gata.aligner
Class AlignerPreferences

java.lang.Object
  gata.aligner.AlignerPreferences

All Implemented Interfaces:

java.io.Serializable

public class AlignerPreferences

extends java.lang.Object

implements java.io.Serializable

Author:

nix Container class to hold aligment preferences, this is saved after running GATAligner as a serialized object and used in subsequent GATAligner runs so the user doesn't have to reset the defaults every run.

See Also:

Serialized Form

Constructor Summary

AlignerPreferences()

Method Summary

java.lang.String	getBaseName()
java.lang.String	getBl2SeqProg()
java.lang.String	getCompSeq()
java.lang.String	getCompStart()
java.lang.Integer	getCreate()
java.lang.Integer	getExtend()
java.lang.String	getExtract()
java.lang.String	getMask()
java.lang.Integer	getMatch()
java.lang.Integer	getMisMatch()
java.lang.String	getRefSeq()
java.lang.String	getRefStart()
java.lang.String	getScore()
java.lang.String	getStorageLoc()
java.lang.String	getWindow()
void	saveAlignerPreferences()
void	setBl2SeqProg(java.lang.String string)
void	setPreferences(java.lang.String refSeq, java.lang.String compSeq, java.lang.String bl2SeqProg, java.lang.String storageLoc, java.lang.String baseName, java.lang.Integer match, java.lang.Integer misMatch, java.lang.Integer create, java.lang.Integer extend, java.lang.String mask, java.lang.String extract, java.lang.String window, java.lang.String score, java.lang.String refStart, java.lang.String compStart)
java.lang.String	toString()

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

AlignerPreferences

public AlignerPreferences()

Method Detail

toString

public java.lang.String toString()

setPreferences

public void setPreferences(java.lang.String refSeq,
                           java.lang.String compSeq,
                           java.lang.String bl2SeqProg,
                           java.lang.String storageLoc,
                           java.lang.String baseName,
                           java.lang.Integer match,
                           java.lang.Integer misMatch,
                           java.lang.Integer create,
                           java.lang.Integer extend,
                           java.lang.String mask,
                           java.lang.String extract,
                           java.lang.String window,
                           java.lang.String score,
                           java.lang.String refStart,
                           java.lang.String compStart)

saveAlignerPreferences

public void saveAlignerPreferences()

getBl2SeqProg

public java.lang.String getBl2SeqProg()

getCompSeq

public java.lang.String getCompSeq()

getCreate

public java.lang.Integer getCreate()

getExtend

public java.lang.Integer getExtend()

getMask

public java.lang.String getMask()

getMatch

public java.lang.Integer getMatch()

getMisMatch

public java.lang.Integer getMisMatch()

getRefSeq

public java.lang.String getRefSeq()

getStorageLoc

public java.lang.String getStorageLoc()

getCompStart

public java.lang.String getCompStart()

getRefStart

public java.lang.String getRefStart()

getScore

public java.lang.String getScore()

getWindow

public java.lang.String getWindow()

getBaseName

public java.lang.String getBaseName()

setBl2SeqProg

public void setBl2SeqProg(java.lang.String string)

getExtract

public java.lang.String getExtract()