org.utgenome.gwt.utgb.client.bio
Class Alignment

java.lang.Object
  org.utgenome.gwt.utgb.client.bio.Alignment

All Implemented Interfaces:

com.google.gwt.user.client.rpc.IsSerializable

public class Alignment
extends Object
implements com.google.gwt.user.client.rpc.IsSerializable

Alignment result

Author:

leo

Constructor Summary

Alignment()

Method Summary

void	addBlockSizes(int blockSize)
void	addQueryStarts(int queryStart)
void	addTargetStarts(int targetStart)
int	getBlockCount()
ArrayList<Integer>	getBlockSizes()
int	getNumMatch()
int	getNumMisMatch()
int	getNumN()
int	getNumRepMatch()
long	getQueryEnd()
int	getQueryLen()
String	getQueryName()
long	getQueryStart()
ArrayList<Integer>	getQueryStarts()
String	getStrand()
int	getTargetEnd()
String	getTargetName()
int	getTargetSize()
int	getTargetStart()
ArrayList<Integer>	getTargetStarts()
boolean	isPlusStrand()
void	setBlockCount(int blockCount)
void	setNumMatch(int numMatch)
void	setNumMisMatch(int numMisMatch)
void	setNumN(int numN)
void	setNumRepMatch(int numRepMatch)
void	setQueryEnd(int queryEnd)
void	setQueryLen(int querySize)
void	setQueryName(String queryName)
void	setQueryStart(int queryStart)
void	setStrand(String strand)
void	setTargetEnd(int targetEnd)
void	setTargetName(String targetName)
void	setTargetSize(int targetSize)
void	setTargetStart(int targetStart)

Methods inherited from class java.lang.Object

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

Constructor Detail

Alignment

public Alignment()

Method Detail

getNumMatch

public int getNumMatch()

getQueryLen

public int getQueryLen()

setQueryLen

public void setQueryLen(int querySize)

getTargetSize

public int getTargetSize()

setTargetSize

public void setTargetSize(int targetSize)

setNumMatch

public void setNumMatch(int numMatch)

getNumMisMatch

public int getNumMisMatch()

setNumMisMatch

public void setNumMisMatch(int numMisMatch)

getNumRepMatch

public int getNumRepMatch()

setNumRepMatch

public void setNumRepMatch(int numRepMatch)

getNumN

public int getNumN()

setNumN

public void setNumN(int numN)

getQueryName

public String getQueryName()

setQueryName

public void setQueryName(String queryName)

getQueryStart

public long getQueryStart()

setQueryStart

public void setQueryStart(int queryStart)

getQueryEnd

public long getQueryEnd()

setQueryEnd

public void setQueryEnd(int queryEnd)

getTargetName

public String getTargetName()

setTargetName

public void setTargetName(String targetName)

getTargetStart

public int getTargetStart()

setTargetStart

public void setTargetStart(int targetStart)

getTargetEnd

public int getTargetEnd()

setTargetEnd

public void setTargetEnd(int targetEnd)

getStrand

public String getStrand()

isPlusStrand

public boolean isPlusStrand()

setStrand

public void setStrand(String strand)

getBlockCount

public int getBlockCount()

setBlockCount

public void setBlockCount(int blockCount)

getBlockSizes

public ArrayList<Integer> getBlockSizes()

getQueryStarts

public ArrayList<Integer> getQueryStarts()

getTargetStarts

public ArrayList<Integer> getTargetStarts()

addBlockSizes

public void addBlockSizes(int blockSize)

addQueryStarts

public void addQueryStarts(int queryStart)

addTargetStarts

public void addTargetStarts(int targetStart)