Class NexusExporter

    • Field Detail

      • treeNameAttributeKey

        public static final java.lang.String treeNameAttributeKey
        See Also:
        Constant Field Values
      • exportExcludeKeys

        public static final java.lang.String[] exportExcludeKeys
    • 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

      • 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
      • exportMatrix

        public void exportMatrix​(DistanceMatrix distanceMatrix)
      • roundDouble

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

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