Package pal.alignment
Class GapBalancedAlignment
- java.lang.Object
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- pal.alignment.AbstractAlignment
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- pal.alignment.GapBalancedAlignment
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public class GapBalancedAlignment extends AbstractAlignment implements java.io.Serializable
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:
- Serialized Form
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Nested Class Summary
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Nested classes/interfaces inherited from interface pal.misc.IdGroup
IdGroup.Utils
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Field Summary
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Fields inherited from class pal.alignment.AbstractAlignment
idGroup, numSeqs, numSites
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Constructor Summary
Constructors Constructor Description GapBalancedAlignment(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
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description char
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 Detail
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GapBalancedAlignment
public GapBalancedAlignment(Alignment base, int startingCodonPosition, boolean alignGap)
The standard GapBalanced constructor- Parameters:
Alignment
- on which to based this gap balanced alignmentthe
- estimated startingCodonPosition of the alignment
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GapBalancedAlignment
public GapBalancedAlignment(Alignment base, int startingCodonPosition, int codonLength)
GapBalanced power user constructor- Parameters:
Alignment
- on which to based this gap balanced alignmentstartingCodonPosition
- the starting codon position of the alignmentcodonLength
- the length of a codon (to make things general, - the author is a Computer Scientist)
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GapBalancedAlignment
public GapBalancedAlignment(Alignment base, int startingCodonPosition, boolean alignGap, int codonLength)
GapBalanced power user constructor- Parameters:
Alignment
- on which to based this gap balanced alignmentstartingCodonPosition
- 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)
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Method Detail
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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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