AlignmentExporter
, SequenceExporter
, TreeExporter
public class NexusExporter extends java.lang.Object implements AlignmentExporter, SequenceExporter, TreeExporter
Modifier and Type | Field | Description |
---|---|---|
static java.lang.String[] |
exportExcludeKeys |
|
static int |
MAX_ROW_LENGTH |
|
static java.lang.String |
treeNameAttributeKey |
Constructor | Description |
---|---|
NexusExporter(java.io.Writer writer) |
|
NexusExporter(java.io.Writer writer,
boolean writeMetaComments) |
|
NexusExporter(java.io.Writer writer,
boolean writeMetaComments,
boolean interleave) |
Modifier and Type | Method | Description |
---|---|---|
void |
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 tree
|
void |
exportTrees(java.util.Collection<? extends Tree> trees) |
Export a collection of trees
|
void |
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> t) |
|
static boolean |
isGeneratedTreeName(java.lang.String name) |
|
static double |
roundDouble(double value,
int decimalPlace) |
public static final java.lang.String treeNameAttributeKey
public static final java.lang.String[] exportExcludeKeys
public static final int MAX_ROW_LENGTH
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 goespublic void exportAlignment(Alignment alignment) throws java.io.IOException
exportAlignment
in interface AlignmentExporter
alignment
- to exportjava.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 exportTrees(java.util.Collection<? extends Tree> trees, boolean writeTaxa) throws java.io.IOException
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)
http://code.google.com/p/jebl2/