gata.aligner
Class AlignParams
java.lang.Object
gata.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
Methods inherited from class java.lang.Object |
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
AlignParams
public AlignParams()
AlignParams
public AlignParams(AlignerPreferences ap)
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)