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java.lang.Object org.strbio.mol.lib.GapModelAdapter org.strbio.mol.lib.GapConstant org.strbio.mol.lib.GapAffine org.strbio.mol.lib.GapDistanceDependent
public class GapDistanceDependent
Distance dependent 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
Field Summary | |
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double |
gapD
Distance penalty. |
Fields inherited from class org.strbio.mol.lib.GapAffine |
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gapE |
Fields inherited from class org.strbio.mol.lib.GapConstant |
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endGapFoldOK, endGapSeqOK, gapI |
Constructor Summary | |
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GapDistanceDependent(double gapi,
double gape,
double gapd)
Set the penalties. |
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GapDistanceDependent(double gapi,
double gape,
double gapd,
boolean seqEndGapOK,
boolean foldEndGapOK)
Set the penalties. |
Method Summary | |
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void |
describe(Printf outfile)
the default function describes only ends. |
void |
describeBriefly(Printf outfile)
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void |
finished(Polymer seq,
Polymer fold)
Forget about distance matrix. |
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 |
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. |
void |
setOptimizableParameters(double[] x)
set all the optimizable (double) parameters from a vector. |
void |
setup(Polymer seq,
Polymer fold)
Calculate distance matrix. |
Methods inherited from class org.strbio.mol.lib.GapAffine |
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printParameters |
Methods inherited from class org.strbio.mol.lib.GapConstant |
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isEndGapFoldOK, isEndGapSeqOK |
Methods inherited from class org.strbio.mol.lib.GapModelAdapter |
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calculateFirstPosition, dealWithEndPenalties, describeEnds |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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public double gapD
Constructor Detail |
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public GapDistanceDependent(double gapi, double gape, double gapd)
public GapDistanceDependent(double gapi, double gape, double gapd, boolean seqEndGapOK, boolean foldEndGapOK)
Method Detail |
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public void setup(Polymer seq, Polymer fold)
setup
in interface GapModel
setup
in class GapModelAdapter
public void finished(Polymer seq, Polymer fold)
finished
in interface GapModel
finished
in class GapModelAdapter
public double gapCostDeletion(Polymer seq, Polymer fold, int seqi, int seqj, int foldi, int foldj)
GapModel
seq: i.....j fold: ixxxxxj
gapCostDeletion
in interface GapModel
gapCostDeletion
in class GapAffine
public double gapCostInsertion(Polymer seq, Polymer fold, int seqi, int seqj, int foldi, int foldj)
GapModel
seq: ixxxxxj fold: i.....j
gapCostInsertion
in interface GapModel
gapCostInsertion
in class GapAffine
public void processGlobalMatrix(float[][] mat, int[][] nextX, int[][] nextY, Polymer seq, Polymer fold)
processGlobalMatrix
in interface GapModel
processGlobalMatrix
in class GapAffine
public void describe(Printf outfile)
GapModelAdapter
describe
in interface Description
describe
in class GapAffine
public void describeBriefly(Printf outfile)
describeBriefly
in class GapConstant
public double[] getOptimizableParameters()
getOptimizableParameters
in interface GapModel
getOptimizableParameters
in class GapAffine
public void setOptimizableParameters(double[] x)
setOptimizableParameters
in interface GapModel
setOptimizableParameters
in class GapAffine
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