net.sf.jannot.alignment.maf
Class LazyAlignmentBlock

java.lang.Object
  net.sf.jannot.alignment.maf.AbstractAlignmentBlock
      net.sf.jannot.alignment.maf.LazyAlignmentBlock

All Implemented Interfaces:

java.lang.Comparable<AbstractAlignmentBlock>, java.lang.Iterable<AbstractAlignmentSequence>, Located

public class LazyAlignmentBlock
extends AbstractAlignmentBlock

Author:

Thomas Abeel, thpar

Constructor Summary

LazyAlignmentBlock(long offsetStart, LineBlockCompressedInputStream zr, int start, int end)

Method Summary

void	add(AbstractAlignmentSequence as)
AbstractAlignmentSequence	getAlignmentSequence(int i)
java.util.Iterator<AbstractAlignmentSequence>	iterator()
void	lazyLoad() Load the actual alignment block from the zipped maf file and fill in the gaps in the alignment sequences
int	size()

Methods inherited from class net.sf.jannot.alignment.maf.AbstractAlignmentBlock

compareTo, end, length, start

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

LazyAlignmentBlock

public LazyAlignmentBlock(long offsetStart,
                          LineBlockCompressedInputStream zr,
                          int start,
                          int end)

Method Detail

add

public void add(AbstractAlignmentSequence as)

Specified by:

add in class AbstractAlignmentBlock

lazyLoad

public void lazyLoad()

Load the actual alignment block from the zipped maf file and fill in the gaps in the alignment sequences

iterator

public java.util.Iterator<AbstractAlignmentSequence> iterator()

getAlignmentSequence

public AbstractAlignmentSequence getAlignmentSequence(int i)

Specified by:

getAlignmentSequence in class AbstractAlignmentBlock

Returns:

size

public int size()

Specified by:

size in class AbstractAlignmentBlock

Returns: