org.strbio.mol.lib
Class GapAffine

java.lang.Object
  org.strbio.mol.lib.GapModelAdapter
      org.strbio.mol.lib.GapConstant
          org.strbio.mol.lib.GapAffine

All Implemented Interfaces:

Description, GapModel

Direct Known Subclasses:

GapDistanceDependent

public class GapAffine
extends GapConstant
implements Description

Affine gap penalties. (cost = gapI + (n-1) * gapE)

  Version 1.1, 7/1/99 - conforms to GapModel 1.1 interface
  Version 1.0, 2/25/99 - original version
  

Version:

1.1, 7/1/99

Author:

JMC

Field Summary

double

gapE Gap extention penalty.

Fields inherited from class org.strbio.mol.lib.GapConstant

endGapFoldOK, endGapSeqOK, gapI

Constructor Summary

GapAffine(double gapi, double gape)
Set the penalties.

GapAffine(double gapi, double gape, boolean seqEndGapOK, boolean foldEndGapOK)
Set the penalties.

Method Summary

void	describe(Printf outfile) the default function describes only ends.
double	gapCostDeletion(Polymer seq, Polymer fold, int seqi, int seqj, int foldi, int foldj) This function should return the gap cost for aligning residues seqi and foldi, then seqj and foldj.
double	gapCostInsertion(Polymer seq, Polymer fold, int seqi, int seqj, int foldi, int foldj) This function should return the gap cost for aligning residues seqi and foldi, then seqj and foldj.
double[]	getOptimizableParameters() get all the optimizable (double) parameters as a vector.
void	printParameters(Printf outfile) default printParameters function does nothing.
void	processGlobalMatrix(float[][] mat, int[][] nextX, int[][] nextY, Polymer seq, Polymer fold) This function is optimized for affine gap penalties.
void	setOptimizableParameters(double[] x) set all the optimizable (double) parameters from a vector.

Methods inherited from class org.strbio.mol.lib.GapConstant

describeBriefly, isEndGapFoldOK, isEndGapSeqOK

Methods inherited from class org.strbio.mol.lib.GapModelAdapter

calculateFirstPosition, dealWithEndPenalties, describeEnds, finished, setup

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

gapE

public double gapE

Gap extention penalty.

Constructor Detail

GapAffine

public GapAffine(double gapi,
                 double gape)

Set the penalties. Ends treated like standard n-w.

GapAffine

public GapAffine(double gapi,
                 double gape,
                 boolean seqEndGapOK,
                 boolean foldEndGapOK)

Set the penalties.

Method Detail

gapCostDeletion

public double gapCostDeletion(Polymer seq,
                              Polymer fold,
                              int seqi,
                              int seqj,
                              int foldi,
                              int foldj)

Description copied from interface: GapModel

This function should return the gap cost for aligning residues seqi and foldi, then seqj and foldj. foldi and foldj should not be consecutive; seqi and seqj should if you're doing needleman-wunsch alignments. i and j are 0-based integers, with no relation to n in Monomer. -1 means off the end. Otherwise, j should always be higher than i.

      seq:   i.....j
      fold:  ixxxxxj
      


Specified by:
gapCostDeletion in interface GapModel
Overrides:
gapCostDeletion in class GapConstant

gapCostInsertion

public double gapCostInsertion(Polymer seq,
                               Polymer fold,
                               int seqi,
                               int seqj,
                               int foldi,
                               int foldj)

Description copied from interface: GapModel

This function should return the gap cost for aligning residues seqi and foldi, then seqj and foldj. seqi and seqj should not be consecutive; foldi and foldj should if you're doing needleman-wunsch alignments. i and j are 0-based integers, with no relation to n in Monomer. -1 means off the end. Otherwise, j should always be higher than i.

      seq:   ixxxxxj
      fold:  i.....j
      


Specified by:
gapCostInsertion in interface GapModel
Overrides:
gapCostInsertion in class GapConstant

processGlobalMatrix

public void processGlobalMatrix(float[][] mat,
                                int[][] nextX,
                                int[][] nextY,
                                Polymer seq,
                                Polymer fold)

This function is optimized for affine gap penalties.

Specified by:

processGlobalMatrix in interface GapModel

Overrides:

processGlobalMatrix in class GapConstant

describe

public void describe(Printf outfile)

Description copied from class: GapModelAdapter

the default function describes only ends.

Specified by:

describe in interface Description

Overrides:

describe in class GapConstant

printParameters

public void printParameters(Printf outfile)

Description copied from class: GapModelAdapter

default printParameters function does nothing.

Specified by:

printParameters in interface GapModel

Overrides:

printParameters in class GapModelAdapter

getOptimizableParameters

public double[] getOptimizableParameters()

get all the optimizable (double) parameters as a vector.

Specified by:

getOptimizableParameters in interface GapModel

Overrides:

getOptimizableParameters in class GapConstant

setOptimizableParameters

public void setOptimizableParameters(double[] x)

set all the optimizable (double) parameters from a vector.

Specified by:

setOptimizableParameters in interface GapModel

Overrides:

setOptimizableParameters in class GapConstant