org.broad.igv.data
Class BasicScore

java.lang.Object
  org.broad.igv.data.BasicScore

All Implemented Interfaces:

LocusScore, Feature

public class BasicScore
extends java.lang.Object
implements LocusScore

Author:

jrobinso

Constructor Summary

BasicScore(BasicScore bs)

BasicScore(java.lang.String chromosome, int start, int end, float score)

Method Summary

BasicScore	copy()
java.lang.String	getChr() Return the features reference sequence name, e.g chromosome or contig
java.lang.String	getChromosome()
float	getConfidence()
int	getEnd() Return the end position following 1-based fully closed conventions.
int	getExtendedEnd()
int	getExtendedStart()
float	getScore()
int	getStart() Return the start position in 1-based coordinates (first base is 1)
java.lang.String	getValueString(double position, WindowFunction windowFunction) Return a string to be used for popup text.
void	setConfidence(float confidence)
void	setEnd(int end)
void	setStart(int start)

Methods inherited from class java.lang.Object

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

Constructor Detail

BasicScore

public BasicScore(java.lang.String chromosome,
                  int start,
                  int end,
                  float score)

BasicScore

public BasicScore(BasicScore bs)

Method Detail

copy

public BasicScore copy()

Specified by:

copy in interface LocusScore

getChromosome

public java.lang.String getChromosome()

getChr

public java.lang.String getChr()

Description copied from interface: Feature

Return the features reference sequence name, e.g chromosome or contig

Specified by:

getChr in interface Feature

getStart

public int getStart()

Description copied from interface: Feature

Return the start position in 1-based coordinates (first base is 1)

Specified by:

getStart in interface Feature

getScore

public float getScore()

Specified by:

getScore in interface LocusScore

setStart

public void setStart(int start)

Specified by:

setStart in interface LocusScore

getEnd

public int getEnd()

Description copied from interface: Feature

Return the end position following 1-based fully closed conventions. The length of a feature is end - start + 1;

Specified by:

getEnd in interface Feature

setEnd

public void setEnd(int end)

Specified by:

setEnd in interface LocusScore

setConfidence

public void setConfidence(float confidence)

Specified by:

setConfidence in interface LocusScore

getConfidence

public float getConfidence()

Specified by:

getConfidence in interface LocusScore

getValueString

public java.lang.String getValueString(double position,
                                       WindowFunction windowFunction)

Description copied from interface: LocusScore

Return a string to be used for popup text. The WindowFunction is passed in so it can be used t annotate the value. The LocusScore object itself does not "know" from what window function it was derived

Specified by:

getValueString in interface LocusScore

Returns:

getExtendedStart

public int getExtendedStart()

getExtendedEnd

public int getExtendedEnd()