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java.lang.Object org.strbio.mol.lib.AlignmentParameters
public class AlignmentParameters
Alignment parameters. This consists of a gap model and a list of scoring functions.
Field Summary | |
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GapModel |
gapModel
The gap model used. |
ScoreList |
scoreList
The scoring functions used. |
Constructor Summary | |
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AlignmentParameters()
Default is everything null. |
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AlignmentParameters(GapModel gm,
ScoreList sl)
Provide an initial gap model and score list. |
Method Summary | |
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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 |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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public GapModel gapModel
public ScoreList scoreList
Constructor Detail |
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public AlignmentParameters(GapModel gm, ScoreList sl)
public AlignmentParameters()
Method Detail |
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public void describe(Printf outfile)
describe
in interface Description
public final void addScoreFunction(ScoreFunction s, double weight)
public final void addScoreFunction(ScoreFunction s)
public final void normalizeWeights()
public void setup(Polymer seq, Polymer fold)
public void setAlignment(Alignment al)
public void finished(Polymer seq, Polymer fold)
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