Package jebl.evolution.io
Class NexusExporter
java.lang.Object
jebl.evolution.io.NexusExporter
- All Implemented Interfaces:
AlignmentExporter
,SequenceExporter
,TreeExporter
public class NexusExporter
extends 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
-
Field Summary
Fields -
Constructor Summary
ConstructorsConstructorDescriptionNexusExporter
(Writer writer) NexusExporter
(Writer writer, boolean writeMetaComments) NexusExporter
(Writer writer, boolean writeMetaComments, boolean interleave) -
Method Summary
Modifier and TypeMethodDescriptionvoid
close()
void
close an existing open trees blockvoid
exportAlignment
(Alignment alignment) exportAlignment.void
exportMatrix
(DistanceMatrix distanceMatrix) void
exportSequences
(Collection<? extends Sequence> sequences) export alignment.void
exportTree
(Tree tree) Export a single treevoid
exportTrees
(Collection<? extends Tree> trees) Export a collection of treesvoid
exportTrees
(Collection<? extends Tree> trees, boolean writeTaxa) void
exportTreesWithTranslation
(Collection<? extends Tree> trees, Map<String, String> translationMap) static boolean
isGeneratedTreeName
(String name)
-
Field Details
-
treeNameAttributeKey
- See Also:
-
exportExcludeKeys
-
MAX_ROW_LENGTH
public static final int MAX_ROW_LENGTH- See Also:
-
-
Constructor Details
-
NexusExporter
-
NexusExporter
- Parameters:
writer
- where export text goes
-
NexusExporter
- Parameters:
writer
- where export text goes
-
-
Method Details
-
exportAlignment
exportAlignment.- Specified by:
exportAlignment
in interfaceAlignmentExporter
- Parameters:
alignment
- to export
-
exportSequences
public void exportSequences(Collection<? extends Sequence> sequences) throws IllegalArgumentException export alignment.- Specified by:
exportSequences
in interfaceSequenceExporter
- Throws:
IllegalArgumentException
-
closeBlock
public void closeBlock()close an existing open trees block -
exportTree
Export a single tree- Specified by:
exportTree
in interfaceTreeExporter
- Parameters:
tree
-- Throws:
IOException
-
exportTrees
Description copied from interface:TreeExporter
Export a collection of trees- Specified by:
exportTrees
in interfaceTreeExporter
- Parameters:
trees
-
-
exportTrees
-
exportTreesWithTranslation
public void exportTreesWithTranslation(Collection<? extends Tree> trees, Map<String, String> translationMap) throws IOException- Throws:
IOException
-
close
public void close()- Specified by:
close
in interfaceTreeExporter
-
exportMatrix
-
isGeneratedTreeName
-