Class PhylogenyWriter


  • public final class PhylogenyWriter
    extends java.lang.Object
    • Field Detail

      • INDENT_PHYLOXML_DEAFULT

        public static final boolean INDENT_PHYLOXML_DEAFULT
        See Also:
        Constant Field Values
      • PHYLO_XML_INTENDATION_BASE

        public static final java.lang.String PHYLO_XML_INTENDATION_BASE
        See Also:
        Constant Field Values
      • PHYLO_XML_VERSION_ENCODING_LINE

        public static final java.lang.String PHYLO_XML_VERSION_ENCODING_LINE
        See Also:
        Constant Field Values
      • PHYLO_XML_NAMESPACE_LINE

        public static final java.lang.String PHYLO_XML_NAMESPACE_LINE
        See Also:
        Constant Field Values
    • Constructor Detail

      • PhylogenyWriter

        public PhylogenyWriter()
    • Method Detail

      • setIndentPhyloxml

        public void setIndentPhyloxml​(boolean indent_phyloxml)
      • toNewHampshire

        public void toNewHampshire​(java.util.List<Phylogeny> trees,
                                   boolean write_distance_to_parent,
                                   java.io.File out_file,
                                   java.lang.String separator)
                            throws java.io.IOException
        Throws:
        java.io.IOException
      • toNewHampshire

        public java.lang.StringBuffer toNewHampshire​(Phylogeny tree,
                                                     boolean nh_write_distance_to_parent)
                                              throws java.io.IOException
        Throws:
        java.io.IOException
      • toNewHampshire

        public void toNewHampshire​(Phylogeny tree,
                                   boolean write_distance_to_parent,
                                   java.io.File out_file)
                            throws java.io.IOException
        Throws:
        java.io.IOException
      • toNewHampshire

        public void toNewHampshire​(Phylogeny[] trees,
                                   boolean write_distance_to_parent,
                                   java.io.File out_file,
                                   java.lang.String separator)
                            throws java.io.IOException
        Throws:
        java.io.IOException
      • toNewHampshireX

        public void toNewHampshireX​(java.util.List<Phylogeny> trees,
                                    java.io.File out_file,
                                    java.lang.String separator)
                             throws java.io.IOException
        Throws:
        java.io.IOException
      • toNewHampshireX

        public java.lang.StringBuffer toNewHampshireX​(Phylogeny tree)
                                               throws java.io.IOException
        Throws:
        java.io.IOException
      • toNewHampshireX

        public void toNewHampshireX​(Phylogeny tree,
                                    java.io.File out_file)
                             throws java.io.IOException
        Throws:
        java.io.IOException
      • toNewHampshireX

        public void toNewHampshireX​(Phylogeny[] trees,
                                    java.io.File out_file,
                                    java.lang.String separator)
                             throws java.io.IOException
        Throws:
        java.io.IOException
      • toPhyloXML

        public void toPhyloXML​(java.io.File out_file,
                               java.util.List<Phylogeny> trees,
                               int phyloxml_level,
                               java.lang.String separator)
                        throws java.io.IOException
        Throws:
        java.io.IOException
      • toPhyloXML

        public void toPhyloXML​(java.io.File out_file,
                               Phylogeny tree,
                               int phyloxml_level)
                        throws java.io.IOException
        Throws:
        java.io.IOException
      • toPhyloXML

        public java.lang.StringBuffer toPhyloXML​(Phylogeny tree,
                                                 int phyloxml_level)
                                          throws java.io.IOException
        Throws:
        java.io.IOException
      • toPhyloXML

        public void toPhyloXML​(Phylogeny[] trees,
                               int phyloxml_level,
                               java.io.File out_file,
                               java.lang.String separator)
                        throws java.io.IOException
        Throws:
        java.io.IOException
      • toPhyloXML

        public void toPhyloXML​(Phylogeny phy,
                               int phyloxml_level,
                               java.io.File out_file)
                        throws java.io.IOException
        Throws:
        java.io.IOException
      • toPhyloXML

        public void toPhyloXML​(java.io.Writer writer,
                               java.util.List<Phylogeny> trees,
                               int phyloxml_level,
                               java.lang.String separator)
                        throws java.io.IOException
        Throws:
        java.io.IOException
      • toPhyloXML

        public void toPhyloXML​(java.io.Writer writer,
                               Phylogeny tree,
                               int phyloxml_level)
                        throws java.io.IOException
        Throws:
        java.io.IOException
      • toPhyloXML

        public void toPhyloXML​(java.io.Writer writer,
                               Phylogeny[] trees,
                               int phyloxml_level,
                               java.lang.String separator)
                        throws java.io.IOException
        Throws:
        java.io.IOException
      • createPhylogenyWriter

        public static PhylogenyWriter createPhylogenyWriter()
      • writeNexusTaxaBlock

        public static void writeNexusTaxaBlock​(java.io.Writer writer,
                                               Phylogeny tree)
                                        throws java.io.IOException
        Throws:
        java.io.IOException