public class GapBalancedAlignment extends AbstractAlignment implements java.io.Serializable
IdGroup.Utils
idGroup, numSeqs, numSites
Constructor and Description |
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GapBalancedAlignment(Alignment base,
int startingCodonPosition,
boolean alignGap)
The standard GapBalanced constructor
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GapBalancedAlignment(Alignment base,
int startingCodonPosition,
boolean alignGap,
int codonLength)
GapBalanced power user constructor
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GapBalancedAlignment(Alignment base,
int startingCodonPosition,
int codonLength)
GapBalanced power user constructor
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Modifier and Type | Method and Description |
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char |
getData(int seq,
int site)
sequence alignment at (sequence, site)
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getAlignedSequenceString, getChar, getDataType, getIdCount, getIdentifier, getLength, getSequenceCount, getSiteCount, getState, getStates, guessDataType, isGap, isUnknownState, report, setDataType, setIdentifier, toString, whichIdNumber
public GapBalancedAlignment(Alignment base, int startingCodonPosition, boolean alignGap)
Alignment
- on which to based this gap balanced alignmentthe
- estimated startingCodonPosition of the alignmentpublic GapBalancedAlignment(Alignment base, int startingCodonPosition, int codonLength)
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)public GapBalancedAlignment(Alignment base, int startingCodonPosition, boolean alignGap, int codonLength)
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)public char getData(int seq, int site)
getData
in interface Alignment
getData
in class AbstractAlignment