Package | Description |
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Alignments |
Provides class for dealing with "alignments" and the sites in an alignment.
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Modifier and Type | Method and Description |
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static Ambiguous |
Ambiguous.fromFile(java.io.File f)
Reads in amiguous data information from a file.
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Constructor and Description |
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DuplicationAlignment(java.io.File f,
Ambiguous ambig)
Creates a duplication alignment which contains ambiguous data.
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SequenceAlignment(java.io.File f,
Ambiguous ambig)
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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