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java.lang.Objectorg.biojava.bio.dp.WeightMatrixAnnotator
public class WeightMatrixAnnotator
Annotates a sequence with hits to a weight-matrix.
This SequenceAnnotator implementation returns a new ViewSequence wrapping the underlying Sequence
Constructor Summary | |
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WeightMatrixAnnotator(WeightMatrix wm,
double threshold)
Create a new annotator that uses PROBABILITY score type. |
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WeightMatrixAnnotator(WeightMatrix wm,
ScoreType scoreType,
double threshold)
Create a new annotator that uses a specific score type. |
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WeightMatrixAnnotator(WeightMatrix wm,
ScoreType scoreType,
double threshold,
String wmID)
Create a new annotator that uses the PROBABILITY score type and an ID for the weight matrix. |
Method Summary | |
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Sequence |
annotate(Sequence seq)
Return an annotated version of a sequence. |
String |
getWeightMatrixID()
Get the value of the weight matrix id. |
void |
setWeightMatrixID(String id)
Set the weight matrix id. |
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 WeightMatrixAnnotator(WeightMatrix wm, ScoreType scoreType, double threshold, String wmID)
wm
- the weight matrixthreshold
- the thresholdwmID
- the weight matrix IDpublic WeightMatrixAnnotator(WeightMatrix wm, double threshold)
wm
- a WeightMatrix
valuethreshold
- a double
valuepublic WeightMatrixAnnotator(WeightMatrix wm, ScoreType scoreType, double threshold)
wm
- the weigth matrixscoreType
- the score typethreshold
- the thresholdMethod Detail |
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public Sequence annotate(Sequence seq) throws IllegalAlphabetException, BioException, ChangeVetoException
SequenceAnnotator
annotate
in interface SequenceAnnotator
seq
- The sequence to be annotated.
seq
(may be the
same object).
IllegalAlphabetException
- If the sequence is over
an inappropriate alphabet for
the annotated method being
encapsulated
BioException
- if the sequence fails to be annotated
ChangeVetoException
- if either the sequence doesn't allow
annotation or if the change was vetoedpublic String getWeightMatrixID()
public void setWeightMatrixID(String id)
id
- Value to assign to the weight matrix id.
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