Package org.forester.rio
Class RIO
- java.lang.Object
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- org.forester.rio.RIO
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public final class RIO extends java.lang.Object
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
RIO.REROOTING
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Field Summary
Fields Modifier and Type Field Description static int
DEFAULT_RANGE
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description static IntMatrix
calculateOrthologTable(Phylogeny[] analyzed_gene_trees, boolean sort)
static RIO
executeAnalysis(java.io.File gene_trees_file, java.io.File species_tree_file, SDIutil.ALGORITHM algorithm, RIO.REROOTING rerooting, java.lang.String outgroup, int first, int last, boolean produce_log, boolean verbose, boolean transfer_taxonomy)
static RIO
executeAnalysis(java.io.File gene_trees_file, Phylogeny species_tree, SDIutil.ALGORITHM algorithm, RIO.REROOTING rerooting, java.lang.String outgroup, boolean produce_log, boolean verbose, boolean transfer_taxonomy)
static RIO
executeAnalysis(java.io.File gene_trees_file, Phylogeny species_tree, SDIutil.ALGORITHM algorithm, RIO.REROOTING rerooting, java.lang.String outgroup, int first, int last, boolean produce_log, boolean verbose, boolean transfer_taxonomy)
static RIO
executeAnalysis(IteratingPhylogenyParser p, java.io.File species_tree_file, SDIutil.ALGORITHM algorithm, RIO.REROOTING rerooting, java.lang.String outgroup, int first, int last, boolean produce_log, boolean verbose, boolean transfer_taxonomy)
static RIO
executeAnalysis(IteratingPhylogenyParser p, Phylogeny species_tree, SDIutil.ALGORITHM algorithm, RIO.REROOTING rerooting, java.lang.String outgroup, boolean produce_log, boolean verbose, boolean transfer_taxonomy)
static RIO
executeAnalysis(IteratingPhylogenyParser p, Phylogeny species_tree, SDIutil.ALGORITHM algorithm, RIO.REROOTING rerooting, java.lang.String outgroup, int first, int last, boolean produce_log, boolean verbose, boolean transfer_taxonomy)
static RIO
executeAnalysis(Phylogeny[] gene_trees, Phylogeny species_tree)
static RIO
executeAnalysis(Phylogeny[] gene_trees, Phylogeny species_tree, SDIutil.ALGORITHM algorithm, RIO.REROOTING rerooting, java.lang.String outgroup, boolean produce_log, boolean verbose, boolean transfer_taxonomy)
static RIO
executeAnalysis(Phylogeny[] gene_trees, Phylogeny species_tree, SDIutil.ALGORITHM algorithm, RIO.REROOTING rerooting, java.lang.String outgroup, int first, int last, boolean produce_log, boolean verbose, boolean transfer_taxonomy)
Phylogeny[]
getAnalyzedGeneTrees()
BasicDescriptiveStatistics
getDuplicationsStatistics()
int
getExtNodesOfAnalyzedGeneTrees()
Returns the numbers of number of ext nodes in gene trees analyzed (after stripping).SDIutil.TaxonomyComparisonBase
getGSDIRtaxCompBase()
int
getIntNodesOfAnalyzedGeneTrees()
Returns the numbers of number of int nodes in gene trees analyzed (after stripping).java.lang.StringBuilder
getLog()
Phylogeny
getMinDuplicationsGeneTree()
IntMatrix
getOrthologTable()
java.util.List<PhylogenyNode>
getRemovedGeneTreeNodes()
Phylogeny
getSpeciesTree()
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Field Detail
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DEFAULT_RANGE
public static final int DEFAULT_RANGE
- See Also:
- Constant Field Values
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Method Detail
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getAnalyzedGeneTrees
public final Phylogeny[] getAnalyzedGeneTrees()
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getDuplicationsStatistics
public final BasicDescriptiveStatistics getDuplicationsStatistics()
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getExtNodesOfAnalyzedGeneTrees
public final int getExtNodesOfAnalyzedGeneTrees()
Returns the numbers of number of ext nodes in gene trees analyzed (after stripping).- Returns:
- number of ext nodes in gene trees analyzed (after stripping)
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getGSDIRtaxCompBase
public final SDIutil.TaxonomyComparisonBase getGSDIRtaxCompBase()
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getIntNodesOfAnalyzedGeneTrees
public final int getIntNodesOfAnalyzedGeneTrees()
Returns the numbers of number of int nodes in gene trees analyzed (after stripping).- Returns:
- number of int nodes in gene trees analyzed (after stripping)
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getLog
public final java.lang.StringBuilder getLog()
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getMinDuplicationsGeneTree
public final Phylogeny getMinDuplicationsGeneTree()
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getOrthologTable
public final IntMatrix getOrthologTable()
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getRemovedGeneTreeNodes
public final java.util.List<PhylogenyNode> getRemovedGeneTreeNodes()
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getSpeciesTree
public final Phylogeny getSpeciesTree()
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calculateOrthologTable
public static final IntMatrix calculateOrthologTable(Phylogeny[] analyzed_gene_trees, boolean sort) throws RIOException
- Throws:
RIOException
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executeAnalysis
public static final RIO executeAnalysis(java.io.File gene_trees_file, java.io.File species_tree_file, SDIutil.ALGORITHM algorithm, RIO.REROOTING rerooting, java.lang.String outgroup, int first, int last, boolean produce_log, boolean verbose, boolean transfer_taxonomy) throws java.io.IOException, SDIException, RIOException
- Throws:
java.io.IOException
SDIException
RIOException
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executeAnalysis
public static final RIO executeAnalysis(java.io.File gene_trees_file, Phylogeny species_tree, SDIutil.ALGORITHM algorithm, RIO.REROOTING rerooting, java.lang.String outgroup, boolean produce_log, boolean verbose, boolean transfer_taxonomy) throws java.io.IOException, SDIException, RIOException
- Throws:
java.io.IOException
SDIException
RIOException
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executeAnalysis
public static final RIO executeAnalysis(java.io.File gene_trees_file, Phylogeny species_tree, SDIutil.ALGORITHM algorithm, RIO.REROOTING rerooting, java.lang.String outgroup, int first, int last, boolean produce_log, boolean verbose, boolean transfer_taxonomy) throws java.io.IOException, SDIException, RIOException
- Throws:
java.io.IOException
SDIException
RIOException
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executeAnalysis
public static final RIO executeAnalysis(IteratingPhylogenyParser p, java.io.File species_tree_file, SDIutil.ALGORITHM algorithm, RIO.REROOTING rerooting, java.lang.String outgroup, int first, int last, boolean produce_log, boolean verbose, boolean transfer_taxonomy) throws java.io.IOException, SDIException, RIOException
- Throws:
java.io.IOException
SDIException
RIOException
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executeAnalysis
public static final RIO executeAnalysis(IteratingPhylogenyParser p, Phylogeny species_tree, SDIutil.ALGORITHM algorithm, RIO.REROOTING rerooting, java.lang.String outgroup, boolean produce_log, boolean verbose, boolean transfer_taxonomy) throws java.io.IOException, SDIException, RIOException
- Throws:
java.io.IOException
SDIException
RIOException
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executeAnalysis
public static final RIO executeAnalysis(IteratingPhylogenyParser p, Phylogeny species_tree, SDIutil.ALGORITHM algorithm, RIO.REROOTING rerooting, java.lang.String outgroup, int first, int last, boolean produce_log, boolean verbose, boolean transfer_taxonomy) throws java.io.IOException, SDIException, RIOException
- Throws:
java.io.IOException
SDIException
RIOException
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executeAnalysis
public static final RIO executeAnalysis(Phylogeny[] gene_trees, Phylogeny species_tree) throws java.io.IOException, SDIException, RIOException
- Throws:
java.io.IOException
SDIException
RIOException
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executeAnalysis
public static final RIO executeAnalysis(Phylogeny[] gene_trees, Phylogeny species_tree, SDIutil.ALGORITHM algorithm, RIO.REROOTING rerooting, java.lang.String outgroup, boolean produce_log, boolean verbose, boolean transfer_taxonomy) throws java.io.IOException, SDIException, RIOException
- Throws:
java.io.IOException
SDIException
RIOException
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executeAnalysis
public static final RIO executeAnalysis(Phylogeny[] gene_trees, Phylogeny species_tree, SDIutil.ALGORITHM algorithm, RIO.REROOTING rerooting, java.lang.String outgroup, int first, int last, boolean produce_log, boolean verbose, boolean transfer_taxonomy) throws java.io.IOException, SDIException, RIOException
- Throws:
java.io.IOException
SDIException
RIOException
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