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

java.lang.Object
  extended by 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)


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