org.strbio.raf
Class GapRAF

java.lang.Object
  org.strbio.mol.lib.GapModelAdapter
      org.strbio.raf.GapRAF

All Implemented Interfaces:

Description, GapModel

public class GapRAF
extends GapModelAdapter
implements Description

Gap penalties for RAF. Constant (1.0) for sequence (seqres), Constant (1.0) for fold, unless difference in monomer n matches gap length; i.e. A101 . B103 would have no gap penalty. There is a small, constant penalty (0.1) where adjacent residues have monomer n differences other than 0 or 1.

  Version 1.0, 10/4/01 - original version
  

Version:

1.0, 10/4/01

Author:

JMC

Field Summary

boolean	endGapFoldOK Gaps at the end of the fold - ok?
boolean	endGapSeqOK Gaps at the end of the sequence - ok?

Constructor Summary

GapRAF()
Set the penalties.

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.
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 gap penalties which are affine in only 1 direction, and have to be fully looked at in the other direction.

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

calculateFirstPosition, dealWithEndPenalties, describeEnds, finished, getOptimizableParameters, printParameters, setOptimizableParameters, 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?

Constructor Detail

GapRAF

public GapRAF()

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

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 gap penalties which are affine in only 1 direction, and have to be fully looked at in the other direction.

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)