gata.aligner
Class AlignParams

java.lang.Object
  extended bygata.aligner.AlignParams
All Implemented Interfaces:
java.io.Serializable

public class AlignParams
extends java.lang.Object
implements java.io.Serializable

Author:
nix A class to represent alignment parameters entered for a particular alignment. This is saved and made availible to GATAPlotter.
See Also:
Serialized Form

Constructor Summary
AlignParams()
           
AlignParams(AlignerPreferences ap)
           
 
Method Summary
 java.lang.String getBaseName()
           
 java.lang.String getBl2seq()
           
 java.lang.String getCompSeqFile()
           
 java.lang.String[] getDNAFILES()
           
 boolean getDUST()
           
 double getEFF_M()
           
 double getEFF_N()
           
 int getGAP_CREATE()
           
 int getGAP_EXT()
           
 double getH()
           
 double getK()
           
 double getLAMBDA()
           
 int getLENGTH_COMPSEQ()
           
 int getLENGTH_REFSEQ()
           
 int getMATCH()
           
 int getMAX_SCORE()
           
 int getMIN_SCORE()
           
 int getMISMATCH()
           
 java.lang.String getNAME_COMPSEQ()
           
 java.lang.String getNAME_REFSEQ()
           
 java.lang.String getPathToResults()
           
 java.lang.String getRefSeqFile()
           
 int getSTART_INDEX_COMPSEQ()
           
 int getSTART_INDEX_REFSEQ()
           
 int getWIN_SIZE()
           
 boolean isCompVisible()
           
 boolean isEXTRACT()
           
 void setCompVisible(boolean compVisible)
           
 void setEFF_M(double d)
           
 void setEFF_N(double d)
           
 void setEXTRACT(boolean extract)
           
 void setH(double d)
           
 void setK(double d)
           
 void setLAMBDA(double d)
           
 void setLENGTH_COMPSEQ(int l)
           
 void setLENGTH_REFSEQ(int l)
           
 void setNAME_COMPSEQ(java.lang.String s)
           
 void setNAME_REFSEQ(java.lang.String s)
           
 void setSTART_INDEX_COMPSEQ(int start_index_compseq)
           
 void setSTART_INDEX_REFSEQ(int start_index_refseq)
           
 java.lang.String toHTMLString()
           
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

AlignParams

public AlignParams()

AlignParams

public AlignParams(AlignerPreferences ap)
Method Detail

getWIN_SIZE

public int getWIN_SIZE()

getMATCH

public int getMATCH()

getMISMATCH

public int getMISMATCH()

getGAP_CREATE

public int getGAP_CREATE()

getGAP_EXT

public int getGAP_EXT()

getMIN_SCORE

public int getMIN_SCORE()

getMAX_SCORE

public int getMAX_SCORE()

getSTART_INDEX_REFSEQ

public int getSTART_INDEX_REFSEQ()

getSTART_INDEX_COMPSEQ

public int getSTART_INDEX_COMPSEQ()

getLENGTH_REFSEQ

public int getLENGTH_REFSEQ()

getLENGTH_COMPSEQ

public int getLENGTH_COMPSEQ()

getDNAFILES

public java.lang.String[] getDNAFILES()

getNAME_REFSEQ

public java.lang.String getNAME_REFSEQ()

getNAME_COMPSEQ

public java.lang.String getNAME_COMPSEQ()

getPathToResults

public java.lang.String getPathToResults()

getDUST

public boolean getDUST()

setLENGTH_REFSEQ

public void setLENGTH_REFSEQ(int l)

setLENGTH_COMPSEQ

public void setLENGTH_COMPSEQ(int l)

setNAME_REFSEQ

public void setNAME_REFSEQ(java.lang.String s)

setNAME_COMPSEQ

public void setNAME_COMPSEQ(java.lang.String s)

toHTMLString

public java.lang.String toHTMLString()

getEFF_M

public double getEFF_M()

getEFF_N

public double getEFF_N()

getH

public double getH()

getK

public double getK()

getLAMBDA

public double getLAMBDA()

setEFF_M

public void setEFF_M(double d)

setEFF_N

public void setEFF_N(double d)

setH

public void setH(double d)

setK

public void setK(double d)

setLAMBDA

public void setLAMBDA(double d)

getBaseName

public java.lang.String getBaseName()

getBl2seq

public java.lang.String getBl2seq()

getCompSeqFile

public java.lang.String getCompSeqFile()

getRefSeqFile

public java.lang.String getRefSeqFile()

setSTART_INDEX_COMPSEQ

public void setSTART_INDEX_COMPSEQ(int start_index_compseq)

setSTART_INDEX_REFSEQ

public void setSTART_INDEX_REFSEQ(int start_index_refseq)

isEXTRACT

public boolean isEXTRACT()

setEXTRACT

public void setEXTRACT(boolean extract)

isCompVisible

public boolean isCompVisible()

setCompVisible

public void setCompVisible(boolean compVisible)