public final class PhylogenyDecorator {
- public final static boolean SANITIZE = false;
final private static String TP_NODE_NAME = "NODE_NAME";
final private static String TP_SEQ_ACCESSION = "SEQ_ACCESSION";
final private static String TP_SEQ_ACCESSION_SOURCE = "SEQ_ACCESSION_SOURCE";
public static void decorate( final Phylogeny phylogeny,
final Map<String, Map<String, String>> map,
- final boolean picky,
- final int numbers_of_chars_allowed_to_remove_if_not_found_in_map )
- throws IllegalArgumentException, PhyloXmlDataFormatException {
+ final boolean picky ) throws IllegalArgumentException, PhyloXmlDataFormatException {
for( final PhylogenyNodeIterator iter = phylogeny.iteratorPostorder(); iter.hasNext(); ) {
final PhylogenyNode node = iter.next();
final String name = node.getName();
if ( !ForesterUtil.isEmpty( name ) ) {
- if ( map.containsKey( name ) || ( numbers_of_chars_allowed_to_remove_if_not_found_in_map > 0 ) ) {
- Map<String, String> new_values = map.get( name );
- int x = 0;
- while ( ( new_values == null ) && ( numbers_of_chars_allowed_to_remove_if_not_found_in_map > 0 )
- && ( x <= numbers_of_chars_allowed_to_remove_if_not_found_in_map ) ) {
- new_values = map.get( name.substring( 0, name.length() - x ) );
- ++x;
- }
+ if ( map.containsKey( name ) ) {
+ final Map<String, String> new_values = map.get( name );
if ( new_values != null ) {
if ( new_values.containsKey( TP_TAXONOMY_CODE ) ) {
ForesterUtil.ensurePresenceOfTaxonomy( node );
}
}
- public static void decorate( final Phylogeny phylogeny,
- final Map<String, String> map,
- final FIELD field,
- final boolean extract_bracketed_scientific_name,
- final boolean extract_bracketed_tax_code,
- final boolean picky,
- final boolean cut_name_after_space,
- final boolean process_name_intelligently,
- final boolean process_similar_to,
- final int numbers_of_chars_allowed_to_remove_if_not_found_in_map,
- final boolean trim_after_tilde,
- final boolean verbose ) throws IllegalArgumentException, NHXFormatException,
+ public static String decorate( final Phylogeny phylogeny,
+ final Map<String, String> map,
+ final FIELD field,
+ final boolean extract_bracketed_scientific_name,
+ final boolean extract_bracketed_tax_code,
+ final boolean picky,
+ final boolean cut_name_after_space,
+ final boolean trim_after_tilde,
+ final boolean verbose ) throws IllegalArgumentException, NHXFormatException,
PhyloXmlDataFormatException {
- PhylogenyDecorator.decorate( phylogeny,
- map,
- field,
- extract_bracketed_scientific_name,
- extract_bracketed_tax_code,
- picky,
- null,
- cut_name_after_space,
- process_name_intelligently,
- process_similar_to,
- numbers_of_chars_allowed_to_remove_if_not_found_in_map,
- trim_after_tilde,
- verbose );
+ return PhylogenyDecorator.decorate( phylogeny,
+ map,
+ field,
+ extract_bracketed_scientific_name,
+ extract_bracketed_tax_code,
+ picky,
+ null,
+ cut_name_after_space,
+ trim_after_tilde,
+ verbose );
}
/**
* @throws IllegalArgumentException
* @throws PhyloXmlDataFormatException
*/
- public static void decorate( final Phylogeny phylogeny,
- final Map<String, String> map,
- final FIELD field,
- final boolean extract_bracketed_scientific_name,
- final boolean extract_bracketed_tax_code,
- final boolean picky,
- final Map<String, String> intermediate_map,
- final boolean cut_name_after_space,
- final boolean process_name_intelligently,
- final boolean process_similar_to,
- final int numbers_of_chars_allowed_to_remove_if_not_found_in_map,
- final boolean trim_after_tilde,
- final boolean verbose ) throws IllegalArgumentException, PhyloXmlDataFormatException {
+ public static String decorate( final Phylogeny phylogeny,
+ final Map<String, String> map,
+ final FIELD field,
+ final boolean extract_bracketed_scientific_name,
+ final boolean extract_bracketed_tax_code,
+ final boolean picky,
+ final Map<String, String> intermediate_map,
+ final boolean cut_name_after_space,
+ final boolean trim_after_tilde,
+ final boolean verbose ) throws IllegalArgumentException, PhyloXmlDataFormatException {
if ( extract_bracketed_scientific_name && ( field == FIELD.TAXONOMY_SCIENTIFIC_NAME ) ) {
throw new IllegalArgumentException( "attempt to extract bracketed scientific name together with data field pointing to scientific name" );
}
if ( map.isEmpty() ) {
throw new IllegalArgumentException( "map is empty" );
}
+ int ext_nodes = 0;
+ int ext_nodes_updated = 0;
+ int int_nodes = 0;
+ int int_nodes_updated = 0;
for( final PhylogenyNodeIterator iter = phylogeny.iteratorPostorder(); iter.hasNext(); ) {
final PhylogenyNode node = iter.next();
+ if ( node.isExternal() ) {
+ ++ext_nodes;
+ }
+ else {
+ ++int_nodes;
+ }
String name = node.getName();
+ if ( picky && node.isExternal() && ForesterUtil.isEmpty( name ) ) {
+ throw new IllegalArgumentException( "external node with no name present" );
+ }
String tilde_annotation = null;
if ( trim_after_tilde && ( name.indexOf( '~' ) > 0 ) ) {
final int ti = name.indexOf( '~' );
+ final String orig = name;
tilde_annotation = name.substring( ti );
name = name.substring( 0, ti );
+ if ( node.isExternal() && ForesterUtil.isEmpty( name ) ) {
+ throw new IllegalArgumentException( "external node with illegal name: " + orig );
+ }
}
if ( !ForesterUtil.isEmpty( name ) ) {
if ( intermediate_map != null ) {
name = PhylogenyDecorator.extractIntermediate( intermediate_map, name, verbose );
}
- if ( map.containsKey( name ) || ( numbers_of_chars_allowed_to_remove_if_not_found_in_map > 0 ) ) {
- String new_value = map.get( name );
- int x = 0;
- while ( ( new_value == null ) && ( numbers_of_chars_allowed_to_remove_if_not_found_in_map > 0 )
- && ( x <= numbers_of_chars_allowed_to_remove_if_not_found_in_map ) ) {
- new_value = map.get( name.substring( 0, name.length() - x ) );
- ++x;
- }
- if ( new_value != null ) {
- new_value = new_value.trim();
- new_value.replaceAll( "/\\s+/", " " );
+ if ( map.containsKey( name ) ) {
+ String new_value = map.get( name ).trim().replaceAll( "/\\s+/", " " );
+ if ( !ForesterUtil.isEmpty( new_value ) ) {
+ if ( node.isExternal() ) {
+ ++ext_nodes_updated;
+ }
+ else {
+ ++int_nodes_updated;
+ }
if ( extract_bracketed_scientific_name && new_value.endsWith( "]" ) ) {
new_value = extractBracketedScientificNames( node, new_value );
}
}
new_value = PhylogenyDecorator.deleteAtFirstSpace( new_value );
}
- else if ( process_name_intelligently ) {
- if ( verbose ) {
- System.out.print( new_value + " -> " );
- }
- new_value = PhylogenyDecorator.processNameIntelligently( new_value );
- }
- else if ( process_similar_to ) {
- if ( verbose ) {
- System.out.print( new_value + " -> " );
- }
- new_value = PhylogenyDecorator.processSimilarTo( new_value );
- }
- if ( PhylogenyDecorator.SANITIZE ) {
- new_value = PhylogenyDecorator.sanitize( new_value );
- }
if ( trim_after_tilde ) {
new_value = addTildeAnnotation( tilde_annotation, new_value );
}
throw new RuntimeException( "unknown field \"" + field + "\"" );
}
}
+ else {
+ throw new IllegalArgumentException( "node name \"" + name + "\" maps to empty value" );
+ }
}
else if ( picky ) {
- throw new IllegalArgumentException( "\"" + name + "\" not found in name map" );
+ throw new IllegalArgumentException( "node name \"" + name + "\" not found in map" );
}
}
}
- }
-
- public static void decorate( final Phylogeny[] phylogenies,
- final Map<String, Map<String, String>> map,
- final boolean picky,
- final int numbers_of_chars_allowed_to_remove_if_not_found_in_map )
- throws IllegalArgumentException, NHXFormatException, PhyloXmlDataFormatException {
- for( final Phylogeny phylogenie : phylogenies ) {
- PhylogenyDecorator
- .decorate( phylogenie, map, picky, numbers_of_chars_allowed_to_remove_if_not_found_in_map );
- }
- }
-
- public static void decorate( final Phylogeny[] phylogenies,
- final Map<String, String> map,
- final FIELD field,
- final boolean extract_bracketed_scientific_name,
- final boolean extract_bracketed_tax_code,
- final boolean picky,
- final boolean cut_name_after_space,
- final boolean process_name_intelligently,
- final boolean process_similar_to,
- final int numbers_of_chars_allowed_to_remove_if_not_found_in_map,
- final boolean trim_after_tilde,
- final boolean verbose ) throws IllegalArgumentException, NHXFormatException,
- PhyloXmlDataFormatException {
- for( final Phylogeny phylogenie : phylogenies ) {
- PhylogenyDecorator.decorate( phylogenie,
- map,
- field,
- extract_bracketed_scientific_name,
- extract_bracketed_tax_code,
- picky,
- cut_name_after_space,
- process_name_intelligently,
- process_similar_to,
- numbers_of_chars_allowed_to_remove_if_not_found_in_map,
- trim_after_tilde,
- verbose );
- }
- }
-
- public static void decorate( final Phylogeny[] phylogenies,
- final Map<String, String> map,
- final FIELD field,
- final boolean extract_bracketed_scientific_name,
- final boolean extract_bracketed_tax_code,
- final boolean picky,
- final Map<String, String> intermediate_map,
- final boolean cut_name_after_space,
- final boolean process_name_intelligently,
- final boolean process_similar_to,
- final int numbers_of_chars_allowed_to_remove_if_not_found_in_map,
- final boolean trim_after_tilde,
- final boolean verbose ) throws IllegalArgumentException, NHXFormatException,
- PhyloXmlDataFormatException {
- for( final Phylogeny phylogenie : phylogenies ) {
- PhylogenyDecorator.decorate( phylogenie,
- map,
- field,
- extract_bracketed_scientific_name,
- extract_bracketed_tax_code,
- picky,
- intermediate_map,
- cut_name_after_space,
- process_name_intelligently,
- process_similar_to,
- numbers_of_chars_allowed_to_remove_if_not_found_in_map,
- trim_after_tilde,
- verbose );
- }
+ return "updated " + ext_nodes_updated + "/" + ext_nodes + " external nodes, updated " + int_nodes_updated + "/"
+ + int_nodes + " internal nodes";
}
public static Map<String, Map<String, String>> parseMappingTable( final File mapping_table_file )
return new_name;
}
- private static String processNameIntelligently( final String name ) {
- final String[] s = name.split( " " );
- if ( s.length < 2 ) {
- return name;
- }
- else if ( ( s[ 0 ].indexOf( "_" ) > 0 ) && ( s[ 0 ].indexOf( "|" ) > 0 ) ) {
- return s[ 0 ];
- }
- else if ( ( s[ 1 ].indexOf( "_" ) > 0 ) && ( s[ 1 ].indexOf( "|" ) > 0 ) ) {
- return s[ 1 ];
- }
- else if ( ( s[ 0 ].indexOf( "_" ) > 0 ) && ( s[ 0 ].indexOf( "." ) > 0 ) ) {
- return s[ 0 ];
- }
- else if ( ( s[ 1 ].indexOf( "_" ) > 0 ) && ( s[ 1 ].indexOf( "." ) > 0 ) ) {
- return s[ 1 ];
- }
- else if ( s[ 0 ].indexOf( "_" ) > 0 ) {
- return s[ 0 ];
- }
- else if ( s[ 1 ].indexOf( "_" ) > 0 ) {
- return s[ 1 ];
- }
- else {
- return s[ 0 ];
- }
- }
-
- private static String processSimilarTo( final String name ) {
- final int i = name.toLowerCase().indexOf( "similar to" );
- String similar_to = "";
- if ( i >= 0 ) {
- similar_to = " similarity=" + name.substring( i + 10 ).trim();
- }
- final String pi = processNameIntelligently( name );
- return pi + similar_to;
- }
-
- private static String sanitize( String s ) {
- s = s.replace( ' ', '_' );
- s = s.replace( '(', '{' );
- s = s.replace( ')', '}' );
- s = s.replace( '[', '{' );
- s = s.replace( ']', '}' );
- s = s.replace( ',', '_' );
- return s;
- }
-
public static enum FIELD {
DOMAIN_STRUCTURE,
MOL_SEQ,
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