public final class PhylogenyWriter
extends java.lang.Object
Modifier and Type | Class and Description |
---|---|
static class |
PhylogenyWriter.FORMAT |
Modifier and Type | Field and Description |
---|---|
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 and Description |
---|
PhylogenyWriter() |
Modifier and Type | Method and Description |
---|---|
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) |
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,
java.util.List<Phylogeny> trees) |
void |
toNexus(java.io.File out_file,
Phylogeny tree) |
java.lang.StringBuffer |
toNexus(Phylogeny tree) |
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(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) |
public static final boolean INDENT_PHYLOXML_DEAFULT
public static final java.lang.String PHYLO_XML_INTENDATION_BASE
public static final java.lang.String PHYLO_XML_VERSION_ENCODING_LINE
public static final java.lang.String PHYLO_XML_NAMESPACE_LINE
public static final java.lang.String PHYLO_XML_END
public void setIndentPhyloxml(boolean indent_phyloxml)
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
java.io.IOException
public java.lang.StringBuffer toNewHampshire(Phylogeny tree, boolean simple_nh, boolean nh_write_distance_to_parent) throws java.io.IOException
java.io.IOException
public void toNewHampshire(Phylogeny tree, boolean simple_nh, boolean write_distance_to_parent, java.io.File out_file) throws java.io.IOException
java.io.IOException
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
java.io.IOException
public void toNewHampshireX(java.util.List<Phylogeny> trees, java.io.File out_file, java.lang.String separator) throws java.io.IOException
java.io.IOException
public java.lang.StringBuffer toNewHampshireX(Phylogeny tree) throws java.io.IOException
java.io.IOException
public void toNewHampshireX(Phylogeny tree, java.io.File out_file) throws java.io.IOException
java.io.IOException
public void toNewHampshireX(Phylogeny[] trees, java.io.File out_file, java.lang.String separator) throws java.io.IOException
java.io.IOException
public void toNexus(java.io.File out_file, java.util.List<Phylogeny> trees) throws java.io.IOException
java.io.IOException
public void toNexus(java.io.File out_file, Phylogeny tree) throws java.io.IOException
java.io.IOException
public java.lang.StringBuffer toNexus(Phylogeny tree) throws java.io.IOException
java.io.IOException
public void toPhyloXML(java.io.File out_file, java.util.List<Phylogeny> trees, int phyloxml_level, java.lang.String separator) throws java.io.IOException
java.io.IOException
public void toPhyloXML(java.io.File out_file, Phylogeny tree, int phyloxml_level) throws java.io.IOException
java.io.IOException
public java.lang.StringBuffer toPhyloXML(Phylogeny tree, int phyloxml_level) throws java.io.IOException
java.io.IOException
public void toPhyloXML(Phylogeny[] trees, int phyloxml_level, java.io.File out_file, java.lang.String separator) throws java.io.IOException
java.io.IOException
public void toPhyloXML(java.io.Writer writer, java.util.List<Phylogeny> trees, int phyloxml_level, java.lang.String separator) throws java.io.IOException
java.io.IOException
public void toPhyloXML(java.io.Writer writer, Phylogeny tree, int phyloxml_level) throws java.io.IOException
java.io.IOException
public void toPhyloXML(java.io.Writer writer, Phylogeny[] trees, int phyloxml_level, java.lang.String separator) throws java.io.IOException
java.io.IOException
public static PhylogenyWriter createPhylogenyWriter()
public static void writeNexusTaxaBlock(java.io.Writer writer, Phylogeny tree) throws java.io.IOException
java.io.IOException
public static void writeNexusTreesBlock(java.io.Writer writer, java.util.List<Phylogeny> trees) throws java.io.IOException
java.io.IOException