X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fws%2Funiprot%2FUniProtWsTools.java;h=73399ba590579ac3ccf9a2f1f72b210e6f20c6bf;hb=050c1eb17e94f7f78535cd7730fc7024c437ccad;hp=dd8d7603be674fea16e573210cc4a18321e20fc9;hpb=0368d0ed99717796cff01aad68cf176338652354;p=jalview.git diff --git a/forester/java/src/org/forester/ws/uniprot/UniProtWsTools.java b/forester/java/src/org/forester/ws/uniprot/UniProtWsTools.java index dd8d760..73399ba 100644 --- a/forester/java/src/org/forester/ws/uniprot/UniProtWsTools.java +++ b/forester/java/src/org/forester/ws/uniprot/UniProtWsTools.java @@ -41,17 +41,21 @@ import org.forester.util.ForesterUtil; public final class UniProtWsTools { + private static final boolean ALLOW_TAXONOMY_CODE_HACKS = true; //TODO turn off for final realease! + public enum Db { UNKNOWN, UNIPROT; } public final static String BASE_URL = "http://www.uniprot.org/"; - public final static String BASE_EMBL_DB_URL = "http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/embl/"; private final static String URL_ENC = "UTF-8"; // uniprot/expasy accession number format (6 chars): // letter digit letter-or-digit letter-or-digit letter-or-digit digit + // ?: => no back-reference + // \A => begin of String + // \Z => end of String private final static Pattern UNIPROT_AC_PATTERN = Pattern - .compile( "^.*[^a-zA-Z0-9]?([A-NR-ZOPQ]\\d[A-Z0-9]{3}\\d)[^a-zA-Z0-9]?" ); + .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]\\d[A-Z0-9]{3}\\d)(?:[^a-zA-Z0-9]|\\Z)" ); private final static boolean DEBUG = false; private static String encode( final String str ) throws UnsupportedEncodingException { @@ -74,8 +78,6 @@ public final class UniProtWsTools { return null; } } - - public static List getTaxonomiesFromCommonName( final String cn, final int max_taxonomies_return ) throws IOException { @@ -116,11 +118,14 @@ public final class UniProtWsTools { throws IOException { // Hack! Craniata? .. if ( sn.equals( "Drosophila" ) ) { - return hack( UniProtTaxonomy.DROSOPHILA_GENUS ); + return uniProtTaxonomyToList( UniProtTaxonomy.DROSOPHILA_GENUS ); } else if ( sn.equals( "Xenopus" ) ) { - return hack( UniProtTaxonomy.XENOPUS_GENUS ); + return uniProtTaxonomyToList( UniProtTaxonomy.XENOPUS_GENUS ); } + // else if ( sn.equals( "Nucleariidae and Fonticula group" ) ) { + // return hack( UniProtTaxonomy.NUCLEARIIDAE_AND_FONTICULA ); + // } final List result = getTaxonomyStringFromScientificName( sn, max_taxonomies_return ); if ( result.size() > 0 ) { return parseUniProtTaxonomy( result ); @@ -153,13 +158,12 @@ public final class UniProtWsTools { public static List getTaxonomiesFromTaxonomyCode( final String code, final int max_taxonomies_return ) throws IOException { - String my_code = new String( code ); - // Hacks! - if ( my_code.equals( "FUGRU" ) ) { - my_code = "TAKRU"; - } - else if ( my_code.equals( "CAP" ) ) { - return hack( UniProtTaxonomy.CAPITELLA_TELATA_SPECIES ); + final String my_code = new String( code ); + if ( ALLOW_TAXONOMY_CODE_HACKS ) { + final List l = resolveFakeTaxonomyCodes( max_taxonomies_return, my_code ); + if ( l != null ) { + return l; + } } final List result = getTaxonomyStringFromTaxonomyCode( my_code, max_taxonomies_return ); if ( result.size() > 0 ) { @@ -168,6 +172,100 @@ public final class UniProtWsTools { return null; } + private static List resolveFakeTaxonomyCodes( final int max_taxonomies_return, final String code ) + throws IOException { + if ( code.equals( "CAP" ) ) { + return getTaxonomiesFromId( "283909", max_taxonomies_return ); + } + else if ( code.equals( "FUGRU" ) ) { + return getTaxonomiesFromId( "31033", max_taxonomies_return ); + } + else if ( code.equals( "GIALA" ) ) { + return getTaxonomiesFromId( "5741", max_taxonomies_return ); + } + else if ( code.equals( "TRIVE" ) ) { + return getTaxonomiesFromId( "413071", max_taxonomies_return ); + } + else if ( code.equals( "CAPOWC" ) ) { + return getTaxonomiesFromId( "192875", max_taxonomies_return ); + } + else if ( code.equals( "SPHARC" ) ) { + return getTaxonomiesFromId( "667725", max_taxonomies_return ); + } + else if ( code.equals( "THETRA" ) ) { + return getTaxonomiesFromId( "529818", max_taxonomies_return ); + } + else if ( code.equals( "CHLVUL" ) ) { + return getTaxonomiesFromId( "574566", max_taxonomies_return ); + } + else if ( code.equals( "CITCLE" ) ) { + return getTaxonomiesFromId( "85681", max_taxonomies_return ); + } + else if ( code.equals( "MYCPOP" ) ) { + return getTaxonomiesFromId( "85929", max_taxonomies_return ); + } + else if ( code.equals( "AGABB" ) ) { + return getTaxonomiesFromId( "597362", max_taxonomies_return ); + } + else if ( code.equals( "BAUCOM" ) ) { + return getTaxonomiesFromId( "430998", max_taxonomies_return ); + } + else if ( code.equals( "DICSQU" ) ) { + return getTaxonomiesFromId( "114155", max_taxonomies_return ); + } + else if ( code.equals( "FOMPIN" ) ) { + return getTaxonomiesFromId( "40483", max_taxonomies_return ); + } + else if ( code.equals( "HYDMA" ) ) { + return getTaxonomiesFromId( "6085", max_taxonomies_return ); + } + else if ( code.equals( "MYCFI" ) ) { + return getTaxonomiesFromId( "83344", max_taxonomies_return ); + } + else if ( code.equals( "OIDMAI" ) ) { + return getTaxonomiesFromId( "78148", max_taxonomies_return ); + } + else if ( code.equals( "OSTRC" ) ) { + return getTaxonomiesFromId( "385169", max_taxonomies_return ); + } + else if ( code.equals( "POSPL" ) ) { + return getTaxonomiesFromId( "104341", max_taxonomies_return ); + } + else if ( code.equals( "SAICOM" ) ) { + return getTaxonomiesFromId( "5606", max_taxonomies_return ); + } + else if ( code.equals( "SERLA" ) ) { + return getTaxonomiesFromId( "85982", max_taxonomies_return ); + } + else if ( code.equals( "SPORO" ) ) { + return getTaxonomiesFromId( "40563", max_taxonomies_return ); + } + else if ( code.equals( "ACRALC" ) ) { + return getTaxonomiesFromId( "398408", max_taxonomies_return ); + } + else if ( code.equals( "THITER" ) ) { + return getTaxonomiesFromId( "35720", max_taxonomies_return ); + } + else if ( code.equals( "MYCTHE" ) ) { + return getTaxonomiesFromId( "78579", max_taxonomies_return ); + } + else if ( code.equals( "CONPUT" ) ) { + return getTaxonomiesFromId( "80637", max_taxonomies_return ); + } + else if ( code.equals( "WOLCOC" ) ) { + return getTaxonomiesFromId( "81056", max_taxonomies_return ); + } + else if ( code.equals( "CLAGRA" ) ) { + return getTaxonomiesFromId( "27339", max_taxonomies_return ); + } + else if ( code.equals( "XANPAR" ) ) { + return getTaxonomiesFromId( "107463", max_taxonomies_return ); + } + else { + return null; + } + } + private static List getTaxonomyStringFromCommonName( final String cn, final int max_lines_to_return ) throws IOException { return queryUniprot( "taxonomy/?query=common%3a%22" + encode( cn ) + "%22&format=tab", max_lines_to_return ); @@ -188,7 +286,7 @@ public final class UniProtWsTools { return queryUniprot( "taxonomy/?query=mnemonic%3a%22" + encode( code ) + "%22&format=tab", max_lines_to_return ); } - private static List hack( final UniProtTaxonomy tax ) { + private static List uniProtTaxonomyToList( final UniProtTaxonomy tax ) { final List l = new ArrayList(); l.add( tax ); return l; @@ -201,7 +299,13 @@ public final class UniProtWsTools { // Ignore empty lines. } else if ( line.startsWith( "Taxon" ) ) { - //TODO next the check format FIXME + final String[] items = line.split( "\t" ); + if ( !( items[ 1 ].equalsIgnoreCase( "Mnemonic" ) && items[ 2 ].equalsIgnoreCase( "Scientific name" ) + && items[ 3 ].equalsIgnoreCase( "Common name" ) && items[ 4 ].equalsIgnoreCase( "Synonym" ) + && items[ 5 ].equalsIgnoreCase( "Other Names" ) && items[ 6 ].equalsIgnoreCase( "Reviewed" ) + && items[ 7 ].equalsIgnoreCase( "Rank" ) && items[ 8 ].equalsIgnoreCase( "Lineage" ) ) ) { + throw new IOException( "Unreconized UniProt Taxonomy format: " + line ); + } } else { if ( line.split( "\t" ).length > 4 ) { @@ -212,26 +316,16 @@ public final class UniProtWsTools { return taxonomies; } - - public static List queryEmblDb( final String query, int max_lines_to_return ) throws IOException { - return queryDb( query, - max_lines_to_return, - BASE_EMBL_DB_URL ) ; + public static List queryEmblDb( final String query, final int max_lines_to_return ) throws IOException { + return queryDb( query, max_lines_to_return, BASE_EMBL_DB_URL ); } - - - - public static List queryUniprot( final String query, int max_lines_to_return ) throws IOException { - return queryDb( query, - max_lines_to_return, - BASE_URL ) ; - - + + public static List queryUniprot( final String query, final int max_lines_to_return ) throws IOException { + return queryDb( query, max_lines_to_return, BASE_URL ); } - public static List queryDb( final String query, - int max_lines_to_return, - final String base_url ) throws IOException { + public static List queryDb( final String query, int max_lines_to_return, final String base_url ) + throws IOException { if ( ForesterUtil.isEmpty( query ) ) { throw new IllegalArgumentException( "illegal attempt to use empty query " ); } @@ -247,6 +341,9 @@ public final class UniProtWsTools { String line; final List result = new ArrayList(); while ( ( line = in.readLine() ) != null ) { + if ( DEBUG ) { + System.out.println( line ); + } result.add( line ); if ( result.size() > max_lines_to_return ) { break; @@ -255,16 +352,16 @@ public final class UniProtWsTools { in.close(); return result; } - - + public static SequenceDatabaseEntry obtainUniProtEntry( final String query, final int max_lines_to_return ) throws IOException { final List lines = queryUniprot( "uniprot/" + query + ".txt", max_lines_to_return ); return UniProtEntry.createInstanceFromPlainText( lines ); } - public static SequenceDatabaseEntry obtainEmblEntry( String query, int max_lines_to_return ) throws IOException { - final List lines = queryEmblDb( "query", max_lines_to_return ); + public static SequenceDatabaseEntry obtainEmblEntry( final String query, final int max_lines_to_return ) + throws IOException { + final List lines = queryEmblDb( query, max_lines_to_return ); return EbiDbEntry.createInstanceFromPlainText( lines ); } }