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Packages that use OutputException | |
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Alignments | Provides class for dealing with "alignments" and the sites in an alignment. |
Optimizers | Provides classes for optimising a likelihood. |
Parameters | Provides classes for defining parameters used in the various calculations. |
Simulations | Provides a class to create simulate data. |
Trees | Provides classes to define a tree and any constraints on that tree. |
Uses of OutputException in Alignments |
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Methods in Alignments that throw OutputException | |
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static void |
DuplicationAlignment.writeFile(Alignment a,
java.io.File f)
Writes a alignment to a file in the duplication alignment format described above. |
static void |
FastaAlignment.writeFile(Alignment a,
java.io.File f)
Writes a alignment to a file in the format described in FastaAlignment.FastaAlignment(java.io.File) . |
static void |
PhylipAlignment.writeFile(Alignment a,
java.io.File f)
Writes a alignment to a file in the format described in PhylipAlignment.PhylipAlignment(java.io.File) . |
static void |
SequenceAlignment.writeFile(Alignment a,
java.io.File f)
Deprecated. Writes a alignment to a file in the format described in SequenceAlignment.SequenceAlignment(java.io.File) . |
Uses of OutputException in Optimizers |
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Methods in Optimizers that throw OutputException | |
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Likelihood |
GoldenSection.maximise(Calculator l,
Parameters params)
|
Likelihood |
NelderMead.maximise(Calculator l,
Parameters params)
|
Likelihood |
Optimizer.maximise(Calculator l,
Parameters p)
Maximises the likelihood, logging to screen. |
Likelihood |
GoldenSection.maximise(Calculator l,
Parameters params,
java.io.File log)
|
Likelihood |
NelderMead.maximise(Calculator l,
Parameters params,
java.io.File log)
|
Likelihood |
Optimizer.maximise(Calculator l,
Parameters params,
java.io.File log)
Maximises the likelihood, logging to a file. |
Likelihood |
GoldenSection.restart(Calculator l,
java.io.File checkPoint)
|
Likelihood |
NelderMead.restart(Calculator l,
java.io.File checkPoint)
|
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)
|
Likelihood |
NelderMead.restart(Calculator l,
java.io.File checkPoint,
java.io.File log)
|
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 OutputException in Parameters |
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Methods in Parameters that throw OutputException | |
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void |
Parameters.toFile(java.io.File f)
Writes the parameter values to a file. |
void |
Parameters.toFile(java.io.File f,
double like)
Writes the parameter values to a file and writes a line labeled likelihood and which gives the likelihood given as input. |
Uses of OutputException in Simulations |
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Methods in Simulations that throw OutputException | |
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double |
HypothesisTest.test(Tree t,
Alignment a,
Alignment unobserved,
Parameters nullParams,
Parameters altParams)
Does a hpyothesis test on the given data and gives a p-value |
double |
HypothesisTest.test(Tree t,
Alignment a,
Alignment unobserved,
Parameters nullParams,
Parameters altParams,
java.util.Map<java.lang.String,java.lang.String> recode)
Does a hpyothesis test on the given data and gives a p-value |
Uses of OutputException in Trees |
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Methods in Trees that throw OutputException | |
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void |
Tree.toFile(java.io.File f)
Writes the tree to a file in Newick format. |
void |
Tree.toFile(java.io.File f,
boolean nameInternal)
Write the tree to a file in Newick format. |
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