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java.lang.Object org.emboss.jemboss.editor.Consensus
Calculate a consensus using the same method as 'cons' in the EMBOSS suite.
Field Summary | |
private java.lang.String |
cons
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private int[][] |
matrix
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Constructor Summary | |
Consensus(java.io.File matrixFile,
java.util.Vector seqs,
float fplural,
float setcase,
int identity)
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Consensus(Matrix mat,
java.util.Vector seqs,
float fplural,
float setcase,
int identity)
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Consensus(java.lang.String matrixJar,
java.lang.String matrixFileName,
java.util.Vector seqs,
float fplural,
float setcase,
int identity)
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Method Summary | |
private void |
calculateCons(Matrix mat,
java.util.Vector seqs,
float fplural,
float setcase,
int identity)
Routine to calculate the consensus of a set of sequences |
Sequence |
getConsensusSequence()
Get the consensus sequence |
int |
getMaxSequenceLength(java.util.Vector seqs)
Check all sequences lengths and return length of the longest sequence |
java.lang.String |
getResidue(java.util.Vector seqs,
int i,
int k)
Get the residue at a given position from a given sequence |
float |
getSequenceWeight(java.util.Vector seqs,
int i)
Get the sequence weight |
boolean |
isEqualSequenceLength(java.util.Vector seqs)
Check all sequences are the same length |
static void |
main(java.lang.String[] args)
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Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
private int[][] matrix
private java.lang.String cons
Constructor Detail |
public Consensus(java.io.File matrixFile, java.util.Vector seqs, float fplural, float setcase, int identity)
matrixFile
- scoring matrix fileseqs
- vector of Sequence objectsfplural
- defines no. of +ve scoring matches below
which there is no consensus.setcase
- upper/lower case given if score above/below
user defined +ve matching threshold.identity
- defines the number of identical symbols
requires in an alignment column for it to
included in the consensus.public Consensus(java.lang.String matrixJar, java.lang.String matrixFileName, java.util.Vector seqs, float fplural, float setcase, int identity)
matrixJar
- jar file containing scoring matrixmatrixFileName
- scoring matrix file nameseqs
- vector of Sequence objectsfplural
- defines no. of +ve scoring matches below
which there is no consensus.setcase
- upper/lower case given if score above/below
user defined +ve matching threshold.identity
- defines the number of identical symbols
requires in an alignment column for it to
included in the consensus.public Consensus(Matrix mat, java.util.Vector seqs, float fplural, float setcase, int identity)
mat
- scoring matrixseqs
- vector of Sequence objectsfplural
- defines no. of +ve scoring matches below
which there is no consensus.setcase
- upper/lower case given if score above/below
user defined +ve matching threshold.identity
- defines the number of identical symbols
requires in an alignment column for it to
included in the consensus.Method Detail |
private void calculateCons(Matrix mat, java.util.Vector seqs, float fplural, float setcase, int identity)
mat
- scoring matrixseqs
- vector of Sequence objectsfplural
- defines no. of +ve scoring matches below
which there is no consensus.setcase
- upper/lower case given if score above/below
user defined +ve matching threshold.identity
- defines the number of identical symbols
requires in an alignment column for it to
included in the consensus.public boolean isEqualSequenceLength(java.util.Vector seqs)
seqs
- collection of sequences
public int getMaxSequenceLength(java.util.Vector seqs)
seqs
- collection of sequences
public Sequence getConsensusSequence()
public float getSequenceWeight(java.util.Vector seqs, int i)
seqs
- set of sequencesi
- index of a sequence in the set
public java.lang.String getResidue(java.util.Vector seqs, int i, int k)
seqs
- set of sequencesi
- index of a sequence in the set
public static void main(java.lang.String[] args)
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