org.biojava.bio.structure.align.pairwise
Interface Alignable

All Known Implementing Classes:
StrCompAlignment

public interface Alignable


Method Summary
 AligMatEl[][] getAligMat()
           
 int getCols()
           
 float getGapExtCol()
           
 float getGapExtRow()
           
 float getGapOpenCol()
           
 float getGapOpenRow()
           
 IndexPair[] getPath()
           
 int getPathSize()
           
 int getRows()
           
 float getScore()
           
 void setAligMat(AligMatEl[][] alignmentMatrix)
           
 void setGapExtCol(float penalty)
           
 void setGapExtRow(float penalty)
           
 void setGapOpenCol(float penalty)
           
 void setGapOpenRow(float penalty)
           
 void setPath(IndexPair[] path)
           
 void setPathSize(int pathSize)
           
 void setScore(float score)
           
 

Method Detail

getRows

int getRows()

getCols

int getCols()

getAligMat

AligMatEl[][] getAligMat()

setAligMat

void setAligMat(AligMatEl[][] alignmentMatrix)

getGapExtCol

float getGapExtCol()

setGapExtCol

void setGapExtCol(float penalty)

getGapExtRow

float getGapExtRow()

setGapExtRow

void setGapExtRow(float penalty)

getGapOpenCol

float getGapOpenCol()

setGapOpenCol

void setGapOpenCol(float penalty)

getGapOpenRow

float getGapOpenRow()

setGapOpenRow

void setGapOpenRow(float penalty)

setScore

void setScore(float score)

getScore

float getScore()

getPathSize

int getPathSize()

setPathSize

void setPathSize(int pathSize)

setPath

void setPath(IndexPair[] path)

getPath

IndexPair[] getPath()