Field Detail

• treeNameAttributeKey

  public static final java.lang.String treeNameAttributeKey

  See Also:

  Constant Field Values

• exportExcludeKeys

  public static final java.lang.String[] exportExcludeKeys

• MAX_ROW_LENGTH

  public static final int MAX_ROW_LENGTH

  See Also:

  Constant Field Values

Constructor Detail

• NexusExporter

  public NexusExporter​(java.io.Writer writer)

• NexusExporter

  public NexusExporter​(java.io.Writer writer,
                       boolean writeMetaComments)

  Parameters:

  writer - where export text goes

• NexusExporter

  public NexusExporter​(java.io.Writer writer,
                       boolean writeMetaComments,
                       boolean interleave)

  Parameters:

  writer - where export text goes

Method Detail

• exportAlignment

  public void exportAlignment​(Alignment alignment)

  exportAlignment.

  Specified by:

  exportAlignment in interface AlignmentExporter

  Parameters:

  alignment - to export

• exportSequences

  public void exportSequences​(java.util.Collection<? extends Sequence> sequences)
                       throws java.lang.IllegalArgumentException

  export alignment.

  Specified by:

  exportSequences in interface SequenceExporter

  Throws:

  java.lang.IllegalArgumentException

• exportTree

  public void exportTree​(Tree tree)

  Export a single tree

  Specified by:

  exportTree in interface TreeExporter

  Parameters:

  tree -

  Throws:

  java.io.IOException

• exportTrees

  public void exportTrees​(java.util.Collection<? extends Tree> trees)

  Description copied from interface: TreeExporter
  Export a collection of trees

  Specified by:

  exportTrees in interface TreeExporter

• exportTrees

  public void exportTrees​(java.util.Collection<? extends Tree> trees,
                          boolean writeTaxa)

• 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

• close

  public void close()

  Specified by:

  close in interface TreeExporter

• exportMatrix

  public void exportMatrix​(DistanceMatrix distanceMatrix)

• roundDouble

  public static double roundDouble​(double value,
                                   int decimalPlace)

• isGeneratedTreeName

  public static boolean isGeneratedTreeName​(java.lang.String name)