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java.lang.Object org.strbio.mol.lib.ScorePSIBlast
public class ScorePSIBlast
A scoring function that uses PSI-BLAST matrices.
Version 1.1, 6/7/99 - moved to org.strbio.mol.lib Version 1.0, 1/28/99 - original version
Constructor Summary | |
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ScorePSIBlast()
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Method Summary | |
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void |
describe(Printf outfile)
This should print info about the object to an output file. |
void |
finished(Polymer p)
This function is called when you are done using the function on a polymer. |
double |
score(Monomer a,
Monomer b)
This function should return a score for aligning two monomers of a polymer, preferably with low = good, high = bad. |
double |
score(ProfResPSI a,
ProfResPSI b)
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void |
setup(Polymer p)
This function is to set up the scoring function for use on a polymer. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public ScorePSIBlast()
Method Detail |
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public double score(ProfResPSI a, ProfResPSI b)
public double score(Monomer a, Monomer b)
ScoreFunction
score
in interface ScoreFunction
public void setup(Polymer p)
ScoreSetup
setup
in interface ScoreSetup
public void finished(Polymer p)
ScoreSetup
finished
in interface ScoreSetup
public void describe(Printf outfile)
Description
describe
in interface Description
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