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Packages that use AlignmentException | |
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Alignments | Provides class for dealing with "alignments" and the sites in an alignment. |
Ancestors | Provides classed to calculate ancestral reconstruction. |
Simulations | Provides a class to create simulate data. |
Uses of AlignmentException in Alignments |
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Constructors in Alignments that throw AlignmentException | |
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Alignment(java.util.List<Site> data)
Creates an alignment |
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DuplicationAlignment(java.io.File f)
Creates a duplication alignment from a file. |
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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)
Creates a sequence alignment from a file. |
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SequenceAlignment(java.io.File f,
Ambiguous ambig)
Creates a sequence alignment from a file with ambiguouis data. |
Uses of AlignmentException in Ancestors |
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Methods in Ancestors that throw AlignmentException | |
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abstract Alignment |
AncestralJoint.calculate(Parameters params)
Calculates the reconstruction |
Alignment |
AncestralJointBB.calculate(Parameters p)
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Alignment |
AncestralJointDP.calculate(Parameters params)
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AncestralMarginal.Result |
AncestralMarginal.calculate(Parameters params)
Calculates the reconstruction |
Uses of AlignmentException in Simulations |
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Methods in Simulations that throw AlignmentException | |
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Alignment |
Simulate.getAlignment(int length)
Gets a simulated alignment, not returing the state of internal nodes |
Alignment |
Simulate.getAlignment(int length,
boolean internal)
Gets a simulated alignment |
Alignment |
Simulate.getAlignment(int length,
boolean internal,
java.util.Map<java.lang.String,java.lang.String> recode)
Gets a simulated alignment. |
Alignment |
Simulate.getAlignment(int length,
java.util.Map<java.lang.String,java.lang.String> recode)
Gets a simulated alignment, not returing the state of internal nodes. |
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