X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fio%2Fparsers%2Futil%2FParserUtils.java;h=51f7f892b03b4545e6961933e092d0d54143f027;hb=1051703a697d29be2dc59ed1ed26b7ce5665ad66;hp=58a48ff7e498943c32473785d6faca7214cf6348;hpb=12298ec6ab774c405b20389b81f73329ea3323a0;p=jalview.git diff --git a/forester/java/src/org/forester/io/parsers/util/ParserUtils.java b/forester/java/src/org/forester/io/parsers/util/ParserUtils.java index 58a48ff..51f7f89 100644 --- a/forester/java/src/org/forester/io/parsers/util/ParserUtils.java +++ b/forester/java/src/org/forester/io/parsers/util/ParserUtils.java @@ -41,17 +41,30 @@ import java.util.regex.Pattern; import org.forester.io.parsers.PhylogenyParser; import org.forester.io.parsers.nexus.NexusPhylogeniesParser; import org.forester.io.parsers.nhx.NHXParser; +import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION; +import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException; import org.forester.io.parsers.phyloxml.PhyloXmlParser; import org.forester.io.parsers.tol.TolParser; import org.forester.phylogeny.Phylogeny; import org.forester.phylogeny.PhylogenyMethods; +import org.forester.phylogeny.PhylogenyNode; +import org.forester.phylogeny.data.Identifier; +import org.forester.phylogeny.data.Taxonomy; import org.forester.util.ForesterConstants; import org.forester.util.ForesterUtil; public final class ParserUtils { - final private static Pattern TAXOMONY_CODE_PATTERN_1 = Pattern.compile( "[A-Z0-9]{5}" ); - final private static Pattern TAXOMONY_CODE_PATTERN_2 = Pattern.compile( "([A-Z0-9]{5})[^A-Z].*" ); + final public static Pattern TAXOMONY_SN_PATTERN = Pattern + .compile( "[^_]{2,}_([A-Z][a-z]+_[a-z]{2,}(_[A-Za-z]\\w+|))\\b" ); + final public static Pattern TAXOMONY_CODE_PATTERN_1 = Pattern.compile( "\\b[A-Z0-9]{5}|RAT|PIG|PEA|CAP\\b" ); + final private static Pattern TAXOMONY_CODE_PATTERN_2 = Pattern + .compile( "([A-Z0-9]{5}|RAT|PIG|PEA|CAP)[^0-9A-Za-z].*" ); + final private static Pattern TAXOMONY_CODE_PATTERN_PF = Pattern + .compile( "([A-Z0-9]{5}|RAT|PIG|PEA|CAP)/\\d+-\\d+" ); + final private static Pattern TAXOMONY_UNIPROT_ID_PATTERN_1 = Pattern.compile( "\\b\\d{1,7}\\b" ); + final private static Pattern TAXOMONY_UNIPROT_ID_PATTERN_2 = Pattern.compile( "(\\d{1,7})[^0-9A-Za-z].*" ); + final private static Pattern TAXOMONY_UNIPROT_ID_PATTERN_PF = Pattern.compile( "(\\d{1,7})/\\d+-\\d+" ); final public static PhylogenyParser createParserDependingFileContents( final File file, final boolean phyloxml_validate_against_xsd ) @@ -209,57 +222,122 @@ public final class ParserUtils { return reader; } - /** - * Extracts a code if and only if: - * one and only one _, - * shorter than 25, - * no |, - * no ., - * if / present it has to be after the _, - * if PFAM_STYLE_ONLY: / must be present, - * tax code can only contain uppercase letters and numbers, - * and must contain at least one uppercase letter. - * Return null if no code extractable. - * - * @param name - * @return - */ - public static String extractTaxonomyCodeFromNodeName( final String name, - final PhylogenyMethods.TAXONOMY_EXTRACTION taxonomy_extraction ) { + public final static String extractTaxonomyCodeFromNodeName( final String name, + final TAXONOMY_EXTRACTION taxonomy_extraction ) { if ( ( name.indexOf( "_" ) > 0 ) - && ( name.length() < 31 ) - // && ( name.lastIndexOf( "_" ) == name.indexOf( "_" ) ) - && ( name.indexOf( "|" ) < 0 ) - && ( name.indexOf( "." ) < 0 ) - && ( ( taxonomy_extraction != PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ) || ( name - .indexOf( "/" ) >= 0 ) ) - && ( ( ( name.indexOf( "/" ) ) < 0 ) || ( name.indexOf( "/" ) > name.indexOf( "_" ) ) ) ) { - final String[] s = name.split( "[_/]" ); + && ( ( taxonomy_extraction != TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ) || ( name.indexOf( "/" ) > 4 ) ) ) { + final String[] s = name.split( "[_\\s]" ); if ( s.length > 1 ) { final String str = s[ 1 ]; - // if ( str.length() < 6 ) { - if ( ( str.length() < 5 ) && ( str.startsWith( "RAT" ) || str.startsWith( "PIG" ) ) ) { - return str.substring( 0, 3 ); + if ( !ForesterUtil.isEmpty( str ) ) { + if ( taxonomy_extraction == TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ) { + final Matcher m = TAXOMONY_CODE_PATTERN_PF.matcher( str ); + if ( m.matches() ) { + return m.group( 1 ); + } + } + else { + final Matcher m1 = TAXOMONY_CODE_PATTERN_1.matcher( str ); + if ( m1.matches() ) { + return m1.group(); + } + final Matcher m2 = TAXOMONY_CODE_PATTERN_2.matcher( str ); + if ( m2.matches() ) { + return m2.group( 1 ); + } + } + } + } + } + else if ( taxonomy_extraction == TAXONOMY_EXTRACTION.YES ) { + final Matcher m1 = TAXOMONY_CODE_PATTERN_1.matcher( name ); + if ( m1.matches() ) { + return name; + } + } + return null; + } + + public final static String extractScientificNameFromNodeName( final String name ) { + final Matcher m1 = TAXOMONY_SN_PATTERN.matcher( name ); + if ( m1.matches() ) { + return m1.group( 1 ).replace( '_', ' ' ); + } + return null; + } + + public final static String extractTaxonomyDataFromNodeName( final PhylogenyNode node, + final NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction ) + throws PhyloXmlDataFormatException { + final String id = extractUniprotTaxonomyIdFromNodeName( node.getName(), taxonomy_extraction ); + if ( !ForesterUtil.isEmpty( id ) ) { + if ( !node.getNodeData().isHasTaxonomy() ) { + node.getNodeData().setTaxonomy( new Taxonomy() ); + } + if ( ( node.getNodeData().getTaxonomy().getIdentifier() == null ) + || ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getIdentifier().getValue() ) ) { + node.getNodeData().getTaxonomy().setIdentifier( new Identifier( id, "uniprot" ) ); + return id; + } + } + else { + final String code = extractTaxonomyCodeFromNodeName( node.getName(), taxonomy_extraction ); + if ( !ForesterUtil.isEmpty( code ) ) { + if ( !node.getNodeData().isHasTaxonomy() ) { + node.getNodeData().setTaxonomy( new Taxonomy() ); } - final Matcher m1 = TAXOMONY_CODE_PATTERN_1.matcher( str ); - if ( m1.matches() ) { - return m1.group(); + if ( ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getTaxonomyCode() ) ) { + node.getNodeData().getTaxonomy().setTaxonomyCode( code ); + return code; + } + } + else if ( taxonomy_extraction == TAXONOMY_EXTRACTION.YES ) { + final String sn = extractScientificNameFromNodeName( node.getName() ); + if ( !ForesterUtil.isEmpty( sn ) ) { + if ( !node.getNodeData().isHasTaxonomy() ) { + node.getNodeData().setTaxonomy( new Taxonomy() ); + } + if ( ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) ) { + node.getNodeData().getTaxonomy().setScientificName( sn ); + return sn; + } } - final Matcher m2 = TAXOMONY_CODE_PATTERN_2.matcher( str ); - if ( m2.matches() ) { - return m2.group( 1 ); + } + } + return null; + } + + public final static String extractUniprotTaxonomyIdFromNodeName( final String name, + final TAXONOMY_EXTRACTION taxonomy_extraction ) { + if ( ( name.indexOf( "_" ) > 0 ) + && ( ( taxonomy_extraction != TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ) || ( name.indexOf( "/" ) > 4 ) ) ) { + final String[] s = name.split( "[_\\s]" ); + if ( s.length > 1 ) { + final String str = s[ 1 ]; + if ( !ForesterUtil.isEmpty( str ) ) { + if ( taxonomy_extraction == TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ) { + final Matcher m = TAXOMONY_UNIPROT_ID_PATTERN_PF.matcher( str ); + if ( m.matches() ) { + return m.group( 1 ); + } + } + else { + final Matcher m1 = TAXOMONY_UNIPROT_ID_PATTERN_1.matcher( str ); + if ( m1.matches() ) { + return m1.group(); + } + final Matcher m2 = TAXOMONY_UNIPROT_ID_PATTERN_2.matcher( str ); + if ( m2.matches() ) { + return m2.group( 1 ); + } + } } - // return null; - // final Matcher uc_letters_and_numbers = NHXParser.UC_LETTERS_NUMBERS_PATTERN.matcher( str ); - // if ( !uc_letters_and_numbers.matches() ) { - // return null; - // } - // final Matcher numbers_only = NHXParser.NUMBERS_ONLY_PATTERN.matcher( str ); - // if ( numbers_only.matches() ) { - // return null; - // } - // return str; - // } + } + } + else if ( taxonomy_extraction == TAXONOMY_EXTRACTION.YES ) { + final Matcher m1 = TAXOMONY_UNIPROT_ID_PATTERN_1.matcher( name ); + if ( m1.matches() ) { + return name; } } return null;