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public interface CharacterAlignment
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.
Nested Class Summary |
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Nested classes/interfaces inherited from interface pal.misc.IdGroup |
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IdGroup.Utils |
Field Summary | |
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static double |
MISSING
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Method Summary | |
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java.lang.String |
getEnvironmentName(int trait)
Return name of the environments for this trait number |
int |
getSequenceCount()
Return number of sequences(taxa) in this alignment |
double |
getTrait(int seq,
int trait)
Return the trait value for a given sequence (taxon) and trait number |
int |
getTraitCount()
Return number of traits for each sequence in this alignment |
java.lang.String |
getTraitName(int trait)
Return name of the trait for this trait number |
Methods inherited from interface pal.misc.IdGroup |
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getIdCount, getIdentifier, setIdentifier, whichIdNumber |
Methods inherited from interface pal.misc.Report |
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report |
Methods inherited from interface pal.misc.TableReport |
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getTableColumnNames, getTableData, getTableTitle |
Field Detail |
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static final double MISSING
Method Detail |
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java.lang.String getTraitName(int trait)
java.lang.String getEnvironmentName(int trait)
double getTrait(int seq, int trait)
int getSequenceCount()
int getTraitCount()
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