org.strbio.mol.lib
Class GapConstant

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

All Implemented Interfaces:

Description, GapModel

Direct Known Subclasses:

GapAffine

public class GapConstant
extends GapModelAdapter
implements Description

Constant gap penalties.

  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

boolean	endGapFoldOK Gaps at the end of the fold - ok?
boolean	endGapSeqOK Gaps at the end of the sequence - ok?
double	gapI Gap opening penalty.

Constructor Summary

GapConstant(double gapi)
Set the penalty.

GapConstant(double gapi, boolean seqEndGapOK, boolean foldEndGapOK)
Set the penalty.

Method Summary

void	describe(Printf outfile) the default function describes only ends.
void	describeBriefly(Printf outfile)
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.
boolean	isEndGapFoldOK() See if aligning the end of the fold vs a gap is OK (not penalized)
boolean	isEndGapSeqOK() See if aligning the end of the sequence vs a gap is OK (not penalized)
void	processGlobalMatrix(float[][] mat, int[][] nextX, int[][] nextY, Polymer seq, Polymer fold) This function is optimized for constant gap penalties.
void	setOptimizableParameters(double[] x) set all the optimizable (double) parameters from a vector.

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

calculateFirstPosition, dealWithEndPenalties, describeEnds, finished, printParameters, setup

Methods inherited from class java.lang.Object

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

Field Detail

endGapSeqOK

public boolean endGapSeqOK

Gaps at the end of the sequence - ok?

endGapFoldOK

public boolean endGapFoldOK

Gaps at the end of the fold - ok?

gapI

public double gapI

Gap opening penalty.

Constructor Detail

GapConstant

public GapConstant(double gapi)

Set the penalty. Standard n-w.

GapConstant

public GapConstant(double gapi,
                   boolean seqEndGapOK,
                   boolean foldEndGapOK)

Set the penalty.

Method Detail

isEndGapSeqOK

public boolean isEndGapSeqOK()

Description copied from interface: GapModel

See if aligning the end of the sequence vs a gap is OK (not penalized)

Specified by:

isEndGapSeqOK in interface GapModel

isEndGapFoldOK

public boolean isEndGapFoldOK()

Description copied from interface: GapModel

See if aligning the end of the fold vs a gap is OK (not penalized)

Specified by:

isEndGapFoldOK in interface GapModel

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

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

processGlobalMatrix

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

This function is optimized for constant gap penalties.

Specified by:

processGlobalMatrix in interface GapModel

Overrides:

processGlobalMatrix in class GapModelAdapter

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 GapModelAdapter

describeBriefly

public void describeBriefly(Printf outfile)

getOptimizableParameters

public double[] getOptimizableParameters()

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

Specified by:

getOptimizableParameters in interface GapModel

Overrides:

getOptimizableParameters in class GapModelAdapter

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 GapModelAdapter