Package pal.alignment
Class GapBalancedAlignment
java.lang.Object
pal.alignment.AbstractAlignment
pal.alignment.GapBalancedAlignment
- All Implemented Interfaces:
Serializable
,Alignment
,IdGroup
,Report
Creates a "Gap-Balanced" alignment.
- Version:
- $Id: GapBalancedAlignment.java,v 1.14 2003/04/10 05:53:47 matt Exp $
- Author:
- Matthew Goode
- See Also:
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Nested Class Summary
Nested classes/interfaces inherited from interface pal.misc.IdGroup
IdGroup.Utils
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Field Summary
Fields inherited from class pal.alignment.AbstractAlignment
idGroup, numSeqs, numSites
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Constructor Summary
ConstructorsConstructorDescriptionGapBalancedAlignment
(Alignment base, int startingCodonPosition, boolean alignGap) The standard GapBalanced constructorGapBalancedAlignment
(Alignment base, int startingCodonPosition, boolean alignGap, int codonLength) GapBalanced power user constructorGapBalancedAlignment
(Alignment base, int startingCodonPosition, int codonLength) GapBalanced power user constructor -
Method Summary
Modifier and TypeMethodDescriptionchar
getData
(int seq, int site) sequence alignment at (sequence, site)Methods inherited from class pal.alignment.AbstractAlignment
getAlignedSequenceString, getChar, getDataType, getIdCount, getIdentifier, getLength, getSequenceCount, getSiteCount, getState, getStates, guessDataType, isGap, isUnknownState, report, setDataType, setIdentifier, toString, whichIdNumber
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Constructor Details
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GapBalancedAlignment
The standard GapBalanced constructor- Parameters:
Alignment
- on which to based this gap balanced alignmentthe
- estimated startingCodonPosition of the alignment
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GapBalancedAlignment
GapBalanced power user constructor- Parameters:
startingCodonPosition
- the starting codon position of the alignmentcodonLength
- the length of a codon (to make things general, - the author is a Computer Scientist)Alignment
- on which to based this gap balanced alignment
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GapBalancedAlignment
public GapBalancedAlignment(Alignment base, int startingCodonPosition, boolean alignGap, int codonLength) GapBalanced power user constructor- Parameters:
startingCodonPosition
- the starting codon position of the alignmentalignGap
- sometimes a large cap may occur in the middle of a sequence's codon. If this is true than no columns can match up in this area (it's hard to explain - for safety choose true!)codonLength
- the length of a codon (to make things general, - the author is a Computer Scientist)Alignment
- on which to based this gap balanced alignment
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Method Details
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getData
public char getData(int seq, int site) sequence alignment at (sequence, site)- Specified by:
getData
in interfaceAlignment
- Specified by:
getData
in classAbstractAlignment
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