java.lang.Object

org.forester.io.writers.PhylogenyWriter

public final class PhylogenyWriter extends Object

Nested Class Summary

Nested Classes

Modifier and Type

Class

Description

static enum

PhylogenyWriter.FORMAT
Field Summary

Fields

Modifier and Type

Field

Description

static final boolean

INDENT_PHYLOXML_DEAFULT

static final String

PHYLO_XML_END

static final String

PHYLO_XML_INTENDATION_BASE

static final String

PHYLO_XML_NAMESPACE_LINE

static final String

PHYLO_XML_VERSION_ENCODING_LINE
Constructor Summary

Constructors

Constructor

Description

PhylogenyWriter()
Method Summary

Modifier and Type

Method

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(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)

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)

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 Details
- 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 Details
- PhylogenyWriter
  
  public PhylogenyWriter()
Method Details
- 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

Class PhylogenyWriter

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Details

INDENT_PHYLOXML_DEAFULT

PHYLO_XML_INTENDATION_BASE

PHYLO_XML_VERSION_ENCODING_LINE

PHYLO_XML_NAMESPACE_LINE

PHYLO_XML_END

Constructor Details

PhylogenyWriter

Method Details

setIndentPhyloxml

toNewHampshire

toNewHampshire

toNewHampshire

toNewHampshire

toNewHampshire

toNewHampshire

toNewHampshireX

toNewHampshireX

toNewHampshireX

toNewHampshireX

toNexus

toNexus

toPhyloXML

toPhyloXML

toPhyloXML

toPhyloXML

toPhyloXML

toPhyloXML

toPhyloXML

toPhyloXML

createPhylogenyWriter

writeNexusTaxaBlock

writeNexusTreesBlock