org.forester.io.writers

Class PhylogenyWriter

java.lang.Object

org.forester.io.writers.PhylogenyWriter

public final class PhylogenyWriter
extends Object

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	PhylogenyWriter.FORMAT

Field Summary

Fields

Modifier and Type	Field and Description
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

Constructors

Constructor and Description
PhylogenyWriter()

Method Summary

Modifier and Type	Method and Description
static PhylogenyWriter	createPhylogenyWriter()
void	setIndentPhyloxml(boolean indent_phyloxml)
void	toNewHampshire(List<Phylogeny> trees, boolean write_distance_to_parent, File out_file, String separator)
void	toNewHampshire(Phylogeny[] trees, boolean write_distance_to_parent, File out_file, String separator)
StringBuffer	toNewHampshire(Phylogeny tree, boolean nh_write_distance_to_parent)
void	toNewHampshire(Phylogeny tree, boolean write_distance_to_parent, File out_file)
StringBuffer	toNewHampshire(Phylogeny tree, boolean nh_write_distance_to_parent, PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE svs)
void	toNewHampshire(Phylogeny tree, boolean write_distance_to_parent, PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE svs, 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, Phylogeny tree, PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE svs)
StringBuffer	toNexus(Phylogeny tree, PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE svs)
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(Phylogeny phy, int phyloxml_level, File out_file)
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, PhylogenyNode.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 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 write_distance_to_parent,
                           File out_file,
                           String separator)
                    throws IOException

Throws:

IOException

toNewHampshire

public StringBuffer toNewHampshire(Phylogeny tree,
                                   boolean nh_write_distance_to_parent,
                                   PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE svs)
                            throws IOException

Throws:

IOException

toNewHampshire

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

Throws:

IOException

toNewHampshire

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

Throws:

IOException

toNewHampshire

public void toNewHampshire(Phylogeny tree,
                           boolean write_distance_to_parent,
                           PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE svs,
                           File out_file)
                    throws IOException

Throws:

IOException

toNewHampshire

public void toNewHampshire(Phylogeny[] trees,
                           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,
                    Phylogeny tree,
                    PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE svs)
             throws IOException

Throws:

IOException

toNexus

public StringBuffer toNexus(Phylogeny tree,
                            PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE svs)
                     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(Phylogeny phy,
                       int phyloxml_level,
                       File out_file)
                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,
                                        PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE svs)
                                 throws IOException

Throws:

IOException