org.forester.io.writers
Class PhylogenyWriter

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

public final class PhylogenyWriter
extends java.lang.Object

Nested Class Summary

static class

PhylogenyWriter.FORMAT

Field Summary

static boolean	INDENT_PHYLOXML_DEAFULT
static java.lang.String	PHYLO_XML_END
static java.lang.String	PHYLO_XML_INTENDATION_BASE
static java.lang.String	PHYLO_XML_NAMESPACE_LINE
static java.lang.String	PHYLO_XML_VERSION_ENCODING_LINE

Constructor Summary

PhylogenyWriter()

Method Summary

static PhylogenyWriter	createPhylogenyWriter()
void	setIndentPhyloxml(boolean indent_phyloxml)
void	toNewHampshire(java.util.List<Phylogeny> trees, boolean simple_nh, boolean write_distance_to_parent, java.io.File out_file, java.lang.String separator)
void	toNewHampshire(Phylogeny[] trees, boolean simple_nh, boolean write_distance_to_parent, java.io.File out_file, java.lang.String separator)
java.lang.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, java.io.File out_file)
java.lang.StringBuffer	toNewHampshire(Phylogeny tree, boolean simple_nh, boolean nh_write_distance_to_parent, PhylogenyNodeI.NH_CONVERSION_SUPPORT_VALUE_STYLE svs)
void	toNewHampshire(Phylogeny tree, boolean simple_nh, boolean write_distance_to_parent, PhylogenyNodeI.NH_CONVERSION_SUPPORT_VALUE_STYLE svs, java.io.File out_file)
void	toNewHampshireX(java.util.List<Phylogeny> trees, java.io.File out_file, java.lang.String separator)
java.lang.StringBuffer	toNewHampshireX(Phylogeny tree)
void	toNewHampshireX(Phylogeny[] trees, java.io.File out_file, java.lang.String separator)
void	toNewHampshireX(Phylogeny tree, java.io.File out_file)
void	toNexus(java.io.File out_file, Phylogeny tree, PhylogenyNodeI.NH_CONVERSION_SUPPORT_VALUE_STYLE svs)
java.lang.StringBuffer	toNexus(Phylogeny tree, PhylogenyNodeI.NH_CONVERSION_SUPPORT_VALUE_STYLE svs)
void	toPhyloXML(java.io.File out_file, java.util.List<Phylogeny> trees, int phyloxml_level, java.lang.String separator)
void	toPhyloXML(java.io.File out_file, Phylogeny tree, int phyloxml_level)
void	toPhyloXML(Phylogeny[] trees, int phyloxml_level, java.io.File out_file, java.lang.String separator)
java.lang.StringBuffer	toPhyloXML(Phylogeny tree, int phyloxml_level)
void	toPhyloXML(Phylogeny phy, int phyloxml_level, java.io.File out_file)
void	toPhyloXML(java.io.Writer writer, java.util.List<Phylogeny> trees, int phyloxml_level, java.lang.String separator)
void	toPhyloXML(java.io.Writer writer, Phylogeny[] trees, int phyloxml_level, java.lang.String separator)
void	toPhyloXML(java.io.Writer writer, Phylogeny tree, int phyloxml_level)
static void	writeNexusTaxaBlock(java.io.Writer writer, Phylogeny tree)
static void	writeNexusTreesBlock(java.io.Writer writer, java.util.List<Phylogeny> trees, PhylogenyNodeI.NH_CONVERSION_SUPPORT_VALUE_STYLE svs)

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 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 simple_nh,
                           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 simple_nh,
                                             boolean nh_write_distance_to_parent,
                                             PhylogenyNodeI.NH_CONVERSION_SUPPORT_VALUE_STYLE svs)
                                      throws java.io.IOException

Throws:

java.io.IOException

toNewHampshire

public java.lang.StringBuffer toNewHampshire(Phylogeny tree,
                                             boolean simple_nh,
                                             boolean nh_write_distance_to_parent)
                                      throws java.io.IOException

Throws:

java.io.IOException

toNewHampshire

public void toNewHampshire(Phylogeny tree,
                           boolean simple_nh,
                           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 simple_nh,
                           boolean write_distance_to_parent,
                           PhylogenyNodeI.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 simple_nh,
                           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,
                    PhylogenyNodeI.NH_CONVERSION_SUPPORT_VALUE_STYLE svs)
             throws java.io.IOException

Throws:

java.io.IOException

toNexus

public java.lang.StringBuffer toNexus(Phylogeny tree,
                                      PhylogenyNodeI.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,
                                        PhylogenyNodeI.NH_CONVERSION_SUPPORT_VALUE_STYLE svs)
                                 throws java.io.IOException

Throws:

java.io.IOException