org.forester.io.writers
Class PhylogenyWriter
java.lang.Object
org.forester.io.writers.PhylogenyWriter
public final class PhylogenyWriter
- extends Object
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 |
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
PhylogenyWriter
public PhylogenyWriter()
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