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Packages that use InputException | |
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Alignments | Provides class for dealing with "alignments" and the sites in an alignment. |
Models | Provides classes for defing a phylogenetic model. |
Optimizers | Provides classes for optimising a likelihood. |
Parameters | Provides classes for defining parameters used in the various calculations. |
Trees | Provides classes to define a tree and any constraints on that tree. |
Uses of InputException in Alignments |
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Methods in Alignments that throw InputException | |
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static Ambiguous |
Ambiguous.fromFile(java.io.File f)
Reads in amiguous data information from a file. |
Constructors in Alignments that throw InputException | |
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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 InputException in Models |
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Methods in Models that throw InputException | |
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static Model |
Model.fromFile(java.io.File f)
Creates a new model from a file. |
static RateCategory |
RateCategory.fromFile(java.io.File mfile)
Creates an instance from the information in a file. |
Uses of InputException in Optimizers |
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Methods in Optimizers that throw InputException | |
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Likelihood |
GoldenSection.restart(Calculator l,
java.io.File checkPoint)
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Likelihood |
NelderMead.restart(Calculator l,
java.io.File checkPoint)
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Likelihood |
Optimizer.restart(Calculator l,
java.io.File checkPoint)
Maximises the likelihood starting from a checkpoint file (see Optimizer.setCheckPointFile(java.io.File) ,
logging to the screen. |
Likelihood |
GoldenSection.restart(Calculator l,
java.io.File checkPoint,
java.io.File log)
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Likelihood |
NelderMead.restart(Calculator l,
java.io.File checkPoint,
java.io.File log)
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Likelihood |
Optimizer.restart(Calculator l,
java.io.File checkPoint,
java.io.File log)
Maximises the likelihood starting from a checkpoint file (see Optimizer.setCheckPointFile(java.io.File) ,
logging to a file. |
Uses of InputException in Parameters |
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Methods in Parameters that throw InputException | |
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static Parameters |
Parameters.fromFile(java.io.File f)
Reads parameters from a file. |
Uses of InputException in Trees |
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Methods in Trees that throw InputException | |
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static Tree |
Tree.fromFile(java.io.File f)
Creates a tree from a file containing a Newick string |
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