A B C D E F G H I K L M N O P Q R S T U V W Z _

A

AbstractAlignmentBlock - Class in net.sf.jannot.alignment.maf
 
AbstractAlignmentBlock(int, int) - Constructor for class net.sf.jannot.alignment.maf.AbstractAlignmentBlock
 
AbstractAlignmentSequence - Class in net.sf.jannot.alignment.maf
 
AbstractAlignmentSequence(String, int, int, Strand) - Constructor for class net.sf.jannot.alignment.maf.AbstractAlignmentSequence
 
AbstractMAFMultipleAlignment - Class in net.sf.jannot.alignment.maf
 
AbstractMAFMultipleAlignment() - Constructor for class net.sf.jannot.alignment.maf.AbstractMAFMultipleAlignment
 
AbstractStreamDataSource - Class in net.sf.jannot.source
Extends DataSource.
AbstractStreamDataSource(Locator) - Constructor for class net.sf.jannot.source.AbstractStreamDataSource
 
AbstractUnivariateStatistic - Class in org.apache.commons.math.stat
Abstract base class for all implementations of the UnivariateStatistic interface.
AbstractUnivariateStatistic() - Constructor for class org.apache.commons.math.stat.AbstractUnivariateStatistic
 
AbstractWiggle - Class in net.sf.jannot.wiggle
 
AbstractWiggle() - Constructor for class net.sf.jannot.wiggle.AbstractWiggle
 
Accumulator - Class in org.broad.igv.tools
Estimating percentiles -- weighted average of multiple estimates
Accumulator(Collection<WindowFunction>) - Constructor for class org.broad.igv.tools.Accumulator
 
add(int) - Method in class gnu.trove.map.hash.TIntFloatHashMap.TKeyView
Unsupported when operating upon a Key Set view of a TIntFloatMap

Inserts a value into the set.

add(float) - Method in class gnu.trove.map.hash.TIntFloatHashMap.TValueView
 
add(long) - Method in class gnu.trove.map.hash.TLongDoubleHashMap.TKeyView
Unsupported when operating upon a Key Set view of a TLongDoubleMap

Inserts a value into the set.

add(double) - Method in class gnu.trove.map.hash.TLongDoubleHashMap.TValueView
 
add(E) - Method in class gnu.trove.set.hash.THashSet
Inserts a value into the set.
add(int) - Method in class gnu.trove.set.hash.TIntHashSet
Inserts a value into the set.
add(long) - Method in class gnu.trove.set.hash.TLongHashSet
Inserts a value into the set.
add(int) - Method in interface gnu.trove.set.TIntSet
Inserts a value into the set.
add(long) - Method in interface gnu.trove.set.TLongSet
Inserts a value into the set.
add(double) - Method in interface gnu.trove.TDoubleCollection
Inserts a value into the collection.
add(float) - Method in interface gnu.trove.TFloatCollection
Inserts a value into the collection.
add(int) - Method in interface gnu.trove.TIntCollection
Inserts a value into the collection.
add(long) - Method in interface gnu.trove.TLongCollection
Inserts a value into the collection.
add(short) - Method in interface gnu.trove.TShortCollection
Inserts a value into the collection.
add(AbstractAlignmentSequence) - Method in class net.sf.jannot.alignment.maf.AbstractAlignmentBlock
 
add(AbstractAlignmentSequence) - Method in class net.sf.jannot.alignment.maf.LazyAlignmentBlock
 
add(MemoryAlignmentBlock) - Method in class net.sf.jannot.alignment.maf.MAFMemoryMultipleAlignment
 
add(AbstractAlignmentSequence) - Method in class net.sf.jannot.alignment.maf.MemoryAlignmentBlock
 
add(String, String) - Method in class net.sf.jannot.Description
Add a value to a key.
add(DataKey, Data<?>) - Method in class net.sf.jannot.Entry
 
add(T) - Method in class net.sf.jannot.EntrySetAnnotation
 
add(Feature) - Method in class net.sf.jannot.MemoryFeatureAnnotation
 
add(SAMRecord) - Method in class net.sf.jannot.shortread.MemoryReadSet
 
add(SyntenicBlock) - Method in class net.sf.jannot.SyntenicAnnotation
 
add(float) - Method in class org.broad.igv.tools.Accumulator
 
add(double) - Method in class org.broad.igv.util.collections.DoubleArrayList
 
add(float) - Method in class org.broad.igv.util.collections.FloatArrayList
 
add(int) - Method in class org.broad.igv.util.collections.IntArrayList
 
addAll(Collection<? extends Integer>) - Method in class gnu.trove.map.hash.TIntFloatHashMap.TKeyView
Unsupported when operating upon a Key Set view of a TIntFloatMap

Adds all of the elements in collection to the set.

addAll(TIntCollection) - Method in class gnu.trove.map.hash.TIntFloatHashMap.TKeyView
Unsupported when operating upon a Key Set view of a TIntFloatMap

Adds all of the elements in the TIntCollection to the set.

addAll(int[]) - Method in class gnu.trove.map.hash.TIntFloatHashMap.TKeyView
Unsupported when operating upon a Key Set view of a TIntFloatMap

Adds all of the elements in the array to the set.

addAll(Collection<? extends Float>) - Method in class gnu.trove.map.hash.TIntFloatHashMap.TValueView
Adds all of the elements in collection to the collection.
addAll(TFloatCollection) - Method in class gnu.trove.map.hash.TIntFloatHashMap.TValueView
Adds all of the elements in the TFloatCollection to the collection.
addAll(float[]) - Method in class gnu.trove.map.hash.TIntFloatHashMap.TValueView
Adds all of the elements in the array to the collection.
addAll(Collection<? extends Long>) - Method in class gnu.trove.map.hash.TLongDoubleHashMap.TKeyView
Unsupported when operating upon a Key Set view of a TLongDoubleMap

Adds all of the elements in collection to the set.

addAll(TLongCollection) - Method in class gnu.trove.map.hash.TLongDoubleHashMap.TKeyView
Unsupported when operating upon a Key Set view of a TLongDoubleMap

Adds all of the elements in the TLongCollection to the set.

addAll(long[]) - Method in class gnu.trove.map.hash.TLongDoubleHashMap.TKeyView
Unsupported when operating upon a Key Set view of a TLongDoubleMap

Adds all of the elements in the array to the set.

addAll(Collection<? extends Double>) - Method in class gnu.trove.map.hash.TLongDoubleHashMap.TValueView
Adds all of the elements in collection to the collection.
addAll(TDoubleCollection) - Method in class gnu.trove.map.hash.TLongDoubleHashMap.TValueView
Adds all of the elements in the TDoubleCollection to the collection.
addAll(double[]) - Method in class gnu.trove.map.hash.TLongDoubleHashMap.TValueView
Adds all of the elements in the array to the collection.
addAll(Collection<? extends E>) - Method in class gnu.trove.set.hash.THashSet
Adds all of the elements in collection to the set.
addAll(Collection<? extends Integer>) - Method in class gnu.trove.set.hash.TIntHashSet
Adds all of the elements in collection to the set.
addAll(TIntCollection) - Method in class gnu.trove.set.hash.TIntHashSet
Adds all of the elements in the TIntCollection to the set.
addAll(int[]) - Method in class gnu.trove.set.hash.TIntHashSet
Adds all of the elements in the array to the set.
addAll(Collection<? extends Long>) - Method in class gnu.trove.set.hash.TLongHashSet
Adds all of the elements in collection to the set.
addAll(TLongCollection) - Method in class gnu.trove.set.hash.TLongHashSet
Adds all of the elements in the TLongCollection to the set.
addAll(long[]) - Method in class gnu.trove.set.hash.TLongHashSet
Adds all of the elements in the array to the set.
addAll(Collection<? extends Integer>) - Method in interface gnu.trove.set.TIntSet
Adds all of the elements in collection to the set.
addAll(TIntCollection) - Method in interface gnu.trove.set.TIntSet
Adds all of the elements in the TIntCollection to the set.
addAll(int[]) - Method in interface gnu.trove.set.TIntSet
Adds all of the elements in the array to the set.
addAll(Collection<? extends Long>) - Method in interface gnu.trove.set.TLongSet
Adds all of the elements in collection to the set.
addAll(TLongCollection) - Method in interface gnu.trove.set.TLongSet
Adds all of the elements in the TLongCollection to the set.
addAll(long[]) - Method in interface gnu.trove.set.TLongSet
Adds all of the elements in the array to the set.
addAll(Collection<? extends Double>) - Method in interface gnu.trove.TDoubleCollection
Adds all of the elements in collection to the collection.
addAll(TDoubleCollection) - Method in interface gnu.trove.TDoubleCollection
Adds all of the elements in the TDoubleCollection to the collection.
addAll(double[]) - Method in interface gnu.trove.TDoubleCollection
Adds all of the elements in the array to the collection.
addAll(Collection<? extends Float>) - Method in interface gnu.trove.TFloatCollection
Adds all of the elements in collection to the collection.
addAll(TFloatCollection) - Method in interface gnu.trove.TFloatCollection
Adds all of the elements in the TFloatCollection to the collection.
addAll(float[]) - Method in interface gnu.trove.TFloatCollection
Adds all of the elements in the array to the collection.
addAll(Collection<? extends Integer>) - Method in interface gnu.trove.TIntCollection
Adds all of the elements in collection to the collection.
addAll(TIntCollection) - Method in interface gnu.trove.TIntCollection
Adds all of the elements in the TIntCollection to the collection.
addAll(int[]) - Method in interface gnu.trove.TIntCollection
Adds all of the elements in the array to the collection.
addAll(Collection<? extends Long>) - Method in interface gnu.trove.TLongCollection
Adds all of the elements in collection to the collection.
addAll(TLongCollection) - Method in interface gnu.trove.TLongCollection
Adds all of the elements in the TLongCollection to the collection.
addAll(long[]) - Method in interface gnu.trove.TLongCollection
Adds all of the elements in the array to the collection.
addAll(Collection<? extends Short>) - Method in interface gnu.trove.TShortCollection
Adds all of the elements in collection to the collection.
addAll(TShortCollection) - Method in interface gnu.trove.TShortCollection
Adds all of the elements in the TShortCollection to the collection.
addAll(short[]) - Method in interface gnu.trove.TShortCollection
Adds all of the elements in the array to the collection.
addAll(Iterable<Alignment>) - Method in class net.sf.jannot.alignment.mfa.AlignmentAnnotation
 
addAll(MemoryListData<T>) - Method in class net.sf.jannot.MemoryListData
 
addAll(Iterable<T>) - Method in class net.sf.jannot.MemoryListData
 
addAll(Data<SAMRecord>) - Method in class net.sf.jannot.shortread.MemoryReadSet
 
addAll(double[]) - Method in class org.broad.igv.util.collections.DoubleArrayList
 
addAll(DoubleArrayList) - Method in class org.broad.igv.util.collections.DoubleArrayList
 
addAll(float[]) - Method in class org.broad.igv.util.collections.FloatArrayList
 
addAll(FloatArrayList) - Method in class org.broad.igv.util.collections.FloatArrayList
 
addAll(int[]) - Method in class org.broad.igv.util.collections.IntArrayList
 
addAll(IntArrayList) - Method in class org.broad.igv.util.collections.IntArrayList
 
addLocation(Location) - Method in class net.sf.jannot.Feature
 
addQualifier(String, String) - Method in class net.sf.jannot.Feature
 
addSequence(String) - Method in class net.sf.jannot.alignment.ReferenceSequence
 
addSequence(String) - Method in class net.sf.jannot.refseq.MemorySequence
 
addSpecies(String) - Method in class net.sf.jannot.alignment.maf.AbstractMAFMultipleAlignment
 
adjustOrPutValue(int, float, float) - Method in class gnu.trove.map.hash.TIntFloatHashMap
Adjusts the primitive value mapped to the key if the key is present in the map.
adjustOrPutValue(long, double, double) - Method in class gnu.trove.map.hash.TLongDoubleHashMap
Adjusts the primitive value mapped to the key if the key is present in the map.
adjustOrPutValue(int, float, float) - Method in interface gnu.trove.map.TIntFloatMap
Adjusts the primitive value mapped to the key if the key is present in the map.
adjustOrPutValue(long, double, double) - Method in interface gnu.trove.map.TLongDoubleMap
Adjusts the primitive value mapped to the key if the key is present in the map.
adjustValue(int, float) - Method in class gnu.trove.map.hash.TIntFloatHashMap
Adjusts the primitive value mapped to key.
adjustValue(long, double) - Method in class gnu.trove.map.hash.TLongDoubleHashMap
Adjusts the primitive value mapped to key.
adjustValue(int, float) - Method in interface gnu.trove.map.TIntFloatMap
Adjusts the primitive value mapped to key.
adjustValue(long, double) - Method in interface gnu.trove.map.TLongDoubleMap
Adjusts the primitive value mapped to key.
advance() - Method in interface gnu.trove.iterator.TAdvancingIterator
Moves the iterator forward to the next entry.
Alignment - Class in net.sf.jannot.alignment.mfa
 
Alignment(String, MemorySequence, ReferenceSequence) - Constructor for class net.sf.jannot.alignment.mfa.Alignment
 
AlignmentAnnotation - Class in net.sf.jannot.alignment.mfa
 
AlignmentAnnotation() - Constructor for class net.sf.jannot.alignment.mfa.AlignmentAnnotation
 
ALNParser - Class in net.sf.jannot.parser
 
ALNParser(DataKey) - Constructor for class net.sf.jannot.parser.ALNParser
 
AminoAcidMapping - Enum in net.sf.jannot
Enumerates different genetic codes.
annotation - Variable in class net.sf.jannot.event.AnnotationEvent
 
AnnotationEvent - Class in net.sf.jannot.event
 
AnnotationEvent(FeatureAnnotation) - Constructor for class net.sf.jannot.event.AnnotationEvent
 
AnnotationEvent(FeatureAnnotation, String) - Constructor for class net.sf.jannot.event.AnnotationEvent
 
ArrayIterable<T> - Class in net.sf.jannot.utils
This Iterator is used to iterate over Arrays.
ArrayIterable(Object) - Constructor for class net.sf.jannot.utils.ArrayIterable
create an Iterator for the Array array.
ArrayIterator<T> - Class in net.sf.jannot.utils
This Iterator is used to iterate over Arrays.
ArrayIterator(Object) - Constructor for class net.sf.jannot.utils.ArrayIterator
create an Iterator for the Array array.
availableWindowFunctions() - Method in class net.sf.jannot.tdf.TDFData
 

B

BAMreads - Class in net.sf.jannot.shortread
 
BAMreads(SAMDataSource, Entry) - Constructor for class net.sf.jannot.shortread.BAMreads
 
BasicScore - Class in org.broad.igv.data
 
BasicScore(String, int, int, float) - Constructor for class org.broad.igv.data.BasicScore
 
BasicScore(BasicScore) - Constructor for class org.broad.igv.data.BasicScore
 
BasicShortRead - Class in net.sf.jannot.shortread
 
BasicShortRead(char[], int, boolean) - Constructor for class net.sf.jannot.shortread.BasicShortRead
 
BasicShortRead(byte[], int, boolean) - Constructor for class net.sf.jannot.shortread.BasicShortRead
 
BBCompressionUtils - Class in org.broad.igv.bbfile
File retrieved from BigWig project at Google code on July 26, 2011, revision 36 http://code.google.com/p/bigwig/ This project provides java readers for the UCSC's BigWig and BigBed formats.
BBCompressionUtils() - Constructor for class org.broad.igv.bbfile.BBCompressionUtils
 
BBFILE_HEADER_OFFSET - Static variable in class org.broad.igv.bbfile.BBFileReader
 
BBFILE_HEADER_SIZE - Static variable in class org.broad.igv.bbfile.BBFileHeader
 
BBFileHeader - Class in org.broad.igv.bbfile
File retrieved from BigWig project at Google code on July 26, 2011, revision 36 http://code.google.com/p/bigwig/ This project provides java readers for the UCSC's BigWig and BigBed formats.
BBFileHeader(SeekableStream, long) - Constructor for class org.broad.igv.bbfile.BBFileHeader
 
BBFileHeader(int, short, short, long, long, long, short, short, long, long, int, long) - Constructor for class org.broad.igv.bbfile.BBFileHeader
 
BBFileReader - Class in org.broad.igv.bbfile
File retrieved from BigWig project at Google code on July 26, 2011, revision 36 http://code.google.com/p/bigwig/ This project provides java readers for the UCSC's BigWig and BigBed formats.
BBFileReader(String) - Constructor for class org.broad.igv.bbfile.BBFileReader
 
BBFileReader(Locator, SeekableStream) - Constructor for class org.broad.igv.bbfile.BBFileReader
 
BBTotalSummaryBlock - Class in org.broad.igv.bbfile
File retrieved from BigWig project at Google code on July 26, 2011, revision 36 http://code.google.com/p/bigwig/ This project provides java readers for the UCSC's BigWig and BigBed formats.
BBTotalSummaryBlock(SeekableStream, long, boolean) - Constructor for class org.broad.igv.bbfile.BBTotalSummaryBlock
 
BBTotalSummaryBlock(long, float, float, float, float) - Constructor for class org.broad.igv.bbfile.BBTotalSummaryBlock
 
BBZoomLevelFormat - Class in org.broad.igv.bbfile
File retrieved from BigWig project at Google code on July 26, 2011, revision 36 http://code.google.com/p/bigwig/ This project provides java readers for the UCSC's BigWig and BigBed formats.
BBZoomLevelFormat(int, SeekableStream, long, long, boolean, int) - Constructor for class org.broad.igv.bbfile.BBZoomLevelFormat
 
BBZoomLevelHeader - Class in org.broad.igv.bbfile
File retrieved from BigWig project at Google code on July 26, 2011, revision 36 http://code.google.com/p/bigwig/ This project provides java readers for the UCSC's BigWig and BigBed formats.
BBZoomLevelHeader(SeekableStream, long, int, boolean) - Constructor for class org.broad.igv.bbfile.BBZoomLevelHeader
 
BBZoomLevelHeader(int, int, int, long, long) - Constructor for class org.broad.igv.bbfile.BBZoomLevelHeader
 
BBZoomLevels - Class in org.broad.igv.bbfile
File retrieved from BigWig project at Google code on July 26, 2011, revision 36 http://code.google.com/p/bigwig/ This project provides java readers for the UCSC's BigWig and BigBed formats.
BBZoomLevels(SeekableStream, long, int, boolean, int) - Constructor for class org.broad.igv.bbfile.BBZoomLevels
 
BED_CONF - Static variable in class net.sf.jannot.tabix.TabixWriter
 
BEDCodec - Class in net.sf.jannot.tabix.codec
 
BEDCodec(FeatureWrapper, Iterable<TabixLine>) - Constructor for class net.sf.jannot.tabix.codec.BEDCodec
 
BedFeature - Class in org.broad.igv.bbfile
File retrieved from BigWig project at Google code on July 26, 2011, revision 36 http://code.google.com/p/bigwig/ This project provides java readers for the UCSC's BigWig and BigBed formats.
BedFeature(int, String, int, int, String) - Constructor for class org.broad.igv.bbfile.BedFeature
 
BEDGRAPH_ITEM_SIZE - Static variable in class org.broad.igv.bbfile.BigWigSectionHeader
 
BedGraphParser - Class in net.sf.jannot.parser
 
BedGraphParser(DataKey) - Constructor for class net.sf.jannot.parser.BedGraphParser
 
BEDParser - Class in net.sf.jannot.parser
 
BEDParser() - Constructor for class net.sf.jannot.parser.BEDParser
 
BEDTools - Class in net.sf.jannot.parser
 
BEDTools() - Constructor for class net.sf.jannot.parser.BEDTools
 
BEDWrapper - Class in net.sf.jannot.tabix
 
BIGBED_MAGIC_HTL - Static variable in class org.broad.igv.bbfile.BBFileHeader
 
BIGBED_MAGIC_LTH - Static variable in class org.broad.igv.bbfile.BBFileHeader
 
BigBedDataBlock - Class in org.broad.igv.bbfile
File retrieved from BigWig project at Google code on July 26, 2011, revision 36 http://code.google.com/p/bigwig/ This project provides java readers for the UCSC's BigWig and BigBed formats.
BigBedDataBlock(SeekableStream, RPTreeLeafNodeItem, HashMap<Integer, String>, boolean, int) - Constructor for class org.broad.igv.bbfile.BigBedDataBlock
 
BigBedIterator - Class in org.broad.igv.bbfile
File retrieved from BigWig project at Google code on July 26, 2011, revision 36 http://code.google.com/p/bigwig/ This project provides java readers for the UCSC's BigWig and BigBed formats.
BigBedIterator(SeekableStream, BPTree, RPTree, RPChromosomeRegion, boolean) - Constructor for class org.broad.igv.bbfile.BigBedIterator
Constructor for a BigBed iterator over the specified chromosome region

Parameters: fis - file input stream handle chromIDTree - B+ index tree returns chromomosme ID's for chromosome names chromDataTree - R+ chromosome data locations tree selectionRegion - chromosome region for selection of Bed feature extraction consists of: startChromID - ID of start chromosome startBase - starting base position for features endChromID - ID of end chromosome endBase - starting base position for features contained - specifies bed features must be contained by region, if true; else return any intersecting region features

BigBedIterator() - Constructor for class org.broad.igv.bbfile.BigBedIterator
 
BIGWIG_MAGIC_HTL - Static variable in class org.broad.igv.bbfile.BBFileHeader
 
BIGWIG_MAGIC_LTH - Static variable in class org.broad.igv.bbfile.BBFileHeader
 
BigWigData - Class in net.sf.jannot.bigwig
 
BigWigData(String, BBFileReader) - Constructor for class net.sf.jannot.bigwig.BigWigData
 
BigWigDataBlock - Class in org.broad.igv.bbfile
File retrieved from BigWig project at Google code on July 26, 2011, revision 36 http://code.google.com/p/bigwig/ This project provides java readers for the UCSC's BigWig and BigBed formats.
BigWigDataBlock(SeekableStream, RPTreeLeafNodeItem, HashMap<Integer, String>, boolean, int) - Constructor for class org.broad.igv.bbfile.BigWigDataBlock
 
BigWigDataSource - Class in net.sf.jannot.bigwig
Data source for BigWig files.
BigWigDataSource(Locator) - Constructor for class net.sf.jannot.bigwig.BigWigDataSource
 
BigWigIterator - Class in org.broad.igv.bbfile
File retrieved from BigWig project at Google code on July 26, 2011, revision 36 http://code.google.com/p/bigwig/ This project provides java readers for the UCSC's BigWig and BigBed formats.
BigWigIterator(SeekableStream, BPTree, RPTree, RPChromosomeRegion, boolean) - Constructor for class org.broad.igv.bbfile.BigWigIterator
Constructor for a BigWig iterator over the specified chromosome region

Parameters: fis - file input stream handle chromIDTree - B+ chromosome index tree provides chromosome ID's for chromosome names chromDataTree - R+ chromosome data locations tree selectionRegion - chromosome region for selection of Wig feature extraction consists of: startChromID - ID of start chromosome startBase - starting base position for values endChromID - ID of end chromosome endBase - ending base position for values contained - specifies wig values must be contained by region, if true; else return any intersecting region values

BigWigIterator() - Constructor for class org.broad.igv.bbfile.BigWigIterator
Constructor for an empty iterator
BigWigSection - Class in org.broad.igv.bbfile
File retrieved from BigWig project at Google code on July 26, 2011, revision 36 http://code.google.com/p/bigwig/ This project provides java readers for the UCSC's BigWig and BigBed formats.
BigWigSection(byte[], HashMap<Integer, String>, boolean, RPTreeLeafNodeItem) - Constructor for class org.broad.igv.bbfile.BigWigSection
 
BigWigSectionHeader - Class in org.broad.igv.bbfile
File retrieved from BigWig project at Google code on July 26, 2011, revision 36 http://code.google.com/p/bigwig/ This project provides java readers for the UCSC's BigWig and BigBed formats.
BigWigSectionHeader(LittleEndianInputStream) - Constructor for class org.broad.igv.bbfile.BigWigSectionHeader
 
BigWigSectionHeader(DataInputStream) - Constructor for class org.broad.igv.bbfile.BigWigSectionHeader
 
BigWigSectionHeader.WigItemType - Enum in org.broad.igv.bbfile
 
BinaryBlob - Class in net.sf.jannot.picard
 
BinaryBlob(long) - Constructor for class net.sf.jannot.picard.BinaryBlob
 
BinaryCodec - Class in net.sf.jannot.tabix
Encapsulates file representation of various primitive data types.
BinaryCodec(File, boolean) - Constructor for class net.sf.jannot.tabix.BinaryCodec
Constructs BinaryCodec from a file and set it's mode to writing or not
BinaryCodec(String, boolean) - Constructor for class net.sf.jannot.tabix.BinaryCodec
Constructs BinaryCodec from a file name and set it's mode to writing or not
BinaryCodec(OutputStream) - Constructor for class net.sf.jannot.tabix.BinaryCodec
Constructs BinaryCodec from an output stream
BinaryCodec(InputStream) - Constructor for class net.sf.jannot.tabix.BinaryCodec
Constructs BinaryCodec from an input stream
BinaryCodec() - Constructor for class net.sf.jannot.tabix.BinaryCodec
Ambiguous whether reading or writing until set{In,Out}putStream is called
BlastM8Parser - Class in net.sf.jannot.parser.software
 
BlastM8Parser() - Constructor for class net.sf.jannot.parser.software.BlastM8Parser
 
BPTree - Class in org.broad.igv.bbfile
File retrieved from BigWig project at Google code on July 26, 2011, revision 36 http://code.google.com/p/bigwig/ This project provides java readers for the UCSC's BigWig and BigBed formats.
BPTree(SeekableStream, long, boolean) - Constructor for class org.broad.igv.bbfile.BPTree
 
BPTREE_HEADER_SIZE - Static variable in class org.broad.igv.bbfile.BPTreeHeader
 
BPTREE_MAGIC_HTL - Static variable in class org.broad.igv.bbfile.BPTreeHeader
 
BPTREE_MAGIC_LTH - Static variable in class org.broad.igv.bbfile.BPTreeHeader
 
BPTREE_NODE_FORMAT_SIZE - Static variable in class org.broad.igv.bbfile.BPTree
 
BPTREE_NODE_ITEM_SIZE - Static variable in class org.broad.igv.bbfile.BPTree
 
BPTreeChildNode - Class in org.broad.igv.bbfile
File retrieved from BigWig project at Google code on July 26, 2011, revision 36 http://code.google.com/p/bigwig/ This project provides java readers for the UCSC's BigWig and BigBed formats.
BPTreeChildNode(long) - Constructor for class org.broad.igv.bbfile.BPTreeChildNode
 
BPTreeChildNodeItem - Class in org.broad.igv.bbfile
File retrieved from BigWig project at Google code on July 26, 2011, revision 36 http://code.google.com/p/bigwig/ This project provides java readers for the UCSC's BigWig and BigBed formats.
BPTreeChildNodeItem(int, String, BPTreeNode) - Constructor for class org.broad.igv.bbfile.BPTreeChildNodeItem
 
BPTreeHeader - Class in org.broad.igv.bbfile
File retrieved from BigWig project at Google code on July 26, 2011, revision 36 http://code.google.com/p/bigwig/ This project provides java readers for the UCSC's BigWig and BigBed formats.
BPTreeHeader(SeekableStream, long, boolean) - Constructor for class org.broad.igv.bbfile.BPTreeHeader
 
BPTreeLeafNode - Class in org.broad.igv.bbfile
File retrieved from BigWig project at Google code on July 26, 2011, revision 36 http://code.google.com/p/bigwig/ This project provides java readers for the UCSC's BigWig and BigBed formats.
BPTreeLeafNode(long) - Constructor for class org.broad.igv.bbfile.BPTreeLeafNode
 
BPTreeLeafNodeItem - Class in org.broad.igv.bbfile
File retrieved from BigWig project at Google code on July 26, 2011, revision 36 http://code.google.com/p/bigwig/ This project provides java readers for the UCSC's BigWig and BigBed formats.
BPTreeLeafNodeItem(long, String, int, int) - Constructor for class org.broad.igv.bbfile.BPTreeLeafNodeItem
 
BPTreeNode - Interface in org.broad.igv.bbfile
File retrieved from BigWig project at Google code on July 26, 2011, revision 36 http://code.google.com/p/bigwig/ This project provides java readers for the UCSC's BigWig and BigBed formats.
breakQuotedString(String, char) - Static method in class org.broad.igv.util.StringUtils
 
BroadSolexa - Class in net.sf.jannot.parser.software
A short read parser for Broad data
BroadSolexa(DataKey) - Constructor for class net.sf.jannot.parser.software.BroadSolexa
 
BufferedByteWriter - Class in org.broad.igv.tdf
 
BufferedByteWriter() - Constructor for class org.broad.igv.tdf.BufferedByteWriter
 
BufferedByteWriter(int) - Constructor for class org.broad.igv.tdf.BufferedByteWriter
 
bytesWritten() - Method in class org.broad.igv.tdf.BufferedByteWriter
 

C

cachedCount() - Method in class net.sf.jannot.MemoryFeatureAnnotation
Returns the number of features that resides in memory.
cacheDir - Static variable in class net.sf.jannot.source.cache.SourceCache
 
cacheDir - Static variable in class net.sf.jannot.source.IndexManager
 
CachedURLSource - Class in net.sf.jannot.source.cache
 
CachedURLSource(URL) - Constructor for class net.sf.jannot.source.cache.CachedURLSource
 
CachingQueryReader - Class in net.sf.jannot.shortread
A wrapper for SAMDataSource that supports query by interval and is cached
CachingQueryReader.TiledIterator - Class in net.sf.jannot.shortread
 
calculateGrownCapacity() - Method in class gnu.trove.impl.hash.THash
 
canBuildIndex(Locator) - Static method in class net.sf.jannot.source.IndexManager
 
canSave() - Method in class net.sf.jannot.alignment.maf.AbstractMAFMultipleAlignment
 
canSave() - Method in class net.sf.jannot.alignment.mfa.AlignmentAnnotation
 
canSave() - Method in class net.sf.jannot.bigwig.BigWigData
 
canSave() - Method in interface net.sf.jannot.Data
 
canSave() - Method in class net.sf.jannot.mafix.IndexedMAF
 
canSave() - Method in class net.sf.jannot.MemoryFeatureAnnotation
 
canSave() - Method in class net.sf.jannot.MemoryListData
 
canSave() - Method in class net.sf.jannot.refseq.Sequence
 
canSave() - Method in class net.sf.jannot.shortread.ReadGroup
 
canSave() - Method in class net.sf.jannot.tabix.TabixWrapper
 
canSave() - Method in class net.sf.jannot.tdf.TDFData
 
canSave() - Method in class net.sf.jannot.wiggle.DiskArrayWiggle
 
canSave() - Method in class net.sf.jannot.wiggle.FloatArrayWiggle
 
canSave() - Method in class net.sf.jannot.wiggle.TroveArrayWiggle
 
capacity() - Method in class gnu.trove.impl.hash.THash
 
capacity() - Method in class gnu.trove.impl.hash.TObjectHash
 
capacity() - Method in class gnu.trove.impl.hash.TPrimitiveHash
Returns the capacity of the hash table.
certify(URL) - Static method in class net.sf.jannot.source.SSL
 
ChangeEvent - Interface in net.sf.jannot.event
 
chr2tid(String) - Method in class net.sf.jannot.tabix.TabixReader
 
chr2tid(String) - Method in class net.sf.jannot.tabix.TabixWriter
Override chr2tid so that getInv() adds new chromosomes as we read the source file.
chrColumn - Variable in class net.sf.jannot.tabix.TabixWriter.Conf
 
chromKeysMatch(String) - Method in class org.broad.igv.bbfile.BPTreeChildNodeItem
 
chromKeysMatch(String) - Method in class org.broad.igv.bbfile.BPTreeLeafNodeItem
 
Cleaner - Class in net.sf.jannot
Registry for random access files that need to be closed.
Cleaner() - Constructor for class net.sf.jannot.Cleaner
 
clear() - Method in class gnu.trove.impl.hash.THash
Empties the collection.
clear() - Method in class gnu.trove.map.hash.THashMap
Empties the map.
clear() - Method in class gnu.trove.map.hash.TIntFloatHashMap
Empties the collection.
clear() - Method in class gnu.trove.map.hash.TIntFloatHashMap.TKeyView
Empties the set.
clear() - Method in class gnu.trove.map.hash.TIntFloatHashMap.TValueView
Empties the collection.
clear() - Method in class gnu.trove.map.hash.TLongDoubleHashMap
Empties the collection.
clear() - Method in class gnu.trove.map.hash.TLongDoubleHashMap.TKeyView
Empties the set.
clear() - Method in class gnu.trove.map.hash.TLongDoubleHashMap.TValueView
Empties the collection.
clear() - Method in interface gnu.trove.map.TIntFloatMap
Empties the map.
clear() - Method in interface gnu.trove.map.TLongDoubleMap
Empties the map.
clear() - Method in class gnu.trove.set.hash.THashSet
Empties the set.
clear() - Method in class gnu.trove.set.hash.TIntHashSet
Empties the collection.
clear() - Method in class gnu.trove.set.hash.TLongHashSet
Empties the collection.
clear() - Method in interface gnu.trove.set.TIntSet
Empties the set.
clear() - Method in interface gnu.trove.set.TLongSet
Empties the set.
clear() - Method in interface gnu.trove.TDoubleCollection
Empties the collection.
clear() - Method in interface gnu.trove.TFloatCollection
Empties the collection.
clear() - Method in interface gnu.trove.TIntCollection
Empties the collection.
clear() - Method in interface gnu.trove.TLongCollection
Empties the collection.
clear() - Method in interface gnu.trove.TShortCollection
Empties the collection.
clear() - Method in class net.sf.jannot.EntrySet
 
clear() - Method in class net.sf.jannot.shortread.MemoryReadSet
 
clear() - Method in class net.sf.jannot.SyntenicAnnotation
 
clear() - Method in class org.apache.commons.collections.map.Flat3Map
Clears the map, resetting the size to zero and nullifying references to avoid garbage collection issues.
clear() - Method in class org.broad.igv.util.collections.DoubleArrayList
Empty all elements.
clear() - Method in class org.broad.igv.util.collections.FloatArrayList
Empty all elements.
clear() - Method in class org.broad.igv.util.collections.IntArrayList
Empty all elements.
clearQualifiers() - Method in class net.sf.jannot.Feature
 
close() - Method in class net.sf.jannot.shortread.CachingQueryReader.TiledIterator
 
close() - Method in class net.sf.jannot.shortread.EmptyIterator
 
close() - Method in class net.sf.jannot.tabix.BinaryCodec
Close the appropriate stream
close() - Method in class org.broad.igv.tdf.TDFReader
 
closeAll() - Method in class net.sf.jannot.picard.SeekableFileCachedHTTPStream
Closes this SeekableFileCachedHTTPStream and its entire lineage.
closeFile() - Method in class org.broad.igv.tdf.TDFWriter
Write out the group and dataset index and close the underlying file.
Codec<T> - Class in net.sf.jannot.tabix.codec
 
Codec(Iterable<TabixLine>, int) - Constructor for class net.sf.jannot.tabix.codec.Codec
 
compact() - Method in class gnu.trove.impl.hash.THash
Compresses the hashtable to the minimum prime size (as defined by PrimeFinder) that will hold all of the elements currently in the table.
compareRegions(RPChromosomeRegion) - Method in class org.broad.igv.bbfile.RPChromosomeRegion
 
compareRegions(RPChromosomeRegion) - Method in class org.broad.igv.bbfile.RPTreeChildNode
 
compareRegions(RPChromosomeRegion) - Method in class org.broad.igv.bbfile.RPTreeChildNodeItem
 
compareRegions(RPChromosomeRegion) - Method in class org.broad.igv.bbfile.RPTreeLeafNode
 
compareRegions(RPChromosomeRegion) - Method in interface org.broad.igv.bbfile.RPTreeNode
 
compareTo(AbstractAlignmentBlock) - Method in class net.sf.jannot.alignment.maf.AbstractAlignmentBlock
 
compareTo(Entry) - Method in class net.sf.jannot.Entry
 
compareTo(Feature) - Method in class net.sf.jannot.Feature
 
compareTo(Location) - Method in class net.sf.jannot.Location
 
compareTo(ShortRead) - Method in class net.sf.jannot.shortread.ShortRead
 
compareTo(DataSource) - Method in class net.sf.jannot.source.DataSource
 
compareTo(DataKey) - Method in class net.sf.jannot.StringKey
 
compareTo(Pair64) - Method in class net.sf.jannot.tabix.Pair64
 
compareTo(TabixReader.TPair64) - Method in class net.sf.jannot.tabix.TabixReader.TPair64
 
compareTo(DataKey) - Method in class net.sf.jannot.Type
 
complement(char) - Static method in class net.sf.jannot.utils.SequenceTools
 
compress(byte[], int) - Static method in class org.broad.igv.bbfile.BBCompressionUtils
 
compress(byte[]) - Static method in class org.broad.igv.util.CompressionUtils
 
compress(byte[], int) - Static method in class org.broad.igv.util.CompressionUtils
 
CompressionUtils - Class in org.broad.igv.util
Created by IntelliJ IDEA.
CompressionUtils() - Constructor for class org.broad.igv.util.CompressionUtils
 
computeHashCode(T) - Method in interface gnu.trove.strategy.HashingStrategy
Computes a hash code for the specified object.
computeHashCode(K) - Method in class gnu.trove.strategy.IdentityHashingStrategy
 
computeMaxSize(int) - Method in class gnu.trove.impl.hash.THash
Computes the values of maxSize.
computeNextAutoCompactionAmount(int) - Method in class gnu.trove.impl.hash.THash
Computes the number of removes that need to happen before the next auto-compaction will occur.
Constants - Class in gnu.trove.impl
Central location for constants needed by various implementations.
Constants() - Constructor for class gnu.trove.impl.Constants
 
construct(SAMRecord) - Static method in class net.sf.jannot.shortread.ShortReadTools
 
containedIn(RPChromosomeRegion) - Method in class org.broad.igv.bbfile.RPChromosomeRegion
 
contains(int) - Method in class gnu.trove.impl.hash.TIntFloatHash
Searches the set for val
contains(int) - Method in class gnu.trove.impl.hash.TIntHash
Searches the set for val
contains(long) - Method in class gnu.trove.impl.hash.TLongDoubleHash
Searches the set for val
contains(long) - Method in class gnu.trove.impl.hash.TLongHash
Searches the set for val
contains(Object) - Method in class gnu.trove.impl.hash.TObjectHash
Searches the set for obj
contains(int) - Method in class gnu.trove.map.hash.TIntFloatHashMap.TKeyView
Returns true if this set contains the specified element.
contains(float) - Method in class gnu.trove.map.hash.TIntFloatHashMap.TValueView
Returns true if this collection contains the specified element.
contains(long) - Method in class gnu.trove.map.hash.TLongDoubleHashMap.TKeyView
Returns true if this set contains the specified element.
contains(double) - Method in class gnu.trove.map.hash.TLongDoubleHashMap.TValueView
Returns true if this collection contains the specified element.
contains(int) - Method in interface gnu.trove.set.TIntSet
Returns true if this set contains the specified element.
contains(long) - Method in interface gnu.trove.set.TLongSet
Returns true if this set contains the specified element.
contains(double) - Method in interface gnu.trove.TDoubleCollection
Returns true if this collection contains the specified element.
contains(float) - Method in interface gnu.trove.TFloatCollection
Returns true if this collection contains the specified element.
contains(int) - Method in interface gnu.trove.TIntCollection
Returns true if this collection contains the specified element.
contains(long) - Method in interface gnu.trove.TLongCollection
Returns true if this collection contains the specified element.
contains(short) - Method in interface gnu.trove.TShortCollection
Returns true if this collection contains the specified element.
contains(DataKey) - Method in class net.sf.jannot.Entry
 
contains(T) - Method in class net.sf.jannot.EntrySetAnnotation
 
contains(URL) - Static method in class net.sf.jannot.source.cache.SourceCache
 
contains(SyntenicBlock) - Method in class net.sf.jannot.SyntenicAnnotation
 
containsAll(Collection<?>) - Method in class gnu.trove.map.hash.TIntFloatHashMap.TKeyView
Tests the set to determine if all of the elements in collection are present.
containsAll(TIntCollection) - Method in class gnu.trove.map.hash.TIntFloatHashMap.TKeyView
Tests the set to determine if all of the elements in TIntCollection are present.
containsAll(int[]) - Method in class gnu.trove.map.hash.TIntFloatHashMap.TKeyView
Tests the set to determine if all of the elements in array are present.
containsAll(Collection<?>) - Method in class gnu.trove.map.hash.TIntFloatHashMap.TValueView
Tests the collection to determine if all of the elements in collection are present.
containsAll(TFloatCollection) - Method in class gnu.trove.map.hash.TIntFloatHashMap.TValueView
Tests the collection to determine if all of the elements in TFloatCollection are present.
containsAll(float[]) - Method in class gnu.trove.map.hash.TIntFloatHashMap.TValueView
Tests the collection to determine if all of the elements in array are present.
containsAll(Collection<?>) - Method in class gnu.trove.map.hash.TLongDoubleHashMap.TKeyView
Tests the set to determine if all of the elements in collection are present.
containsAll(TLongCollection) - Method in class gnu.trove.map.hash.TLongDoubleHashMap.TKeyView
Tests the set to determine if all of the elements in TLongCollection are present.
containsAll(long[]) - Method in class gnu.trove.map.hash.TLongDoubleHashMap.TKeyView
Tests the set to determine if all of the elements in array are present.
containsAll(Collection<?>) - Method in class gnu.trove.map.hash.TLongDoubleHashMap.TValueView
Tests the collection to determine if all of the elements in collection are present.
containsAll(TDoubleCollection) - Method in class gnu.trove.map.hash.TLongDoubleHashMap.TValueView
Tests the collection to determine if all of the elements in TDoubleCollection are present.
containsAll(double[]) - Method in class gnu.trove.map.hash.TLongDoubleHashMap.TValueView
Tests the collection to determine if all of the elements in array are present.
containsAll(Collection<?>) - Method in class gnu.trove.set.hash.THashSet
Tests the set to determine if all of the elements in collection are present.
containsAll(Collection<?>) - Method in class gnu.trove.set.hash.TIntHashSet
Tests the set to determine if all of the elements in collection are present.
containsAll(TIntCollection) - Method in class gnu.trove.set.hash.TIntHashSet
Tests the set to determine if all of the elements in TIntCollection are present.
containsAll(int[]) - Method in class gnu.trove.set.hash.TIntHashSet
Tests the set to determine if all of the elements in array are present.
containsAll(Collection<?>) - Method in class gnu.trove.set.hash.TLongHashSet
Tests the set to determine if all of the elements in collection are present.
containsAll(TLongCollection) - Method in class gnu.trove.set.hash.TLongHashSet
Tests the set to determine if all of the elements in TLongCollection are present.
containsAll(long[]) - Method in class gnu.trove.set.hash.TLongHashSet
Tests the set to determine if all of the elements in array are present.
containsAll(Collection<?>) - Method in interface gnu.trove.set.TIntSet
Tests the set to determine if all of the elements in collection are present.
containsAll(TIntCollection) - Method in interface gnu.trove.set.TIntSet
Tests the set to determine if all of the elements in TIntCollection are present.
containsAll(int[]) - Method in interface gnu.trove.set.TIntSet
Tests the set to determine if all of the elements in array are present.
containsAll(Collection<?>) - Method in interface gnu.trove.set.TLongSet
Tests the set to determine if all of the elements in collection are present.
containsAll(TLongCollection) - Method in interface gnu.trove.set.TLongSet
Tests the set to determine if all of the elements in TLongCollection are present.
containsAll(long[]) - Method in interface gnu.trove.set.TLongSet
Tests the set to determine if all of the elements in array are present.
containsAll(Collection<?>) - Method in interface gnu.trove.TDoubleCollection
Tests the collection to determine if all of the elements in collection are present.
containsAll(TDoubleCollection) - Method in interface gnu.trove.TDoubleCollection
Tests the collection to determine if all of the elements in TDoubleCollection are present.
containsAll(double[]) - Method in interface gnu.trove.TDoubleCollection
Tests the collection to determine if all of the elements in array are present.
containsAll(Collection<?>) - Method in interface gnu.trove.TFloatCollection
Tests the collection to determine if all of the elements in collection are present.
containsAll(TFloatCollection) - Method in interface gnu.trove.TFloatCollection
Tests the collection to determine if all of the elements in TFloatCollection are present.
containsAll(float[]) - Method in interface gnu.trove.TFloatCollection
Tests the collection to determine if all of the elements in array are present.
containsAll(Collection<?>) - Method in interface gnu.trove.TIntCollection
Tests the collection to determine if all of the elements in collection are present.
containsAll(TIntCollection) - Method in interface gnu.trove.TIntCollection
Tests the collection to determine if all of the elements in TIntCollection are present.
containsAll(int[]) - Method in interface gnu.trove.TIntCollection
Tests the collection to determine if all of the elements in array are present.
containsAll(Collection<?>) - Method in interface gnu.trove.TLongCollection
Tests the collection to determine if all of the elements in collection are present.
containsAll(TLongCollection) - Method in interface gnu.trove.TLongCollection
Tests the collection to determine if all of the elements in TLongCollection are present.
containsAll(long[]) - Method in interface gnu.trove.TLongCollection
Tests the collection to determine if all of the elements in array are present.
containsAll(Collection<?>) - Method in interface gnu.trove.TShortCollection
Tests the collection to determine if all of the elements in collection are present.
containsAll(TShortCollection) - Method in interface gnu.trove.TShortCollection
Tests the collection to determine if all of the elements in TShortCollection are present.
containsAll(short[]) - Method in interface gnu.trove.TShortCollection
Tests the collection to determine if all of the elements in array are present.
containsElement(Map.Entry<K, V>) - Method in class gnu.trove.map.hash.THashMap.EntryView
 
containsElement(K) - Method in class gnu.trove.map.hash.THashMap.KeyView
 
containsElement(V) - Method in class gnu.trove.map.hash.THashMap.ValueView
 
containsKey(Object) - Method in class gnu.trove.map.hash.THashMap
checks for the present of key in the keys of the map.
containsKey(int) - Method in class gnu.trove.map.hash.TIntFloatHashMap
Checks for the present of key in the keys of the map.
containsKey(long) - Method in class gnu.trove.map.hash.TLongDoubleHashMap
Checks for the present of key in the keys of the map.
containsKey(int) - Method in interface gnu.trove.map.TIntFloatMap
Checks for the present of key in the keys of the map.
containsKey(long) - Method in interface gnu.trove.map.TLongDoubleMap
Checks for the present of key in the keys of the map.
containsKey(Object) - Method in class org.apache.commons.collections.map.Flat3Map
Checks whether the map contains the specified key.
containsValue(Object) - Method in class gnu.trove.map.hash.THashMap
checks for the presence of val in the values of the map.
containsValue(float) - Method in class gnu.trove.map.hash.TIntFloatHashMap
Checks for the presence of val in the values of the map.
containsValue(double) - Method in class gnu.trove.map.hash.TLongDoubleHashMap
Checks for the presence of val in the values of the map.
containsValue(float) - Method in interface gnu.trove.map.TIntFloatMap
Checks for the presence of val in the values of the map.
containsValue(double) - Method in interface gnu.trove.map.TLongDoubleMap
Checks for the presence of val in the values of the map.
containsValue(Object) - Method in class org.apache.commons.collections.map.Flat3Map
Checks whether the map contains the specified value.
ConvertBAM2TDF - Class in org.broad.tools
Program to create tdf files from bam files.
ConvertBAM2TDF() - Constructor for class org.broad.tools.ConvertBAM2TDF
 
copy() - Method in class net.sf.jannot.Feature
Creates a deep copy of this feature.
copy() - Method in class net.sf.jannot.Location
 
copy() - Method in class org.broad.igv.data.BasicScore
 
copy() - Method in interface org.broad.igv.feature.LocusScore
 
create(int, float...) - Static method in class net.sf.jannot.pileup.PileTools
Creates the most memory efficient pile implementation for the given values.
create(int, byte[]) - Static method in class net.sf.jannot.pileup.ReadDetailPile
Creates a pile up for read data from a pile up file
create(SAMDataSource) - Static method in class net.sf.jannot.shortread.CachingQueryReader
 
create(Locator, Locator) - Static method in class net.sf.jannot.source.DataSourceFactory
 
createDataset(String, TDFDataset.DataType, int, int) - Method in class org.broad.igv.tdf.TDFWriter
 
createGroup(String) - Method in class org.broad.igv.tdf.TDFWriter
 
createIndex(Locator) - Static method in class net.sf.jannot.source.IndexManager
A potentially long-running method that will create an index for the provided locator
createIndex(Locator) - Method in class net.sf.jannot.tabix.TabixWriter
 
createTile(byte[], int) - Static method in class org.broad.igv.tdf.TileFactory
 

D

DAS - Class in net.sf.jannot.source.das
 
DAS(String) - Constructor for class net.sf.jannot.source.das.DAS
 
DAS.EntryPoint - Class in net.sf.jannot.source.das
 
DAS.EntryPoint() - Constructor for class net.sf.jannot.source.das.DAS.EntryPoint
 
Data<K> - Interface in net.sf.jannot
Data for an entry
data - Variable in class net.sf.jannot.tabix.TabixWrapper
 
DataKey - Interface in net.sf.jannot
Keys for the entry data
dataKey - Variable in class net.sf.jannot.parser.Parser
 
DataSource - Class in net.sf.jannot.source
 
DataSource(Locator) - Constructor for class net.sf.jannot.source.DataSource
 
DataSource - Interface in org.broad.igv.data
 
DataSourceFactory - Class in net.sf.jannot.source
 
DataSourceFactory() - Constructor for class net.sf.jannot.source.DataSourceFactory
 
DataSourceFactory.Sources - Enum in net.sf.jannot.source
 
decompress(byte[], int) - Static method in class org.broad.igv.bbfile.BBCompressionUtils
 
decompress(byte[]) - Static method in class org.broad.igv.util.CompressionUtils
 
decompress(byte[], int) - Static method in class org.broad.igv.util.CompressionUtils
 
DEFAULT_BYTE_NO_ENTRY_VALUE - Static variable in class gnu.trove.impl.Constants
the default value that represents for byte types.
DEFAULT_CAPACITY - Static variable in class gnu.trove.impl.Constants
the default capacity for new collections
DEFAULT_CAPACITY - Static variable in class gnu.trove.impl.hash.THash
the default initial capacity for the hash table.
DEFAULT_CHAR_NO_ENTRY_VALUE - Static variable in class gnu.trove.impl.Constants
the default value that represents for char types.
DEFAULT_DOUBLE_NO_ENTRY_VALUE - Static variable in class gnu.trove.impl.Constants
the default value that represents for double types.
DEFAULT_FLOAT_NO_ENTRY_VALUE - Static variable in class gnu.trove.impl.Constants
the default value that represents for float types.
DEFAULT_INT_NO_ENTRY_VALUE - Static variable in class gnu.trove.impl.Constants
the default value that represents for int types.
DEFAULT_LOAD_FACTOR - Static variable in class gnu.trove.impl.Constants
the load above which rehashing occurs.
DEFAULT_LOAD_FACTOR - Static variable in class gnu.trove.impl.hash.THash
the load above which rehashing occurs.
DEFAULT_LONG_NO_ENTRY_VALUE - Static variable in class gnu.trove.impl.Constants
the default value that represents for long types.
DEFAULT_SHORT_NO_ENTRY_VALUE - Static variable in class gnu.trove.impl.Constants
the default value that represents for short types.
deleteItem(int) - Method in class org.broad.igv.bbfile.BPTreeChildNode
 
deleteItem(int) - Method in class org.broad.igv.bbfile.BPTreeLeafNode
 
deleteItem(int) - Method in interface org.broad.igv.bbfile.BPTreeNode
 
deleteItem(int) - Method in class org.broad.igv.bbfile.RPTreeChildNode
 
deleteItem(int) - Method in class org.broad.igv.bbfile.RPTreeLeafNode
 
deleteItem(int) - Method in interface org.broad.igv.bbfile.RPTreeNode
 
DensityEstimate - Interface in net.sf.jannot
 
Description - Class in net.sf.jannot
 
Description() - Constructor for class net.sf.jannot.Description
 
description - Variable in class net.sf.jannot.Entry
 
detectParser(InputStream, Object) - Static method in class net.sf.jannot.parser.Parser
 
disableURLCaching - Static variable in class net.sf.jannot.source.DataSourceFactory
 
disjointAbove(RPChromosomeRegion) - Method in class org.broad.igv.bbfile.RPChromosomeRegion
 
disjointBelow(RPChromosomeRegion) - Method in class org.broad.igv.bbfile.RPChromosomeRegion
 
DiskArrayWiggle - Class in net.sf.jannot.wiggle
Make wiggle Fill it with setMethod Initialize with init();
DiskArrayWiggle(int) - Constructor for class net.sf.jannot.wiggle.DiskArrayWiggle
 
doChange() - Method in interface net.sf.jannot.event.ChangeEvent
 
doCount(String, String, Collection<WindowFunction>) - Method in class org.broad.tools.TDFTools
Compute coverage or density of an alignment or feature file.
DoubleArrayList - Class in org.broad.igv.util.collections
Author: jrobinso Date: Jul 22, 2010

ArrayList type collection for int types.

DoubleArrayList() - Constructor for class org.broad.igv.util.collections.DoubleArrayList
 
DoubleArrayList(int) - Constructor for class org.broad.igv.util.collections.DoubleArrayList
 
DoubleArrayList(double[]) - Constructor for class org.broad.igv.util.collections.DoubleArrayList
 
DoublePile - Class in net.sf.jannot.pileup
 
DoublePile(int, float, float) - Constructor for class net.sf.jannot.pileup.DoublePile
 
DSN - Class in net.sf.jannot.source.das
 
DSN(String) - Constructor for class net.sf.jannot.source.das.DSN
 
DualPivotQuicksort - Class in gnu.trove.impl
 
DualPivotQuicksort() - Constructor for class gnu.trove.impl.DualPivotQuicksort
 
dumpAllTiles(String) - Static method in class org.broad.igv.tdf.TDFUtils
 
dumpDatasets(String) - Static method in class org.broad.igv.tdf.TDFUtils
 
dumpRange(String, String, int, int) - Static method in class org.broad.igv.tdf.TDFUtils
 
dumpRootAttributes(String) - Static method in class org.broad.igv.tdf.TDFUtils
 
dumpSummary(String) - Static method in class org.broad.igv.tdf.TDFUtils
 
dumpTile(String, String, int) - Static method in class org.broad.igv.tdf.TDFUtils
 

E

EMBLParser - Class in net.sf.jannot.parser
 
EMBLParser() - Constructor for class net.sf.jannot.parser.EMBLParser
 
EmptyIterator<T> - Class in net.sf.jannot.shortread
 
EmptyIterator() - Constructor for class net.sf.jannot.shortread.EmptyIterator
 
EmptyIterator - Class in org.apache.commons.collections.iterators
Provides an implementation of an empty iterator.
EmptyIterator() - Constructor for class org.apache.commons.collections.iterators.EmptyIterator
Constructor.
end() - Method in class net.sf.jannot.alignment.maf.AbstractAlignmentBlock
 
end() - Method in class net.sf.jannot.alignment.maf.AbstractAlignmentSequence
 
end() - Method in class net.sf.jannot.alignment.maf.LazyAlignmentSequence
 
end() - Method in class net.sf.jannot.alignment.mfa.Alignment
 
end() - Method in class net.sf.jannot.Feature
 
end() - Method in interface net.sf.jannot.Located
 
end - Variable in class net.sf.jannot.Location
These fields are public for efficient getter access.
end() - Method in class net.sf.jannot.Location
 
end() - Method in interface net.sf.jannot.pileup.Pile
 
end() - Method in class net.sf.jannot.pileup.SinglePile
 
end() - Method in class net.sf.jannot.shortread.BasicShortRead
 
end() - Method in class net.sf.jannot.shortread.ShortRead
 
end(SAMRecord) - Static method in class net.sf.jannot.shortread.ShortReadTools
 
end - Variable in class net.sf.jannot.tabix.Pair64
Pair value
endColumn - Variable in class net.sf.jannot.tabix.TabixWriter.Conf
 
ensureCapacity(int) - Method in class gnu.trove.impl.hash.THash
Ensure that this hashtable has sufficient capacity to hold desiredCapacity additional elements without requiring a rehash.
Entry - Class in net.sf.jannot
Each Entry contains information about a specific genome/chromossomes or any chunck of DNA.
Entry(String) - Constructor for class net.sf.jannot.Entry
 
entrySet() - Method in class gnu.trove.map.hash.THashMap
Returns a Set view on the entries of the map.
EntrySet - Class in net.sf.jannot
Top level class for JAnnot, this class represents a set of Entry.
EntrySet() - Constructor for class net.sf.jannot.EntrySet
 
entrySet() - Method in class org.apache.commons.collections.map.Flat3Map
Gets the entrySet view of the map.
EntrySetAnnotation<T> - Class in net.sf.jannot
Interface for annotation associated with an EntrySet of type T.
EntrySetAnnotation() - Constructor for class net.sf.jannot.EntrySetAnnotation
 
equals(Object) - Method in class gnu.trove.map.hash.THashMap
Compares this map with another map for equality of their stored entries.
equals(Object) - Method in class gnu.trove.map.hash.TIntFloatHashMap
equals(Object) - Method in class gnu.trove.map.hash.TIntFloatHashMap.TKeyView
 
equals(Object) - Method in class gnu.trove.map.hash.TLongDoubleHashMap
equals(Object) - Method in class gnu.trove.map.hash.TLongDoubleHashMap.TKeyView
 
equals(Object) - Method in class gnu.trove.set.hash.THashSet
 
equals(Object) - Method in class gnu.trove.set.hash.TIntHashSet
Compares the specified object with this set for equality.
equals(Object) - Method in class gnu.trove.set.hash.TLongHashSet
Compares the specified object with this set for equality.
equals(Object) - Method in interface gnu.trove.set.TIntSet
Compares the specified object with this set for equality.
equals(Object) - Method in interface gnu.trove.set.TLongSet
Compares the specified object with this set for equality.
equals(T, T) - Method in interface gnu.trove.strategy.HashingStrategy
Compares o1 and o2 for equality.
equals(K, K) - Method in class gnu.trove.strategy.IdentityHashingStrategy
 
equals(Object) - Method in interface gnu.trove.TDoubleCollection
Compares the specified object with this collection for equality.
equals(Object) - Method in interface gnu.trove.TFloatCollection
Compares the specified object with this collection for equality.
equals(Object) - Method in interface gnu.trove.TIntCollection
Compares the specified object with this collection for equality.
equals(Object) - Method in interface gnu.trove.TLongCollection
Compares the specified object with this collection for equality.
equals(Object) - Method in interface gnu.trove.TShortCollection
Compares the specified object with this collection for equality.
equals(Object) - Method in class net.sf.jannot.Feature
 
equals(Object) - Method in class net.sf.jannot.Location
 
equals(Object) - Method in class net.sf.jannot.shortread.ShortRead
 
equals(Object) - Method in class net.sf.jannot.source.SAMDataSource
 
equals(Object) - Method in class net.sf.jannot.StringKey
 
equals(Object) - Method in class org.apache.commons.collections.map.Flat3Map
Compares this map with another.
equals(RPChromosomeRegion) - Method in class org.broad.igv.bbfile.RPChromosomeRegion
 
evaluate(double[]) - Method in class org.apache.commons.math.stat.AbstractUnivariateStatistic
 
evaluate(double[], int, int) - Method in class org.apache.commons.math.stat.AbstractUnivariateStatistic
 
evaluate(double[], double) - Method in class org.apache.commons.math.stat.Percentile
Returns an estimate of the pth percentile of the values in the values array.
evaluate(double[], int, int) - Method in class org.apache.commons.math.stat.Percentile
Returns an estimate of the quantileth percentile of the designated values in the values array.
evaluate(double[], int, int, double) - Method in class org.apache.commons.math.stat.Percentile
Returns an estimate of the pth percentile of the values in the values array, starting with the element in (0-based) position begin in the array and including length values.
execute(byte) - Method in interface gnu.trove.function.TByteFunction
Execute this function with value
execute(char) - Method in interface gnu.trove.function.TCharFunction
Execute this function with value
execute(double) - Method in interface gnu.trove.function.TDoubleFunction
Execute this function with value
execute(float) - Method in interface gnu.trove.function.TFloatFunction
Execute this function with value
execute(int) - Method in interface gnu.trove.function.TIntFunction
Execute this function with value
execute(long) - Method in interface gnu.trove.function.TLongFunction
Execute this function with value
execute(T) - Method in interface gnu.trove.function.TObjectFunction
Execute this function with value
execute(short) - Method in interface gnu.trove.function.TShortFunction
Execute this function with value
execute(T) - Method in class gnu.trove.procedure.array.ToObjectArrayProceedure
 
execute(byte) - Method in interface gnu.trove.procedure.TByteProcedure
Executes this procedure.
execute(char) - Method in interface gnu.trove.procedure.TCharProcedure
Executes this procedure.
execute(double) - Method in interface gnu.trove.procedure.TDoubleProcedure
Executes this procedure.
execute(float) - Method in interface gnu.trove.procedure.TFloatProcedure
Executes this procedure.
execute(int, float) - Method in interface gnu.trove.procedure.TIntFloatProcedure
Executes this procedure.
execute(int) - Method in interface gnu.trove.procedure.TIntProcedure
Executes this procedure.
execute(long, double) - Method in interface gnu.trove.procedure.TLongDoubleProcedure
Executes this procedure.
execute(long) - Method in interface gnu.trove.procedure.TLongProcedure
Executes this procedure.
execute(K, V) - Method in interface gnu.trove.procedure.TObjectObjectProcedure
Executes this procedure.
execute(T) - Method in interface gnu.trove.procedure.TObjectProcedure
Executes this procedure.
execute(short) - Method in interface gnu.trove.procedure.TShortProcedure
Executes this procedure.
exists() - Method in class net.sf.jannot.source.Locator
 
exit() - Static method in class net.sf.jannot.Cleaner
 
expand(RPChromosomeRegion) - Method in class org.broad.igv.bbfile.RPChromosomeRegion
 
extractParent(Map<String, String>, String) - Static method in class net.sf.jannot.parser.GFF3Parser
 
extractSequence(Sequence, Feature) - Static method in class net.sf.jannot.utils.SequenceTools
 

F

Faidx - Class in net.sf.jannot.indexing
 
Faidx() - Constructor for class net.sf.jannot.indexing.Faidx
 
FaidxData - Class in net.sf.jannot.refseq
 
FaidxData(FaidxIndex, SeekableStream, String) - Constructor for class net.sf.jannot.refseq.FaidxData
 
FaidxIndex - Class in net.sf.jannot.refseq
 
FaidxIndex(InputStream) - Constructor for class net.sf.jannot.refseq.FaidxIndex
 
FaixDataIterable - Class in net.sf.jannot.refseq
 
FaixDataIterable(SeekableStream, int, int, long, long, long, long) - Constructor for class net.sf.jannot.refseq.FaixDataIterable
 
FastaParser - Class in net.sf.jannot.parser
In case of multiple alignments it is strongly advised to set the dataKey
FastaParser() - Constructor for class net.sf.jannot.parser.FastaParser
 
FastaParser(DataKey) - Constructor for class net.sf.jannot.parser.FastaParser
 
fastCeil(float) - Static method in class gnu.trove.impl.HashFunctions
In profiling, it has been found to be faster to have our own local implementation of "ceil" rather than to call to Math.ceil(double).
Feature - Class in net.sf.jannot
Features are set of characteristics which describe a genome.
Feature() - Constructor for class net.sf.jannot.Feature
 
Feature - Interface in org.broad.tribble
Represents a locus on a reference sequence.
FeatureAnnotation - Interface in net.sf.jannot
Represents the annotation of a single type
FeatureEvent - Class in net.sf.jannot.event
 
FeatureEvent(Feature) - Constructor for class net.sf.jannot.event.FeatureEvent
 
FeatureEvent(Feature, String) - Constructor for class net.sf.jannot.event.FeatureEvent
 
FeatureWrapper - Class in net.sf.jannot.tabix
 
FeatureWrapper(String, IndexedFeatureFile, TabIndex) - Constructor for class net.sf.jannot.tabix.FeatureWrapper
 
file() - Method in class net.sf.jannot.source.Locator
 
FileSource - Class in net.sf.jannot.source
Extends AbstractStreamDataSource.
FileSource(File) - Constructor for class net.sf.jannot.source.FileSource
 
FileSource(String) - Constructor for class net.sf.jannot.source.FileSource
 
FileSource(File, boolean) - Constructor for class net.sf.jannot.source.FileSource
 
fill(ByteBuffer, int) - Method in class org.broad.igv.tdf.TDFFixedTile
 
fill(ByteBuffer, int) - Method in class org.broad.igv.tdf.TDFVaryTile
 
finalize() - Method in class net.sf.jannot.source.das.DAS
 
finalize() - Method in class net.sf.jannot.source.IndexedFastaDataSource
 
finalize() - Method in class net.sf.jannot.source.IndexedMAFDataSource
 
finalize() - Method in class net.sf.jannot.source.SAMDataSource
 
findAllChromosomeNames(BPTreeNode, ArrayList<String>) - Method in class org.broad.igv.bbfile.BPTree
 
FindPeaksParser - Class in net.sf.jannot.parser.software
 
FindPeaksParser() - Constructor for class net.sf.jannot.parser.software.FindPeaksParser
 
finish(URL) - Static method in class net.sf.jannot.source.cache.SourceCache
This method should only be called when the data is completely written.
finish() - Method in class org.broad.igv.tools.Accumulator
 
FIXEDSTEP_ITEM_SIZE - Static variable in class org.broad.igv.bbfile.BigWigSectionHeader
 
Flat3Map<K,V> - Class in org.apache.commons.collections.map
A Map implementation that stores data in simple fields until the size is greater than 3.
Flat3Map() - Constructor for class org.apache.commons.collections.map.Flat3Map
Constructor.
Flat3Map(Map) - Constructor for class org.apache.commons.collections.map.Flat3Map
Constructor copying elements from another map.
flip() - Method in class net.sf.jannot.SyntenicBlock
Flip reference and target
FloatArrayList - Class in org.broad.igv.util.collections
Author: jrobinso Date: Jul 22, 2010

ArrayList type collection for int types.

FloatArrayList() - Constructor for class org.broad.igv.util.collections.FloatArrayList
 
FloatArrayList(int) - Constructor for class org.broad.igv.util.collections.FloatArrayList
 
FloatArrayList(float[]) - Constructor for class org.broad.igv.util.collections.FloatArrayList
 
FloatArrayWiggle - Class in net.sf.jannot.wiggle
 
FloatArrayWiggle(float[]) - Constructor for class net.sf.jannot.wiggle.FloatArrayWiggle
 
forEach(TIntProcedure) - Method in class gnu.trove.impl.hash.TIntFloatHash
Executes procedure for each key in the map.
forEach(TIntProcedure) - Method in class gnu.trove.impl.hash.TIntHash
Executes procedure for each element in the set.
forEach(TLongProcedure) - Method in class gnu.trove.impl.hash.TLongDoubleHash
Executes procedure for each key in the map.
forEach(TLongProcedure) - Method in class gnu.trove.impl.hash.TLongHash
Executes procedure for each element in the set.
forEach(TObjectProcedure<T>) - Method in class gnu.trove.impl.hash.TObjectHash
Executes procedure for each element in the set.
forEach(TIntProcedure) - Method in class gnu.trove.map.hash.TIntFloatHashMap.TKeyView
Executes procedure for each element in the set.
forEach(TFloatProcedure) - Method in class gnu.trove.map.hash.TIntFloatHashMap.TValueView
Executes procedure for each element in the collection.
forEach(TLongProcedure) - Method in class gnu.trove.map.hash.TLongDoubleHashMap.TKeyView
Executes procedure for each element in the set.
forEach(TDoubleProcedure) - Method in class gnu.trove.map.hash.TLongDoubleHashMap.TValueView
Executes procedure for each element in the collection.
forEach(TIntProcedure) - Method in interface gnu.trove.set.TIntSet
Executes procedure for each element in the set.
forEach(TLongProcedure) - Method in interface gnu.trove.set.TLongSet
Executes procedure for each element in the set.
forEach(TDoubleProcedure) - Method in interface gnu.trove.TDoubleCollection
Executes procedure for each element in the collection.
forEach(TFloatProcedure) - Method in interface gnu.trove.TFloatCollection
Executes procedure for each element in the collection.
forEach(TIntProcedure) - Method in interface gnu.trove.TIntCollection
Executes procedure for each element in the collection.
forEach(TLongProcedure) - Method in interface gnu.trove.TLongCollection
Executes procedure for each element in the collection.
forEach(TShortProcedure) - Method in interface gnu.trove.TShortCollection
Executes procedure for each element in the collection.
forEachEntry(TObjectObjectProcedure<K, V>) - Method in class gnu.trove.map.hash.THashMap
Executes procedure for each key/value entry in the map.
forEachEntry(TIntFloatProcedure) - Method in class gnu.trove.map.hash.TIntFloatHashMap
Executes procedure for each key/value entry in the map.
forEachEntry(TLongDoubleProcedure) - Method in class gnu.trove.map.hash.TLongDoubleHashMap
Executes procedure for each key/value entry in the map.
forEachEntry(TIntFloatProcedure) - Method in interface gnu.trove.map.TIntFloatMap
Executes procedure for each key/value entry in the map.
forEachEntry(TLongDoubleProcedure) - Method in interface gnu.trove.map.TLongDoubleMap
Executes procedure for each key/value entry in the map.
forEachKey(TObjectProcedure<K>) - Method in class gnu.trove.map.hash.THashMap
Executes procedure for each key in the map.
forEachKey(TIntProcedure) - Method in class gnu.trove.map.hash.TIntFloatHashMap
Executes procedure for each key in the map.
forEachKey(TLongProcedure) - Method in class gnu.trove.map.hash.TLongDoubleHashMap
Executes procedure for each key in the map.
forEachKey(TIntProcedure) - Method in interface gnu.trove.map.TIntFloatMap
Executes procedure for each key in the map.
forEachKey(TLongProcedure) - Method in interface gnu.trove.map.TLongDoubleMap
Executes procedure for each key in the map.
forEachValue(TObjectProcedure<V>) - Method in class gnu.trove.map.hash.THashMap
Executes procedure for each value in the map.
forEachValue(TFloatProcedure) - Method in class gnu.trove.map.hash.TIntFloatHashMap
Executes procedure for each value in the map.
forEachValue(TDoubleProcedure) - Method in class gnu.trove.map.hash.TLongDoubleHashMap
Executes procedure for each value in the map.
forEachValue(TFloatProcedure) - Method in interface gnu.trove.map.TIntFloatMap
Executes procedure for each value in the map.
forEachValue(TDoubleProcedure) - Method in interface gnu.trove.map.TLongDoubleMap
Executes procedure for each value in the map.
FREE - Static variable in class gnu.trove.impl.hash.TObjectHash
 
FREE - Static variable in class gnu.trove.impl.hash.TPrimitiveHash
flag indicating that a slot in the hashtable is available
fromSymbol(char) - Static method in enum net.sf.jannot.Strand
 
FULL - Static variable in class gnu.trove.impl.hash.TPrimitiveHash
flag indicating that a slot in the hashtable is occupied

G

geDataSize() - Method in class org.broad.igv.bbfile.RPTreeLeafNodeItem
 
GenbankParser - Class in net.sf.jannot.parser
 
GenbankParser() - Constructor for class net.sf.jannot.parser.GenbankParser
 
GenbankParser(DataKey) - Constructor for class net.sf.jannot.parser.GenbankParser
 
GeneMarkParser - Class in net.sf.jannot.parser.software
Parser for the output of the GeneMark gene caller
GeneMarkParser() - Constructor for class net.sf.jannot.parser.software.GeneMarkParser
 
generateBlockZippedFile(InputStream, File) - Static method in class net.sf.jannot.mafix.MafixFactory
Read the original MAF file and write it to the block zipped stream.
generateIndex(SeekableStream, File) - Static method in class net.sf.jannot.mafix.MafixFactory
 
genoToShort(String) - Static method in class org.broad.igv.util.StringUtils
 
get(Object) - Method in class gnu.trove.map.hash.THashMap
retrieves the value for key
get(int) - Method in class gnu.trove.map.hash.TIntFloatHashMap
Retrieves the value for key
get(long) - Method in class gnu.trove.map.hash.TLongDoubleHashMap
Retrieves the value for key
get(int) - Method in interface gnu.trove.map.TIntFloatMap
Retrieves the value for key
get(long) - Method in interface gnu.trove.map.TLongDoubleMap
Retrieves the value for key
get(int, int) - Method in class net.sf.jannot.alignment.maf.AbstractMAFMultipleAlignment
 
get() - Method in class net.sf.jannot.alignment.maf.AbstractMAFMultipleAlignment
 
get(int, int) - Method in class net.sf.jannot.alignment.maf.MAFMemoryMultipleAlignment
 
get() - Method in class net.sf.jannot.alignment.maf.MAFMemoryMultipleAlignment
 
get(int, int) - Method in class net.sf.jannot.alignment.mfa.AlignmentAnnotation
 
get() - Method in class net.sf.jannot.alignment.mfa.AlignmentAnnotation
 
get(String) - Method in enum net.sf.jannot.AminoAcidMapping
 
get(int, int) - Method in class net.sf.jannot.bigwig.BigWigData
 
get() - Method in class net.sf.jannot.bigwig.BigWigData
 
get(int, int) - Method in interface net.sf.jannot.Data
Gets data.
get() - Method in interface net.sf.jannot.Data
 
get(String) - Method in class net.sf.jannot.Description
 
get(DataKey) - Method in class net.sf.jannot.Entry
 
get(Entry, Location) - Method in class net.sf.jannot.EntrySetAnnotation
Returns all object of type T that overlap with the provided location.
get(Entry, Location, int) - Method in class net.sf.jannot.EntrySetAnnotation
Returns all object of type T that overlap with the provided location.
get(int, int) - Method in class net.sf.jannot.mafix.IndexedMAF
 
get() - Method in class net.sf.jannot.mafix.IndexedMAF
 
get(int, int) - Method in class net.sf.jannot.MemoryFeatureAnnotation
 
get() - Method in class net.sf.jannot.MemoryFeatureAnnotation
 
get(int, int) - Method in class net.sf.jannot.MemoryListData
 
get() - Method in class net.sf.jannot.MemoryListData
 
get(int, int) - Method in class net.sf.jannot.refseq.FaidxData
 
get() - Method in class net.sf.jannot.refseq.FaidxData
 
get(String) - Method in class net.sf.jannot.refseq.FaidxIndex
 
get(int) - Method in class net.sf.jannot.refseq.MemorySequence
 
get(int, int) - Method in class net.sf.jannot.refseq.MemorySequence
 
get() - Method in class net.sf.jannot.refseq.MemorySequence
 
get(int, int) - Method in class net.sf.jannot.refseq.Sequence
Gets a subsequence from this sequence.
get() - Method in class net.sf.jannot.refseq.Sequence
 
get(int, int) - Method in class net.sf.jannot.refseq.SubSequence
 
get() - Method in class net.sf.jannot.refseq.SubSequence
 
get(int, int) - Method in class net.sf.jannot.shortread.BAMreads
 
get() - Method in class net.sf.jannot.shortread.BAMreads
 
get(int, int) - Method in class net.sf.jannot.shortread.MemoryReadSet
 
get() - Method in class net.sf.jannot.shortread.MemoryReadSet
 
get(URL) - Static method in class net.sf.jannot.source.cache.SourceCache
 
get(int) - Static method in enum net.sf.jannot.Strand
 
get(Entry, Location) - Method in class net.sf.jannot.SyntenicAnnotation
 
get(int, int) - Method in class net.sf.jannot.tabix.BEDWrapper
 
get(int, int) - Method in class net.sf.jannot.tabix.GFFWrapper
 
get(int, int) - Method in class net.sf.jannot.tabix.PileupWrapper
 
get(int, int) - Method in class net.sf.jannot.tabix.SWigWrapper
 
get(int) - Method in class net.sf.jannot.tabix.TabixLine
 
get() - Method in class net.sf.jannot.tabix.TabixWrapper
 
get(int, int) - Method in class net.sf.jannot.tdf.TDFData
 
get() - Method in class net.sf.jannot.tdf.TDFData
 
get(String) - Static method in class net.sf.jannot.Type
Return key
get(int, int, int) - Method in class net.sf.jannot.wiggle.AbstractWiggle
 
get(int, int) - Method in class net.sf.jannot.wiggle.AbstractWiggle
 
get() - Method in class net.sf.jannot.wiggle.DiskArrayWiggle
 
get() - Method in class net.sf.jannot.wiggle.FloatArrayWiggle
 
get(int, int, int) - Method in interface net.sf.jannot.wiggle.Graph
Returns float array with float[i] containing a value Resolutions should be powers of two: 1,2,4,8,16,32,64,128,256,...
get() - Method in class net.sf.jannot.wiggle.TroveArrayWiggle
 
get(Object) - Method in class org.apache.commons.collections.map.Flat3Map
Gets the value mapped to the key specified.
get(int) - Method in class org.broad.igv.util.collections.DoubleArrayList
 
get(int) - Method in class org.broad.igv.util.collections.FloatArrayList
 
get(int) - Method in class org.broad.igv.util.collections.IntArrayList
 
getAlignmentSequence(int) - Method in class net.sf.jannot.alignment.maf.AbstractAlignmentBlock
 
getAlignmentSequence(int) - Method in class net.sf.jannot.alignment.maf.LazyAlignmentBlock
 
getAlignmentSequence(int) - Method in class net.sf.jannot.alignment.maf.MemoryAlignmentBlock
 
getAll(Entry) - Method in class net.sf.jannot.EntrySetAnnotation
 
getAll(Entry) - Method in class net.sf.jannot.SyntenicAnnotation
 
getAllChromosomeRegions() - Method in class org.broad.igv.bbfile.RPTree
 
getAminoAcid(int, AminoAcidMapping) - Method in class net.sf.jannot.refseq.MemorySequence
Deprecated. 
getAttribute(String) - Method in class org.broad.igv.tdf.TDFEntity
 
getAttributeNames() - Method in class org.broad.igv.tdf.TDFEntity
 
getAutoCompactionFactor() - Method in class gnu.trove.impl.hash.THash
 
getAutoSqlOffset() - Method in class org.broad.igv.bbfile.BBFileHeader
 
getAvailableMemoryFraction() - Method in class org.broad.LRUCache
 
getAvailableWindowFunctions() - Method in interface org.broad.igv.data.DataSource
 
getBases() - Method in interface net.sf.jannot.pileup.Pile
 
getBases() - Method in class net.sf.jannot.pileup.ReadDetailPile
Gives you the actual bases that are present in this pile.
getBases() - Method in class net.sf.jannot.pileup.SinglePile
Gives you the actual bases that are present in this pile.
getBasesCovered() - Method in class org.broad.igv.bbfile.BBTotalSummaryBlock
 
getBasesCovered() - Method in class org.broad.igv.bbfile.ZoomDataRecord
 
getBBFileHeader() - Method in class org.broad.igv.bbfile.BBFileReader
 
getBBFis() - Method in class org.broad.igv.bbfile.BBFileReader
 
getBBFis() - Method in class org.broad.igv.bbfile.BBZoomLevelFormat
 
getBBFis() - Method in class org.broad.igv.bbfile.BigBedIterator
 
getBBFis() - Method in class org.broad.igv.bbfile.BigWigIterator
 
getBBFis() - Method in class org.broad.igv.bbfile.ZoomLevelIterator
 
getBedData(RPChromosomeRegion, boolean) - Method in class org.broad.igv.bbfile.BigBedDataBlock
 
getBigBedIterator(String, int, String, int, boolean) - Method in class org.broad.igv.bbfile.BBFileReader
Returns an iterator for BigBed features which occupy a chromosome selection region.
getBigBedIterator() - Method in class org.broad.igv.bbfile.BBFileReader
Returns an iterator for BigBed features for all chromosome regions.
getBigWigIterator(String, int, String, int, boolean) - Method in class org.broad.igv.bbfile.BBFileReader
Returns an iterator for BigWig values which occupy the specified startChromosome region.
getBigWigIterator() - Method in class org.broad.igv.bbfile.BBFileReader
Returns an iterator for BigWig values for all chromosome regions.
getBlockSize() - Method in class org.broad.igv.bbfile.BPTree
 
getBlockSize() - Method in class org.broad.igv.bbfile.BPTreeHeader
 
getBlockSize() - Method in class org.broad.igv.bbfile.RPTreeHeader
 
getBPTreeOffset() - Method in class org.broad.igv.bbfile.BPTree
 
getBytes() - Method in class org.broad.igv.tdf.BufferedByteWriter
 
getCached(int) - Method in class net.sf.jannot.MemoryFeatureAnnotation
 
getCachedIndexOf(Feature) - Method in class net.sf.jannot.MemoryFeatureAnnotation
 
getChildItems() - Method in class org.broad.igv.bbfile.BPTreeChildNode
 
getChildNode() - Method in class org.broad.igv.bbfile.BPTreeChildNodeItem
 
getChildNode() - Method in class org.broad.igv.bbfile.RPTreeChildNodeItem
 
getChr() - Method in class org.broad.igv.data.BasicScore
 
getChr() - Method in interface org.broad.tribble.Feature
Return the features reference sequence name, e.g chromosome or contig
getChromEnd() - Method in class org.broad.igv.bbfile.ZoomDataRecord
 
getChromID() - Method in class org.broad.igv.bbfile.BigWigSectionHeader
 
getChromID() - Method in class org.broad.igv.bbfile.BPTreeLeafNodeItem
 
getChromId() - Method in class org.broad.igv.bbfile.ZoomDataRecord
 
getChromKey() - Method in class org.broad.igv.bbfile.BPTreeChildNodeItem
 
getChromKey() - Method in class org.broad.igv.bbfile.BPTreeLeafNodeItem
 
getChromName() - Method in class org.broad.igv.bbfile.ZoomDataRecord
 
getChromosome() - Method in class org.broad.igv.bbfile.BedFeature
 
getChromosome() - Method in class org.broad.igv.bbfile.WigItem
 
getChromosome() - Method in class org.broad.igv.data.BasicScore
 
getChromosomeBounds(int, int) - Method in class org.broad.igv.bbfile.BBFileReader
 
getChromosomeBounds() - Method in class org.broad.igv.bbfile.BBFileReader
 
getChromosomeBounds() - Method in class org.broad.igv.bbfile.RPTree
 
getChromosomeBounds() - Method in class org.broad.igv.bbfile.RPTreeChildNode
 
getChromosomeBounds() - Method in class org.broad.igv.bbfile.RPTreeChildNodeItem
 
getChromosomeBounds() - Method in class org.broad.igv.bbfile.RPTreeLeafNode
 
getChromosomeBounds() - Method in class org.broad.igv.bbfile.RPTreeLeafNodeItem
 
getChromosomeBounds() - Method in interface org.broad.igv.bbfile.RPTreeNode
 
getChromosomeDataHits(RPChromosomeRegion, boolean) - Method in class org.broad.igv.bbfile.RPTree
 
getChromosomeDataTree() - Method in class org.broad.igv.bbfile.BBFileReader
 
getChromosomeDataTree() - Method in class org.broad.igv.bbfile.BigBedIterator
 
getChromosomeDataTree() - Method in class org.broad.igv.bbfile.BigWigIterator
 
getChromosomeEnd() - Method in class org.broad.igv.bbfile.BigWigSectionHeader
 
getChromosomeID(String) - Method in class org.broad.igv.bbfile.BBFileReader
 
getChromosomeID(String) - Method in class org.broad.igv.bbfile.BPTree
 
getChromosomeIDMap(int, int) - Method in class org.broad.igv.bbfile.BPTree
 
getChromosomeIDTree() - Method in class org.broad.igv.bbfile.BBFileReader
 
getChromosomeIDTree() - Method in class org.broad.igv.bbfile.BigBedIterator
 
getChromosomeIDTree() - Method in class org.broad.igv.bbfile.BigWigIterator
 
getChromosomeIDTree() - Method in class org.broad.igv.bbfile.ZoomLevelIterator
 
getChromosomeKey(String) - Method in class org.broad.igv.bbfile.BPTree
 
getChromosomeName(int) - Method in class org.broad.igv.bbfile.BBFileReader
 
getChromosomeName(int) - Method in class org.broad.igv.bbfile.BPTree
 
getChromosomeNameCount() - Method in class org.broad.igv.bbfile.BBFileReader
 
getChromosomeNames() - Method in class org.broad.igv.bbfile.BBFileReader
 
getChromosomeNames() - Method in class org.broad.igv.bbfile.BPTree
 
getChromosomeRegion(int, int) - Method in class org.broad.igv.bbfile.RPTree
 
getChromosomeRegionCount() - Method in class org.broad.igv.bbfile.BBFileReader
 
getChromosomeRegions() - Method in class org.broad.igv.bbfile.BBFileReader
 
getChromosomeStart() - Method in class org.broad.igv.bbfile.BigWigSectionHeader
 
getChromosomeTreeOffset() - Method in class org.broad.igv.bbfile.BBFileHeader
 
getChromSize() - Method in class org.broad.igv.bbfile.BPTreeLeafNodeItem
 
getChromStart() - Method in class org.broad.igv.bbfile.ZoomDataRecord
 
getColor() - Method in class net.sf.jannot.Feature
 
getConfidence() - Method in class org.broad.igv.data.BasicScore
 
getConfidence() - Method in interface org.broad.igv.feature.LocusScore
 
getConservation(int) - Method in class net.sf.jannot.alignment.mfa.AlignmentAnnotation
Position in the reference This coordinate is one based
getDataCount() - Method in class org.broad.igv.bbfile.BBFileReader
 
getDataMax() - Method in interface org.broad.igv.data.DataSource
 
getDataMax() - Method in class org.broad.igv.tdf.TDFReader
 
getDataMin() - Method in interface org.broad.igv.data.DataSource
 
getDataMin() - Method in class org.broad.igv.tdf.TDFReader
 
getDataOffset() - Method in class org.broad.igv.bbfile.BBZoomLevelHeader
 
getDataOffset() - Method in class org.broad.igv.bbfile.RPTreeLeafNodeItem
 
getDataset(String, int, WindowFunction) - Method in class org.broad.igv.tdf.TDFReader
 
getDataset(String) - Method in class org.broad.igv.tdf.TDFReader
 
getDatasetNames() - Method in class org.broad.igv.tdf.TDFReader
 
getDecompressionBufSize() - Method in class org.broad.igv.bbfile.BBFileReader
 
getDefinedFieldCount() - Method in class org.broad.igv.bbfile.BBFileHeader
 
getDescription() - Method in enum net.sf.jannot.AminoAcidMapping
 
getDisplayName() - Method in enum org.broad.igv.track.WindowFunction
 
getDouble(int) - Method in class net.sf.jannot.tabix.TabixLine
 
getEnd() - Method in class org.broad.igv.data.BasicScore
 
getEnd() - Method in interface org.broad.tribble.Feature
Return the end position following 1-based fully closed conventions.
getEndBase() - Method in class org.broad.igv.bbfile.BedFeature
 
getEndBase() - Method in class org.broad.igv.bbfile.RPChromosomeRegion
 
getEndBase() - Method in class org.broad.igv.bbfile.RPTreeHeader
 
getEndBase() - Method in class org.broad.igv.bbfile.WigItem
 
getEndChromID() - Method in class org.broad.igv.bbfile.RPChromosomeRegion
 
getEndChromID() - Method in class org.broad.igv.bbfile.RPTreeHeader
 
getEndPosition(int) - Method in class org.broad.igv.tdf.TDFBedTile
 
getEndPosition(int) - Method in class org.broad.igv.tdf.TDFFixedTile
 
getEndPosition(int) - Method in interface org.broad.igv.tdf.TDFTile
 
getEndPosition(int) - Method in class org.broad.igv.tdf.TDFVaryTile
 
getEntry() - Method in class net.sf.jannot.EntrySet
Returns the default entry.
getEntry(String) - Method in class net.sf.jannot.EntrySet
 
getEntryPoints(String) - Method in class net.sf.jannot.source.das.DAS
 
getEstimateCount(Location) - Method in interface net.sf.jannot.DensityEstimate
 
getEstimateCount(Location) - Method in class net.sf.jannot.MemoryFeatureAnnotation
 
getEstimateCount(Location) - Method in class net.sf.jannot.tabix.TabixWrapper
 
getExtendedEnd() - Method in class org.broad.igv.data.BasicScore
 
getExtendedStart() - Method in class org.broad.igv.data.BasicScore
 
getExtremes(RPChromosomeRegion) - Method in class org.broad.igv.bbfile.RPChromosomeRegion
 
getFeature() - Method in class net.sf.jannot.event.FeatureEvent
 
getFieldCount() - Method in class org.broad.igv.bbfile.BBFileHeader
 
getFile() - Method in class net.sf.jannot.source.FileSource
 
getFileHeaderSize() - Method in class org.broad.igv.bbfile.BBFileHeader
 
getFirstRead(SAMRecord) - Method in class net.sf.jannot.shortread.BAMreads
 
getFirstRead(SAMRecord) - Method in class net.sf.jannot.shortread.MemoryReadSet
 
getFirstRead(SAMRecord) - Method in class net.sf.jannot.shortread.ReadGroup
 
getFis() - Method in class org.broad.igv.bbfile.BPTree
 
getFloat(int) - Method in class net.sf.jannot.picard.BinaryBlob
 
getFootprint(int) - Method in class net.sf.jannot.alignment.mfa.AlignmentAnnotation
 
getFrame() - Method in class net.sf.jannot.Feature
 
getFullDataOffset() - Method in class org.broad.igv.bbfile.BBFileHeader
 
getFullIndexOffset() - Method in class org.broad.igv.bbfile.BBFileHeader
 
getGroup(String) - Method in class org.broad.igv.tdf.TDFReader
 
getGroup(String) - Method in class org.broad.igv.tdf.TDFWriter
 
getGroupNames() - Method in class org.broad.igv.tdf.TDFReader
 
getHeaderOffset() - Method in class org.broad.igv.bbfile.BPTreeHeader
 
getHeaderSize() - Static method in class org.broad.igv.bbfile.BPTreeHeader
 
getHeaderSize() - Method in class org.broad.igv.bbfile.RPTreeHeader
 
getHighestChromID() - Method in class org.broad.igv.bbfile.BPTreeChildNode
 
getHighestChromID() - Method in class org.broad.igv.bbfile.BPTreeLeafNode
 
getHighestChromID() - Method in interface org.broad.igv.bbfile.BPTreeNode
 
getHighestChromKey() - Method in class org.broad.igv.bbfile.BPTreeChildNode
 
getHighestChromKey() - Method in class org.broad.igv.bbfile.BPTreeLeafNode
 
getHighestChromKey() - Method in interface org.broad.igv.bbfile.BPTreeNode
 
getID() - Method in class net.sf.jannot.Entry
Shortcut to access the id
getIndex(Locator) - Static method in class net.sf.jannot.source.IndexManager
 
getIndex() - Method in class net.sf.jannot.tabix.IndexedFeatureFile
 
getIndexOffset() - Method in class org.broad.igv.bbfile.BBZoomLevelHeader
 
getInputFileName() - Method in class net.sf.jannot.tabix.BinaryCodec
 
getInputStream() - Method in class net.sf.jannot.tabix.BinaryCodec
 
getInt(int) - Method in class net.sf.jannot.tabix.TabixLine
 
getIntv(String) - Method in class net.sf.jannot.tabix.TabixReader
 
getIntv(String) - Method in class net.sf.jannot.tabix.TabixWriter
Override getIntv because it's a good time to figure out which bin things should go into.
getIos() - Method in class net.sf.jannot.source.AbstractStreamDataSource
 
getItem(int) - Method in class org.broad.igv.bbfile.BPTreeChildNode
 
getItem(int) - Method in class org.broad.igv.bbfile.BPTreeLeafNode
 
getItem(int) - Method in interface org.broad.igv.bbfile.BPTreeNode
 
getItem(int) - Method in class org.broad.igv.bbfile.RPTreeChildNode
 
getItem(int) - Method in class org.broad.igv.bbfile.RPTreeLeafNode
 
getItem(int) - Method in interface org.broad.igv.bbfile.RPTreeNode
 
getItemCount() - Method in class org.broad.igv.bbfile.BigWigSection
 
getItemCount() - Method in class org.broad.igv.bbfile.BigWigSectionHeader
 
getItemCount() - Method in class org.broad.igv.bbfile.BPTree
 
getItemCount() - Method in class org.broad.igv.bbfile.BPTreeChildNode
 
getItemCount() - Method in class org.broad.igv.bbfile.BPTreeHeader
 
getItemCount() - Method in class org.broad.igv.bbfile.BPTreeLeafNode
 
getItemCount() - Method in interface org.broad.igv.bbfile.BPTreeNode
 
getItemCount() - Method in class org.broad.igv.bbfile.RPTree
 
getItemCount() - Method in class org.broad.igv.bbfile.RPTreeChildNode
 
getItemCount() - Method in class org.broad.igv.bbfile.RPTreeHeader
 
getItemCount() - Method in class org.broad.igv.bbfile.RPTreeLeafNode
 
getItemCount() - Method in interface org.broad.igv.bbfile.RPTreeNode
 
getItemIndex() - Method in class org.broad.igv.bbfile.BedFeature
 
getItemIndex() - Method in class org.broad.igv.bbfile.BPTreeChildNodeItem
 
getItemIndex() - Method in class org.broad.igv.bbfile.BPTreeLeafNodeItem
 
getItemNumber() - Method in class org.broad.igv.bbfile.WigItem
 
getItemSpan() - Method in class org.broad.igv.bbfile.BigWigSectionHeader
 
getItemsPerSlot() - Method in class org.broad.igv.bbfile.RPTreeHeader
 
getItemStep() - Method in class org.broad.igv.bbfile.BigWigSectionHeader
 
getItemType() - Method in class org.broad.igv.bbfile.BigWigSectionHeader
 
getKey() - Method in class net.sf.jannot.shortread.BAMreads
 
getKeySize() - Method in class org.broad.igv.bbfile.BPTree
 
getKeySize() - Method in class org.broad.igv.bbfile.BPTreeHeader
 
getLeafItems() - Method in class org.broad.igv.bbfile.BigBedIterator
 
getLeafItems() - Method in class org.broad.igv.bbfile.BPTreeLeafNode
 
getLength() - Method in interface net.sf.jannot.pileup.Pile
 
getLength() - Method in class net.sf.jannot.pileup.SinglePile
 
getLocator() - Method in class net.sf.jannot.source.DataSource
 
getLocator() - Method in class org.broad.igv.bbfile.BBFileReader
 
getLocator() - Method in class org.broad.igv.tdf.TDFReader
 
getLowerLimit() - Method in class org.broad.igv.tdf.TDFReader
 
getLowestChromID() - Method in class org.broad.igv.bbfile.BPTreeChildNode
 
getLowestChromID() - Method in class org.broad.igv.bbfile.BPTreeLeafNode
 
getLowestChromID() - Method in interface org.broad.igv.bbfile.BPTreeNode
 
getLowestChromKey() - Method in class org.broad.igv.bbfile.BPTreeChildNode
 
getLowestChromKey() - Method in class org.broad.igv.bbfile.BPTreeLeafNode
 
getLowestChromKey() - Method in interface org.broad.igv.bbfile.BPTreeNode
 
getMagic() - Method in class org.broad.igv.bbfile.BBFileHeader
 
getMagic() - Method in class org.broad.igv.bbfile.BPTreeHeader
 
getMagic() - Method in class org.broad.igv.bbfile.RPTreeHeader
 
getMaximumCoordinate() - Method in interface net.sf.jannot.DensityEstimate
 
getMaximumCoordinate() - Method in class net.sf.jannot.MemoryFeatureAnnotation
 
getMaximumCoordinate() - Method in class net.sf.jannot.tabix.TabixWrapper
 
getMaximumLength() - Method in class net.sf.jannot.Entry
Returns the highest position for which there is data
getMaxScore() - Method in interface net.sf.jannot.FeatureAnnotation
Gives the most reliable estimate of the maximum score.
getMaxScore() - Method in class net.sf.jannot.MemoryFeatureAnnotation
 
getMaxScore() - Method in class net.sf.jannot.tabix.FeatureWrapper
 
getMaxVal() - Method in class org.broad.igv.bbfile.BBTotalSummaryBlock
 
getMaxVal() - Method in class org.broad.igv.bbfile.ZoomDataRecord
 
getMaxZoom() - Method in class org.broad.igv.tdf.TDFReader
 
getMBBFis() - Method in class org.broad.igv.bbfile.BBTotalSummaryBlock
 
getMeanVal() - Method in class org.broad.igv.bbfile.ZoomDataRecord
 
getMemoryAnnotation(DataKey) - Method in class net.sf.jannot.Entry
 
getMEndFileOffset() - Method in class org.broad.igv.bbfile.RPTreeHeader
 
getMinScore() - Method in interface net.sf.jannot.FeatureAnnotation
Gives the most reliable estimate of the mininum score.
getMinScore() - Method in class net.sf.jannot.MemoryFeatureAnnotation
 
getMinScore() - Method in class net.sf.jannot.tabix.FeatureWrapper
 
getMinVal() - Method in class org.broad.igv.bbfile.BBTotalSummaryBlock
 
getMinVal() - Method in class org.broad.igv.bbfile.ZoomDataRecord
 
getName() - Method in class net.sf.jannot.alignment.maf.AbstractAlignmentSequence
 
getName() - Method in class net.sf.jannot.source.Locator
 
getName(int) - Method in class org.broad.igv.tdf.TDFBedTile
 
getName() - Method in class org.broad.igv.tdf.TDFEntity
 
getName(int) - Method in class org.broad.igv.tdf.TDFFixedTile
 
getName(int) - Method in interface org.broad.igv.tdf.TDFTile
 
getName(int) - Method in class org.broad.igv.tdf.TDFVaryTile
 
getNames() - Method in class net.sf.jannot.mafix.IndexedMAF
 
getNodeCount() - Method in class org.broad.igv.bbfile.BPTree
 
getNodeCount() - Method in class org.broad.igv.bbfile.RPTree
 
getNodeIndex() - Method in class org.broad.igv.bbfile.BPTreeChildNode
 
getNodeIndex() - Method in class org.broad.igv.bbfile.BPTreeLeafNode
 
getNodeIndex() - Method in interface org.broad.igv.bbfile.BPTreeNode
 
getNoEntryKey() - Method in class gnu.trove.impl.hash.TIntFloatHash
Returns the value that is used to represent null as a key.
getNoEntryKey() - Method in class gnu.trove.impl.hash.TLongDoubleHash
Returns the value that is used to represent null as a key.
getNoEntryKey() - Method in interface gnu.trove.map.TIntFloatMap
Returns the value that will be returned from TIntFloatMap.get(int) or TIntFloatMap.put(int, float) if no entry exists for a given key.
getNoEntryKey() - Method in interface gnu.trove.map.TLongDoubleMap
Returns the value that will be returned from TLongDoubleMap.get(long) or TLongDoubleMap.put(long, double) if no entry exists for a given key.
getNoEntryValue() - Method in class gnu.trove.impl.hash.TIntFloatHash
Returns the value that is used to represent null.
getNoEntryValue() - Method in class gnu.trove.impl.hash.TIntHash
Returns the value that is used to represent null.
getNoEntryValue() - Method in class gnu.trove.impl.hash.TLongDoubleHash
Returns the value that is used to represent null.
getNoEntryValue() - Method in class gnu.trove.impl.hash.TLongHash
Returns the value that is used to represent null.
getNoEntryValue() - Method in class gnu.trove.map.hash.TIntFloatHashMap.TKeyView
Returns the value that is used to represent null.
getNoEntryValue() - Method in class gnu.trove.map.hash.TIntFloatHashMap.TValueView
Returns the value that is used to represent null.
getNoEntryValue() - Method in class gnu.trove.map.hash.TLongDoubleHashMap.TKeyView
Returns the value that is used to represent null.
getNoEntryValue() - Method in class gnu.trove.map.hash.TLongDoubleHashMap.TValueView
Returns the value that is used to represent null.
getNoEntryValue() - Method in interface gnu.trove.map.TIntFloatMap
Returns the value that will be returned from TIntFloatMap.get(int) or TIntFloatMap.put(int, float) if no entry exists for a given key.
getNoEntryValue() - Method in interface gnu.trove.map.TLongDoubleMap
Returns the value that will be returned from TLongDoubleMap.get(long) or TLongDoubleMap.put(long, double) if no entry exists for a given key.
getNoEntryValue() - Method in interface gnu.trove.set.TIntSet
Returns the value that is used to represent null.
getNoEntryValue() - Method in interface gnu.trove.set.TLongSet
Returns the value that is used to represent null.
getNoEntryValue() - Method in interface gnu.trove.TDoubleCollection
Returns the value that is used to represent null.
getNoEntryValue() - Method in interface gnu.trove.TFloatCollection
Returns the value that is used to represent null.
getNoEntryValue() - Method in interface gnu.trove.TIntCollection
Returns the value that is used to represent null.
getNoEntryValue() - Method in interface gnu.trove.TLongCollection
Returns the value that is used to represent null.
getNoEntryValue() - Method in interface gnu.trove.TShortCollection
Returns the value that is used to represent null.
getNucleotide(int) - Method in class net.sf.jannot.alignment.mfa.Alignment
Gives the nucleotide that appears at the given position in the alignment.
getNucleotide(int) - Method in class net.sf.jannot.refseq.MemorySequence
Deprecated. 
getNucleotide(int) - Method in class net.sf.jannot.shortread.BasicShortRead
 
getNucleotide(int) - Method in class net.sf.jannot.shortread.ShortRead
 
getNucleotide(SAMRecord, int) - Static method in class net.sf.jannot.shortread.ShortReadTools
Deprecated. 
getNucleotideCount(char, int) - Method in class net.sf.jannot.alignment.mfa.AlignmentAnnotation
 
getNumberOfTiles() - Method in class org.broad.igv.tdf.TDFDataset
 
getOrCreateEntry(String) - Method in class net.sf.jannot.EntrySet
 
getOrder() - Method in class org.broad.igv.bbfile.RPTree
 
getOutputFileName() - Method in class net.sf.jannot.tabix.BinaryCodec
 
getOutputStream() - Method in class net.sf.jannot.tabix.BinaryCodec
 
getPairLength() - Method in class net.sf.jannot.shortread.BAMreads
 
getPairLength() - Method in class net.sf.jannot.shortread.MemoryReadSet
 
getPairLength() - Method in class net.sf.jannot.shortread.ReadGroup
Returns the maximum length of a pair of reads.
getParent() - Method in class net.sf.jannot.Location
 
getParser() - Method in class net.sf.jannot.source.AbstractStreamDataSource
 
getPercentile(WindowFunction) - Method in class org.broad.igv.tools.Accumulator
 
getPhase(int) - Method in class net.sf.jannot.Feature
 
getPostfix() - Method in class net.sf.jannot.source.Locator
 
getQualifiersKeys() - Method in class net.sf.jannot.Feature
 
getQuantile() - Method in class org.apache.commons.math.stat.Percentile
Returns the value of the quantile field (determines what percentile is computed when evaluate() is called with no quantile argument).
getQuery(int) - Static method in class net.sf.jannot.shortread.ShortRead
 
getRawRange(int, int) - Method in class net.sf.jannot.wiggle.AbstractWiggle
 
getRawRange(int, int) - Method in class net.sf.jannot.wiggle.DiskArrayWiggle
 
getRawRange(int, int) - Method in class net.sf.jannot.wiggle.FloatArrayWiggle
 
getRawRange(int, int) - Method in interface net.sf.jannot.wiggle.Query
 
getRawRange(int, int) - Method in class net.sf.jannot.wiggle.TroveArrayWiggle
 
getReader() - Method in class net.sf.jannot.source.SAMDataSource
 
getReader(SeekableStream) - Static method in class org.broad.igv.tdf.TDFReader
 
getRecordNumber() - Method in class org.broad.igv.bbfile.ZoomDataRecord
 
getReductionLevel() - Method in class org.broad.igv.bbfile.BBZoomLevelHeader
 
getReferenceNames() - Method in class net.sf.jannot.tabix.TabixReader
 
getReferenceNucleotide(int) - Method in class net.sf.jannot.alignment.mfa.Alignment
Gives the nucleotide that appears at the given position in the reference sequence.
getReferences() - Method in class net.sf.jannot.source.das.DAS
 
getReferences() - Method in class net.sf.jannot.source.das.DSN
 
getRefGapCount() - Method in class net.sf.jannot.alignment.ReferenceSequence
 
getReserved() - Method in class org.broad.igv.bbfile.BBZoomLevelHeader
 
getReserved() - Method in class org.broad.igv.bbfile.BigWigSectionHeader
 
getReserved() - Method in class org.broad.igv.bbfile.BPTreeHeader
 
getReserved() - Method in class org.broad.igv.bbfile.RPTreeHeader
 
getRestOfFields() - Method in class org.broad.igv.bbfile.BedFeature
 
getReverseAminoAcid(int, AminoAcidMapping) - Method in class net.sf.jannot.refseq.MemorySequence
Deprecated. 
getReverseNucleotide(int) - Method in class net.sf.jannot.refseq.MemorySequence
Deprecated. 
getReverseTranslationTable() - Method in class net.sf.jannot.alignment.maf.SequenceTranslator
 
getRootGroup() - Method in class org.broad.igv.tdf.TDFWriter
 
getRootNode() - Method in class org.broad.igv.bbfile.BPTree
 
getRPTreeHeader() - Method in class org.broad.igv.bbfile.RPTree
 
getScore() - Method in class net.sf.jannot.Feature
 
getScore() - Method in class org.broad.igv.data.BasicScore
 
getScore() - Method in interface org.broad.igv.feature.LocusScore
 
getSecondRead(SAMRecord) - Method in class net.sf.jannot.shortread.BAMreads
 
getSecondRead(SAMRecord) - Method in class net.sf.jannot.shortread.MemoryReadSet
 
getSecondRead(SAMRecord) - Method in class net.sf.jannot.shortread.ReadGroup
Get the second read in a mate-pair.
getSectionData(RPChromosomeRegion, boolean, ArrayList<WigItem>) - Method in class org.broad.igv.bbfile.BigWigSection
 
getSectionDataSize() - Method in class org.broad.igv.bbfile.BigWigSection
 
getSectionHeader() - Method in class org.broad.igv.bbfile.BigWigSection
 
getSelectionRegion() - Method in class org.broad.igv.bbfile.BigBedIterator
 
getSelectionRegion() - Method in class org.broad.igv.bbfile.BigWigIterator
 
getSelectionRegion() - Method in class org.broad.igv.bbfile.ZoomLevelIterator
 
getSize() - Method in class org.broad.igv.tdf.TDFBedTile
 
getSize() - Method in class org.broad.igv.tdf.TDFFixedTile
 
getSize() - Method in interface org.broad.igv.tdf.TDFTile
 
getSize() - Method in class org.broad.igv.tdf.TDFVaryTile
 
getSourceKey() - Method in class net.sf.jannot.source.SAMDataSource
 
getSources(String) - Method in class net.sf.jannot.source.das.DSN
 
getStart() - Method in class org.broad.igv.data.BasicScore
 
getStart() - Method in interface org.broad.tribble.Feature
Return the start position in 1-based coordinates (first base is 1)
getStartBase() - Method in class org.broad.igv.bbfile.BedFeature
 
getStartBase() - Method in class org.broad.igv.bbfile.RPChromosomeRegion
 
getStartBase() - Method in class org.broad.igv.bbfile.RPTreeHeader
 
getStartBase() - Method in class org.broad.igv.bbfile.WigItem
 
getStartChromID() - Method in class org.broad.igv.bbfile.RPChromosomeRegion
 
getStartChromID() - Method in class org.broad.igv.bbfile.RPTreeHeader
 
getStartPosition(int) - Method in class org.broad.igv.tdf.TDFBedTile
 
getStartPosition(int) - Method in class org.broad.igv.tdf.TDFFixedTile
 
getStartPosition(int) - Method in interface org.broad.igv.tdf.TDFTile
 
getStartPosition(int) - Method in class org.broad.igv.tdf.TDFVaryTile
 
getStrand(String) - Static method in class net.sf.jannot.parser.ParserTools
 
getSumData() - Method in class org.broad.igv.bbfile.BBTotalSummaryBlock
 
getSumData() - Method in class org.broad.igv.bbfile.ZoomDataRecord
 
getSummaryBlockOffset() - Method in class org.broad.igv.bbfile.BBTotalSummaryBlock
 
getSummaryBlockSize() - Static method in class org.broad.igv.bbfile.BBTotalSummaryBlock
 
getSummaryScoresForRange(String, int, int, int) - Method in interface org.broad.igv.data.DataSource
 
getSumSquares() - Method in class org.broad.igv.bbfile.BBTotalSummaryBlock
 
getSumSquares() - Method in class org.broad.igv.bbfile.ZoomDataRecord
 
getTabixConfiguration() - Method in class net.sf.jannot.source.Locator
 
getTargets() - Method in class net.sf.jannot.SyntenicAnnotation
 
getTile(int) - Method in class org.broad.igv.tdf.TDFDataset
 
getTileEnd() - Method in class org.broad.igv.tdf.TDFBedTile
 
getTileEnd() - Method in class org.broad.igv.tdf.TDFFixedTile
 
getTiles(int, int) - Method in class org.broad.igv.tdf.TDFDataset
 
getTiles(String, int, int, int) - Method in class org.broad.igv.tdf.TileManager
 
getTileSize(String) - Method in class net.sf.jannot.shortread.CachingQueryReader
 
getTileStart() - Method in class org.broad.igv.tdf.TDFBedTile
 
getTileStart() - Method in class org.broad.igv.tdf.TDFFixedTile
 
getTileStart() - Method in interface org.broad.igv.tdf.TDFTile
 
getTileStart() - Method in class org.broad.igv.tdf.TDFVaryTile
 
getTileWidth() - Method in class org.broad.igv.tdf.TDFDataset
 
getTotal() - Method in class net.sf.jannot.pileup.DoublePile
 
getTotal() - Method in class net.sf.jannot.pileup.MultiPile
 
getTotal() - Method in interface net.sf.jannot.pileup.Pile
 
getTotal() - Method in class net.sf.jannot.pileup.SinglePile
 
getTotalSummaryBlock() - Method in class org.broad.igv.bbfile.BBFileReader
 
getTotalSummaryOffset() - Method in class org.broad.igv.bbfile.BBFileHeader
 
getTrackLine() - Method in class org.broad.igv.tdf.TDFReader
 
getTrackNames() - Method in class org.broad.igv.tdf.TDFReader
 
getTreeHeader() - Method in class org.broad.igv.bbfile.BPTree
 
getTreeOffset() - Method in class org.broad.igv.bbfile.RPTreeHeader
 
getUncompressBuffSize() - Method in class org.broad.igv.bbfile.BBFileHeader
 
getUncompressBuffSize() - Method in class org.broad.igv.bbfile.RPTree
 
getUpperLimit() - Method in class org.broad.igv.tdf.TDFReader
Return the default upper value for the data range.
getURL() - Method in class net.sf.jannot.source.URLSource
 
getValSize() - Method in class org.broad.igv.bbfile.BPTreeHeader
 
getValue(int) - Method in class net.sf.jannot.pileup.DoublePile
 
getValue(int) - Method in class net.sf.jannot.pileup.MultiPile
 
getValue(int) - Method in interface net.sf.jannot.pileup.Pile
 
getValue(int) - Method in class net.sf.jannot.pileup.SinglePile
 
getValue() - Method in enum net.sf.jannot.Strand
 
getValue(int, int) - Method in class org.broad.igv.tdf.TDFBedTile
 
getValue(int, int) - Method in class org.broad.igv.tdf.TDFFixedTile
 
getValue(int, int) - Method in interface org.broad.igv.tdf.TDFTile
 
getValue(int, int) - Method in class org.broad.igv.tdf.TDFVaryTile
 
getValue(WindowFunction) - Method in class org.broad.igv.tools.Accumulator
 
getValueCount() - Method in class net.sf.jannot.pileup.DoublePile
 
getValueCount() - Method in class net.sf.jannot.pileup.MultiPile
 
getValueCount() - Method in interface net.sf.jannot.pileup.Pile
 
getValueCount() - Method in class net.sf.jannot.pileup.SinglePile
 
getValueSize() - Method in class org.broad.igv.bbfile.BPTree
 
getValueString(double, WindowFunction) - Method in class org.broad.igv.data.BasicScore
 
getValueString(double, WindowFunction) - Method in interface org.broad.igv.feature.LocusScore
Return a string to be used for popup text.
getVersion() - Method in class org.broad.igv.bbfile.BBFileHeader
 
getVersion() - Method in class org.broad.igv.tdf.TDFReader
 
getWigData(RPChromosomeRegion, boolean) - Method in class org.broad.igv.bbfile.BigWigDataBlock
 
getWigValue() - Method in class org.broad.igv.bbfile.WigItem
 
getWindowFunction() - Method in interface org.broad.igv.data.DataSource
 
getWindowFunction(String) - Static method in enum org.broad.igv.track.WindowFunction
 
getWindowFunctions() - Method in class org.broad.igv.tdf.TDFReader
 
getZoomData(RPChromosomeRegion, boolean) - Method in class org.broad.igv.bbfile.ZoomDataBlock
 
getZoomDataOffset() - Method in class org.broad.igv.bbfile.BBZoomLevelFormat
 
getZoomDataSize() - Method in class org.broad.igv.bbfile.BBZoomLevelFormat
 
getZoomDataTree() - Method in class org.broad.igv.bbfile.ZoomLevelIterator
 
getZoomFormatLocation() - Method in class org.broad.igv.bbfile.BBZoomLevelFormat
 
getZoomHeaderCount() - Method in class org.broad.igv.bbfile.BBZoomLevels
 
getZoomHeadersOffset() - Method in class org.broad.igv.bbfile.BBZoomLevels
 
getZoomIndexOffset() - Method in class org.broad.igv.bbfile.BBZoomLevelFormat
 
getZoomLevel() - Method in class org.broad.igv.bbfile.BBZoomLevelFormat
 
getZoomLevel() - Method in class org.broad.igv.bbfile.BBZoomLevelHeader
 
getZoomLevel() - Method in class org.broad.igv.bbfile.ZoomDataRecord
 
getZoomLevel() - Method in class org.broad.igv.bbfile.ZoomLevelIterator
 
getZoomLevelBounds(int, int, int) - Method in class org.broad.igv.bbfile.BBFileReader
 
getZoomLevelBounds(int) - Method in class org.broad.igv.bbfile.BBFileReader
 
getZoomLevelCount() - Method in class org.broad.igv.bbfile.BBFileReader
 
getZoomLevelFormats() - Method in class org.broad.igv.bbfile.BBZoomLevels
 
getZoomLevelHeader(int) - Method in class org.broad.igv.bbfile.BBZoomLevels
 
getZoomLevelHeaders() - Method in class org.broad.igv.bbfile.BBZoomLevels
 
getZoomLevelIterator(int, String, int, String, int, boolean) - Method in class org.broad.igv.bbfile.BBFileReader
Returns an iterator for zoom level records for the chromosome selection region.
getZoomLevelIterator(int) - Method in class org.broad.igv.bbfile.BBFileReader
Returns an iterator for zoom level records for all chromosome regions.
getZoomLevelIterator(int, RPChromosomeRegion, boolean) - Method in class org.broad.igv.bbfile.BBFileReader
Returns an iterator for zoom level records for the chromosome selection region.
getZoomLevelRecordCount(int) - Method in class org.broad.igv.bbfile.BBFileReader
 
getZoomLevelRegions(int) - Method in class org.broad.igv.bbfile.BBFileReader
 
getZoomLevelRPTree(int) - Method in class org.broad.igv.bbfile.BBZoomLevels
 
getZoomLevels() - Method in class org.broad.igv.bbfile.BBFileHeader
 
getZoomLevels() - Method in class org.broad.igv.bbfile.BBFileReader
 
getZoomRecordCount() - Method in class org.broad.igv.bbfile.BBZoomLevelFormat
 
GFF3Parser - Class in net.sf.jannot.parser
 
GFF3Parser() - Constructor for class net.sf.jannot.parser.GFF3Parser
 
GFF_CONF - Static variable in class net.sf.jannot.tabix.TabixWriter
 
GFFCodec - Class in net.sf.jannot.tabix.codec
 
GFFCodec(FeatureWrapper, Iterable<TabixLine>) - Constructor for class net.sf.jannot.tabix.codec.GFFCodec
 
GFFWrapper - Class in net.sf.jannot.tabix
 
GFFWrapper(String, IndexedFeatureFile, TabIndex) - Constructor for class net.sf.jannot.tabix.GFFWrapper
 
gnu.trove - package gnu.trove
 
gnu.trove.function - package gnu.trove.function
 
gnu.trove.impl - package gnu.trove.impl
 
gnu.trove.impl.hash - package gnu.trove.impl.hash
 
gnu.trove.iterator - package gnu.trove.iterator
 
gnu.trove.iterator.hash - package gnu.trove.iterator.hash
 
gnu.trove.map - package gnu.trove.map
 
gnu.trove.map.hash - package gnu.trove.map.hash
 
gnu.trove.procedure - package gnu.trove.procedure
 
gnu.trove.procedure.array - package gnu.trove.procedure.array
 
gnu.trove.set - package gnu.trove.set
 
gnu.trove.set.hash - package gnu.trove.set.hash
 
gnu.trove.strategy - package gnu.trove.strategy
 
Graph - Interface in net.sf.jannot.wiggle
 
GZIP_FLAG - Static variable in class org.broad.igv.tdf.TDFReader
 

H

hash(double) - Static method in class gnu.trove.impl.HashFunctions
Returns a hashcode for the specified value.
hash(float) - Static method in class gnu.trove.impl.HashFunctions
Returns a hashcode for the specified value.
hash(int) - Static method in class gnu.trove.impl.HashFunctions
Returns a hashcode for the specified value.
hash(long) - Static method in class gnu.trove.impl.HashFunctions
Returns a hashcode for the specified value.
hash(Object) - Static method in class gnu.trove.impl.HashFunctions
Returns a hashcode for the specified object.
hashCode() - Method in class gnu.trove.map.hash.THashMap
 
hashCode() - Method in class gnu.trove.map.hash.TIntFloatHashMap
hashCode() - Method in class gnu.trove.map.hash.TIntFloatHashMap.TKeyView
 
hashCode() - Method in class gnu.trove.map.hash.TLongDoubleHashMap
hashCode() - Method in class gnu.trove.map.hash.TLongDoubleHashMap.TKeyView
 
hashCode() - Method in class gnu.trove.set.hash.THashSet
 
hashCode() - Method in class gnu.trove.set.hash.TIntHashSet
Returns the hash code value for this set.
hashCode() - Method in class gnu.trove.set.hash.TLongHashSet
Returns the hash code value for this set.
hashCode() - Method in interface gnu.trove.set.TIntSet
Returns the hash code value for this set.
hashCode() - Method in interface gnu.trove.set.TLongSet
Returns the hash code value for this set.
hashCode() - Method in interface gnu.trove.TDoubleCollection
Returns the hash code value for this collection.
hashCode() - Method in interface gnu.trove.TFloatCollection
Returns the hash code value for this collection.
hashCode() - Method in interface gnu.trove.TIntCollection
Returns the hash code value for this collection.
hashCode() - Method in interface gnu.trove.TLongCollection
Returns the hash code value for this collection.
hashCode() - Method in interface gnu.trove.TShortCollection
Returns the hash code value for this collection.
hashCode() - Method in class net.sf.jannot.Location
 
hashCode() - Method in class net.sf.jannot.source.SAMDataSource
 
hashCode() - Method in class org.apache.commons.collections.map.Flat3Map
Gets the standard Map hashCode.
HashFunctions - Class in gnu.trove.impl
Provides various hash functions.
HashFunctions() - Constructor for class gnu.trove.impl.HashFunctions
 
HashingStrategy<T> - Interface in gnu.trove.strategy
Interface to support pluggable hashing strategies in maps and sets.
hasNext() - Method in class gnu.trove.impl.hash.THashIterator
Returns true if the iterator can be advanced past its current location.
hasNext() - Method in class gnu.trove.impl.hash.THashPrimitiveIterator
Returns true if the iterator can be advanced past its current location.
hasNext() - Method in interface gnu.trove.iterator.TIterator
Returns true if the iterator can be advanced past its current location.
hasNext() - Method in interface gnu.trove.iterator.TPrimitiveIterator
Returns true if the iterator can be advanced past its current location.
hasNext() - Method in class net.sf.jannot.ListIterator
Returns true if the iteration has more elements.
hasNext() - Method in class net.sf.jannot.LocatedListIterator
Returns true if the iteration has more elements.
hasNext() - Method in class net.sf.jannot.shortread.CachingQueryReader.TiledIterator
 
hasNext() - Method in class net.sf.jannot.shortread.EmptyIterator
 
hasNext() - Method in class net.sf.jannot.utils.ArrayIterator
Returns true if the iteration has more elements.
hasNext() - Method in class org.broad.igv.bbfile.BigBedIterator
 
hasNext() - Method in class org.broad.igv.bbfile.BigWigIterator
 
hasNext() - Method in class org.broad.igv.bbfile.ZoomLevelIterator.EmptyIterator
 
hasNext() - Method in class org.broad.igv.bbfile.ZoomLevelIterator
 

I

id - Variable in class net.sf.jannot.alignment.maf.AbstractAlignmentSequence
 
IdentityHashingStrategy<K> - Class in gnu.trove.strategy
A HashingStrategy that does identity comparisons (==) and uses System.identityHashCode(Object) for hashCode generation.
IdentityHashingStrategy() - Constructor for class gnu.trove.strategy.IdentityHashingStrategy
 
idx - Variable in class net.sf.jannot.tabix.TabixWrapper
 
increment(int) - Method in class gnu.trove.map.hash.TIntFloatHashMap
Increments the primitive value mapped to key by 1
increment(long) - Method in class gnu.trove.map.hash.TLongDoubleHashMap
Increments the primitive value mapped to key by 1
increment(int) - Method in interface gnu.trove.map.TIntFloatMap
Increments the primitive value mapped to key by 1
increment(long) - Method in interface gnu.trove.map.TLongDoubleMap
Increments the primitive value mapped to key by 1
index(int) - Method in class gnu.trove.impl.hash.TIntFloatHash
Locates the index of val.
index(int) - Method in class gnu.trove.impl.hash.TIntHash
Locates the index of val.
index(long) - Method in class gnu.trove.impl.hash.TLongDoubleHash
Locates the index of val.
index(long) - Method in class gnu.trove.impl.hash.TLongHash
Locates the index of val.
index(Object) - Method in class gnu.trove.impl.hash.TObjectHash
Locates the index of obj.
index(Locator, Locator) - Static method in class net.sf.jannot.indexing.Faidx
 
IndexedFastaDataSource - Class in net.sf.jannot.source
 
IndexedFastaDataSource(Locator, Locator) - Constructor for class net.sf.jannot.source.IndexedFastaDataSource
 
IndexedFeatureFile - Class in net.sf.jannot.tabix
 
IndexedFeatureFile(Locator, Locator) - Constructor for class net.sf.jannot.tabix.IndexedFeatureFile
 
IndexedMAF - Class in net.sf.jannot.mafix
 
IndexedMAF(SeekableStream, InputStream) - Constructor for class net.sf.jannot.mafix.IndexedMAF
Looks for a compressed version of the requested MAF file and its index file.
IndexedMAF(String, IndexedMAF) - Constructor for class net.sf.jannot.mafix.IndexedMAF
Creates a new IndexedMaf out of an other one, but setting the selected chromosome and pointing to the content of the original IndexedMaf.
IndexedMAFDataSource - Class in net.sf.jannot.source
 
IndexedMAFDataSource(Locator, Locator) - Constructor for class net.sf.jannot.source.IndexedMAFDataSource
 
IndexManager - Class in net.sf.jannot.source
 
IndexManager() - Constructor for class net.sf.jannot.source.IndexManager
 
init(Query) - Method in class net.sf.jannot.wiggle.AbstractWiggle
 
init() - Method in class net.sf.jannot.wiggle.DiskArrayWiggle
 
init() - Method in class net.sf.jannot.wiggle.TroveArrayWiggle
 
insertionIndex(int) - Method in class gnu.trove.impl.hash.TIntFloatHash
Locates the index at which val can be inserted.
insertionIndex(int) - Method in class gnu.trove.impl.hash.TIntHash
Locates the index at which val can be inserted.
insertionIndex(long) - Method in class gnu.trove.impl.hash.TLongDoubleHash
Locates the index at which val can be inserted.
insertionIndex(long) - Method in class gnu.trove.impl.hash.TLongHash
Locates the index at which val can be inserted.
insertionIndex(T) - Method in class gnu.trove.impl.hash.TObjectHash
Locates the index at which obj can be inserted.
insertItem(BPTreeNodeItem) - Method in class org.broad.igv.bbfile.BPTreeChildNode
 
insertItem(BPTreeNodeItem) - Method in class org.broad.igv.bbfile.BPTreeLeafNode
 
insertItem(BPTreeNodeItem) - Method in interface org.broad.igv.bbfile.BPTreeNode
 
insertItem(RPTreeNodeItem) - Method in class org.broad.igv.bbfile.RPTreeChildNode
 
insertItem(RPTreeNodeItem) - Method in class org.broad.igv.bbfile.RPTreeLeafNode
 
insertItem(RPTreeNodeItem) - Method in interface org.broad.igv.bbfile.RPTreeNode
 
INSTANCE - Static variable in class org.apache.commons.collections.iterators.EmptyIterator
Singleton instance of the iterator.
IntArrayList - Class in org.broad.igv.util.collections
Author: jrobinso Date: Jul 22, 2010

ArrayList type collection for int types.

IntArrayList() - Constructor for class org.broad.igv.util.collections.IntArrayList
 
IntArrayList(int) - Constructor for class org.broad.igv.util.collections.IntArrayList
 
IntArrayList(int[]) - Constructor for class org.broad.igv.util.collections.IntArrayList
 
intersectsAbove(RPChromosomeRegion) - Method in class org.broad.igv.bbfile.RPChromosomeRegion
 
intersectsBelow(RPChromosomeRegion) - Method in class org.broad.igv.bbfile.RPChromosomeRegion
 
isAligned(int) - Method in class net.sf.jannot.alignment.mfa.Alignment
Returns whether the supplied position is aligned.
isAnyCompressed() - Method in class net.sf.jannot.source.Locator
 
isBAM() - Method in class net.sf.jannot.source.Locator
 
isBigBed() - Method in class org.broad.igv.bbfile.BBFileHeader
 
isBigBedFile() - Method in class org.broad.igv.bbfile.BBFileReader
 
isBigWig() - Method in class net.sf.jannot.source.Locator
 
isBigWig() - Method in class org.broad.igv.bbfile.BBFileHeader
 
isBigWigFile() - Method in class org.broad.igv.bbfile.BBFileReader
 
isBlockCompressed() - Method in class net.sf.jannot.source.Locator
 
isContained() - Method in class org.broad.igv.bbfile.BigBedIterator
 
isContained() - Method in class org.broad.igv.bbfile.BigWigIterator
 
isContained() - Method in class org.broad.igv.bbfile.ZoomLevelIterator
 
isCurrentWindowFunction(WindowFunction) - Method in class net.sf.jannot.tdf.TDFData
 
isEmpty() - Method in class gnu.trove.impl.hash.THash
Tells whether this set is currently holding any elements.
isEmpty() - Method in class gnu.trove.map.hash.TIntFloatHashMap
Tells whether this set is currently holding any elements.
isEmpty() - Method in class gnu.trove.map.hash.TIntFloatHashMap.TKeyView
Returns true if this set contains no elements.
isEmpty() - Method in class gnu.trove.map.hash.TIntFloatHashMap.TValueView
Returns true if this collection contains no elements.
isEmpty() - Method in class gnu.trove.map.hash.TLongDoubleHashMap
Tells whether this set is currently holding any elements.
isEmpty() - Method in class gnu.trove.map.hash.TLongDoubleHashMap.TKeyView
Returns true if this set contains no elements.
isEmpty() - Method in class gnu.trove.map.hash.TLongDoubleHashMap.TValueView
Returns true if this collection contains no elements.
isEmpty() - Method in interface gnu.trove.map.TIntFloatMap
Returns true if this map contains no key-value mappings.
isEmpty() - Method in interface gnu.trove.map.TLongDoubleMap
Returns true if this map contains no key-value mappings.
isEmpty() - Method in interface gnu.trove.set.TIntSet
Returns true if this set contains no elements.
isEmpty() - Method in interface gnu.trove.set.TLongSet
Returns true if this set contains no elements.
isEmpty() - Method in interface gnu.trove.TDoubleCollection
Returns true if this collection contains no elements.
isEmpty() - Method in interface gnu.trove.TFloatCollection
Returns true if this collection contains no elements.
isEmpty() - Method in interface gnu.trove.TIntCollection
Returns true if this collection contains no elements.
isEmpty() - Method in interface gnu.trove.TLongCollection
Returns true if this collection contains no elements.
isEmpty() - Method in interface gnu.trove.TShortCollection
Returns true if this collection contains no elements.
isEmpty() - Method in class org.apache.commons.collections.map.Flat3Map
Checks whether the map is currently empty.
isEmpty() - Method in class org.broad.igv.util.collections.DoubleArrayList
 
isEmpty() - Method in class org.broad.igv.util.collections.FloatArrayList
 
isEmpty() - Method in class org.broad.igv.util.collections.IntArrayList
 
isFasta() - Method in class net.sf.jannot.source.Locator
 
isFirstInPair() - Method in class net.sf.jannot.shortread.ShortRead
 
isFirstInPair(SAMRecord) - Static method in class net.sf.jannot.shortread.ShortReadTools
 
isHeaderOK() - Method in class org.broad.igv.bbfile.BBFileHeader
 
isHeaderOK() - Method in class org.broad.igv.bbfile.BPTreeHeader
 
isHeaderOK() - Method in class org.broad.igv.bbfile.RPTreeHeader
 
isIndexed() - Method in class net.sf.jannot.bigwig.BigWigDataSource
 
isIndexed() - Method in class net.sf.jannot.source.das.DAS
 
isIndexed() - Method in class net.sf.jannot.source.DataSource
 
isIndexed() - Method in class net.sf.jannot.source.FileSource
 
isIndexed() - Method in class net.sf.jannot.source.IndexedFastaDataSource
 
isIndexed() - Method in class net.sf.jannot.source.IndexedMAFDataSource
 
isIndexed() - Method in class net.sf.jannot.source.SAMDataSource
 
isIndexed() - Method in class net.sf.jannot.source.URLSource
 
isIndexed() - Method in class net.sf.jannot.tabix.IndexedFeatureFile
 
isIndexed() - Method in class net.sf.jannot.tdf.TDFDataSource
 
isIsLowToHigh() - Method in class org.broad.igv.bbfile.RPTree
 
isLeaf() - Method in class org.broad.igv.bbfile.BPTreeChildNode
 
isLeaf() - Method in class org.broad.igv.bbfile.BPTreeLeafNode
 
isLeaf() - Method in interface org.broad.igv.bbfile.BPTreeNode
 
isLeaf() - Method in class org.broad.igv.bbfile.RPTreeChildNode
 
isLeaf() - Method in class org.broad.igv.bbfile.RPTreeLeafNode
 
isLeaf() - Method in interface org.broad.igv.bbfile.RPTreeNode
 
isLeafItem() - Method in class org.broad.igv.bbfile.BPTreeChildNodeItem
 
isLeafItem() - Method in class org.broad.igv.bbfile.BPTreeLeafNodeItem
 
isLogNormalized() - Method in interface org.broad.igv.data.DataSource
 
isLowToHigh() - Method in class org.broad.igv.bbfile.BBFileHeader
 
isLowToHigh() - Method in class org.broad.igv.bbfile.BBFileReader
 
isMaf() - Method in class net.sf.jannot.source.Locator
 
isPaired() - Method in class net.sf.jannot.shortread.ShortRead
 
isPaired(SAMRecord) - Static method in class net.sf.jannot.shortread.ShortReadTools
 
isSecondInPair(SAMRecord) - Static method in class net.sf.jannot.shortread.ShortReadTools
 
isStart(String) - Method in enum net.sf.jannot.AminoAcidMapping
 
isStop(char) - Method in enum net.sf.jannot.AminoAcidMapping
 
isStreamCompressed() - Method in class net.sf.jannot.source.Locator
 
isTabix() - Method in class net.sf.jannot.source.Locator
 
isTDF() - Method in class net.sf.jannot.source.Locator
 
isURL() - Method in class net.sf.jannot.source.Locator
 
isValidSectionType() - Method in class org.broad.igv.bbfile.BigWigSection
 
IsValidType() - Method in class org.broad.igv.bbfile.BigWigSectionHeader
 
isWebservice() - Method in class net.sf.jannot.source.Locator
 
isWig() - Method in class net.sf.jannot.source.Locator
 
isWriting() - Method in class net.sf.jannot.tabix.BinaryCodec
 
iterator() - Method in class gnu.trove.map.hash.THashMap.EntryView
 
iterator() - Method in class gnu.trove.map.hash.THashMap.KeyView
 
iterator() - Method in class gnu.trove.map.hash.THashMap.ValueView
 
iterator() - Method in class gnu.trove.map.hash.TIntFloatHashMap
iterator() - Method in class gnu.trove.map.hash.TIntFloatHashMap.TKeyView
Creates an iterator over the values of the set.
iterator() - Method in class gnu.trove.map.hash.TIntFloatHashMap.TValueView
Creates an iterator over the values of the collection.
iterator() - Method in class gnu.trove.map.hash.TLongDoubleHashMap
iterator() - Method in class gnu.trove.map.hash.TLongDoubleHashMap.TKeyView
Creates an iterator over the values of the set.
iterator() - Method in class gnu.trove.map.hash.TLongDoubleHashMap.TValueView
Creates an iterator over the values of the collection.
iterator() - Method in interface gnu.trove.map.TIntFloatMap
 
iterator() - Method in interface gnu.trove.map.TLongDoubleMap
 
iterator() - Method in class gnu.trove.set.hash.THashSet
Creates an iterator over the values of the set.
iterator() - Method in class gnu.trove.set.hash.TIntHashSet
Creates an iterator over the values of the set.
iterator() - Method in class gnu.trove.set.hash.TLongHashSet
Creates an iterator over the values of the set.
iterator() - Method in interface gnu.trove.set.TIntSet
Creates an iterator over the values of the set.
iterator() - Method in interface gnu.trove.set.TLongSet
Creates an iterator over the values of the set.
iterator() - Method in interface gnu.trove.TDoubleCollection
Creates an iterator over the values of the collection.
iterator() - Method in interface gnu.trove.TFloatCollection
Creates an iterator over the values of the collection.
iterator() - Method in interface gnu.trove.TIntCollection
Creates an iterator over the values of the collection.
iterator() - Method in interface gnu.trove.TLongCollection
Creates an iterator over the values of the collection.
iterator() - Method in interface gnu.trove.TShortCollection
Creates an iterator over the values of the collection.
iterator() - Method in class net.sf.jannot.alignment.maf.LazyAlignmentBlock
 
iterator() - Method in class net.sf.jannot.alignment.maf.MemoryAlignmentBlock
 
iterator() - Method in class net.sf.jannot.Entry
 
iterator() - Method in class net.sf.jannot.EntrySet
 
iterator() - Method in class net.sf.jannot.EntrySetAnnotation
 
iterator() - Method in class net.sf.jannot.ListIterable
 
iterator() - Method in class net.sf.jannot.LocatedListIterable
 
iterator() - Method in class net.sf.jannot.refseq.FaixDataIterable
 
iterator() - Method in class net.sf.jannot.shortread.BAMreads
 
iterator() - Method in class net.sf.jannot.shortread.CachingQueryReader
 
iterator() - Method in class net.sf.jannot.SyntenicAnnotation
 
iterator() - Method in class net.sf.jannot.tabix.codec.Codec
 
iterator() - Method in class net.sf.jannot.utils.ArrayIterable
 
iterator() - Method in class net.sf.jannot.wiggle.DiskArrayWiggle
 
iterator() - Method in class net.sf.jannot.wiggle.TroveArrayWiggle
 

K

key() - Method in interface gnu.trove.iterator.TIntFloatIterator
Provides access to the key of the mapping at the iterator's position.
key() - Method in interface gnu.trove.iterator.TLongDoubleIterator
Provides access to the key of the mapping at the iterator's position.
key - Variable in class net.sf.jannot.tabix.TabixWrapper
 
keyForEntry(Map.Entry<K, V>) - Method in class gnu.trove.map.hash.THashMap.EntryView
 
keys() - Method in class gnu.trove.map.hash.TIntFloatHashMap
Returns the keys of the map as an array of int values.
keys(int[]) - Method in class gnu.trove.map.hash.TIntFloatHashMap
Returns the keys of the map.
keys() - Method in class gnu.trove.map.hash.TLongDoubleHashMap
Returns the keys of the map as an array of long values.
keys(long[]) - Method in class gnu.trove.map.hash.TLongDoubleHashMap
Returns the keys of the map.
keys() - Method in interface gnu.trove.map.TIntFloatMap
Returns the keys of the map as an array of int values.
keys(int[]) - Method in interface gnu.trove.map.TIntFloatMap
Returns the keys of the map.
keys() - Method in interface gnu.trove.map.TLongDoubleMap
Returns the keys of the map as an array of long values.
keys(long[]) - Method in interface gnu.trove.map.TLongDoubleMap
Returns the keys of the map.
keySet() - Method in class gnu.trove.map.hash.THashMap
returns a Set view on the keys of the map.
keySet() - Method in class gnu.trove.map.hash.TIntFloatHashMap
Returns the keys of the map as a TIntSet
keySet() - Method in class gnu.trove.map.hash.TLongDoubleHashMap
Returns the keys of the map as a TLongSet
keySet() - Method in interface gnu.trove.map.TIntFloatMap
Returns the keys of the map as a TIntSet
keySet() - Method in interface gnu.trove.map.TLongDoubleMap
Returns the keys of the map as a TLongSet
keySet() - Method in class org.apache.commons.collections.map.Flat3Map
Gets the keySet view of the map.
knownAtEof() - Method in class net.sf.jannot.tabix.BinaryCodec
 

L

label() - Method in class net.sf.jannot.alignment.maf.AbstractMAFMultipleAlignment
 
label() - Method in class net.sf.jannot.alignment.mfa.AlignmentAnnotation
 
label() - Method in class net.sf.jannot.bigwig.BigWigData
 
label() - Method in interface net.sf.jannot.Data
 
label() - Method in class net.sf.jannot.MemoryFeatureAnnotation
 
label() - Method in class net.sf.jannot.refseq.Sequence
 
label() - Method in class net.sf.jannot.shortread.BAMreads
 
label() - Method in class net.sf.jannot.shortread.MemoryReadSet
 
label() - Method in class net.sf.jannot.tabix.TabixWrapper
 
label() - Method in class net.sf.jannot.tdf.TDFData
 
label() - Method in class net.sf.jannot.wiggle.AbstractWiggle
 
largestPrime - Static variable in class gnu.trove.impl.PrimeFinder
The largest prime this class can generate; currently equal to Integer.MAX_VALUE.
LazyAlignmentBlock - Class in net.sf.jannot.alignment.maf
 
LazyAlignmentBlock(long, LineBlockCompressedInputStream, int, int) - Constructor for class net.sf.jannot.alignment.maf.LazyAlignmentBlock
 
LazyAlignmentSequence - Class in net.sf.jannot.alignment.maf
 
LazyAlignmentSequence(String, int, int, Strand, LazyAlignmentBlock) - Constructor for class net.sf.jannot.alignment.maf.LazyAlignmentSequence
 
lazyLoad() - Method in class net.sf.jannot.alignment.maf.LazyAlignmentBlock
Load the actual alignment block from the zipped maf file and fill in the gaps in the alignment sequences
length() - Method in class net.sf.jannot.alignment.maf.AbstractAlignmentBlock
 
length() - Method in class net.sf.jannot.Feature
 
length() - Method in class net.sf.jannot.Location
 
length() - Method in class net.sf.jannot.shortread.BasicShortRead
 
length() - Method in class net.sf.jannot.shortread.ShortRead
 
length(SAMRecord) - Static method in class net.sf.jannot.shortread.ShortReadTools
 
length() - Method in class net.sf.jannot.source.Locator
 
length() - Method in class net.sf.jannot.tabix.TabixLine
 
line() - Method in class net.sf.jannot.tabix.TabixLine
 
LineBlockCompressedInputStream - Class in net.sf.jannot.picard
 
LineBlockCompressedInputStream(SeekableStream) - Constructor for class net.sf.jannot.picard.LineBlockCompressedInputStream
 
ListIterable<T> - Class in net.sf.jannot
This Iterator is used to iterate over Lists without fail-fast behavior.
ListIterable(List<T>) - Constructor for class net.sf.jannot.ListIterable
 
ListIterator<T> - Class in net.sf.jannot
This Iterator is used to iterate over Arrays.
ListIterator(List<T>) - Constructor for class net.sf.jannot.ListIterator
create an Iterator for the Array array.
LittleEndianInputStream - Class in org.broad.tribble
File retrieved from BigWig project at Google code on July 26, 2011, revision 36 http://code.google.com/p/bigwig/ This project provides java readers for the UCSC's BigWig and BigBed formats.
LittleEndianInputStream(InputStream) - Constructor for class org.broad.tribble.LittleEndianInputStream
 
Located - Interface in net.sf.jannot
 
LocatedListIterable<T extends Located> - Class in net.sf.jannot
This Iterator is used to iterate over Lists without fail-fast behavior.
LocatedListIterable(List<T>, Location) - Constructor for class net.sf.jannot.LocatedListIterable
 
LocatedListIterable(List<T>) - Constructor for class net.sf.jannot.LocatedListIterable
create an Iterator for the Array array.
LocatedListIterator<T extends Located> - Class in net.sf.jannot
This Iterator is used to iterate over Arrays.
LocatedListIterator(List<T>, Location) - Constructor for class net.sf.jannot.LocatedListIterator
create an Iterator for the Array array.
location() - Method in class net.sf.jannot.Feature
 
Location - Class in net.sf.jannot
 
Location(int, int, boolean, boolean) - Constructor for class net.sf.jannot.Location
 
Location(int, int) - Constructor for class net.sf.jannot.Location
 
locator - Variable in class net.sf.jannot.source.DataSource
 
Locator - Class in net.sf.jannot.source
 
Locator(String) - Constructor for class net.sf.jannot.source.Locator
 
LocusScore - Interface in org.broad.igv.feature
 
lru - Variable in class net.sf.jannot.tabix.codec.Codec
 
LRUCache<K,V> - Class in org.broad
 
LRUCache(int) - Constructor for class org.broad.LRUCache
 

M

MafixFactory - Class in net.sf.jannot.mafix
 
MafixFactory() - Constructor for class net.sf.jannot.mafix.MafixFactory
 
MAFMemoryMultipleAlignment - Class in net.sf.jannot.alignment.maf
 
MAFMemoryMultipleAlignment() - Constructor for class net.sf.jannot.alignment.maf.MAFMemoryMultipleAlignment
 
MAFParser - Class in net.sf.jannot.parser
 
MAFParser(DataKey) - Constructor for class net.sf.jannot.parser.MAFParser
 
main(String[]) - Static method in class org.broad.igv.util.StringUtils
 
main(String[]) - Static method in class org.broad.tools.ConvertBAM2TDF
 
MapViewParser - Class in net.sf.jannot.parser.software
 
MapViewParser(DataKey) - Constructor for class net.sf.jannot.parser.software.MapViewParser
 
MaqSNPParser - Class in net.sf.jannot.parser.software
Parser for the Maq SNP format.
MaqSNPParser() - Constructor for class net.sf.jannot.parser.software.MaqSNPParser
 
max() - Method in class net.sf.jannot.wiggle.AbstractWiggle
 
max() - Method in class net.sf.jannot.wiggle.DiskArrayWiggle
 
max() - Method in class net.sf.jannot.wiggle.FloatArrayWiggle
 
max() - Method in interface net.sf.jannot.wiggle.Graph
 
max() - Method in class net.sf.jannot.wiggle.TroveArrayWiggle
 
MAX_VALUE_COUNT - Static variable in class org.broad.igv.tools.Accumulator
 
MAX_ZOOM_DATA_RECORDS - Static variable in class org.broad.igv.bbfile.BBZoomLevelFormat
 
mBc - Variable in class net.sf.jannot.tabix.TabixReader
 
mChr2tid - Variable in class net.sf.jannot.tabix.TabixReader
 
mEc - Variable in class net.sf.jannot.tabix.TabixReader
 
MemoryAlignmentBlock - Class in net.sf.jannot.alignment.maf
 
MemoryAlignmentBlock(int, int) - Constructor for class net.sf.jannot.alignment.maf.MemoryAlignmentBlock
 
MemoryAlignmentSequence - Class in net.sf.jannot.alignment.maf
 
MemoryAlignmentSequence(String, int, int, int, Strand, Sequence) - Constructor for class net.sf.jannot.alignment.maf.MemoryAlignmentSequence
 
MemoryFeatureAnnotation - Class in net.sf.jannot
 
MemoryFeatureAnnotation() - Constructor for class net.sf.jannot.MemoryFeatureAnnotation
 
MemoryListData<T> - Class in net.sf.jannot
Data that is stored in memory in a list of a particular type
MemoryListData() - Constructor for class net.sf.jannot.MemoryListData
 
MemoryReadSet - Class in net.sf.jannot.shortread
 
MemoryReadSet() - Constructor for class net.sf.jannot.shortread.MemoryReadSet
 
MemorySequence - Class in net.sf.jannot.refseq
 
MemorySequence() - Constructor for class net.sf.jannot.refseq.MemorySequence
 
MemorySequence(MemorySequence) - Constructor for class net.sf.jannot.refseq.MemorySequence
Copy constructor
MemorySequence(String) - Constructor for class net.sf.jannot.refseq.MemorySequence
 
MemorySequence(StringBuffer) - Constructor for class net.sf.jannot.refseq.MemorySequence
 
mFn - Variable in class net.sf.jannot.tabix.TabixReader
 
min() - Method in class net.sf.jannot.wiggle.AbstractWiggle
 
min() - Method in class net.sf.jannot.wiggle.DiskArrayWiggle
 
min() - Method in class net.sf.jannot.wiggle.FloatArrayWiggle
 
min() - Method in interface net.sf.jannot.wiggle.Graph
 
min() - Method in class net.sf.jannot.wiggle.TroveArrayWiggle
 
mMeta - Variable in class net.sf.jannot.tabix.TabixReader
 
moveDown(Type) - Static method in class net.sf.jannot.Type
Class Type stores all Types defined in a array.
moveToNextIndex() - Method in class gnu.trove.impl.hash.THashIterator
Sets the internal index so that the `next' object can be returned.
moveToNextIndex() - Method in class gnu.trove.impl.hash.THashPrimitiveIterator
Sets the internal index so that the `next' object can be returned.
moveUp(Type) - Static method in class net.sf.jannot.Type
Class Type stores all Types defined in a array.
mPreset - Variable in class net.sf.jannot.tabix.TabixReader
 
mSc - Variable in class net.sf.jannot.tabix.TabixReader
 
mSeq - Variable in class net.sf.jannot.tabix.TabixReader
 
mSkip - Variable in class net.sf.jannot.tabix.TabixReader
 
MultiPile - Class in net.sf.jannot.pileup
 
MultiPile(int, float[]) - Constructor for class net.sf.jannot.pileup.MultiPile
 

N

name() - Method in class net.sf.jannot.alignment.mfa.Alignment
Returns the name of this alignment
names() - Method in class net.sf.jannot.refseq.FaidxIndex
 
net.sf.jannot - package net.sf.jannot
 
net.sf.jannot.alignment - package net.sf.jannot.alignment
 
net.sf.jannot.alignment.maf - package net.sf.jannot.alignment.maf
 
net.sf.jannot.alignment.mfa - package net.sf.jannot.alignment.mfa
 
net.sf.jannot.bigwig - package net.sf.jannot.bigwig
 
net.sf.jannot.event - package net.sf.jannot.event
 
net.sf.jannot.exception - package net.sf.jannot.exception
 
net.sf.jannot.indexing - package net.sf.jannot.indexing
 
net.sf.jannot.mafix - package net.sf.jannot.mafix
 
net.sf.jannot.parser - package net.sf.jannot.parser
 
net.sf.jannot.parser.software - package net.sf.jannot.parser.software
 
net.sf.jannot.picard - package net.sf.jannot.picard
 
net.sf.jannot.pileup - package net.sf.jannot.pileup
 
net.sf.jannot.refseq - package net.sf.jannot.refseq
 
net.sf.jannot.shortread - package net.sf.jannot.shortread
 
net.sf.jannot.source - package net.sf.jannot.source
 
net.sf.jannot.source.cache - package net.sf.jannot.source.cache
 
net.sf.jannot.source.das - package net.sf.jannot.source.das
 
net.sf.jannot.tabix - package net.sf.jannot.tabix
 
net.sf.jannot.tabix.codec - package net.sf.jannot.tabix.codec
 
net.sf.jannot.tdf - package net.sf.jannot.tdf
 
net.sf.jannot.utils - package net.sf.jannot.utils
 
net.sf.jannot.wiggle - package net.sf.jannot.wiggle
 
next() - Method in class gnu.trove.impl.hash.THashIterator
Moves the iterator to the next Object and returns it.
next() - Method in interface gnu.trove.iterator.TDoubleIterator
Advances the iterator to the next element in the underlying collection and returns it.
next() - Method in interface gnu.trove.iterator.TFloatIterator
Advances the iterator to the next element in the underlying collection and returns it.
next() - Method in interface gnu.trove.iterator.TIntIterator
Advances the iterator to the next element in the underlying collection and returns it.
next() - Method in interface gnu.trove.iterator.TLongIterator
Advances the iterator to the next element in the underlying collection and returns it.
next() - Method in interface gnu.trove.iterator.TShortIterator
Advances the iterator to the next element in the underlying collection and returns it.
next() - Method in class net.sf.jannot.ListIterator
Returns the next element in the interation.
next() - Method in class net.sf.jannot.LocatedListIterator
Returns the next element in the iteration.
next() - Method in class net.sf.jannot.shortread.CachingQueryReader.TiledIterator
 
next() - Method in class net.sf.jannot.shortread.EmptyIterator
 
next() - Method in class net.sf.jannot.tabix.TabixReader.Iterator
 
next() - Method in class net.sf.jannot.utils.ArrayIterator
Returns the next element in the interation.
next() - Method in class org.broad.igv.bbfile.BigBedIterator
Method returns the current bed feature and advances to the next bed record.
next() - Method in class org.broad.igv.bbfile.BigWigIterator
Method returns the current Wig item and advances to the next Wig record.
next() - Method in class org.broad.igv.bbfile.ZoomLevelIterator
Method returns the current bed feature and advances to the next bed record.
nextIndex() - Method in class gnu.trove.impl.hash.THashIterator
Returns the index of the next value in the data structure or a negative value if the iterator is exhausted.
nextIndex() - Method in class gnu.trove.impl.hash.THashPrimitiveIterator
Returns the index of the next value in the data structure or a negative value if the iterator is exhausted.
nextPrime(int) - Static method in class gnu.trove.impl.PrimeFinder
Returns a prime number which is >= desiredCapacity and very close to desiredCapacity (within 11% if desiredCapacity >= 1000).
no_entry_key - Variable in class gnu.trove.impl.hash.TIntFloatHash
key that represents null NOTE: should not be modified after the Hash is created, but is not final because of Externalization
no_entry_key - Variable in class gnu.trove.impl.hash.TLongDoubleHash
key that represents null NOTE: should not be modified after the Hash is created, but is not final because of Externalization
no_entry_value - Variable in class gnu.trove.impl.hash.TIntFloatHash
value that represents null NOTE: should not be modified after the Hash is created, but is not final because of Externalization
no_entry_value - Variable in class gnu.trove.impl.hash.TIntHash
value that represents null NOTE: should not be modified after the Hash is created, but is not final because of Externalization
no_entry_value - Variable in class gnu.trove.impl.hash.TLongDoubleHash
value that represents null NOTE: should not be modified after the Hash is created, but is not final because of Externalization
no_entry_value - Variable in class gnu.trove.impl.hash.TLongHash
value that represents null NOTE: should not be modified after the Hash is created, but is not final because of Externalization
noAlignmentBlocks() - Method in class net.sf.jannot.alignment.maf.AbstractMAFMultipleAlignment
 
noAlignmentBlocks() - Method in class net.sf.jannot.alignment.maf.MAFMemoryMultipleAlignment
 
noAlignmentBlocks() - Method in class net.sf.jannot.mafix.IndexedMAF
 
noNucleotides - Variable in class net.sf.jannot.alignment.maf.AbstractAlignmentSequence
 
noValues() - Method in class org.broad.igv.tdf.TDFBedTile
 
noValues() - Method in class org.broad.igv.tdf.TDFFixedTile
 
noValues() - Method in interface org.broad.igv.tdf.TDFTile
Returns the number of values that are available for each position in this Tile.
noValues() - Method in class org.broad.igv.tdf.TDFVaryTile
 
numAlignments() - Method in class net.sf.jannot.alignment.mfa.AlignmentAnnotation
 

O

objectAtIndex(int) - Method in class gnu.trove.impl.hash.THashIterator
Returns the object at the specified index.
objectAtIndex(int) - Method in class gnu.trove.iterator.hash.TObjectHashIterator
 
org.apache.commons.collections.iterators - package org.apache.commons.collections.iterators
 
org.apache.commons.collections.map - package org.apache.commons.collections.map
 
org.apache.commons.math.stat - package org.apache.commons.math.stat
 
org.broad - package org.broad
 
org.broad.igv.bbfile - package org.broad.igv.bbfile
 
org.broad.igv.data - package org.broad.igv.data
 
org.broad.igv.feature - package org.broad.igv.feature
 
org.broad.igv.tdf - package org.broad.igv.tdf
 
org.broad.igv.tools - package org.broad.igv.tools
 
org.broad.igv.track - package org.broad.igv.track
 
org.broad.igv.util - package org.broad.igv.util
 
org.broad.igv.util.collections - package org.broad.igv.util.collections
 
org.broad.tools - package org.broad.tools
 
org.broad.tribble - package org.broad.tribble
 
overlaps(Location) - Method in class net.sf.jannot.Feature
 
overlaps(Feature) - Method in class net.sf.jannot.Feature
 
overlaps(int, int) - Method in class net.sf.jannot.Location
 

P

padGff(String[]) - Static method in class net.sf.jannot.parser.GFF3Parser
 
Pair64 - Class in net.sf.jannot.tabix
Pair of longs
Pair64(long, long) - Constructor for class net.sf.jannot.tabix.Pair64
 
parse(InputStream, EntrySet) - Method in class net.sf.jannot.parser.ALNParser
 
parse(InputStream, EntrySet) - Method in class net.sf.jannot.parser.BedGraphParser
 
parse(InputStream, EntrySet) - Method in class net.sf.jannot.parser.BEDParser
 
parse(InputStream, EntrySet) - Method in class net.sf.jannot.parser.EMBLParser
 
parse(InputStream, EntrySet) - Method in class net.sf.jannot.parser.FastaParser
 
parse(InputStream, EntrySet) - Method in class net.sf.jannot.parser.GenbankParser
 
parse(InputStream, EntrySet) - Method in class net.sf.jannot.parser.GFF3Parser
Will return an entry for each unique seq_id
parse(InputStream, EntrySet) - Method in class net.sf.jannot.parser.MAFParser
 
parse(InputStream, EntrySet) - Method in class net.sf.jannot.parser.Parser
Read all data from an input stream.
parse(InputStream, EntrySet) - Method in class net.sf.jannot.parser.PTTParser
Will return an entry for each unique seq_id
parse(InputStream, EntrySet) - Method in class net.sf.jannot.parser.software.BlastM8Parser
 
parse(InputStream, EntrySet) - Method in class net.sf.jannot.parser.software.BroadSolexa
 
parse(InputStream, EntrySet) - Method in class net.sf.jannot.parser.software.FindPeaksParser
 
parse(InputStream, EntrySet) - Method in class net.sf.jannot.parser.software.GeneMarkParser
 
parse(InputStream, EntrySet) - Method in class net.sf.jannot.parser.software.MapViewParser
 
parse(InputStream, EntrySet) - Method in class net.sf.jannot.parser.software.MaqSNPParser
 
parse(InputStream, EntrySet) - Method in class net.sf.jannot.parser.software.SIPHTParser
 
parse(InputStream, EntrySet) - Method in class net.sf.jannot.parser.software.TransTermHPParser
 
parse(InputStream, EntrySet) - Method in class net.sf.jannot.parser.software.TRNAscanParser
 
parse(InputStream, EntrySet) - Method in class net.sf.jannot.parser.SyntenicParser
 
parse(InputStream, EntrySet) - Method in class net.sf.jannot.parser.TBLParser
 
parse(InputStream, EntrySet) - Method in class net.sf.jannot.parser.WiggleParser
 
parse(TabixLine) - Method in class net.sf.jannot.tabix.codec.BEDCodec
 
parse(TabixLine) - Method in class net.sf.jannot.tabix.codec.Codec
 
parse(TabixLine) - Method in class net.sf.jannot.tabix.codec.GFFCodec
 
parse(TabixLine) - Method in class net.sf.jannot.tabix.codec.PileupCodec
 
parse(TabixLine) - Method in class net.sf.jannot.tabix.codec.SWigCodec
 
parse(TabIndex, char) - Method in class net.sf.jannot.tabix.TabixLine
 
parseLine(String, Type) - Static method in class net.sf.jannot.parser.BEDTools
 
parseLocation(String) - Static method in class net.sf.jannot.parser.ParserTools
 
Parser - Class in net.sf.jannot.parser
 
Parser(DataKey) - Constructor for class net.sf.jannot.parser.Parser
 
parseReg(String) - Method in class net.sf.jannot.tabix.TabixReader
Parse a region in the format of "chr1", "chr1:100" or "chr1:100-1000"
parsers - Static variable in class net.sf.jannot.parser.Parser
 
ParserTools - Class in net.sf.jannot.parser
 
ParserTools() - Constructor for class net.sf.jannot.parser.ParserTools
 
parseTrack(String) - Static method in class net.sf.jannot.parser.BEDTools
 
Percentile - Class in org.apache.commons.math.stat
Provides percentile computation.
Percentile() - Constructor for class org.apache.commons.math.stat.Percentile
Constructs a Percentile with a default quantile value of 50.0.
Percentile(double) - Constructor for class org.apache.commons.math.stat.Percentile
Constructs a Percentile with the specific quantile value.
Pile - Interface in net.sf.jannot.pileup
 
PileTools - Class in net.sf.jannot.pileup
 
PileTools() - Constructor for class net.sf.jannot.pileup.PileTools
 
PileupCodec - Class in net.sf.jannot.tabix.codec
 
PileupCodec(Iterable<TabixLine>) - Constructor for class net.sf.jannot.tabix.codec.PileupCodec
 
PileupWrapper - Class in net.sf.jannot.tabix
 
postInsertHook(boolean) - Method in class gnu.trove.impl.hash.THash
After an insert, this hook is called to adjust the size/free values of the set and to perform rehashing if necessary.
PrimeFinder - Class in gnu.trove.impl
Used to keep hash table capacities prime numbers.
PrimeFinder() - Constructor for class gnu.trove.impl.PrimeFinder
 
print() - Method in class org.broad.igv.bbfile.BBZoomLevelFormat
 
print() - Method in class org.broad.igv.bbfile.BBZoomLevelHeader
 
print() - Method in class org.broad.igv.bbfile.BedFeature
 
print() - Method in class org.broad.igv.bbfile.BigBedDataBlock
 
print() - Method in class org.broad.igv.bbfile.BigWigDataBlock
 
print() - Method in class org.broad.igv.bbfile.BigWigSection
 
print() - Method in class org.broad.igv.bbfile.BigWigSectionHeader
 
print() - Method in class org.broad.igv.bbfile.BPTree
 
print() - Method in class org.broad.igv.bbfile.BPTreeChildNodeItem
 
print() - Method in class org.broad.igv.bbfile.BPTreeHeader
 
print() - Method in class org.broad.igv.bbfile.BPTreeLeafNodeItem
 
print() - Method in class org.broad.igv.bbfile.RPChromosomeRegion
 
print() - Method in class org.broad.igv.bbfile.RPTree
 
print() - Method in class org.broad.igv.bbfile.RPTreeChildNodeItem
 
print() - Method in class org.broad.igv.bbfile.RPTreeHeader
 
print() - Method in class org.broad.igv.bbfile.RPTreeLeafNodeItem
 
print() - Method in class org.broad.igv.bbfile.WigItem
 
print() - Method in class org.broad.igv.bbfile.ZoomDataBlock
 
print() - Method in class org.broad.igv.bbfile.ZoomDataRecord
 
printItems() - Method in class org.broad.igv.bbfile.BPTreeChildNode
 
printItems() - Method in class org.broad.igv.bbfile.BPTreeLeafNode
 
printItems() - Method in interface org.broad.igv.bbfile.BPTreeNode
 
printItems() - Method in class org.broad.igv.bbfile.RPTreeChildNode
 
printItems() - Method in class org.broad.igv.bbfile.RPTreeLeafNode
 
printItems() - Method in interface org.broad.igv.bbfile.RPTreeNode
 
printTotalSummaryBlock() - Method in class org.broad.igv.bbfile.BBTotalSummaryBlock
 
printZoomHeaders() - Method in class org.broad.igv.bbfile.BBZoomLevels
 
PSLTBL_CONF - Static variable in class net.sf.jannot.tabix.TabixWriter
 
PTTParser - Class in net.sf.jannot.parser
 
PTTParser() - Constructor for class net.sf.jannot.parser.PTTParser
 
put(K, V) - Method in class gnu.trove.map.hash.THashMap
Inserts a key/value pair into the map.
put(int, float) - Method in class gnu.trove.map.hash.TIntFloatHashMap
Inserts a key/value pair into the map.
put(long, double) - Method in class gnu.trove.map.hash.TLongDoubleHashMap
Inserts a key/value pair into the map.
put(int, float) - Method in interface gnu.trove.map.TIntFloatMap
Inserts a key/value pair into the map.
put(long, double) - Method in interface gnu.trove.map.TLongDoubleMap
Inserts a key/value pair into the map.
put(String, String) - Method in class net.sf.jannot.Description
 
put(K, V) - Method in class org.apache.commons.collections.map.Flat3Map
Puts a key-value mapping into this map.
put(int) - Method in class org.broad.igv.tdf.BufferedByteWriter
Writes the specified byte to this buffered output stream.
put(byte[]) - Method in class org.broad.igv.tdf.BufferedByteWriter
 
put(byte[], int, int) - Method in class org.broad.igv.tdf.BufferedByteWriter
Writes len bytes from the specified byte array starting at offset off to this buffered output stream.
putAll(Map<? extends K, ? extends V>) - Method in class gnu.trove.map.hash.THashMap
copies the key/value mappings in map into this map.
putAll(Map<? extends Integer, ? extends Float>) - Method in class gnu.trove.map.hash.TIntFloatHashMap
Put all the entries from the given Map into this map.
putAll(TIntFloatMap) - Method in class gnu.trove.map.hash.TIntFloatHashMap
Put all the entries from the given map into this map.
putAll(Map<? extends Long, ? extends Double>) - Method in class gnu.trove.map.hash.TLongDoubleHashMap
Put all the entries from the given Map into this map.
putAll(TLongDoubleMap) - Method in class gnu.trove.map.hash.TLongDoubleHashMap
Put all the entries from the given map into this map.
putAll(Map<? extends Integer, ? extends Float>) - Method in interface gnu.trove.map.TIntFloatMap
Put all the entries from the given Map into this map.
putAll(TIntFloatMap) - Method in interface gnu.trove.map.TIntFloatMap
Put all the entries from the given map into this map.
putAll(Map<? extends Long, ? extends Double>) - Method in interface gnu.trove.map.TLongDoubleMap
Put all the entries from the given Map into this map.
putAll(TLongDoubleMap) - Method in interface gnu.trove.map.TLongDoubleMap
Put all the entries from the given map into this map.
putAll(Map<? extends K, ? extends V>) - Method in class org.apache.commons.collections.map.Flat3Map
Puts all the values from the specified map into this map.
putFloat(long, float) - Method in class net.sf.jannot.picard.BinaryBlob
 
putFloat(float) - Method in class org.broad.igv.tdf.BufferedByteWriter
 
putIfAbsent(K, V) - Method in class gnu.trove.map.hash.THashMap
Inserts a key/value pair into the map if the specified key is not already associated with a value.
putIfAbsent(int, float) - Method in class gnu.trove.map.hash.TIntFloatHashMap
Inserts a key/value pair into the map if the specified key is not already associated with a value.
putIfAbsent(long, double) - Method in class gnu.trove.map.hash.TLongDoubleHashMap
Inserts a key/value pair into the map if the specified key is not already associated with a value.
putIfAbsent(int, float) - Method in interface gnu.trove.map.TIntFloatMap
Inserts a key/value pair into the map if the specified key is not already associated with a value.
putIfAbsent(long, double) - Method in interface gnu.trove.map.TLongDoubleMap
Inserts a key/value pair into the map if the specified key is not already associated with a value.
putInt(int) - Method in class org.broad.igv.tdf.BufferedByteWriter
 
putLong(long) - Method in class org.broad.igv.tdf.BufferedByteWriter
Writes a long to the underlying output stream as eight bytes, little endian.
putNullTerminatedString(String) - Method in class org.broad.igv.tdf.BufferedByteWriter
 

Q

qualifier(String) - Method in class net.sf.jannot.Feature
 
qualifierKeys() - Method in interface net.sf.jannot.FeatureAnnotation
List of keys of qualifiers that are oresent in this data set.
qualifierKeys() - Method in class net.sf.jannot.MemoryFeatureAnnotation
 
qualifierKeys() - Method in class net.sf.jannot.tabix.FeatureWrapper
 
query(String, int, int, boolean) - Method in class net.sf.jannot.shortread.CachingQueryReader
 
query(String, int, int) - Method in class net.sf.jannot.tabix.IndexedFeatureFile
 
query(int, int, int) - Method in class net.sf.jannot.tabix.TabixReader
 
query(String) - Method in class net.sf.jannot.tabix.TabixReader
 
Query - Interface in net.sf.jannot.wiggle
 

R

read(EntrySet) - Method in class net.sf.jannot.bigwig.BigWigDataSource
 
read(byte[], int, int) - Method in class net.sf.jannot.picard.SeekableFileCachedHTTPStream
 
read(EntrySet) - Method in class net.sf.jannot.source.AbstractStreamDataSource
 
read(EntrySet) - Method in class net.sf.jannot.source.cache.CachedURLSource
 
read(EntrySet) - Method in class net.sf.jannot.source.das.DAS
 
read() - Method in class net.sf.jannot.source.DataSource
 
read(EntrySet) - Method in class net.sf.jannot.source.DataSource
 
read(EntrySet) - Method in class net.sf.jannot.source.IndexedFastaDataSource
 
read(EntrySet) - Method in class net.sf.jannot.source.IndexedMAFDataSource
 
read(EntrySet) - Method in class net.sf.jannot.source.SAMDataSource
 
read(EntrySet) - Method in class net.sf.jannot.tabix.IndexedFeatureFile
 
read(EntrySet) - Method in class net.sf.jannot.tdf.TDFDataSource
 
readBoolean() - Method in class net.sf.jannot.tabix.BinaryCodec
Reads a boolean off the input stream, represented as a byte with value 1 or 0
readBoolean() - Method in class org.broad.tribble.LittleEndianInputStream
 
readByte() - Method in class net.sf.jannot.tabix.BinaryCodec
 
readByte() - Method in class org.broad.tribble.LittleEndianInputStream
 
readBytes(byte[]) - Method in class net.sf.jannot.tabix.BinaryCodec
Read a byte array from the input stream.
readBytes(byte[], int, int) - Method in class net.sf.jannot.tabix.BinaryCodec
Read a byte array from the input stream
readBytes(long, int) - Method in class org.broad.igv.tdf.TDFReader
 
readBytesOrFewer(byte[], int, int) - Method in class net.sf.jannot.tabix.BinaryCodec
Reads a byte array from the input stream.
readChar() - Method in class org.broad.tribble.LittleEndianInputStream
 
ReadDetailPile - Class in net.sf.jannot.pileup
 
ReadDetailPile(int, float, float, byte[]) - Constructor for class net.sf.jannot.pileup.ReadDetailPile
 
readDouble() - Method in class net.sf.jannot.tabix.BinaryCodec
Reads a double off the input stream
readDouble() - Method in class org.broad.tribble.LittleEndianInputStream
 
readExternal(ObjectInput) - Method in class gnu.trove.impl.hash.THash
 
readExternal(ObjectInput) - Method in class gnu.trove.impl.hash.TIntFloatHash
readExternal(ObjectInput) - Method in class gnu.trove.impl.hash.TLongDoubleHash
readExternal(ObjectInput) - Method in class gnu.trove.impl.hash.TObjectHash
 
readExternal(ObjectInput) - Method in class gnu.trove.map.hash.THashMap
 
readExternal(ObjectInput) - Method in class gnu.trove.map.hash.TIntFloatHashMap
readExternal(ObjectInput) - Method in class gnu.trove.map.hash.TLongDoubleHashMap
readExternal(ObjectInput) - Method in class gnu.trove.set.hash.THashSet
 
readExternal(ObjectInput) - Method in class gnu.trove.set.hash.TIntHashSet
readExternal(ObjectInput) - Method in class gnu.trove.set.hash.TLongHashSet
ReadFailedException - Exception in net.sf.jannot.exception
 
ReadFailedException(IOException) - Constructor for exception net.sf.jannot.exception.ReadFailedException
 
ReadFailedException(Throwable) - Constructor for exception net.sf.jannot.exception.ReadFailedException
 
ReadFailedException(String) - Constructor for exception net.sf.jannot.exception.ReadFailedException
 
readFloat() - Method in class net.sf.jannot.tabix.BinaryCodec
Reads a float off the input stream
readFloat() - Method in class org.broad.tribble.LittleEndianInputStream
 
readFully(byte[], SeekableStream) - Static method in class org.broad.tribble.SeekableStreamUtils
 
ReadGroup - Class in net.sf.jannot.shortread
 
ReadGroup() - Constructor for class net.sf.jannot.shortread.ReadGroup
 
readIndex(File) - Method in class net.sf.jannot.tabix.TabixReader
Read the Tabix index from a file
readIndex() - Method in class net.sf.jannot.tabix.TabixReader
Read the Tabix index from the default file.
readInt() - Method in class net.sf.jannot.tabix.BinaryCodec
Read an int off the input stream
readInt(InputStream) - Static method in class net.sf.jannot.tabix.TabixReader
 
readInt() - Method in class org.broad.tribble.LittleEndianInputStream
 
readLength() - Method in class net.sf.jannot.shortread.BAMreads
 
readLength() - Method in class net.sf.jannot.shortread.MemoryReadSet
 
readLength() - Method in class net.sf.jannot.shortread.ReadGroup
Returns the maximum length of a read.
readLengthAndString(boolean) - Method in class net.sf.jannot.tabix.BinaryCodec
Read an int length, and then a String of that length
readLine() - Method in class net.sf.jannot.picard.LineBlockCompressedInputStream
Reads a line from the inputstream until a \n or \n\r is encountered.
readLine(InputStream) - Static method in class net.sf.jannot.tabix.TabixReader
 
readLine() - Method in class net.sf.jannot.tabix.TabixReader
Read one line from the data file.
readLong() - Method in class net.sf.jannot.tabix.BinaryCodec
Reads a long off the input stream
readLong(InputStream) - Static method in class net.sf.jannot.tabix.TabixReader
 
readLong() - Method in class org.broad.tribble.LittleEndianInputStream
 
readNullTerminatedString() - Method in class net.sf.jannot.tabix.BinaryCodec
Read ASCII bytes from the input stream until a null byte is read
readShort() - Method in class net.sf.jannot.tabix.BinaryCodec
 
readShort() - Method in class org.broad.tribble.LittleEndianInputStream
 
readString(int) - Method in class net.sf.jannot.tabix.BinaryCodec
Read a string off the input stream, as ASCII bytes
readString(ByteBuffer) - Static method in class org.broad.igv.util.StringUtils
 
readString() - Method in class org.broad.tribble.LittleEndianInputStream
Read a null terminated byte array and return result as a string
readTile(TDFDataset, int) - Method in class org.broad.igv.tdf.TDFReader
 
readUByte() - Method in class net.sf.jannot.tabix.BinaryCodec
Reads an 8-bit unsigned byte from the input stream.
readUInt() - Method in class net.sf.jannot.tabix.BinaryCodec
Reads a 32-bit unsigned int from the input stream.
readULong() - Method in class net.sf.jannot.tabix.BinaryCodec
Reads a 64-bit unsigned long from the input stream.
readUnsignedByte() - Method in class org.broad.tribble.LittleEndianInputStream
 
readUnsignedShort() - Method in class org.broad.tribble.LittleEndianInputStream
 
readUShort() - Method in class net.sf.jannot.tabix.BinaryCodec
Reads a 16-bit unsigned short from the input stream.
recommendedIndex() - Method in class net.sf.jannot.source.Locator
 
RECORD_SIZE - Static variable in class org.broad.igv.bbfile.ZoomDataRecord
 
reenableAutoCompaction(boolean) - Method in class gnu.trove.impl.hash.THash
Re-enable auto-compaction after it was disabled via THash.tempDisableAutoCompaction().
ref2aln(int) - Method in class net.sf.jannot.alignment.ReferenceSequence
Returns the alignment position if you know the position in the reference sequence.
ReferenceSequence - Class in net.sf.jannot.alignment
Sequence that can be used as reference for multiple alignments.
ReferenceSequence(StringBuffer) - Constructor for class net.sf.jannot.alignment.ReferenceSequence
 
ReferenceSequence(MemorySequence) - Constructor for class net.sf.jannot.alignment.ReferenceSequence
 
refLength() - Method in class net.sf.jannot.alignment.mfa.Alignment
Returns the length of the reference sequence.
refLocation() - Method in class net.sf.jannot.SyntenicBlock
 
refreshData(long) - Method in interface org.broad.igv.data.DataSource
 
register(SAMFileReader, SeekableStream, File) - Static method in class net.sf.jannot.Cleaner
 
register(RandomAccessFile, File) - Static method in class net.sf.jannot.Cleaner
 
rehash(int) - Method in class gnu.trove.impl.hash.THash
Rehashes the set.
rehash(int) - Method in class gnu.trove.map.hash.THashMap
rehashes the map to the new capacity.
rehash(int) - Method in class gnu.trove.map.hash.TIntFloatHashMap
Rehashes the set.
rehash(int) - Method in class gnu.trove.map.hash.TLongDoubleHashMap
Rehashes the set.
rehash(int) - Method in class gnu.trove.set.hash.THashSet
Expands the set to accommodate new values.
rehash(int) - Method in class gnu.trove.set.hash.TIntHashSet
Rehashes the set.
rehash(int) - Method in class gnu.trove.set.hash.TLongHashSet
Rehashes the set.
remove() - Method in class gnu.trove.impl.hash.THashIterator
Removes the last entry returned by the iterator.
remove() - Method in class gnu.trove.impl.hash.THashPrimitiveIterator
Removes the last entry returned by the iterator.
remove() - Method in interface gnu.trove.iterator.TIterator
Removes the last entry returned by the iterator.
remove() - Method in interface gnu.trove.iterator.TPrimitiveIterator
Removes the last entry returned by the iterator.
remove(Object) - Method in class gnu.trove.map.hash.THashMap
Deletes a key/value pair from the map.
remove(int) - Method in class gnu.trove.map.hash.TIntFloatHashMap
Deletes a key/value pair from the map.
remove(int) - Method in class gnu.trove.map.hash.TIntFloatHashMap.TKeyView
Removes entry from the set.
remove(float) - Method in class gnu.trove.map.hash.TIntFloatHashMap.TValueView
Removes entry from the collection.
remove(long) - Method in class gnu.trove.map.hash.TLongDoubleHashMap
Deletes a key/value pair from the map.
remove(long) - Method in class gnu.trove.map.hash.TLongDoubleHashMap.TKeyView
Removes entry from the set.
remove(double) - Method in class gnu.trove.map.hash.TLongDoubleHashMap.TValueView
Removes entry from the collection.
remove(int) - Method in interface gnu.trove.map.TIntFloatMap
Deletes a key/value pair from the map.
remove(long) - Method in interface gnu.trove.map.TLongDoubleMap
Deletes a key/value pair from the map.
remove(Object) - Method in class gnu.trove.set.hash.THashSet
Removes obj from the set.
remove(int) - Method in class gnu.trove.set.hash.TIntHashSet
Removes entry from the set.
remove(long) - Method in class gnu.trove.set.hash.TLongHashSet
Removes entry from the set.
remove(int) - Method in interface gnu.trove.set.TIntSet
Removes entry from the set.
remove(long) - Method in interface gnu.trove.set.TLongSet
Removes entry from the set.
remove(double) - Method in interface gnu.trove.TDoubleCollection
Removes entry from the collection.
remove(float) - Method in interface gnu.trove.TFloatCollection
Removes entry from the collection.
remove(int) - Method in interface gnu.trove.TIntCollection
Removes entry from the collection.
remove(long) - Method in interface gnu.trove.TLongCollection
Removes entry from the collection.
remove(short) - Method in interface gnu.trove.TShortCollection
Removes entry from the collection.
remove(DataKey) - Method in class net.sf.jannot.Entry
 
remove() - Method in class net.sf.jannot.ListIterator
Removes from the underlying collection the last element returned by the iterator (optional operation).
remove() - Method in class net.sf.jannot.LocatedListIterator
Removes from the underlying collection the last element returned by the iterator (optional operation).
remove(Feature) - Method in class net.sf.jannot.MemoryFeatureAnnotation
 
remove() - Method in class net.sf.jannot.shortread.CachingQueryReader.TiledIterator
 
remove() - Method in class net.sf.jannot.shortread.EmptyIterator
 
remove() - Method in class net.sf.jannot.utils.ArrayIterator
Removes from the underlying collection the last element returned by the iterator (optional operation).
remove(Object) - Method in class org.apache.commons.collections.map.Flat3Map
Removes the specified mapping from this map.
remove() - Method in class org.broad.igv.bbfile.BigBedIterator
 
remove() - Method in class org.broad.igv.bbfile.BigWigIterator
 
remove() - Method in class org.broad.igv.bbfile.ZoomLevelIterator
 
removeAll(Collection<?>) - Method in class gnu.trove.map.hash.TIntFloatHashMap.TKeyView
Removes all of the elements in collection from the set.
removeAll(TIntCollection) - Method in class gnu.trove.map.hash.TIntFloatHashMap.TKeyView
Removes all of the elements in TIntCollection from the set.
removeAll(int[]) - Method in class gnu.trove.map.hash.TIntFloatHashMap.TKeyView
Removes all of the elements in array from the set.
removeAll(Collection<?>) - Method in class gnu.trove.map.hash.TIntFloatHashMap.TValueView
Removes all of the elements in collection from the collection.
removeAll(TFloatCollection) - Method in class gnu.trove.map.hash.TIntFloatHashMap.TValueView
Removes all of the elements in TFloatCollection from the collection.
removeAll(float[]) - Method in class gnu.trove.map.hash.TIntFloatHashMap.TValueView
Removes all of the elements in array from the collection.
removeAll(Collection<?>) - Method in class gnu.trove.map.hash.TLongDoubleHashMap.TKeyView
Removes all of the elements in collection from the set.
removeAll(TLongCollection) - Method in class gnu.trove.map.hash.TLongDoubleHashMap.TKeyView
Removes all of the elements in TLongCollection from the set.
removeAll(long[]) - Method in class gnu.trove.map.hash.TLongDoubleHashMap.TKeyView
Removes all of the elements in array from the set.
removeAll(Collection<?>) - Method in class gnu.trove.map.hash.TLongDoubleHashMap.TValueView
Removes all of the elements in collection from the collection.
removeAll(TDoubleCollection) - Method in class gnu.trove.map.hash.TLongDoubleHashMap.TValueView
Removes all of the elements in TDoubleCollection from the collection.
removeAll(double[]) - Method in class gnu.trove.map.hash.TLongDoubleHashMap.TValueView
Removes all of the elements in array from the collection.
removeAll(Collection<?>) - Method in class gnu.trove.set.hash.THashSet
Removes all of the elements in collection from the set.
removeAll(Collection<?>) - Method in class gnu.trove.set.hash.TIntHashSet
Removes all of the elements in collection from the set.
removeAll(TIntCollection) - Method in class gnu.trove.set.hash.TIntHashSet
Removes all of the elements in TIntCollection from the set.
removeAll(int[]) - Method in class gnu.trove.set.hash.TIntHashSet
Removes all of the elements in array from the set.
removeAll(Collection<?>) - Method in class gnu.trove.set.hash.TLongHashSet
Removes all of the elements in collection from the set.
removeAll(TLongCollection) - Method in class gnu.trove.set.hash.TLongHashSet
Removes all of the elements in TLongCollection from the set.
removeAll(long[]) - Method in class gnu.trove.set.hash.TLongHashSet
Removes all of the elements in array from the set.
removeAll(Collection<?>) - Method in interface gnu.trove.set.TIntSet
Removes all of the elements in collection from the set.
removeAll(TIntCollection) - Method in interface gnu.trove.set.TIntSet
Removes all of the elements in TIntCollection from the set.
removeAll(int[]) - Method in interface gnu.trove.set.TIntSet
Removes all of the elements in array from the set.
removeAll(Collection<?>) - Method in interface gnu.trove.set.TLongSet
Removes all of the elements in collection from the set.
removeAll(TLongCollection) - Method in interface gnu.trove.set.TLongSet
Removes all of the elements in TLongCollection from the set.
removeAll(long[]) - Method in interface gnu.trove.set.TLongSet
Removes all of the elements in array from the set.
removeAll(Collection<?>) - Method in interface gnu.trove.TDoubleCollection
Removes all of the elements in collection from the collection.
removeAll(TDoubleCollection) - Method in interface gnu.trove.TDoubleCollection
Removes all of the elements in TDoubleCollection from the collection.
removeAll(double[]) - Method in interface gnu.trove.TDoubleCollection
Removes all of the elements in array from the collection.
removeAll(Collection<?>) - Method in interface gnu.trove.TFloatCollection
Removes all of the elements in collection from the collection.
removeAll(TFloatCollection) - Method in interface gnu.trove.TFloatCollection
Removes all of the elements in TFloatCollection from the collection.
removeAll(float[]) - Method in interface gnu.trove.TFloatCollection
Removes all of the elements in array from the collection.
removeAll(Collection<?>) - Method in interface gnu.trove.TIntCollection
Removes all of the elements in collection from the collection.
removeAll(TIntCollection) - Method in interface gnu.trove.TIntCollection
Removes all of the elements in TIntCollection from the collection.
removeAll(int[]) - Method in interface gnu.trove.TIntCollection
Removes all of the elements in array from the collection.
removeAll(Collection<?>) - Method in interface gnu.trove.TLongCollection
Removes all of the elements in collection from the collection.
removeAll(TLongCollection) - Method in interface gnu.trove.TLongCollection
Removes all of the elements in TLongCollection from the collection.
removeAll(long[]) - Method in interface gnu.trove.TLongCollection
Removes all of the elements in array from the collection.
removeAll(Collection<?>) - Method in interface gnu.trove.TShortCollection
Removes all of the elements in collection from the collection.
removeAll(TShortCollection) - Method in interface gnu.trove.TShortCollection
Removes all of the elements in TShortCollection from the collection.
removeAll(short[]) - Method in interface gnu.trove.TShortCollection
Removes all of the elements in array from the collection.
removeAt(int) - Method in class gnu.trove.impl.hash.THash
Delete the record at index.
removeAt(int) - Method in class gnu.trove.impl.hash.TIntFloatHash
Releases the element currently stored at index.
removeAt(int) - Method in class gnu.trove.impl.hash.TIntHash
Releases the element currently stored at index.
removeAt(int) - Method in class gnu.trove.impl.hash.TLongDoubleHash
Releases the element currently stored at index.
removeAt(int) - Method in class gnu.trove.impl.hash.TLongHash
Releases the element currently stored at index.
removeAt(int) - Method in class gnu.trove.impl.hash.TObjectHash
 
removeAt(int) - Method in class gnu.trove.impl.hash.TPrimitiveHash
Delete the record at index.
removeAt(int) - Method in class gnu.trove.map.hash.THashMap
removes the mapping at index from the map.
removeAt(int) - Method in class gnu.trove.map.hash.TIntFloatHashMap
Releases the element currently stored at index.
removeAt(int) - Method in class gnu.trove.map.hash.TLongDoubleHashMap
Releases the element currently stored at index.
REMOVED - Static variable in class gnu.trove.impl.hash.TObjectHash
 
REMOVED - Static variable in class gnu.trove.impl.hash.TPrimitiveHash
flag indicating that the value of a slot in the hashtable was deleted
removeEldestEntry(Map.Entry<K, V>) - Method in class org.broad.LRUCache
 
removeElement(Map.Entry<K, V>) - Method in class gnu.trove.map.hash.THashMap.EntryView
 
removeElement(K) - Method in class gnu.trove.map.hash.THashMap.KeyView
 
removeElement(V) - Method in class gnu.trove.map.hash.THashMap.ValueView
 
removeLocation(Location) - Method in class net.sf.jannot.Feature
 
requestWindowFunction(WindowFunction) - Method in class net.sf.jannot.tdf.TDFData
 
requiresIndex() - Method in class net.sf.jannot.source.Locator
 
retainAll(Collection<?>) - Method in class gnu.trove.map.hash.TIntFloatHashMap.TKeyView
Removes any values in the set which are not contained in collection.
retainAll(TIntCollection) - Method in class gnu.trove.map.hash.TIntFloatHashMap.TKeyView
Removes any values in the set which are not contained in TIntCollection.
retainAll(int[]) - Method in class gnu.trove.map.hash.TIntFloatHashMap.TKeyView
Removes any values in the set which are not contained in array.
retainAll(Collection<?>) - Method in class gnu.trove.map.hash.TIntFloatHashMap.TValueView
Removes any values in the collection which are not contained in collection.
retainAll(TFloatCollection) - Method in class gnu.trove.map.hash.TIntFloatHashMap.TValueView
Removes any values in the collection which are not contained in TFloatCollection.
retainAll(float[]) - Method in class gnu.trove.map.hash.TIntFloatHashMap.TValueView
Removes any values in the collection which are not contained in array.
retainAll(Collection<?>) - Method in class gnu.trove.map.hash.TLongDoubleHashMap.TKeyView
Removes any values in the set which are not contained in collection.
retainAll(TLongCollection) - Method in class gnu.trove.map.hash.TLongDoubleHashMap.TKeyView
Removes any values in the set which are not contained in TLongCollection.
retainAll(long[]) - Method in class gnu.trove.map.hash.TLongDoubleHashMap.TKeyView
Removes any values in the set which are not contained in array.
retainAll(Collection<?>) - Method in class gnu.trove.map.hash.TLongDoubleHashMap.TValueView
Removes any values in the collection which are not contained in collection.
retainAll(TDoubleCollection) - Method in class gnu.trove.map.hash.TLongDoubleHashMap.TValueView
Removes any values in the collection which are not contained in TDoubleCollection.
retainAll(double[]) - Method in class gnu.trove.map.hash.TLongDoubleHashMap.TValueView
Removes any values in the collection which are not contained in array.
retainAll(Collection<?>) - Method in class gnu.trove.set.hash.THashSet
Removes any values in the set which are not contained in collection.
retainAll(Collection<?>) - Method in class gnu.trove.set.hash.TIntHashSet
Removes any values in the set which are not contained in collection.
retainAll(TIntCollection) - Method in class gnu.trove.set.hash.TIntHashSet
Removes any values in the set which are not contained in TIntCollection.
retainAll(int[]) - Method in class gnu.trove.set.hash.TIntHashSet
Removes any values in the set which are not contained in array.
retainAll(Collection<?>) - Method in class gnu.trove.set.hash.TLongHashSet
Removes any values in the set which are not contained in collection.
retainAll(TLongCollection) - Method in class gnu.trove.set.hash.TLongHashSet
Removes any values in the set which are not contained in TLongCollection.
retainAll(long[]) - Method in class gnu.trove.set.hash.TLongHashSet
Removes any values in the set which are not contained in array.
retainAll(Collection<?>) - Method in interface gnu.trove.set.TIntSet
Removes any values in the set which are not contained in collection.
retainAll(TIntCollection) - Method in interface gnu.trove.set.TIntSet
Removes any values in the set which are not contained in TIntCollection.
retainAll(int[]) - Method in interface gnu.trove.set.TIntSet
Removes any values in the set which are not contained in array.
retainAll(Collection<?>) - Method in interface gnu.trove.set.TLongSet
Removes any values in the set which are not contained in collection.
retainAll(TLongCollection) - Method in interface gnu.trove.set.TLongSet
Removes any values in the set which are not contained in TLongCollection.
retainAll(long[]) - Method in interface gnu.trove.set.TLongSet
Removes any values in the set which are not contained in array.
retainAll(Collection<?>) - Method in interface gnu.trove.TDoubleCollection
Removes any values in the collection which are not contained in collection.
retainAll(TDoubleCollection) - Method in interface gnu.trove.TDoubleCollection
Removes any values in the collection which are not contained in TDoubleCollection.
retainAll(double[]) - Method in interface gnu.trove.TDoubleCollection
Removes any values in the collection which are not contained in array.
retainAll(Collection<?>) - Method in interface gnu.trove.TFloatCollection
Removes any values in the collection which are not contained in collection.
retainAll(TFloatCollection) - Method in interface gnu.trove.TFloatCollection
Removes any values in the collection which are not contained in TFloatCollection.
retainAll(float[]) - Method in interface gnu.trove.TFloatCollection
Removes any values in the collection which are not contained in array.
retainAll(Collection<?>) - Method in interface gnu.trove.TIntCollection
Removes any values in the collection which are not contained in collection.
retainAll(TIntCollection) - Method in interface gnu.trove.TIntCollection
Removes any values in the collection which are not contained in TIntCollection.
retainAll(int[]) - Method in interface gnu.trove.TIntCollection
Removes any values in the collection which are not contained in array.
retainAll(Collection<?>) - Method in interface gnu.trove.TLongCollection
Removes any values in the collection which are not contained in collection.
retainAll(TLongCollection) - Method in interface gnu.trove.TLongCollection
Removes any values in the collection which are not contained in TLongCollection.
retainAll(long[]) - Method in interface gnu.trove.TLongCollection
Removes any values in the collection which are not contained in array.
retainAll(Collection<?>) - Method in interface gnu.trove.TShortCollection
Removes any values in the collection which are not contained in collection.
retainAll(TShortCollection) - Method in interface gnu.trove.TShortCollection
Removes any values in the collection which are not contained in TShortCollection.
retainAll(short[]) - Method in interface gnu.trove.TShortCollection
Removes any values in the collection which are not contained in array.
retainEntries(TObjectObjectProcedure<K, V>) - Method in class gnu.trove.map.hash.THashMap
Retains only those entries in the map for which the procedure returns a true value.
retainEntries(TIntFloatProcedure) - Method in class gnu.trove.map.hash.TIntFloatHashMap
Retains only those entries in the map for which the procedure returns a true value.
retainEntries(TLongDoubleProcedure) - Method in class gnu.trove.map.hash.TLongDoubleHashMap
Retains only those entries in the map for which the procedure returns a true value.
retainEntries(TIntFloatProcedure) - Method in interface gnu.trove.map.TIntFloatMap
Retains only those entries in the map for which the procedure returns a true value.
retainEntries(TLongDoubleProcedure) - Method in interface gnu.trove.map.TLongDoubleMap
Retains only those entries in the map for which the procedure returns a true value.
reverseComplement(Sequence) - Static method in class net.sf.jannot.utils.SequenceTools
Create a reverse complement sequence to the supplied sequence
RPChromosomeRegion - Class in org.broad.igv.bbfile
File retrieved from BigWig project at Google code on July 26, 2011, revision 36 http://code.google.com/p/bigwig/ This project provides java readers for the UCSC's BigWig and BigBed formats.
RPChromosomeRegion(int, int, int, int) - Constructor for class org.broad.igv.bbfile.RPChromosomeRegion
 
RPChromosomeRegion(RPChromosomeRegion) - Constructor for class org.broad.igv.bbfile.RPChromosomeRegion
 
RPChromosomeRegion() - Constructor for class org.broad.igv.bbfile.RPChromosomeRegion
 
RPTree - Class in org.broad.igv.bbfile
File retrieved from BigWig project at Google code on July 26, 2011, revision 36 http://code.google.com/p/bigwig/ This project provides java readers for the UCSC's BigWig and BigBed formats.
RPTree(SeekableStream, long, boolean, int) - Constructor for class org.broad.igv.bbfile.RPTree
 
RPTree(int) - Constructor for class org.broad.igv.bbfile.RPTree
 
RPTREE_HEADER_SIZE - Variable in class org.broad.igv.bbfile.RPTreeHeader
 
RPTREE_MAGIC_HTL - Variable in class org.broad.igv.bbfile.RPTreeHeader
 
RPTREE_MAGIC_LTH - Variable in class org.broad.igv.bbfile.RPTreeHeader
 
RPTREE_NODE_CHILD_ITEM_SIZE - Variable in class org.broad.igv.bbfile.RPTree
 
RPTREE_NODE_FORMAT_SIZE - Variable in class org.broad.igv.bbfile.RPTree
 
RPTREE_NODE_LEAF_ITEM_SIZE - Variable in class org.broad.igv.bbfile.RPTree
 
RPTreeChildNode - Class in org.broad.igv.bbfile
File retrieved from BigWig project at Google code on July 26, 2011, revision 36 http://code.google.com/p/bigwig/ This project provides java readers for the UCSC's BigWig and BigBed formats.
RPTreeChildNode() - Constructor for class org.broad.igv.bbfile.RPTreeChildNode
 
RPTreeChildNodeItem - Class in org.broad.igv.bbfile
File retrieved from BigWig project at Google code on July 26, 2011, revision 36 http://code.google.com/p/bigwig/ This project provides java readers for the UCSC's BigWig and BigBed formats.
RPTreeChildNodeItem(int, int, int, int, RPTreeNode) - Constructor for class org.broad.igv.bbfile.RPTreeChildNodeItem
 
RPTreeHeader - Class in org.broad.igv.bbfile
File retrieved from BigWig project at Google code on July 26, 2011, revision 36 http://code.google.com/p/bigwig/ This project provides java readers for the UCSC's BigWig and BigBed formats.
RPTreeHeader(SeekableStream, long, boolean) - Constructor for class org.broad.igv.bbfile.RPTreeHeader
 
RPTreeLeafNode - Class in org.broad.igv.bbfile
File retrieved from BigWig project at Google code on July 26, 2011, revision 36 http://code.google.com/p/bigwig/ This project provides java readers for the UCSC's BigWig and BigBed formats.
RPTreeLeafNode() - Constructor for class org.broad.igv.bbfile.RPTreeLeafNode
 
RPTreeLeafNodeItem - Class in org.broad.igv.bbfile
File retrieved from BigWig project at Google code on July 26, 2011, revision 36 http://code.google.com/p/bigwig/ This project provides java readers for the UCSC's BigWig and BigBed formats.
RPTreeLeafNodeItem(int, int, int, int, long, long) - Constructor for class org.broad.igv.bbfile.RPTreeLeafNodeItem
 
RPTreeNode - Interface in org.broad.igv.bbfile
File retrieved from BigWig project at Google code on July 26, 2011, revision 36 http://code.google.com/p/bigwig/ This project provides java readers for the UCSC's BigWig and BigBed formats.
RuntimeEOFException - Exception in net.sf.jannot.tabix
Thrown by various codecs to indicate EOF without having to clutter the API with throws clauses
RuntimeEOFException() - Constructor for exception net.sf.jannot.tabix.RuntimeEOFException
 
RuntimeEOFException(String) - Constructor for exception net.sf.jannot.tabix.RuntimeEOFException
 
RuntimeEOFException(String, Throwable) - Constructor for exception net.sf.jannot.tabix.RuntimeEOFException
 
RuntimeEOFException(Throwable) - Constructor for exception net.sf.jannot.tabix.RuntimeEOFException
 
RuntimeIOException - Exception in net.sf.jannot.tabix
Thrown by various IO classes to indicate IOException without having to clutter the API with throws clauses
RuntimeIOException() - Constructor for exception net.sf.jannot.tabix.RuntimeIOException
 
RuntimeIOException(String) - Constructor for exception net.sf.jannot.tabix.RuntimeIOException
 
RuntimeIOException(String, Throwable) - Constructor for exception net.sf.jannot.tabix.RuntimeIOException
 
RuntimeIOException(Throwable) - Constructor for exception net.sf.jannot.tabix.RuntimeIOException
 

S

SAM_CONF - Static variable in class net.sf.jannot.tabix.TabixWriter
 
SAMDataSource - Class in net.sf.jannot.source
 
SAMDataSource(Locator, Locator) - Constructor for class net.sf.jannot.source.SAMDataSource
 
SaveFailedException - Exception in net.sf.jannot.exception
 
SaveFailedException() - Constructor for exception net.sf.jannot.exception.SaveFailedException
 
SaveFailedException(String, Throwable) - Constructor for exception net.sf.jannot.exception.SaveFailedException
 
SaveFailedException(String) - Constructor for exception net.sf.jannot.exception.SaveFailedException
 
SaveFailedException(Throwable) - Constructor for exception net.sf.jannot.exception.SaveFailedException
 
SECTION_HEADER_SIZE - Static variable in class org.broad.igv.bbfile.BigWigSectionHeader
 
seek(long) - Method in class net.sf.jannot.picard.LineBlockCompressedInputStream
 
seek(long) - Method in class net.sf.jannot.picard.SeekableFileCachedHTTPStream
 
SeekableFileCachedHTTPStream - Class in net.sf.jannot.picard
 
SeekableFileCachedHTTPStream(URL) - Constructor for class net.sf.jannot.picard.SeekableFileCachedHTTPStream
 
SeekableStreamUtils - Class in org.broad.tribble
 
SeekableStreamUtils() - Constructor for class org.broad.tribble.SeekableStreamUtils
 
seq() - Method in class net.sf.jannot.alignment.maf.AbstractAlignmentSequence
 
seq() - Method in class net.sf.jannot.alignment.maf.LazyAlignmentSequence
 
seq() - Method in class net.sf.jannot.alignment.maf.MemoryAlignmentSequence
 
sequence() - Method in class net.sf.jannot.Entry
 
Sequence - Class in net.sf.jannot.refseq
 
Sequence() - Constructor for class net.sf.jannot.refseq.Sequence
 
SequenceTools - Class in net.sf.jannot.utils
 
SequenceTools() - Constructor for class net.sf.jannot.utils.SequenceTools
 
SequenceTranslator - Class in net.sf.jannot.alignment.maf
 
SequenceTranslator(AbstractAlignmentSequence) - Constructor for class net.sf.jannot.alignment.maf.SequenceTranslator
 
set(int, float) - Method in class net.sf.jannot.wiggle.DiskArrayWiggle
Zero based coordinate
set(int, float) - Method in class net.sf.jannot.wiggle.TroveArrayWiggle
Zero based coordinate
setAttribute(String, String) - Method in class org.broad.igv.tdf.TDFEntity
 
setAutoCompactionFactor(float) - Method in class gnu.trove.impl.hash.THash
The auto-compaction factor controls whether and when a table performs a THash.compact() automatically after a certain number of remove operations.
setConfidence(float) - Method in class org.broad.igv.data.BasicScore
 
setConfidence(float) - Method in interface org.broad.igv.feature.LocusScore
 
setDataKey(String) - Method in class net.sf.jannot.parser.Parser
 
setDefault(String) - Method in class net.sf.jannot.EntrySet
 
setDefault(Entry) - Method in class net.sf.jannot.EntrySet
 
setEnd(int) - Method in class net.sf.jannot.Location
 
setEnd(int) - Method in class org.broad.igv.data.BasicScore
 
setEnd(int) - Method in interface org.broad.igv.feature.LocusScore
 
setEntryPoint(DAS.EntryPoint) - Method in class net.sf.jannot.source.das.DAS
 
setInputFileName(String) - Method in class net.sf.jannot.tabix.BinaryCodec
 
setInputStream(InputStream) - Method in class net.sf.jannot.tabix.BinaryCodec
 
setIos(InputStream) - Method in class net.sf.jannot.source.AbstractStreamDataSource
 
setLength(int) - Method in interface net.sf.jannot.pileup.Pile
 
setLength(int) - Method in class net.sf.jannot.pileup.SinglePile
 
setLine(String) - Method in class net.sf.jannot.tabix.TabixLine
 
setLocation(Collection<Location>) - Method in class net.sf.jannot.Feature
 
setLocation(Location) - Method in class net.sf.jannot.Feature
 
setLocation(Location[]) - Method in class net.sf.jannot.Feature
 
setOutputFileName(String) - Method in class net.sf.jannot.tabix.BinaryCodec
 
setOutputStream(OutputStream) - Method in class net.sf.jannot.tabix.BinaryCodec
 
setParser(Parser) - Method in class net.sf.jannot.source.AbstractStreamDataSource
 
setQuantile(double) - Method in class org.apache.commons.math.stat.Percentile
Sets the value of the quantile field (determines what percentile is computed when evaluate() is called with no quantile argument).
setReference(String) - Method in class net.sf.jannot.source.das.DAS
 
setScore(double) - Method in class net.sf.jannot.Feature
 
setSelectionRegion(RPChromosomeRegion, boolean) - Method in class org.broad.igv.bbfile.BigBedIterator
 
setSelectionRegion(RPChromosomeRegion, boolean) - Method in class org.broad.igv.bbfile.BigWigIterator
 
setSelectionRegion(RPChromosomeRegion, boolean) - Method in class org.broad.igv.bbfile.ZoomLevelIterator
 
setSeq(Sequence) - Method in class net.sf.jannot.alignment.maf.LazyAlignmentSequence
 
setSequence(String) - Method in class net.sf.jannot.alignment.ReferenceSequence
 
setSequence(Sequence) - Method in class net.sf.jannot.Entry
 
setSequence(String) - Method in class net.sf.jannot.refseq.MemorySequence
 
setSequence(StringBuffer) - Method in class net.sf.jannot.refseq.MemorySequence
 
setStart(int) - Method in class net.sf.jannot.Location
 
setStart(int) - Method in class org.broad.igv.data.BasicScore
 
setStart(int) - Method in interface org.broad.igv.feature.LocusScore
 
setStrand(Strand) - Method in class net.sf.jannot.Feature
 
setType(Type) - Method in class net.sf.jannot.Feature
 
setUp(int) - Method in class gnu.trove.impl.hash.THash
initializes the hashtable to a prime capacity which is at least initialCapacity + 1.
setUp(int) - Method in class gnu.trove.impl.hash.TIntFloatHash
initializes the hashtable to a prime capacity which is at least initialCapacity + 1.
setUp(int) - Method in class gnu.trove.impl.hash.TIntHash
initializes the hashtable to a prime capacity which is at least initialCapacity + 1.
setUp(int) - Method in class gnu.trove.impl.hash.TLongDoubleHash
initializes the hashtable to a prime capacity which is at least initialCapacity + 1.
setUp(int) - Method in class gnu.trove.impl.hash.TLongHash
initializes the hashtable to a prime capacity which is at least initialCapacity + 1.
setUp(int) - Method in class gnu.trove.impl.hash.TObjectHash
initializes the Object set of this hash table.
setUp(int) - Method in class gnu.trove.impl.hash.TPrimitiveHash
initializes the hashtable to a prime capacity which is at least initialCapacity + 1.
setUp(int) - Method in class gnu.trove.map.hash.THashMap
initialize the value array of the map.
setUp(int) - Method in class gnu.trove.map.hash.TIntFloatHashMap
initializes the hashtable to a prime capacity which is at least initialCapacity + 1.
setUp(int) - Method in class gnu.trove.map.hash.TLongDoubleHashMap
initializes the hashtable to a prime capacity which is at least initialCapacity + 1.
setValue(float) - Method in interface gnu.trove.iterator.TIntFloatIterator
Replace the value of the mapping at the iterator's position with the specified value.
setValue(double) - Method in interface gnu.trove.iterator.TLongDoubleIterator
Replace the value of the mapping at the iterator's position with the specified value.
setWindowFunction(WindowFunction) - Method in interface org.broad.igv.data.DataSource
 
ShortRead - Class in net.sf.jannot.shortread
 
ShortRead() - Constructor for class net.sf.jannot.shortread.ShortRead
 
shortReads() - Method in class net.sf.jannot.Entry
 
ShortReadTools - Class in net.sf.jannot.shortread
 
ShortReadTools() - Constructor for class net.sf.jannot.shortread.ShortReadTools
 
SinglePile - Class in net.sf.jannot.pileup
Pile representing a single value.
SinglePile(int, float) - Constructor for class net.sf.jannot.pileup.SinglePile
 
SIPHTParser - Class in net.sf.jannot.parser.software
 
SIPHTParser(StringKey) - Constructor for class net.sf.jannot.parser.software.SIPHTParser
 
size() - Method in class gnu.trove.impl.hash.THash
Returns the number of distinct elements in this collection.
size() - Method in class gnu.trove.map.hash.TIntFloatHashMap.TKeyView
Returns the number of elements in this set (its cardinality).
size() - Method in class gnu.trove.map.hash.TIntFloatHashMap.TValueView
Returns the number of elements in this collection (its cardinality).
size() - Method in class gnu.trove.map.hash.TLongDoubleHashMap.TKeyView
Returns the number of elements in this set (its cardinality).
size() - Method in class gnu.trove.map.hash.TLongDoubleHashMap.TValueView
Returns the number of elements in this collection (its cardinality).
size() - Method in interface gnu.trove.map.TIntFloatMap
Returns an int value that is the number of elements in the map.
size() - Method in interface gnu.trove.map.TLongDoubleMap
Returns an int value that is the number of elements in the map.
size() - Method in interface gnu.trove.set.TIntSet
Returns the number of elements in this set (its cardinality).
size() - Method in interface gnu.trove.set.TLongSet
Returns the number of elements in this set (its cardinality).
size() - Method in interface gnu.trove.TDoubleCollection
Returns the number of elements in this collection (its cardinality).
size() - Method in interface gnu.trove.TFloatCollection
Returns the number of elements in this collection (its cardinality).
size() - Method in interface gnu.trove.TIntCollection
Returns the number of elements in this collection (its cardinality).
size() - Method in interface gnu.trove.TLongCollection
Returns the number of elements in this collection (its cardinality).
size() - Method in interface gnu.trove.TShortCollection
Returns the number of elements in this collection (its cardinality).
size() - Method in class net.sf.jannot.alignment.maf.AbstractAlignmentBlock
 
size() - Method in class net.sf.jannot.alignment.maf.LazyAlignmentBlock
 
size() - Method in class net.sf.jannot.alignment.maf.MemoryAlignmentBlock
 
size() - Method in class net.sf.jannot.bigwig.BigWigDataSource
 
size() - Method in class net.sf.jannot.EntrySet
 
size() - Method in class net.sf.jannot.refseq.FaidxData
 
size() - Method in class net.sf.jannot.refseq.MemorySequence
 
size() - Method in class net.sf.jannot.refseq.Sequence
 
size() - Method in class net.sf.jannot.refseq.SubSequence
 
size() - Method in class net.sf.jannot.shortread.MemoryReadSet
 
size() - Method in class net.sf.jannot.source.das.DAS
 
size() - Method in class net.sf.jannot.source.DataSource
 
size(URL, File) - Static method in class net.sf.jannot.source.DataSource
 
size() - Method in class net.sf.jannot.source.FileSource
 
size() - Method in class net.sf.jannot.source.IndexedFastaDataSource
 
size() - Method in class net.sf.jannot.source.IndexedMAFDataSource
 
size() - Method in class net.sf.jannot.source.SAMDataSource
 
size() - Method in class net.sf.jannot.source.URLSource
 
size() - Method in class net.sf.jannot.tabix.IndexedFeatureFile
 
size() - Method in class net.sf.jannot.tdf.TDFDataSource
 
size() - Method in class net.sf.jannot.wiggle.AbstractWiggle
 
size() - Method in class net.sf.jannot.wiggle.DiskArrayWiggle
 
size() - Method in class net.sf.jannot.wiggle.FloatArrayWiggle
 
size() - Method in interface net.sf.jannot.wiggle.Query
 
size() - Method in class net.sf.jannot.wiggle.TroveArrayWiggle
 
size() - Method in class org.apache.commons.collections.map.Flat3Map
Gets the size of the map.
size() - Method in class org.broad.igv.util.collections.DoubleArrayList
 
size() - Method in class org.broad.igv.util.collections.FloatArrayList
 
size() - Method in class org.broad.igv.util.collections.IntArrayList
 
sizeGapAfter(int) - Method in class net.sf.jannot.alignment.mfa.Alignment
 
sort(int[]) - Static method in class gnu.trove.impl.DualPivotQuicksort
 
sort(int[], int, int) - Static method in class gnu.trove.impl.DualPivotQuicksort
 
source() - Method in class net.sf.jannot.tabix.IndexedFeatureFile
 
SourceCache - Class in net.sf.jannot.source.cache
 
SourceCache() - Constructor for class net.sf.jannot.source.cache.SourceCache
 
species() - Method in class net.sf.jannot.alignment.maf.AbstractMAFMultipleAlignment
 
species() - Method in class net.sf.jannot.mafix.IndexedMAF
 
SSL - Class in net.sf.jannot.source
 
SSL() - Constructor for class net.sf.jannot.source.SSL
 
start() - Method in class net.sf.jannot.alignment.maf.AbstractAlignmentBlock
 
start - Variable in class net.sf.jannot.alignment.maf.AbstractAlignmentSequence
 
start() - Method in class net.sf.jannot.alignment.maf.AbstractAlignmentSequence
One based coordinate of this multiple alignment block
start() - Method in class net.sf.jannot.alignment.maf.LazyAlignmentSequence
 
start() - Method in class net.sf.jannot.alignment.mfa.Alignment
 
start() - Method in class net.sf.jannot.Feature
 
start() - Method in interface net.sf.jannot.Located
 
start - Variable in class net.sf.jannot.Location
These fields are public for efficient getter access.
start() - Method in class net.sf.jannot.Location
 
start() - Method in interface net.sf.jannot.pileup.Pile
 
start() - Method in class net.sf.jannot.pileup.SinglePile
 
start() - Method in class net.sf.jannot.shortread.BasicShortRead
 
start() - Method in class net.sf.jannot.shortread.ShortRead
 
start(SAMRecord) - Static method in class net.sf.jannot.shortread.ShortReadTools
 
start - Variable in class net.sf.jannot.tabix.Pair64
Pair value
startCaching(URL) - Static method in class net.sf.jannot.source.cache.SourceCache
 
startColumn - Variable in class net.sf.jannot.tabix.TabixWriter.Conf
 
storeSequence - Variable in class net.sf.jannot.parser.EMBLParser
 
strand - Variable in class net.sf.jannot.alignment.maf.AbstractAlignmentSequence
 
strand() - Method in class net.sf.jannot.alignment.maf.AbstractAlignmentSequence
 
strand() - Method in class net.sf.jannot.Feature
 
strand() - Method in class net.sf.jannot.shortread.BasicShortRead
 
strand() - Method in class net.sf.jannot.shortread.ShortRead
 
strand(SAMRecord) - Static method in class net.sf.jannot.shortread.ShortReadTools
 
Strand - Enum in net.sf.jannot
 
stream() - Method in class net.sf.jannot.picard.SeekableFileCachedHTTPStream
 
stream() - Method in class net.sf.jannot.source.Locator
 
StringKey - Class in net.sf.jannot
 
StringKey(String) - Constructor for class net.sf.jannot.StringKey
 
stringRepresentation() - Method in class net.sf.jannot.refseq.Sequence
Use this method sparingly as it can be a fairly expensive operation
StringUtils - Class in org.broad.igv.util
Created by IntelliJ IDEA.
StringUtils() - Constructor for class org.broad.igv.util.StringUtils
 
stripIndex() - Method in class net.sf.jannot.source.Locator
Removes the index extension from the file name
subsequence(int, int) - Method in class net.sf.jannot.refseq.Sequence
Coordinates are 1-based, cover [start,end[
SubSequence - Class in net.sf.jannot.refseq
 
SubSequence(Sequence, int, int) - Constructor for class net.sf.jannot.refseq.SubSequence
 
supportsIndex() - Method in class net.sf.jannot.source.Locator
 
SWigCodec - Class in net.sf.jannot.tabix.codec
 
SWigCodec(Iterable<TabixLine>) - Constructor for class net.sf.jannot.tabix.codec.SWigCodec
 
SWigWrapper - Class in net.sf.jannot.tabix
 
symbol() - Method in enum net.sf.jannot.Strand
Symbol representing the Strand.
syntenic - Variable in class net.sf.jannot.EntrySet
 
SyntenicAnnotation - Class in net.sf.jannot
 
SyntenicAnnotation() - Constructor for class net.sf.jannot.SyntenicAnnotation
 
SyntenicBlock - Class in net.sf.jannot
Synthenic block provides a syntenic mapping between two entries.
SyntenicBlock(String, String, Location, Location, Strand, Strand) - Constructor for class net.sf.jannot.SyntenicBlock
 
SyntenicParser - Class in net.sf.jannot.parser
This parser read syntenic blocks from an 8 column file that has the following formatting.
SyntenicParser(DataKey) - Constructor for class net.sf.jannot.parser.SyntenicParser
 

T

TabixLine - Class in net.sf.jannot.tabix
 
TabixLine() - Constructor for class net.sf.jannot.tabix.TabixLine
 
TabixReader - Class in net.sf.jannot.tabix
 
TabixReader(Locator) - Constructor for class net.sf.jannot.tabix.TabixReader
The constructor
TabixReader.Iterator - Class in net.sf.jannot.tabix
 
TabixReader.TIndex - Class in net.sf.jannot.tabix
 
TabixReader.TIndex() - Constructor for class net.sf.jannot.tabix.TabixReader.TIndex
 
TabixReader.TIntv - Class in net.sf.jannot.tabix
 
TabixReader.TIntv() - Constructor for class net.sf.jannot.tabix.TabixReader.TIntv
 
TabixReader.TPair64 - Class in net.sf.jannot.tabix
 
TabixReader.TPair64(long, long) - Constructor for class net.sf.jannot.tabix.TabixReader.TPair64
 
TabixReader.TPair64(TabixReader.TPair64) - Constructor for class net.sf.jannot.tabix.TabixReader.TPair64
 
TabixWrapper<T> - Class in net.sf.jannot.tabix
 
TabixWriter - Class in net.sf.jannot.tabix
Tabix writer, based on Heng Li's C implementation.
TabixWriter(Locator, TabixWriter.Conf) - Constructor for class net.sf.jannot.tabix.TabixWriter
 
TabixWriter.Conf - Class in net.sf.jannot.tabix
 
TabixWriter.Conf(int, int, int, int, char, int) - Constructor for class net.sf.jannot.tabix.TabixWriter.Conf
 
TAD_LIDX_SHIFT - Static variable in class net.sf.jannot.tabix.TabixReader
 
TAdvancingIterator - Interface in gnu.trove.iterator
Common interface for iterators that operate via the "advance" method for moving the cursor to the next element.
target() - Method in class net.sf.jannot.SyntenicBlock
 
targetLocation() - Method in class net.sf.jannot.SyntenicBlock
 
TBLParser - Class in net.sf.jannot.parser
Sequin file format parser.
TBLParser() - Constructor for class net.sf.jannot.parser.TBLParser
 
TByteFunction - Interface in gnu.trove.function
Interface for functions that accept and return one byte primitive.
TByteProcedure - Interface in gnu.trove.procedure
Interface for procedures with one byte parameter.
TCharFunction - Interface in gnu.trove.function
Interface for functions that accept and return one char primitive.
TCharProcedure - Interface in gnu.trove.procedure
Interface for procedures with one char parameter.
TDFBedTile - Class in org.broad.igv.tdf
 
TDFBedTile(ByteBuffer, int, TDFTile.Type) - Constructor for class org.broad.igv.tdf.TDFBedTile
 
TDFBedTile(int, int[], int[], float[][]) - Constructor for class org.broad.igv.tdf.TDFBedTile
 
TDFBedTile(int, int[], int[], float[][], String[]) - Constructor for class org.broad.igv.tdf.TDFBedTile
 
TDFData - Class in net.sf.jannot.tdf
 
TDFData(String, TDFReader) - Constructor for class net.sf.jannot.tdf.TDFData
 
TDFDataset - Class in org.broad.igv.tdf
Represents the data for a particular chromosome and zoom level
TDFDataset(String, TDFDataset.DataType, int, int) - Constructor for class org.broad.igv.tdf.TDFDataset
 
TDFDataset(String, ByteBuffer, TDFReader) - Constructor for class org.broad.igv.tdf.TDFDataset
 
TDFDataset.DataType - Enum in org.broad.igv.tdf
 
TDFDataSource - Class in net.sf.jannot.tdf
Data source for TDF files.
TDFDataSource(Locator) - Constructor for class net.sf.jannot.tdf.TDFDataSource
 
TDFEntity - Class in org.broad.igv.tdf
 
TDFEntity(String) - Constructor for class org.broad.igv.tdf.TDFEntity
 
TDFEntity(String, Map<String, String>) - Constructor for class org.broad.igv.tdf.TDFEntity
 
TDFFixedTile - Class in org.broad.igv.tdf
 
TDFFixedTile(ByteBuffer, int) - Constructor for class org.broad.igv.tdf.TDFFixedTile
 
TDFFixedTile(int, int, float, float[][]) - Constructor for class org.broad.igv.tdf.TDFFixedTile
 
TDFGroup - Class in org.broad.igv.tdf
 
TDFGroup(String, ByteBuffer) - Constructor for class org.broad.igv.tdf.TDFGroup
 
TDFReader - Class in org.broad.igv.tdf
 
TDFTile - Interface in org.broad.igv.tdf
 
TDFTile.Type - Enum in org.broad.igv.tdf
 
TDFTools - Class in org.broad.tools
Class to create TDF files from BAM files.
TDFTools() - Constructor for class org.broad.tools.TDFTools
 
TDFUtils - Class in org.broad.igv.tdf
 
TDFUtils() - Constructor for class org.broad.igv.tdf.TDFUtils
 
TDFVaryTile - Class in org.broad.igv.tdf
 
TDFVaryTile(ByteBuffer, int) - Constructor for class org.broad.igv.tdf.TDFVaryTile
 
TDFVaryTile(int, float, int[], float[][]) - Constructor for class org.broad.igv.tdf.TDFVaryTile
 
TDFWriter - Class in org.broad.igv.tdf
Assumptions

Little endian is used throughout Strings are null terminated ascii (single byte

TDFWriter(File, String, String, String, String[], Collection<WindowFunction>, boolean) - Constructor for class org.broad.igv.tdf.TDFWriter
 
TDoubleCollection - Interface in gnu.trove
An interface that mimics the Collection interface.
TDoubleFunction - Interface in gnu.trove.function
Interface for functions that accept and return one double primitive.
TDoubleIterator - Interface in gnu.trove.iterator
Iterator for double collections.
TDoubleProcedure - Interface in gnu.trove.procedure
Interface for procedures with one double parameter.
tempDisableAutoCompaction() - Method in class gnu.trove.impl.hash.THash
Temporarily disables auto-compaction.
test(double[], int, int) - Method in class org.apache.commons.math.stat.AbstractUnivariateStatistic
This method is used by evaluate(double[], int, int) methods to verify that the input parameters designate a subarray of positive length.
TFloatCollection - Interface in gnu.trove
An interface that mimics the Collection interface.
TFloatFunction - Interface in gnu.trove.function
Interface for functions that accept and return one float primitive.
TFloatIterator - Interface in gnu.trove.iterator
Iterator for float collections.
TFloatProcedure - Interface in gnu.trove.procedure
Interface for procedures with one float parameter.
THash - Class in gnu.trove.impl.hash
Base class for hashtables that use open addressing to resolve collisions.
THash() - Constructor for class gnu.trove.impl.hash.THash
Creates a new THash instance with the default capacity and load factor.
THash(int) - Constructor for class gnu.trove.impl.hash.THash
Creates a new THash instance with a prime capacity at or near the specified capacity and with the default load factor.
THash(int, float) - Constructor for class gnu.trove.impl.hash.THash
Creates a new THash instance with a prime capacity at or near the minimum needed to hold initialCapacity elements with load factor loadFactor without triggering a rehash.
THashIterator<V> - Class in gnu.trove.impl.hash
Implements all iterator functions for the hashed object set.
THashIterator(TObjectHash<V>) - Constructor for class gnu.trove.impl.hash.THashIterator
Create an instance of THashIterator over the values of the TObjectHash
THashMap<K,V> - Class in gnu.trove.map.hash
An implementation of the Map interface which uses an open addressed hash table to store its contents.
THashMap() - Constructor for class gnu.trove.map.hash.THashMap
Creates a new THashMap instance with the default capacity and load factor.
THashMap(int) - Constructor for class gnu.trove.map.hash.THashMap
Creates a new THashMap instance with a prime capacity equal to or greater than initialCapacity and with the default load factor.
THashMap(int, float) - Constructor for class gnu.trove.map.hash.THashMap
Creates a new THashMap instance with a prime capacity equal to or greater than initialCapacity and with the specified load factor.
THashMap(Map<K, V>) - Constructor for class gnu.trove.map.hash.THashMap
Creates a new THashMap instance which contains the key/value pairs in map.
THashMap(THashMap<K, V>) - Constructor for class gnu.trove.map.hash.THashMap
Creates a new THashMap instance which contains the key/value pairs in map.
THashMap.EntryView - Class in gnu.trove.map.hash
a view onto the entries of the map.
THashMap.EntryView() - Constructor for class gnu.trove.map.hash.THashMap.EntryView
 
THashMap.KeyView - Class in gnu.trove.map.hash
a view onto the keys of the map.
THashMap.KeyView() - Constructor for class gnu.trove.map.hash.THashMap.KeyView
 
THashMap.ValueView - Class in gnu.trove.map.hash
a view onto the values of the map.
THashMap.ValueView() - Constructor for class gnu.trove.map.hash.THashMap.ValueView
 
THashPrimitiveIterator - Class in gnu.trove.impl.hash
Implements all iterator functions for the hashed object set.
THashPrimitiveIterator(TPrimitiveHash) - Constructor for class gnu.trove.impl.hash.THashPrimitiveIterator
Creates a TPrimitiveIterator for the specified collection.
THashSet<E> - Class in gnu.trove.set.hash
An implementation of the Set interface that uses an open-addressed hash table to store its contents.
THashSet() - Constructor for class gnu.trove.set.hash.THashSet
Creates a new THashSet instance with the default capacity and load factor.
THashSet(int) - Constructor for class gnu.trove.set.hash.THashSet
Creates a new THashSet instance with a prime capacity equal to or greater than initialCapacity and with the default load factor.
THashSet(int, float) - Constructor for class gnu.trove.set.hash.THashSet
Creates a new THashSet instance with a prime capacity equal to or greater than initialCapacity and with the specified load factor.
THashSet(Collection<? extends E>) - Constructor for class gnu.trove.set.hash.THashSet
Creates a new THashSet instance containing the elements of collection.
throwObjectContractViolation(Object, Object) - Method in class gnu.trove.impl.hash.TObjectHash
Convenience methods for subclasses to use in throwing exceptions about badly behaved user objects employed as keys.
TI_FLAG_UCSC - Static variable in class net.sf.jannot.tabix.TabixWriter
 
TI_PRESET_GENERIC - Static variable in class net.sf.jannot.tabix.TabixWriter
 
TI_PRESET_SAM - Static variable in class net.sf.jannot.tabix.TabixWriter
 
TI_PRESET_VCF - Static variable in class net.sf.jannot.tabix.TabixWriter
 
TileFactory - Class in org.broad.igv.tdf
 
TileFactory() - Constructor for class org.broad.igv.tdf.TileFactory
 
TileManager - Class in org.broad.igv.tdf
 
TileManager(TDFReader) - Constructor for class org.broad.igv.tdf.TileManager
 
TIntCollection - Interface in gnu.trove
An interface that mimics the Collection interface.
TIntFloatHash - Class in gnu.trove.impl.hash
An open addressed hashing implementation for int/float primitive entries.
TIntFloatHash() - Constructor for class gnu.trove.impl.hash.TIntFloatHash
Creates a new T#E#Hash instance with the default capacity and load factor.
TIntFloatHash(int) - Constructor for class gnu.trove.impl.hash.TIntFloatHash
Creates a new T#E#Hash instance whose capacity is the next highest prime above initialCapacity + 1 unless that value is already prime.
TIntFloatHash(int, float) - Constructor for class gnu.trove.impl.hash.TIntFloatHash
Creates a new TIntFloatHash instance with a prime value at or near the specified capacity and load factor.
TIntFloatHash(int, float, int, float) - Constructor for class gnu.trove.impl.hash.TIntFloatHash
Creates a new TIntFloatHash instance with a prime value at or near the specified capacity and load factor.
TIntFloatHashMap - Class in gnu.trove.map.hash
An open addressed Map implementation for int keys and float values.
TIntFloatHashMap() - Constructor for class gnu.trove.map.hash.TIntFloatHashMap
Creates a new TIntFloatHashMap instance with the default capacity and load factor.
TIntFloatHashMap(int) - Constructor for class gnu.trove.map.hash.TIntFloatHashMap
Creates a new TIntFloatHashMap instance with a prime capacity equal to or greater than initialCapacity and with the default load factor.
TIntFloatHashMap(int, float) - Constructor for class gnu.trove.map.hash.TIntFloatHashMap
Creates a new TIntFloatHashMap instance with a prime capacity equal to or greater than initialCapacity and with the specified load factor.
TIntFloatHashMap(int, float, int, float) - Constructor for class gnu.trove.map.hash.TIntFloatHashMap
Creates a new TIntFloatHashMap instance with a prime capacity equal to or greater than initialCapacity and with the specified load factor.
TIntFloatHashMap(int[], float[]) - Constructor for class gnu.trove.map.hash.TIntFloatHashMap
Creates a new TIntFloatHashMap instance containing all of the entries in the map passed in.
TIntFloatHashMap(TIntFloatMap) - Constructor for class gnu.trove.map.hash.TIntFloatHashMap
Creates a new TIntFloatHashMap instance containing all of the entries in the map passed in.
TIntFloatHashMap.TKeyView - Class in gnu.trove.map.hash
a view onto the keys of the map.
TIntFloatHashMap.TKeyView() - Constructor for class gnu.trove.map.hash.TIntFloatHashMap.TKeyView
 
TIntFloatHashMap.TValueView - Class in gnu.trove.map.hash
a view onto the values of the map.
TIntFloatHashMap.TValueView() - Constructor for class gnu.trove.map.hash.TIntFloatHashMap.TValueView
 
TIntFloatIterator - Interface in gnu.trove.iterator
Iterator for maps of type int and float.
TIntFloatMap - Interface in gnu.trove.map
Interface for a primitive map of int keys and float values.
TIntFloatProcedure - Interface in gnu.trove.procedure
Interface for procedures that take two parameters of type int and float.
TIntFunction - Interface in gnu.trove.function
Interface for functions that accept and return one int primitive.
TIntHash - Class in gnu.trove.impl.hash
An open addressed hashing implementation for int primitives.
TIntHash() - Constructor for class gnu.trove.impl.hash.TIntHash
Creates a new TIntHash instance with the default capacity and load factor.
TIntHash(int) - Constructor for class gnu.trove.impl.hash.TIntHash
Creates a new TIntHash instance whose capacity is the next highest prime above initialCapacity + 1 unless that value is already prime.
TIntHash(int, float) - Constructor for class gnu.trove.impl.hash.TIntHash
Creates a new TIntHash instance with a prime value at or near the specified capacity and load factor.
TIntHash(int, float, int) - Constructor for class gnu.trove.impl.hash.TIntHash
Creates a new TIntHash instance with a prime value at or near the specified capacity and load factor.
TIntHashSet - Class in gnu.trove.set.hash
An open addressed set implementation for int primitives.
TIntHashSet() - Constructor for class gnu.trove.set.hash.TIntHashSet
Creates a new TIntHashSet instance with the default capacity and load factor.
TIntHashSet(int) - Constructor for class gnu.trove.set.hash.TIntHashSet
Creates a new TIntHashSet instance with a prime capacity equal to or greater than initialCapacity and with the default load factor.
TIntHashSet(int, float) - Constructor for class gnu.trove.set.hash.TIntHashSet
Creates a new TIntHash instance with a prime value at or near the specified capacity and load factor.
TIntHashSet(int, float, int) - Constructor for class gnu.trove.set.hash.TIntHashSet
Creates a new TIntHashSet instance with a prime capacity equal to or greater than initial_capacity and with the specified load factor.
TIntHashSet(Collection<? extends Integer>) - Constructor for class gnu.trove.set.hash.TIntHashSet
Creates a new TIntHashSet instance that is a copy of the existing Collection.
TIntHashSet(TIntCollection) - Constructor for class gnu.trove.set.hash.TIntHashSet
Creates a new TIntHashSet instance that is a copy of the existing set.
TIntHashSet(int[]) - Constructor for class gnu.trove.set.hash.TIntHashSet
Creates a new TIntHashSet instance containing the elements of array.
TIntIterator - Interface in gnu.trove.iterator
Iterator for int collections.
TIntProcedure - Interface in gnu.trove.procedure
Interface for procedures with one int parameter.
TIntSet - Interface in gnu.trove.set
An implementation of the Set interface that uses an open-addressed hash table to store its contents.
TIterator - Interface in gnu.trove.iterator
Common interface for all iterators used in Trove.
TLongCollection - Interface in gnu.trove
An interface that mimics the Collection interface.
TLongDoubleHash - Class in gnu.trove.impl.hash
An open addressed hashing implementation for long/double primitive entries.
TLongDoubleHash() - Constructor for class gnu.trove.impl.hash.TLongDoubleHash
Creates a new T#E#Hash instance with the default capacity and load factor.
TLongDoubleHash(int) - Constructor for class gnu.trove.impl.hash.TLongDoubleHash
Creates a new T#E#Hash instance whose capacity is the next highest prime above initialCapacity + 1 unless that value is already prime.
TLongDoubleHash(int, float) - Constructor for class gnu.trove.impl.hash.TLongDoubleHash
Creates a new TLongDoubleHash instance with a prime value at or near the specified capacity and load factor.
TLongDoubleHash(int, float, long, double) - Constructor for class gnu.trove.impl.hash.TLongDoubleHash
Creates a new TLongDoubleHash instance with a prime value at or near the specified capacity and load factor.
TLongDoubleHashMap - Class in gnu.trove.map.hash
An open addressed Map implementation for long keys and double values.
TLongDoubleHashMap() - Constructor for class gnu.trove.map.hash.TLongDoubleHashMap
Creates a new TLongDoubleHashMap instance with the default capacity and load factor.
TLongDoubleHashMap(int) - Constructor for class gnu.trove.map.hash.TLongDoubleHashMap
Creates a new TLongDoubleHashMap instance with a prime capacity equal to or greater than initialCapacity and with the default load factor.
TLongDoubleHashMap(int, float) - Constructor for class gnu.trove.map.hash.TLongDoubleHashMap
Creates a new TLongDoubleHashMap instance with a prime capacity equal to or greater than initialCapacity and with the specified load factor.
TLongDoubleHashMap(int, float, long, double) - Constructor for class gnu.trove.map.hash.TLongDoubleHashMap
Creates a new TLongDoubleHashMap instance with a prime capacity equal to or greater than initialCapacity and with the specified load factor.
TLongDoubleHashMap(long[], double[]) - Constructor for class gnu.trove.map.hash.TLongDoubleHashMap
Creates a new TLongDoubleHashMap instance containing all of the entries in the map passed in.
TLongDoubleHashMap(TLongDoubleMap) - Constructor for class gnu.trove.map.hash.TLongDoubleHashMap
Creates a new TLongDoubleHashMap instance containing all of the entries in the map passed in.
TLongDoubleHashMap.TKeyView - Class in gnu.trove.map.hash
a view onto the keys of the map.
TLongDoubleHashMap.TKeyView() - Constructor for class gnu.trove.map.hash.TLongDoubleHashMap.TKeyView
 
TLongDoubleHashMap.TValueView - Class in gnu.trove.map.hash
a view onto the values of the map.
TLongDoubleHashMap.TValueView() - Constructor for class gnu.trove.map.hash.TLongDoubleHashMap.TValueView
 
TLongDoubleIterator - Interface in gnu.trove.iterator
Iterator for maps of type long and double.
TLongDoubleMap - Interface in gnu.trove.map
Interface for a primitive map of long keys and double values.
TLongDoubleProcedure - Interface in gnu.trove.procedure
Interface for procedures that take two parameters of type long and double.
TLongFunction - Interface in gnu.trove.function
Interface for functions that accept and return one long primitive.
TLongHash - Class in gnu.trove.impl.hash
An open addressed hashing implementation for long primitives.
TLongHash() - Constructor for class gnu.trove.impl.hash.TLongHash
Creates a new TLongHash instance with the default capacity and load factor.
TLongHash(int) - Constructor for class gnu.trove.impl.hash.TLongHash
Creates a new TLongHash instance whose capacity is the next highest prime above initialCapacity + 1 unless that value is already prime.
TLongHash(int, float) - Constructor for class gnu.trove.impl.hash.TLongHash
Creates a new TLongHash instance with a prime value at or near the specified capacity and load factor.
TLongHash(int, float, long) - Constructor for class gnu.trove.impl.hash.TLongHash
Creates a new TLongHash instance with a prime value at or near the specified capacity and load factor.
TLongHashSet - Class in gnu.trove.set.hash
An open addressed set implementation for long primitives.
TLongHashSet() - Constructor for class gnu.trove.set.hash.TLongHashSet
Creates a new TLongHashSet instance with the default capacity and load factor.
TLongHashSet(int) - Constructor for class gnu.trove.set.hash.TLongHashSet
Creates a new TLongHashSet instance with a prime capacity equal to or greater than initialCapacity and with the default load factor.
TLongHashSet(int, float) - Constructor for class gnu.trove.set.hash.TLongHashSet
Creates a new TIntHash instance with a prime value at or near the specified capacity and load factor.
TLongHashSet(int, float, long) - Constructor for class gnu.trove.set.hash.TLongHashSet
Creates a new TLongHashSet instance with a prime capacity equal to or greater than initial_capacity and with the specified load factor.
TLongHashSet(Collection<? extends Long>) - Constructor for class gnu.trove.set.hash.TLongHashSet
Creates a new TLongHashSet instance that is a copy of the existing Collection.
TLongHashSet(TLongCollection) - Constructor for class gnu.trove.set.hash.TLongHashSet
Creates a new TLongHashSet instance that is a copy of the existing set.
TLongHashSet(long[]) - Constructor for class gnu.trove.set.hash.TLongHashSet
Creates a new TLongHashSet instance containing the elements of array.
TLongIterator - Interface in gnu.trove.iterator
Iterator for long collections.
TLongProcedure - Interface in gnu.trove.procedure
Interface for procedures with one long parameter.
TLongSet - Interface in gnu.trove.set
An implementation of the Set interface that uses an open-addressed hash table to store its contents.
toArray() - Method in class gnu.trove.map.hash.TIntFloatHashMap.TKeyView
Returns an array containing all of the elements in this set.
toArray(int[]) - Method in class gnu.trove.map.hash.TIntFloatHashMap.TKeyView
Returns an array containing elements in this set.
toArray() - Method in class gnu.trove.map.hash.TIntFloatHashMap.TValueView
Returns an array containing all of the elements in this collection.
toArray(float[]) - Method in class gnu.trove.map.hash.TIntFloatHashMap.TValueView
Returns an array containing elements in this collection.
toArray() - Method in class gnu.trove.map.hash.TLongDoubleHashMap.TKeyView
Returns an array containing all of the elements in this set.
toArray(long[]) - Method in class gnu.trove.map.hash.TLongDoubleHashMap.TKeyView
Returns an array containing elements in this set.
toArray() - Method in class gnu.trove.map.hash.TLongDoubleHashMap.TValueView
Returns an array containing all of the elements in this collection.
toArray(double[]) - Method in class gnu.trove.map.hash.TLongDoubleHashMap.TValueView
Returns an array containing elements in this collection.
toArray() - Method in class gnu.trove.set.hash.THashSet
Returns a new array containing the objects in the set.
toArray(T[]) - Method in class gnu.trove.set.hash.THashSet
Returns a typed array of the objects in the set.
toArray() - Method in class gnu.trove.set.hash.TIntHashSet
Returns an array containing all of the elements in this set.
toArray(int[]) - Method in class gnu.trove.set.hash.TIntHashSet
Returns an array containing elements in this set.
toArray() - Method in class gnu.trove.set.hash.TLongHashSet
Returns an array containing all of the elements in this set.
toArray(long[]) - Method in class gnu.trove.set.hash.TLongHashSet
Returns an array containing elements in this set.
toArray() - Method in interface gnu.trove.set.TIntSet
Returns an array containing all of the elements in this set.
toArray(int[]) - Method in interface gnu.trove.set.TIntSet
Returns an array containing elements in this set.
toArray() - Method in interface gnu.trove.set.TLongSet
Returns an array containing all of the elements in this set.
toArray(long[]) - Method in interface gnu.trove.set.TLongSet
Returns an array containing elements in this set.
toArray() - Method in interface gnu.trove.TDoubleCollection
Returns an array containing all of the elements in this collection.
toArray(double[]) - Method in interface gnu.trove.TDoubleCollection
Returns an array containing elements in this collection.
toArray() - Method in interface gnu.trove.TFloatCollection
Returns an array containing all of the elements in this collection.
toArray(float[]) - Method in interface gnu.trove.TFloatCollection
Returns an array containing elements in this collection.
toArray() - Method in interface gnu.trove.TIntCollection
Returns an array containing all of the elements in this collection.
toArray(int[]) - Method in interface gnu.trove.TIntCollection
Returns an array containing elements in this collection.
toArray() - Method in interface gnu.trove.TLongCollection
Returns an array containing all of the elements in this collection.
toArray(long[]) - Method in interface gnu.trove.TLongCollection
Returns an array containing elements in this collection.
toArray() - Method in interface gnu.trove.TShortCollection
Returns an array containing all of the elements in this collection.
toArray(short[]) - Method in interface gnu.trove.TShortCollection
Returns an array containing elements in this collection.
toArray() - Method in class org.broad.igv.util.collections.DoubleArrayList
 
toArray() - Method in class org.broad.igv.util.collections.FloatArrayList
 
toArray() - Method in class org.broad.igv.util.collections.IntArrayList
 
TObjectFunction<T,R> - Interface in gnu.trove.function
Interface for functions that accept and return one Object reference.
TObjectHash<T> - Class in gnu.trove.impl.hash
An open addressed hashing implementation for Object types.
TObjectHash() - Constructor for class gnu.trove.impl.hash.TObjectHash
Creates a new TObjectHash instance with the default capacity and load factor.
TObjectHash(int) - Constructor for class gnu.trove.impl.hash.TObjectHash
Creates a new TObjectHash instance whose capacity is the next highest prime above initialCapacity + 1 unless that value is already prime.
TObjectHash(int, float) - Constructor for class gnu.trove.impl.hash.TObjectHash
Creates a new TObjectHash instance with a prime value at or near the specified capacity and load factor.
TObjectHashIterator<E> - Class in gnu.trove.iterator.hash
Iterator for hashtables that use open addressing to resolve collisions.
TObjectHashIterator(TObjectHash<E>) - Constructor for class gnu.trove.iterator.hash.TObjectHashIterator
 
TObjectObjectProcedure<K,V> - Interface in gnu.trove.procedure
Interface for procedures that take two Object parameters.
TObjectProcedure<T> - Interface in gnu.trove.procedure
Interface for procedures with one Object parameter.
ToObjectArrayProceedure<T> - Class in gnu.trove.procedure.array
A procedure which stores each value it receives into a target array.
ToObjectArrayProceedure(T[]) - Constructor for class gnu.trove.procedure.array.ToObjectArrayProceedure
 
toString() - Method in class gnu.trove.map.hash.THashMap
 
toString() - Method in class gnu.trove.map.hash.TIntFloatHashMap.TKeyView
 
toString() - Method in class gnu.trove.map.hash.TIntFloatHashMap
toString() - Method in class gnu.trove.map.hash.TIntFloatHashMap.TValueView
toString() - Method in class gnu.trove.map.hash.TLongDoubleHashMap.TKeyView
 
toString() - Method in class gnu.trove.map.hash.TLongDoubleHashMap
toString() - Method in class gnu.trove.map.hash.TLongDoubleHashMap.TValueView
toString() - Method in class gnu.trove.set.hash.THashSet
 
toString() - Method in class gnu.trove.set.hash.TIntHashSet
toString() - Method in class gnu.trove.set.hash.TLongHashSet
toString() - Method in class net.sf.jannot.alignment.maf.AbstractAlignmentSequence
 
toString() - Method in class net.sf.jannot.alignment.mfa.Alignment
 
toString() - Method in enum net.sf.jannot.AminoAcidMapping
 
toString() - Method in class net.sf.jannot.Description
 
toString() - Method in class net.sf.jannot.Entry
 
toString() - Method in class net.sf.jannot.event.AnnotationEvent
 
toString() - Method in class net.sf.jannot.event.FeatureEvent
 
toString() - Method in class net.sf.jannot.Feature
 
toString() - Method in class net.sf.jannot.Location
 
toString() - Method in class net.sf.jannot.MemoryFeatureAnnotation
 
toString() - Method in class net.sf.jannot.parser.Parser
 
toString() - Method in class net.sf.jannot.refseq.MemorySequence
 
toString() - Method in class net.sf.jannot.source.das.DAS.EntryPoint
 
toString() - Method in enum net.sf.jannot.source.DataSourceFactory.Sources
 
toString() - Method in class net.sf.jannot.source.FileSource
 
toString() - Method in class net.sf.jannot.source.IndexedFastaDataSource
 
toString() - Method in class net.sf.jannot.source.Locator
 
toString() - Method in class net.sf.jannot.source.SAMDataSource
 
toString() - Method in class net.sf.jannot.source.URLSource
 
toString() - Method in class net.sf.jannot.StringKey
 
toString() - Method in class net.sf.jannot.tabix.IndexedFeatureFile
 
toString() - Method in class net.sf.jannot.tabix.Pair64
 
toString() - Method in class net.sf.jannot.Type
 
toString() - Method in class org.apache.commons.collections.map.Flat3Map
Gets the map as a String.
TOTAL_SUMMARY_BLOCK_SIZE - Static variable in class org.broad.igv.bbfile.BBTotalSummaryBlock
 
TPrimitiveHash - Class in gnu.trove.impl.hash
The base class for hashtables of primitive values.
TPrimitiveHash() - Constructor for class gnu.trove.impl.hash.TPrimitiveHash
Creates a new THash instance with the default capacity and load factor.
TPrimitiveHash(int) - Constructor for class gnu.trove.impl.hash.TPrimitiveHash
Creates a new TPrimitiveHash instance with a prime capacity at or near the specified capacity and with the default load factor.
TPrimitiveHash(int, float) - Constructor for class gnu.trove.impl.hash.TPrimitiveHash
Creates a new TPrimitiveHash instance with a prime capacity at or near the minimum needed to hold initialCapacity elements with load factor loadFactor without triggering a rehash.
TPrimitiveIterator - Interface in gnu.trove.iterator
Implements all iterator functions for the hashed object set.
transformValues(TObjectFunction<V, V>) - Method in class gnu.trove.map.hash.THashMap
Transform the values in this map using function.
transformValues(TFloatFunction) - Method in class gnu.trove.map.hash.TIntFloatHashMap
Transform the values in this map using function.
transformValues(TDoubleFunction) - Method in class gnu.trove.map.hash.TLongDoubleHashMap
Transform the values in this map using function.
transformValues(TFloatFunction) - Method in interface gnu.trove.map.TIntFloatMap
Transform the values in this map using function.
transformValues(TDoubleFunction) - Method in interface gnu.trove.map.TLongDoubleMap
Transform the values in this map using function.
translate(int) - Method in class net.sf.jannot.alignment.maf.SequenceTranslator
 
translate(Sequence, AminoAcidMapping) - Static method in class net.sf.jannot.utils.SequenceTools
 
TransTermHPParser - Class in net.sf.jannot.parser.software
Parser for the output of the TransTermHP program as described in C.
TransTermHPParser() - Constructor for class net.sf.jannot.parser.software.TransTermHPParser
 
trimToSize() - Method in class gnu.trove.impl.hash.THash
This simply calls compact.
TRNAscanParser - Class in net.sf.jannot.parser.software
 
TRNAscanParser() - Constructor for class net.sf.jannot.parser.software.TRNAscanParser
 
TroveArrayWiggle - Class in net.sf.jannot.wiggle
Make wiggle Fill it with setMethod Initialize with init();
TroveArrayWiggle(int) - Constructor for class net.sf.jannot.wiggle.TroveArrayWiggle
 
TShortCollection - Interface in gnu.trove
An interface that mimics the Collection interface.
TShortFunction - Interface in gnu.trove.function
Interface for functions that accept and return one short primitive.
TShortIterator - Interface in gnu.trove.iterator
Iterator for short collections.
TShortProcedure - Interface in gnu.trove.procedure
Interface for procedures with one short parameter.
type() - Method in class net.sf.jannot.Feature
 
Type - Class in net.sf.jannot
I must improve this documentation Class 'Type' contains list of group names which features can be classified.

U

undoChange() - Method in interface net.sf.jannot.event.ChangeEvent
 
UnsupportedException - Exception in net.sf.jannot.parser
 
UnsupportedException(String) - Constructor for exception net.sf.jannot.parser.UnsupportedException
 
update(Feature) - Method in class net.sf.jannot.tabix.FeatureWrapper
 
url() - Method in class net.sf.jannot.source.Locator
 
url - Variable in class net.sf.jannot.source.URLSource
 
URLSource - Class in net.sf.jannot.source
 
URLSource(URL, Object) - Constructor for class net.sf.jannot.source.URLSource
 
URLSource(URL) - Constructor for class net.sf.jannot.source.URLSource
 
USE_PERCENTILE_AUTOSCALING - Static variable in class org.broad.igv.tdf.TDFGroup
 

V

value() - Method in interface gnu.trove.iterator.TIntFloatIterator
Provides access to the value of the mapping at the iterator's position.
value() - Method in interface gnu.trove.iterator.TLongDoubleIterator
Provides access to the value of the mapping at the iterator's position.
value(int) - Method in class net.sf.jannot.wiggle.DiskArrayWiggle
Get a single value, one based coordinate
value(int) - Method in class net.sf.jannot.wiggle.FloatArrayWiggle
Get a single value, one based coordinate
value(int) - Method in interface net.sf.jannot.wiggle.Graph
 
value(int) - Method in class net.sf.jannot.wiggle.TroveArrayWiggle
Get a single value, one based coordinate
valueCollection() - Method in class gnu.trove.map.hash.TIntFloatHashMap
Returns the values of the map as a TFloatCollection
valueCollection() - Method in class gnu.trove.map.hash.TLongDoubleHashMap
Returns the values of the map as a TDoubleCollection
valueCollection() - Method in interface gnu.trove.map.TIntFloatMap
Returns the values of the map as a TFloatCollection
valueCollection() - Method in interface gnu.trove.map.TLongDoubleMap
Returns the values of the map as a TDoubleCollection
valueForEntry(Map.Entry<K, V>) - Method in class gnu.trove.map.hash.THashMap.EntryView
 
valueOf(String) - Static method in enum net.sf.jannot.AminoAcidMapping
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.sf.jannot.source.DataSourceFactory.Sources
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.sf.jannot.Strand
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in class net.sf.jannot.Type
Deprecated. 
valueOf(String) - Static method in enum org.broad.igv.bbfile.BigWigSectionHeader.WigItemType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.broad.igv.tdf.TDFDataset.DataType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.broad.igv.tdf.TDFTile.Type
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.broad.igv.track.WindowFunction
Returns the enum constant of this type with the specified name.
values() - Method in class gnu.trove.map.hash.THashMap
Returns a view on the values of the map.
values() - Method in class gnu.trove.map.hash.TIntFloatHashMap
Returns the values of the map as an array of #e# values.
values(float[]) - Method in class gnu.trove.map.hash.TIntFloatHashMap
Returns the values of the map using an existing array.
values() - Method in class gnu.trove.map.hash.TLongDoubleHashMap
Returns the values of the map as an array of #e# values.
values(double[]) - Method in class gnu.trove.map.hash.TLongDoubleHashMap
Returns the values of the map using an existing array.
values() - Method in interface gnu.trove.map.TIntFloatMap
Returns the values of the map as an array of #e# values.
values(float[]) - Method in interface gnu.trove.map.TIntFloatMap
Returns the values of the map using an existing array.
values() - Method in interface gnu.trove.map.TLongDoubleMap
Returns the values of the map as an array of #e# values.
values(double[]) - Method in interface gnu.trove.map.TLongDoubleMap
Returns the values of the map using an existing array.
values() - Static method in enum net.sf.jannot.AminoAcidMapping
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.sf.jannot.source.DataSourceFactory.Sources
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.sf.jannot.Strand
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in class net.sf.jannot.Type
Return array of declared types.
values() - Method in class org.apache.commons.collections.map.Flat3Map
Gets the values view of the map.
values() - Static method in enum org.broad.igv.bbfile.BigWigSectionHeader.WigItemType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.broad.igv.tdf.TDFDataset.DataType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.broad.igv.tdf.TDFTile.Type
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.broad.igv.track.WindowFunction
Returns an array containing the constants of this enum type, in the order they are declared.
VARSTEP_ITEM_SIZE - Static variable in class org.broad.igv.bbfile.BigWigSectionHeader
 
VCF_CONF - Static variable in class net.sf.jannot.tabix.TabixWriter
 

W

WiggleParser - Class in net.sf.jannot.parser
 
WiggleParser() - Constructor for class net.sf.jannot.parser.WiggleParser
 
WigItem - Class in org.broad.igv.bbfile
File retrieved from BigWig project at Google code on July 26, 2011, revision 36 http://code.google.com/p/bigwig/ This project provides java readers for the UCSC's BigWig and BigBed formats.
WigItem(int, String, int, int, float) - Constructor for class org.broad.igv.bbfile.WigItem
 
WindowFunction - Enum in org.broad.igv.track
 
write(OutputStream, Entry) - Method in class net.sf.jannot.parser.BEDParser
 
write(OutputStream, Entry, DataKey[]) - Method in class net.sf.jannot.parser.EMBLParser
 
write(OutputStream, Entry) - Method in class net.sf.jannot.parser.FastaParser
 
write(OutputStream, Entry, DataKey[]) - Method in class net.sf.jannot.parser.GFF3Parser
 
write(OutputStream, Entry) - Method in class net.sf.jannot.parser.Parser
Output everything from the provided entry to the output stream.
write(OutputStream, Entry, DataKey[]) - Method in class net.sf.jannot.parser.Parser
 
write(BufferedByteWriter) - Method in class org.broad.igv.tdf.TDFDataset
 
writeBoolean(boolean) - Method in class net.sf.jannot.tabix.BinaryCodec
Writes a boolean (1 byte) to the output buffer
writeByte(byte) - Method in class net.sf.jannot.tabix.BinaryCodec
Writes a byte to the output buffer
writeByte(int) - Method in class net.sf.jannot.tabix.BinaryCodec
 
writeBytes(byte[]) - Method in class net.sf.jannot.tabix.BinaryCodec
Writes a byte array to the output buffer
writeBytes(byte[], int, int) - Method in class net.sf.jannot.tabix.BinaryCodec
 
writeDouble(double) - Method in class net.sf.jannot.tabix.BinaryCodec
Write a double (8 bytes) to the output stream
writeExternal(ObjectOutput) - Method in class gnu.trove.impl.hash.THash
 
writeExternal(ObjectOutput) - Method in class gnu.trove.impl.hash.TIntFloatHash
writeExternal(ObjectOutput) - Method in class gnu.trove.impl.hash.TLongDoubleHash
writeExternal(ObjectOutput) - Method in class gnu.trove.impl.hash.TObjectHash
 
writeExternal(ObjectOutput) - Method in class gnu.trove.map.hash.THashMap
 
writeExternal(ObjectOutput) - Method in class gnu.trove.map.hash.TIntFloatHashMap
writeExternal(ObjectOutput) - Method in class gnu.trove.map.hash.TLongDoubleHashMap
writeExternal(ObjectOutput) - Method in class gnu.trove.set.hash.THashSet
 
writeExternal(ObjectOutput) - Method in class gnu.trove.set.hash.TIntHashSet
writeExternal(ObjectOutput) - Method in class gnu.trove.set.hash.TLongHashSet
writeFloat(float) - Method in class net.sf.jannot.tabix.BinaryCodec
Write a float (4 bytes) to the output stream
writeInt(int) - Method in class net.sf.jannot.tabix.BinaryCodec
Write a 32-bit int to the output stream
writeInt(OutputStream, int) - Static method in class net.sf.jannot.tabix.TabixWriter
 
writeLong(long) - Method in class net.sf.jannot.tabix.BinaryCodec
Write a 64-bit long to the output stream
writeLong(OutputStream, long) - Static method in class net.sf.jannot.tabix.TabixWriter
 
writeShort(short) - Method in class net.sf.jannot.tabix.BinaryCodec
Write a 16-bit short to output stream
writeString(String, boolean, boolean) - Method in class net.sf.jannot.tabix.BinaryCodec
Writes a string to the buffer as ASCII bytes
writeString(BufferedByteWriter, String) - Method in class org.broad.igv.tdf.TDFEntity
Write a string as a null terminated character sequence.
writeTile(String, int, TDFTile) - Method in class org.broad.igv.tdf.TDFWriter
 
writeTo(BufferedByteWriter) - Method in class org.broad.igv.tdf.TDFBedTile
 
writeTo(BufferedByteWriter) - Method in class org.broad.igv.tdf.TDFFixedTile
 
writeTo(BufferedByteWriter) - Method in interface org.broad.igv.tdf.TDFTile
 
writeTo(BufferedByteWriter) - Method in class org.broad.igv.tdf.TDFVaryTile
 
writeUByte(short) - Method in class net.sf.jannot.tabix.BinaryCodec
Write an 8-bit unsigned byte.
writeUInt(long) - Method in class net.sf.jannot.tabix.BinaryCodec
Write a 32-bit unsigned int.
writeUShort(int) - Method in class net.sf.jannot.tabix.BinaryCodec
Write a 16-bit unsigned short.

Z

ZOOM_FORMAT_HEADER_SIZE - Static variable in class org.broad.igv.bbfile.BBZoomLevelFormat
 
ZOOM_LEVEL_HEADER_SIZE - Static variable in class org.broad.igv.bbfile.BBZoomLevelHeader
 
ZoomDataBlock - Class in org.broad.igv.bbfile
File retrieved from BigWig project at Google code on July 26, 2011, revision 36 http://code.google.com/p/bigwig/ This project provides java readers for the UCSC's BigWig and BigBed formats.
ZoomDataBlock(int, SeekableStream, RPTreeLeafNodeItem, HashMap<Integer, String>, boolean, int) - Constructor for class org.broad.igv.bbfile.ZoomDataBlock
 
ZoomDataRecord - Class in org.broad.igv.bbfile
File retrieved from BigWig project at Google code on July 26, 2011, revision 36 http://code.google.com/p/bigwig/ This project provides java readers for the UCSC's BigWig and BigBed formats.
ZoomDataRecord(int, int, String, int, int, int, int, float, float, float, float) - Constructor for class org.broad.igv.bbfile.ZoomDataRecord
 
ZoomLevelIterator - Class in org.broad.igv.bbfile
File retrieved from BigWig project at Google code on July 26, 2011, revision 36 http://code.google.com/p/bigwig/ This project provides java readers for the UCSC's BigWig and BigBed formats.
ZoomLevelIterator() - Constructor for class org.broad.igv.bbfile.ZoomLevelIterator
Default constructor.
ZoomLevelIterator(SeekableStream, BPTree, RPTree, int, RPChromosomeRegion, boolean) - Constructor for class org.broad.igv.bbfile.ZoomLevelIterator
Constructs a zoom level iterator over the specified chromosome region

Parameters: fis - file input stream handle chromIDTree - B+ index tree returns chromId for chromosome name key zoomLevelTree - zoom level R+ chromosome index tree zoomLevel - zoom level represented by the R+ tree selectionRegion - chromosome region for selection of Bed feature extraction consists of: startChromID - ID of start chromosome startBase - starting base position for features endChromID - ID of end chromosome endBase - starting base position for features contained - specifies bed features must be contained by region, if true; else return any intersecting region features

ZoomLevelIterator.EmptyIterator - Class in org.broad.igv.bbfile
 
ZoomLevelIterator.EmptyIterator() - Constructor for class org.broad.igv.bbfile.ZoomLevelIterator.EmptyIterator
 

_

_autoCompactionFactor - Variable in class gnu.trove.impl.hash.THash
The auto-compaction factor for the table.
_autoCompactRemovesRemaining - Variable in class gnu.trove.impl.hash.THash
The number of removes that should be performed before an auto-compaction occurs.
_autoCompactTemporaryDisable - Variable in class gnu.trove.impl.hash.THash
 
_expectedSize - Variable in class gnu.trove.impl.hash.THashIterator
the number of elements this iterator believes are in the data structure it accesses.
_expectedSize - Variable in class gnu.trove.impl.hash.THashPrimitiveIterator
the number of elements this iterator believes are in the data structure it accesses.
_free - Variable in class gnu.trove.impl.hash.THash
the current number of free slots in the hash.
_hash - Variable in class gnu.trove.impl.hash.THashIterator
the data structure this iterator traverses
_hash - Variable in class gnu.trove.impl.hash.THashPrimitiveIterator
the data structure this iterator traverses
_index - Variable in class gnu.trove.impl.hash.THashIterator
the index used for iteration.
_index - Variable in class gnu.trove.impl.hash.THashPrimitiveIterator
the index used for iteration.
_loadFactor - Variable in class gnu.trove.impl.hash.THash
Determines how full the internal table can become before rehashing is required.
_maxSize - Variable in class gnu.trove.impl.hash.THash
The maximum number of elements allowed without allocating more space.
_objectHash - Variable in class gnu.trove.iterator.hash.TObjectHashIterator
 
_set - Variable in class gnu.trove.impl.hash.TIntFloatHash
the set of ints
_set - Variable in class gnu.trove.impl.hash.TIntHash
the set of ints
_set - Variable in class gnu.trove.impl.hash.TLongDoubleHash
the set of longs
_set - Variable in class gnu.trove.impl.hash.TLongHash
the set of longs
_set - Variable in class gnu.trove.impl.hash.TObjectHash
the set of Objects
_size - Variable in class gnu.trove.impl.hash.THash
the current number of occupied slots in the hash.
_states - Variable in class gnu.trove.impl.hash.TPrimitiveHash
flags indicating whether each position in the hash is FREE, FULL, or REMOVED
_values - Variable in class gnu.trove.map.hash.THashMap
the values of the map
_values - Variable in class gnu.trove.map.hash.TIntFloatHashMap
the values of the map
_values - Variable in class gnu.trove.map.hash.TLongDoubleHashMap
the values of the map

A B C D E F G H I K L M N O P Q R S T U V W Z _

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