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Packages that use Ambiguous | |
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Alignments | Provides class for dealing with "alignments" and the sites in an alignment. |
Uses of Ambiguous in Alignments |
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Methods in Alignments that return Ambiguous | |
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static Ambiguous |
Ambiguous.fromFile(java.io.File f)
Reads in amiguous data information from a file. |
Ambiguous |
Site.getAmbiguous()
Gets the information about ambiguous states for this site |
Methods in Alignments with parameters of type Ambiguous | |
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Alignment |
Alignment.recode(java.util.Map<java.lang.String,java.lang.String> recode,
Ambiguous ambig)
Recodes the alignment and returns it and also allows the definition of new ambiguous states |
Site |
Site.recode(java.util.Map<java.lang.String,java.lang.String> recode,
Ambiguous ambig)
Recodes the alignment and returns it and also allows the definition of new ambiguous states |
Constructors in Alignments with parameters of type Ambiguous | |
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DuplicationAlignment(java.io.File f,
Ambiguous ambig)
Creates a duplication alignment which contains ambiguous data. |
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FastaAlignment(java.io.File f,
Ambiguous ambig)
Creates a sequence alignment from a file with ambiguouis data. |
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PhylipAlignment(java.io.File f,
Ambiguous ambig)
Creates a sequence alignment from a file with ambiguouis data. |
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SequenceAlignment(java.io.File f,
Ambiguous ambig)
Deprecated. Creates a sequence alignment from a file with ambiguouis data. |
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Site(java.util.LinkedHashMap<java.lang.String,java.lang.String> sites,
Ambiguous ambig)
Creates a site in a alignment with ambiguous data |
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Site(java.util.LinkedHashMap<java.lang.String,java.lang.String> sites,
Ambiguous ambig,
java.lang.String siteClass)
Creates a site in a alignment with ambiguous data and with the given class. |
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