Package org.forester.tools
Class PhylogenyDecorator
- java.lang.Object
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- org.forester.tools.PhylogenyDecorator
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public final class PhylogenyDecorator extends java.lang.Object
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
PhylogenyDecorator.FIELD
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Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method Description static java.lang.String
decorate(Phylogeny phylogeny, java.util.Map<java.lang.String,java.lang.String> map, PhylogenyDecorator.FIELD field, boolean extract_bracketed_scientific_name, boolean extract_bracketed_tax_code, boolean picky, boolean cut_name_after_space, boolean trim_after_tilde, boolean verbose)
static java.lang.String
decorate(Phylogeny phylogeny, java.util.Map<java.lang.String,java.lang.String> map, PhylogenyDecorator.FIELD field, boolean extract_bracketed_scientific_name, boolean extract_bracketed_tax_code, boolean picky, java.util.Map<java.lang.String,java.lang.String> intermediate_map, boolean cut_name_after_space, boolean trim_after_tilde, boolean verbose)
static void
decorate(Phylogeny phylogeny, java.util.Map<java.lang.String,java.util.Map<java.lang.String,java.lang.String>> map, boolean picky)
static java.util.Map<java.lang.String,java.util.Map<java.lang.String,java.lang.String>>
parseMappingTable(java.io.File mapping_table_file)
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Method Detail
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decorate
public static void decorate(Phylogeny phylogeny, java.util.Map<java.lang.String,java.util.Map<java.lang.String,java.lang.String>> map, boolean picky) throws java.lang.IllegalArgumentException, PhyloXmlDataFormatException
- Throws:
java.lang.IllegalArgumentException
PhyloXmlDataFormatException
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decorate
public static java.lang.String decorate(Phylogeny phylogeny, java.util.Map<java.lang.String,java.lang.String> map, PhylogenyDecorator.FIELD field, boolean extract_bracketed_scientific_name, boolean extract_bracketed_tax_code, boolean picky, boolean cut_name_after_space, boolean trim_after_tilde, boolean verbose) throws java.lang.IllegalArgumentException, NHXFormatException, PhyloXmlDataFormatException
- Throws:
java.lang.IllegalArgumentException
NHXFormatException
PhyloXmlDataFormatException
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decorate
public static java.lang.String decorate(Phylogeny phylogeny, java.util.Map<java.lang.String,java.lang.String> map, PhylogenyDecorator.FIELD field, boolean extract_bracketed_scientific_name, boolean extract_bracketed_tax_code, boolean picky, java.util.Map<java.lang.String,java.lang.String> intermediate_map, boolean cut_name_after_space, boolean trim_after_tilde, boolean verbose) throws java.lang.IllegalArgumentException, PhyloXmlDataFormatException
- Parameters:
phylogeny
-map
- maps names (in phylogeny) to new values if intermediate_map is null otherwise maps intermediate value to new valuefield
-picky
-intermediate_map
- maps name (in phylogeny) to a intermediate value- Throws:
java.lang.IllegalArgumentException
PhyloXmlDataFormatException
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parseMappingTable
public static java.util.Map<java.lang.String,java.util.Map<java.lang.String,java.lang.String>> parseMappingTable(java.io.File mapping_table_file) throws java.io.IOException
- Throws:
java.io.IOException
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