org.forester.io.writers
Class PhylogenyWriter

java.lang.Object
  extended by org.forester.io.writers.PhylogenyWriter

public final class PhylogenyWriter
extends Object


Nested Class Summary
static class PhylogenyWriter.FORMAT
           
 
Field Summary
static boolean INDENT_PHYLOXML_DEAFULT
           
static String PHYLO_XML_END
           
static String PHYLO_XML_INTENDATION_BASE
           
static String PHYLO_XML_NAMESPACE_LINE
           
static String PHYLO_XML_VERSION_ENCODING_LINE
           
 
Constructor Summary
PhylogenyWriter()
           
 
Method Summary
static PhylogenyWriter createPhylogenyWriter()
           
 void setIndentPhyloxml(boolean indent_phyloxml)
           
 void toNewHampshire(List<Phylogeny> trees, boolean simple_nh, boolean write_distance_to_parent, File out_file, String separator)
           
 void toNewHampshire(Phylogeny[] trees, boolean simple_nh, boolean write_distance_to_parent, File out_file, String separator)
           
 StringBuffer toNewHampshire(Phylogeny tree, boolean simple_nh, boolean nh_write_distance_to_parent)
           
 void toNewHampshire(Phylogeny tree, boolean simple_nh, boolean write_distance_to_parent, File out_file)
           
 void toNewHampshireX(List<Phylogeny> trees, File out_file, String separator)
           
 StringBuffer toNewHampshireX(Phylogeny tree)
           
 void toNewHampshireX(Phylogeny[] trees, File out_file, String separator)
           
 void toNewHampshireX(Phylogeny tree, File out_file)
           
 void toNexus(File out_file, List<Phylogeny> trees)
           
 void toNexus(File out_file, Phylogeny tree)
           
 StringBuffer toNexus(Phylogeny tree)
           
 void toPhyloXML(File out_file, List<Phylogeny> trees, int phyloxml_level, String separator)
           
 void toPhyloXML(File out_file, Phylogeny tree, int phyloxml_level)
           
 void toPhyloXML(Phylogeny[] trees, int phyloxml_level, File out_file, String separator)
           
 StringBuffer toPhyloXML(Phylogeny tree, int phyloxml_level)
           
 void toPhyloXML(Writer writer, List<Phylogeny> trees, int phyloxml_level, String separator)
           
 void toPhyloXML(Writer writer, Phylogeny[] trees, int phyloxml_level, String separator)
           
 void toPhyloXML(Writer writer, Phylogeny tree, int phyloxml_level)
           
static void writeNexusTaxaBlock(Writer writer, Phylogeny tree)
           
static void writeNexusTreesBlock(Writer writer, List<Phylogeny> trees)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

INDENT_PHYLOXML_DEAFULT

public static final boolean INDENT_PHYLOXML_DEAFULT
See Also:
Constant Field Values

PHYLO_XML_INTENDATION_BASE

public static final String PHYLO_XML_INTENDATION_BASE
See Also:
Constant Field Values

PHYLO_XML_VERSION_ENCODING_LINE

public static final String PHYLO_XML_VERSION_ENCODING_LINE
See Also:
Constant Field Values

PHYLO_XML_NAMESPACE_LINE

public static final String PHYLO_XML_NAMESPACE_LINE
See Also:
Constant Field Values

PHYLO_XML_END

public static final 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(List<Phylogeny> trees,
                           boolean simple_nh,
                           boolean write_distance_to_parent,
                           File out_file,
                           String separator)
                    throws IOException
Throws:
IOException

toNewHampshire

public StringBuffer toNewHampshire(Phylogeny tree,
                                   boolean simple_nh,
                                   boolean nh_write_distance_to_parent)
                            throws IOException
Throws:
IOException

toNewHampshire

public void toNewHampshire(Phylogeny tree,
                           boolean simple_nh,
                           boolean write_distance_to_parent,
                           File out_file)
                    throws IOException
Throws:
IOException

toNewHampshire

public void toNewHampshire(Phylogeny[] trees,
                           boolean simple_nh,
                           boolean write_distance_to_parent,
                           File out_file,
                           String separator)
                    throws IOException
Throws:
IOException

toNewHampshireX

public void toNewHampshireX(List<Phylogeny> trees,
                            File out_file,
                            String separator)
                     throws IOException
Throws:
IOException

toNewHampshireX

public StringBuffer toNewHampshireX(Phylogeny tree)
                             throws IOException
Throws:
IOException

toNewHampshireX

public void toNewHampshireX(Phylogeny tree,
                            File out_file)
                     throws IOException
Throws:
IOException

toNewHampshireX

public void toNewHampshireX(Phylogeny[] trees,
                            File out_file,
                            String separator)
                     throws IOException
Throws:
IOException

toNexus

public void toNexus(File out_file,
                    List<Phylogeny> trees)
             throws IOException
Throws:
IOException

toNexus

public void toNexus(File out_file,
                    Phylogeny tree)
             throws IOException
Throws:
IOException

toNexus

public StringBuffer toNexus(Phylogeny tree)
                     throws IOException
Throws:
IOException

toPhyloXML

public void toPhyloXML(File out_file,
                       List<Phylogeny> trees,
                       int phyloxml_level,
                       String separator)
                throws IOException
Throws:
IOException

toPhyloXML

public void toPhyloXML(File out_file,
                       Phylogeny tree,
                       int phyloxml_level)
                throws IOException
Throws:
IOException

toPhyloXML

public StringBuffer toPhyloXML(Phylogeny tree,
                               int phyloxml_level)
                        throws IOException
Throws:
IOException

toPhyloXML

public void toPhyloXML(Phylogeny[] trees,
                       int phyloxml_level,
                       File out_file,
                       String separator)
                throws IOException
Throws:
IOException

toPhyloXML

public void toPhyloXML(Writer writer,
                       List<Phylogeny> trees,
                       int phyloxml_level,
                       String separator)
                throws IOException
Throws:
IOException

toPhyloXML

public void toPhyloXML(Writer writer,
                       Phylogeny tree,
                       int phyloxml_level)
                throws IOException
Throws:
IOException

toPhyloXML

public void toPhyloXML(Writer writer,
                       Phylogeny[] trees,
                       int phyloxml_level,
                       String separator)
                throws IOException
Throws:
IOException

createPhylogenyWriter

public static PhylogenyWriter createPhylogenyWriter()

writeNexusTaxaBlock

public static void writeNexusTaxaBlock(Writer writer,
                                       Phylogeny tree)
                                throws IOException
Throws:
IOException

writeNexusTreesBlock

public static void writeNexusTreesBlock(Writer writer,
                                        List<Phylogeny> trees)
                                 throws IOException
Throws:
IOException