org.biojava.bio.structure.align.pairwise
Class StrCompAlignment
java.lang.Object
org.biojava.bio.structure.align.pairwise.StrCompAlignment
- All Implemented Interfaces:
- Alignable
public class StrCompAlignment
- extends java.lang.Object
- implements Alignable
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
StrCompAlignment
public StrCompAlignment(int rows,
int cols)
getRows
public int getRows()
- Specified by:
getRows
in interface Alignable
getCols
public int getCols()
- Specified by:
getCols
in interface Alignable
setAligMat
public void setAligMat(int i,
int j,
AligMatEl el)
getAligMat
public AligMatEl getAligMat(int i,
int j)
getAligMat
public AligMatEl[][] getAligMat()
- Specified by:
getAligMat
in interface Alignable
setAligMat
public void setAligMat(AligMatEl[][] al)
- Specified by:
setAligMat
in interface Alignable
getGapExtCol
public float getGapExtCol()
- Specified by:
getGapExtCol
in interface Alignable
setGapExtCol
public void setGapExtCol(float gapExtCol)
- Specified by:
setGapExtCol
in interface Alignable
getGapExtRow
public float getGapExtRow()
- Specified by:
getGapExtRow
in interface Alignable
setGapExtRow
public void setGapExtRow(float gapExtRow)
- Specified by:
setGapExtRow
in interface Alignable
getGapOpenCol
public float getGapOpenCol()
- Specified by:
getGapOpenCol
in interface Alignable
setGapOpenCol
public void setGapOpenCol(float gapOpenCol)
- Specified by:
setGapOpenCol
in interface Alignable
getGapOpenRow
public float getGapOpenRow()
- Specified by:
getGapOpenRow
in interface Alignable
setGapOpenRow
public void setGapOpenRow(float gapOpenRow)
- Specified by:
setGapOpenRow
in interface Alignable
getScore
public float getScore()
- Specified by:
getScore
in interface Alignable
setScore
public void setScore(float score)
- Specified by:
setScore
in interface Alignable
getPath
public IndexPair[] getPath()
- Specified by:
getPath
in interface Alignable
setPath
public void setPath(IndexPair[] path)
- Specified by:
setPath
in interface Alignable
getPathSize
public int getPathSize()
- Specified by:
getPathSize
in interface Alignable
setPathSize
public void setPathSize(int pathSize)
- Specified by:
setPathSize
in interface Alignable