Package pal.alignment
Interface CharacterAlignment
- All Superinterfaces:
IdGroup
,Report
,Serializable
,TableReport
- All Known Implementing Classes:
SimpleCharacterAlignment
This interface is designed to hold quantitative character states.
Each trait (a quantitative character) has two sets of
labels. One is the traitName, and the second is the environmentName. Obviously any
descriptor could be placed in these two labels, however for printing purposes
traitName is printed first. Double.NaN is assumed to be the missing value.
- Version:
- $Id: CharacterAlignment.java,v 1.2 2001/09/02 13:19:41 korbinian Exp $
- Author:
- Ed Buckler
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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 -
Method Summary
Modifier and TypeMethodDescriptiongetEnvironmentName
(int trait) Return name of the environments for this trait numberint
Return number of sequences(taxa) in this alignmentdouble
getTrait
(int seq, int trait) Return the trait value for a given sequence (taxon) and trait numberint
Return number of traits for each sequence in this alignmentgetTraitName
(int trait) Return name of the trait for this trait numberMethods inherited from interface pal.misc.IdGroup
getIdCount, getIdentifier, setIdentifier, whichIdNumber
Methods inherited from interface pal.misc.TableReport
getTableColumnNames, getTableData, getTableTitle
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Field Details
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MISSING
static final double MISSING- See Also:
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Method Details
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getTraitName
Return name of the trait for this trait number -
getEnvironmentName
Return name of the environments for this trait number -
getTrait
double getTrait(int seq, int trait) Return the trait value for a given sequence (taxon) and trait number -
getSequenceCount
int getSequenceCount()Return number of sequences(taxa) in this alignment -
getTraitCount
int getTraitCount()Return number of traits for each sequence in this alignment
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