Package pal.alignment
Interface CharacterAlignment
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- All Superinterfaces:
IdGroup
,Report
,java.io.Serializable
,TableReport
- All Known Implementing Classes:
SimpleCharacterAlignment
public interface CharacterAlignment extends java.io.Serializable, IdGroup, Report, TableReport
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
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Nested classes/interfaces inherited from interface pal.misc.IdGroup
IdGroup.Utils
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Field Summary
Fields Modifier and Type Field Description static double
MISSING
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Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method Description java.lang.String
getEnvironmentName(int trait)
Return name of the environments for this trait numberint
getSequenceCount()
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
getTraitCount()
Return number of traits for each sequence in this alignmentjava.lang.String
getTraitName(int trait)
Return name of the trait for this trait number-
Methods inherited from interface pal.misc.IdGroup
getIdCount, getIdentifier, setIdentifier, whichIdNumber
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Methods inherited from interface pal.misc.TableReport
getTableColumnNames, getTableData, getTableTitle
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Field Detail
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MISSING
static final double MISSING
- See Also:
- Constant Field Values
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Method Detail
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getTraitName
java.lang.String getTraitName(int trait)
Return name of the trait for this trait number
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getEnvironmentName
java.lang.String getEnvironmentName(int trait)
Return name of the environments for this trait number
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getTrait
double getTrait(int seq, int trait)
Return the trait value for a given sequence (taxon) and trait number
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getSequenceCount
int getSequenceCount()
Return number of sequences(taxa) in this alignment
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getTraitCount
int getTraitCount()
Return number of traits for each sequence in this alignment
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