Package jebl.evolution.io
Class NexusExporter
- java.lang.Object
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- jebl.evolution.io.NexusExporter
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- All Implemented Interfaces:
AlignmentExporter
,SequenceExporter
,TreeExporter
public class NexusExporter extends java.lang.Object implements AlignmentExporter, SequenceExporter, TreeExporter
Export sequences and trees to Nexus format.- Version:
- $Id: NexusExporter.java 1060 2010-06-01 08:52:55Z rambaut $
- Author:
- Andrew Rambaut, Alexei Drummond, Joseph Heled
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Field Summary
Fields Modifier and Type Field Description static java.lang.String[]
exportExcludeKeys
static int
MAX_ROW_LENGTH
static java.lang.String
treeNameAttributeKey
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Constructor Summary
Constructors Constructor Description NexusExporter(java.io.Writer writer)
NexusExporter(java.io.Writer writer, boolean writeMetaComments)
NexusExporter(java.io.Writer writer, boolean writeMetaComments, boolean interleave)
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description void
close()
void
closeBlock()
close an existing open trees blockvoid
exportAlignment(Alignment alignment)
exportAlignment.void
exportMatrix(DistanceMatrix distanceMatrix)
void
exportSequences(java.util.Collection<? extends Sequence> sequences)
export alignment.void
exportTree(Tree tree)
Export a single treevoid
exportTrees(java.util.Collection<? extends Tree> trees)
Export a collection of treesvoid
exportTrees(java.util.Collection<? extends Tree> trees, boolean writeTaxa)
void
exportTreesWithTranslation(java.util.Collection<? extends Tree> trees, java.util.Map<java.lang.String,java.lang.String> translationMap)
static boolean
isGeneratedTreeName(java.lang.String name)
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Field Detail
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treeNameAttributeKey
public static final java.lang.String treeNameAttributeKey
- See Also:
- Constant Field Values
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exportExcludeKeys
public static final java.lang.String[] exportExcludeKeys
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MAX_ROW_LENGTH
public static final int MAX_ROW_LENGTH
- See Also:
- Constant Field Values
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Constructor Detail
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NexusExporter
public NexusExporter(java.io.Writer writer)
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NexusExporter
public NexusExporter(java.io.Writer writer, boolean writeMetaComments)
- Parameters:
writer
- where export text goes
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NexusExporter
public NexusExporter(java.io.Writer writer, boolean writeMetaComments, boolean interleave)
- Parameters:
writer
- where export text goes
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Method Detail
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exportAlignment
public void exportAlignment(Alignment alignment)
exportAlignment.- Specified by:
exportAlignment
in interfaceAlignmentExporter
- Parameters:
alignment
- to export
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exportSequences
public void exportSequences(java.util.Collection<? extends Sequence> sequences) throws java.lang.IllegalArgumentException
export alignment.- Specified by:
exportSequences
in interfaceSequenceExporter
- Throws:
java.lang.IllegalArgumentException
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closeBlock
public void closeBlock()
close an existing open trees block
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exportTree
public void exportTree(Tree tree)
Export a single tree- Specified by:
exportTree
in interfaceTreeExporter
- Parameters:
tree
-- Throws:
java.io.IOException
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exportTrees
public void exportTrees(java.util.Collection<? extends Tree> trees)
Description copied from interface:TreeExporter
Export a collection of trees- Specified by:
exportTrees
in interfaceTreeExporter
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exportTrees
public void exportTrees(java.util.Collection<? extends Tree> trees, boolean writeTaxa)
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exportTreesWithTranslation
public void exportTreesWithTranslation(java.util.Collection<? extends Tree> trees, java.util.Map<java.lang.String,java.lang.String> translationMap) throws java.io.IOException
- Throws:
java.io.IOException
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close
public void close()
- Specified by:
close
in interfaceTreeExporter
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exportMatrix
public void exportMatrix(DistanceMatrix distanceMatrix)
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isGeneratedTreeName
public static boolean isGeneratedTreeName(java.lang.String name)
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