java.lang.Object

org.biojava.nbio.structure.align.pairwise.StrCompAlignment

All Implemented Interfaces:: Alignable

public class StrCompAlignment extends Object implements Alignable

Constructor Summary

Constructors

Constructor

Description

StrCompAlignment(int rows, int cols)
Method Summary

Modifier and Type

Method

Description

AligMatEl[][]

getAligMat()

AligMatEl

getAligMat(int i, int j)

int

getCols()

float

getGapExtCol()

float

getGapExtRow()

float

getGapOpenCol()

float

getGapOpenRow()

IndexPair[]

getPath()

int

getPathSize()

int

getRows()

float

getScore()

void

setAligMat(int i, int j, AligMatEl el)

void

setAligMat(AligMatEl[][] al)

void

setGapExtCol(float gapExtCol)

void

setGapExtRow(float gapExtRow)

void

setGapOpenCol(float gapOpenCol)

void

setGapOpenRow(float gapOpenRow)

void

setPath(IndexPair[] path)

void

setPathSize(int pathSize)

void

setScore(float score)

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details
- StrCompAlignment
  
  public StrCompAlignment(int rows, int cols)
Method Details
- 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

Class StrCompAlignment

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Details

StrCompAlignment

Method Details

getRows

getCols

setAligMat

getAligMat

getAligMat

setAligMat

getGapExtCol

setGapExtCol

getGapExtRow

setGapExtRow

getGapOpenCol

setGapOpenCol

getGapOpenRow

setGapOpenRow

getScore

setScore

getPath

setPath

getPathSize

setPathSize