org.kepler.bio.util

Class BlastTabularResult

java.lang.Object

org.kepler.bio.util.BlastTabularResult

All Implemented Interfaces:

java.lang.Comparable<BlastTabularResult>

public class BlastTabularResult
extends java.lang.Object
implements java.lang.Comparable<BlastTabularResult>

This class is for the lines in blast tabular result. Each line will be one object. They are compared by E-Value and Bit.

Author:

Jianwu Wang

Constructor Summary

Constructors

Constructor and Description
BlastTabularResult(java.lang.String result)

Method Summary

Modifier and Type	Method and Description
int	compareTo(BlastTabularResult result)
int	getAlignmentLength()
float	getBitScore()
java.lang.String	geteValue()
int	getGapOpenings()
java.lang.Float	getIdentity()
int	getMismatches()
int	getqEnd()
int	getqStart()
java.lang.String	getQueryId()
int	getsEnd()
int	getsStart()
java.lang.String	getSubjectId()
static void	main(java.lang.String[] args)
void	setAlignmentLength(int alignmentLength)
void	setBitScore(float bitScore)
void	seteValue(java.lang.String eValue)
void	setGapOpenings(int gapOpenings)
void	setIdentity(java.lang.Float identity)
void	setMismatches(int mismatches)
void	setqEnd(int qEnd)
void	setqStart(int qStart)
void	setQueryId(java.lang.String queryId)
void	setsEnd(int sEnd)
void	setsStart(int sStart)
void	setSubjectId(java.lang.String subjectId)
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

BlastTabularResult

public BlastTabularResult(java.lang.String result)

Method Detail

getQueryId

public java.lang.String getQueryId()

setQueryId

public void setQueryId(java.lang.String queryId)

getSubjectId

public java.lang.String getSubjectId()

setSubjectId

public void setSubjectId(java.lang.String subjectId)

geteValue

public java.lang.String geteValue()

seteValue

public void seteValue(java.lang.String eValue)

getIdentity

public java.lang.Float getIdentity()

setIdentity

public void setIdentity(java.lang.Float identity)

getAlignmentLength

public int getAlignmentLength()

setAlignmentLength

public void setAlignmentLength(int alignmentLength)

getMismatches

public int getMismatches()

setMismatches

public void setMismatches(int mismatches)

getGapOpenings

public int getGapOpenings()

setGapOpenings

public void setGapOpenings(int gapOpenings)

getqStart

public int getqStart()

setqStart

public void setqStart(int qStart)

getqEnd

public int getqEnd()

setqEnd

public void setqEnd(int qEnd)

getsStart

public int getsStart()

setsStart

public void setsStart(int sStart)

getsEnd

public int getsEnd()

setsEnd

public void setsEnd(int sEnd)

getBitScore

public float getBitScore()

setBitScore

public void setBitScore(float bitScore)

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

compareTo

public int compareTo(BlastTabularResult result)

Specified by:

compareTo in interface java.lang.Comparable<BlastTabularResult>

main

public static void main(java.lang.String[] args)