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java.lang.Objectjebl.evolution.io.NexusExporter
public class NexusExporter
Export sequences and trees to Nexus format.
Field Summary | |
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static java.lang.String[] |
exportExcludeKeys
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static int |
MAX_ROW_LENGTH
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static java.lang.String |
treeNameAttributeKey
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Constructor Summary | |
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NexusExporter(java.io.Writer writer)
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NexusExporter(java.io.Writer writer,
boolean writeMetaComments)
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NexusExporter(java.io.Writer writer,
boolean writeMetaComments,
boolean interleave)
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Method Summary | |
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void |
exportAlignment(Alignment alignment)
exportAlignment. |
void |
exportMatrix(DistanceMatrix distanceMatrix)
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void |
exportSequences(java.util.Collection<? extends Sequence> sequences)
export alignment. |
void |
exportTree(Tree tree)
Export a single tree |
void |
exportTrees(java.util.Collection<? extends Tree> trees)
Export a collection of trees |
void |
exportTreesWithTranslation(java.util.Collection<? extends Tree> trees,
java.util.Map<java.lang.String,java.lang.String> t)
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static boolean |
isGeneratedTreeName(java.lang.String name)
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static double |
roundDouble(double value,
int decimalPlace)
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Methods inherited from class java.lang.Object |
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equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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public static final java.lang.String treeNameAttributeKey
public static final java.lang.String[] exportExcludeKeys
public static final int MAX_ROW_LENGTH
Constructor Detail |
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public NexusExporter(java.io.Writer writer)
public NexusExporter(java.io.Writer writer, boolean writeMetaComments)
writer
- where export text goespublic NexusExporter(java.io.Writer writer, boolean writeMetaComments, boolean interleave)
writer
- where export text goesMethod Detail |
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public void exportAlignment(Alignment alignment) throws java.io.IOException
exportAlignment
in interface AlignmentExporter
alignment
- to export
java.io.IOException
public void exportSequences(java.util.Collection<? extends Sequence> sequences) throws java.io.IOException, java.lang.IllegalArgumentException
exportSequences
in interface SequenceExporter
java.io.IOException
java.lang.IllegalArgumentException
public void exportTree(Tree tree) throws java.io.IOException
exportTree
in interface TreeExporter
tree
-
java.io.IOException
public void exportTrees(java.util.Collection<? extends Tree> trees) throws java.io.IOException
TreeExporter
exportTrees
in interface TreeExporter
java.io.IOException
public void exportTreesWithTranslation(java.util.Collection<? extends Tree> trees, java.util.Map<java.lang.String,java.lang.String> t) throws java.io.IOException
java.io.IOException
public void exportMatrix(DistanceMatrix distanceMatrix)
public static double roundDouble(double value, int decimalPlace)
public static boolean isGeneratedTreeName(java.lang.String name)
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