Package org.forester.io.writers
Class PhylogenyWriter
- java.lang.Object
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- org.forester.io.writers.PhylogenyWriter
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public final class PhylogenyWriter extends java.lang.Object
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
PhylogenyWriter.FORMAT
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Field Summary
Fields Modifier and Type Field 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
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Constructor Summary
Constructors Constructor Description PhylogenyWriter()
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description static PhylogenyWriter
createPhylogenyWriter()
void
setIndentPhyloxml(boolean indent_phyloxml)
void
toNewHampshire(java.util.List<Phylogeny> trees, boolean write_distance_to_parent, java.io.File out_file, java.lang.String separator)
void
toNewHampshire(Phylogeny[] trees, boolean write_distance_to_parent, java.io.File out_file, java.lang.String separator)
java.lang.StringBuffer
toNewHampshire(Phylogeny tree, boolean nh_write_distance_to_parent)
void
toNewHampshire(Phylogeny tree, boolean write_distance_to_parent, java.io.File out_file)
java.lang.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, 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, PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE svs)
java.lang.StringBuffer
toNexus(Phylogeny tree, PhylogenyNode.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(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)
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)
static void
writeNexusTaxaBlock(java.io.Writer writer, Phylogeny tree)
static void
writeNexusTreesBlock(java.io.Writer writer, java.util.List<Phylogeny> trees, PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE svs)
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Field Detail
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INDENT_PHYLOXML_DEAFULT
public static final boolean INDENT_PHYLOXML_DEAFULT
- See Also:
- Constant Field Values
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PHYLO_XML_INTENDATION_BASE
public static final java.lang.String PHYLO_XML_INTENDATION_BASE
- See Also:
- Constant Field Values
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PHYLO_XML_VERSION_ENCODING_LINE
public static final java.lang.String PHYLO_XML_VERSION_ENCODING_LINE
- See Also:
- Constant Field Values
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PHYLO_XML_NAMESPACE_LINE
public static final java.lang.String PHYLO_XML_NAMESPACE_LINE
- See Also:
- Constant Field Values
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PHYLO_XML_END
public static final java.lang.String PHYLO_XML_END
- See Also:
- Constant Field Values
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Method Detail
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setIndentPhyloxml
public void setIndentPhyloxml(boolean indent_phyloxml)
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toNewHampshire
public void toNewHampshire(java.util.List<Phylogeny> trees, boolean write_distance_to_parent, java.io.File out_file, java.lang.String separator) throws java.io.IOException
- Throws:
java.io.IOException
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toNewHampshire
public java.lang.StringBuffer toNewHampshire(Phylogeny tree, boolean nh_write_distance_to_parent, PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE svs) throws java.io.IOException
- Throws:
java.io.IOException
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toNewHampshire
public java.lang.StringBuffer toNewHampshire(Phylogeny tree, boolean nh_write_distance_to_parent) throws java.io.IOException
- Throws:
java.io.IOException
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toNewHampshire
public void toNewHampshire(Phylogeny tree, boolean write_distance_to_parent, java.io.File out_file) throws java.io.IOException
- Throws:
java.io.IOException
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toNewHampshire
public void toNewHampshire(Phylogeny tree, boolean write_distance_to_parent, PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE svs, java.io.File out_file) throws java.io.IOException
- Throws:
java.io.IOException
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toNewHampshire
public void toNewHampshire(Phylogeny[] trees, boolean write_distance_to_parent, java.io.File out_file, java.lang.String separator) throws java.io.IOException
- Throws:
java.io.IOException
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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
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toNewHampshireX
public java.lang.StringBuffer toNewHampshireX(Phylogeny tree) throws java.io.IOException
- Throws:
java.io.IOException
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toNewHampshireX
public void toNewHampshireX(Phylogeny tree, java.io.File out_file) throws java.io.IOException
- Throws:
java.io.IOException
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toNewHampshireX
public void toNewHampshireX(Phylogeny[] trees, java.io.File out_file, java.lang.String separator) throws java.io.IOException
- Throws:
java.io.IOException
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toNexus
public void toNexus(java.io.File out_file, Phylogeny tree, PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE svs) throws java.io.IOException
- Throws:
java.io.IOException
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toNexus
public java.lang.StringBuffer toNexus(Phylogeny tree, PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE svs) throws java.io.IOException
- Throws:
java.io.IOException
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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
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toPhyloXML
public void toPhyloXML(java.io.File out_file, Phylogeny tree, int phyloxml_level) throws java.io.IOException
- Throws:
java.io.IOException
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toPhyloXML
public java.lang.StringBuffer toPhyloXML(Phylogeny tree, int phyloxml_level) throws java.io.IOException
- Throws:
java.io.IOException
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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
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toPhyloXML
public void toPhyloXML(Phylogeny phy, int phyloxml_level, java.io.File out_file) throws java.io.IOException
- Throws:
java.io.IOException
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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
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toPhyloXML
public void toPhyloXML(java.io.Writer writer, Phylogeny tree, int phyloxml_level) throws java.io.IOException
- Throws:
java.io.IOException
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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
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createPhylogenyWriter
public static PhylogenyWriter createPhylogenyWriter()
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writeNexusTaxaBlock
public static void writeNexusTaxaBlock(java.io.Writer writer, Phylogeny tree) throws java.io.IOException
- Throws:
java.io.IOException
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writeNexusTreesBlock
public static void writeNexusTreesBlock(java.io.Writer writer, java.util.List<Phylogeny> trees, PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE svs) throws java.io.IOException
- Throws:
java.io.IOException
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