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java.lang.Objectprocope.tools.SequenceAligner
public class SequenceAligner
Calculates pairwise sequence alignments using the JAligner library. Implements a caching functionality to avoid multiple calulations of the same alignments.
Before aligning two sequences you have to add them to the
sequence pool
of the aligner object
to provide actual sequence data for the proteins.
Gap penalties are specified as positive values.
Note: Only local alignments (Smith-Waterman) are supported at the moment.
Constructor Summary | |
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SequenceAligner()
Creates a new sequence aligner with activated caching. |
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SequenceAligner(boolean cache)
Creates a new sequence aligner. |
Method Summary | |
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void |
addToSequencePool(Sequences sequences)
Add a set of sequences to the sequence pool of this aligner. |
jaligner.Alignment |
getAlignment(int protein1,
int protein2)
Returns the local sequence alignment for two given proteins. |
static String[] |
getMatrixNames()
Returns a list of possible substitution matrix names. |
Sequences |
getSequencePool()
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void |
setGapExtend(float gapExt)
Sets the gap extension penality. |
void |
setGapOpen(float gapOpen)
Sets the gap open penality. |
void |
setMatrix(String matrixName)
Sets the substitution matrix. |
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 SequenceAligner()
public SequenceAligner(boolean cache)
cache
- cache alignments to avoid multiple pairwise alignment
calculations?Method Detail |
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public static String[] getMatrixNames()
public void setMatrix(String matrixName) throws ProCopeException
getMatrixNames()
.
matrixName
- name of substitution matrix.
ProCopeException
- if the specified substitution matrix
was not foundpublic void setGapOpen(float gapOpen)
gapOpen
- gap open penalitypublic void setGapExtend(float gapExt)
gapExt
- gap extension penaltypublic void addToSequencePool(Sequences sequences)
sequences
- sequences to be added to the poolpublic jaligner.Alignment getAlignment(int protein1, int protein2) throws ProCopeException
protein1
- first proteinprotein2
- second protein
ProCopeException
- if at least one of the proteins has no
sequence in the current sequence pool
public Sequences getSequencePool()
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