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

• PHYLO_XML_END

  public static final java.lang.String PHYLO_XML_END

  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,
                                               PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE svs)
                                        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 tree,
                             boolean write_distance_to_parent,
                             PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE svs,
                             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

• toNexus

  public void toNexus​(java.io.File out_file,
                      Phylogeny tree,
                      PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE svs)
               throws java.io.IOException

  Throws:

  java.io.IOException

• toNexus

  public java.lang.StringBuffer toNexus​(Phylogeny tree,
                                        PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE svs)
                                 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

• writeNexusTreesBlock

  public static void writeNexusTreesBlock​(java.io.Writer writer,
                                          java.util.List<Phylogeny> trees,
                                          PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE svs)
                                   throws java.io.IOException

  Throws:

  java.io.IOException