org.strbio.mol.lib
Class AlignmentParameters

java.lang.Object
  extended by org.strbio.mol.lib.AlignmentParameters
All Implemented Interfaces:
Description
Direct Known Subclasses:
AlignmentParametersEA

public class AlignmentParameters
extends java.lang.Object
implements Description

Alignment parameters. This consists of a gap model and a list of scoring functions.

Version:
1.0, 6/25/99
Author:
JMC

Field Summary
 GapModel gapModel
          The gap model used.
 ScoreList scoreList
          The scoring functions used.
 
Constructor Summary
AlignmentParameters()
          Default is everything null.
AlignmentParameters(GapModel gm, ScoreList sl)
          Provide an initial gap model and score list.
 
Method Summary
 void addScoreFunction(ScoreFunction s)
          Add new scoring function with default weight.
 void addScoreFunction(ScoreFunction s, double weight)
          Add new scoring function with specified weight.
 void describe(Printf outfile)
          Describe prints parameters of the components, if they support it
 void finished(Polymer seq, Polymer fold)
          Tell objects that we're done doing an alignment on a given seq and fold.
 void normalizeWeights()
          make the relative absolute weights for the scoring functions add up to one.
 void setAlignment(Alignment al)
          Set the alignment for scoring functions that require it.
 void setup(Polymer seq, Polymer fold)
          Set up everything for doing an alignment on a given seq and fold.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

gapModel

public GapModel gapModel
The gap model used.


scoreList

public ScoreList scoreList
The scoring functions used.

Constructor Detail

AlignmentParameters

public AlignmentParameters(GapModel gm,
                           ScoreList sl)
Provide an initial gap model and score list.


AlignmentParameters

public AlignmentParameters()
Default is everything null.

Method Detail

describe

public void describe(Printf outfile)
Describe prints parameters of the components, if they support it

Specified by:
describe in interface Description

addScoreFunction

public final void addScoreFunction(ScoreFunction s,
                                   double weight)
Add new scoring function with specified weight.


addScoreFunction

public final void addScoreFunction(ScoreFunction s)
Add new scoring function with default weight.


normalizeWeights

public final void normalizeWeights()
make the relative absolute weights for the scoring functions add up to one.


setup

public void setup(Polymer seq,
                  Polymer fold)
Set up everything for doing an alignment on a given seq and fold.


setAlignment

public void setAlignment(Alignment al)
Set the alignment for scoring functions that require it.


finished

public void finished(Polymer seq,
                     Polymer fold)
Tell objects that we're done doing an alignment on a given seq and fold.