// Copyright (C) 2010 Christian M Zmasek
// Copyright (C) 2010 Sanford-Burnham Medical Research Institute
// All rights reserved
-//
+//
// This library is free software; you can redistribute it and/or
// modify it under the terms of the GNU Lesser General Public
// License as published by the Free Software Foundation; either
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
// Lesser General Public License for more details.
-//
+//
// You should have received a copy of the GNU Lesser General Public
// License along with this library; if not, write to the Free Software
// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
import java.net.URLEncoder;
import java.util.ArrayList;
import java.util.List;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
import org.forester.util.ForesterUtil;
public final class UniProtWsTools {
- public final static String BASE_URL = "http://www.uniprot.org/";
- private final static String URL_ENC = "UTF-8";
- private final static boolean DEBUG = false;
+ 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|.*[^a-zA-Z0-9])([A-Z]\\d[A-Z0-9]{3}\\d)(?:[^a-zA-Z0-9]|\\Z)" );
+ private final static boolean DEBUG = false;
- synchronized private static String encode( final String str ) throws UnsupportedEncodingException {
+ private static String encode( final String str ) throws UnsupportedEncodingException {
return URLEncoder.encode( str.trim(), URL_ENC );
}
- synchronized public static List<UniProtTaxonomy> getTaxonomiesFromCommonName( final String cn,
- final int max_taxonomies_return )
+ /**
+ * Returns null if no match.
+ *
+ * @param query
+ * @param db
+ * @return
+ */
+ static public String parseUniProtAccessor( final String query ) {
+ final Matcher m = UNIPROT_AC_PATTERN.matcher( query );
+ if ( m.lookingAt() ) {
+ return m.group( 1 );
+ }
+ else {
+ return null;
+ }
+ }
+
+ public static List<UniProtTaxonomy> getTaxonomiesFromCommonName( final String cn, final int max_taxonomies_return )
throws IOException {
final List<String> result = getTaxonomyStringFromCommonName( cn, max_taxonomies_return );
if ( result.size() > 0 ) {
return null;
}
- synchronized public static List<UniProtTaxonomy> getTaxonomiesFromCommonNameStrict( final String cn,
- final int max_taxonomies_return )
+ public static List<UniProtTaxonomy> getTaxonomiesFromCommonNameStrict( final String cn,
+ final int max_taxonomies_return )
throws IOException {
final List<UniProtTaxonomy> taxonomies = getTaxonomiesFromCommonName( cn, max_taxonomies_return );
if ( ( taxonomies != null ) && ( taxonomies.size() > 0 ) ) {
return null;
}
- synchronized public static List<UniProtTaxonomy> getTaxonomiesFromId( final String id,
- final int max_taxonomies_return )
+ public static List<UniProtTaxonomy> getTaxonomiesFromId( final String id, final int max_taxonomies_return )
throws IOException {
final List<String> result = getTaxonomyStringFromId( id, max_taxonomies_return );
if ( result.size() > 0 ) {
return null;
}
- synchronized public static List<UniProtTaxonomy> getTaxonomiesFromScientificName( final String sn,
- final int max_taxonomies_return )
+ public static List<UniProtTaxonomy> getTaxonomiesFromScientificName( final String sn,
+ final int max_taxonomies_return )
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<String> result = getTaxonomyStringFromScientificName( sn, max_taxonomies_return );
if ( result.size() > 0 ) {
return parseUniProtTaxonomy( result );
* and not "Mus musculus", "Mus musculus bactrianus", ...
*
*/
- synchronized public static List<UniProtTaxonomy> getTaxonomiesFromScientificNameStrict( final String sn,
- final int max_taxonomies_return )
+ public static List<UniProtTaxonomy> getTaxonomiesFromScientificNameStrict( final String sn,
+ final int max_taxonomies_return )
throws IOException {
final List<UniProtTaxonomy> taxonomies = getTaxonomiesFromScientificName( sn, max_taxonomies_return );
if ( ( taxonomies != null ) && ( taxonomies.size() > 0 ) ) {
return null;
}
- synchronized public static List<UniProtTaxonomy> getTaxonomiesFromTaxonomyCode( final String code,
- final int max_taxonomies_return )
+ public static List<UniProtTaxonomy> 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<UniProtTaxonomy> l = resolveFakeTaxonomyCodes( max_taxonomies_return, my_code );
+ if ( l != null ) {
+ return l;
+ }
}
final List<String> result = getTaxonomyStringFromTaxonomyCode( my_code, max_taxonomies_return );
if ( result.size() > 0 ) {
return null;
}
- synchronized private static List<String> getTaxonomyStringFromCommonName( final String cn,
- final int max_lines_to_return )
+ private static List<UniProtTaxonomy> 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<String> 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 );
}
- synchronized private static List<String> getTaxonomyStringFromId( final String id, final int max_lines_to_return )
+ private static List<String> getTaxonomyStringFromId( final String id, final int max_lines_to_return )
throws IOException {
return queryUniprot( "taxonomy/?query=id%3a%22" + encode( id ) + "%22&format=tab", max_lines_to_return );
}
- synchronized private static List<String> getTaxonomyStringFromScientificName( final String sn,
- final int max_lines_to_return )
+ private static List<String> getTaxonomyStringFromScientificName( final String sn, final int max_lines_to_return )
throws IOException {
return queryUniprot( "taxonomy/?query=scientific%3a%22" + encode( sn ) + "%22&format=tab", max_lines_to_return );
}
- synchronized private static List<String> getTaxonomyStringFromTaxonomyCode( final String code,
- final int max_lines_to_return )
+ private static List<String> getTaxonomyStringFromTaxonomyCode( final String code, final int max_lines_to_return )
throws IOException {
return queryUniprot( "taxonomy/?query=mnemonic%3a%22" + encode( code ) + "%22&format=tab", max_lines_to_return );
}
- synchronized private static List<UniProtTaxonomy> hack( final UniProtTaxonomy tax ) {
+ private static List<UniProtTaxonomy> uniProtTaxonomyToList( final UniProtTaxonomy tax ) {
final List<UniProtTaxonomy> l = new ArrayList<UniProtTaxonomy>();
l.add( tax );
return l;
}
- synchronized private static List<UniProtTaxonomy> parseUniProtTaxonomy( final List<String> result )
- throws IOException {
+ private static List<UniProtTaxonomy> parseUniProtTaxonomy( final List<String> result ) throws IOException {
final List<UniProtTaxonomy> taxonomies = new ArrayList<UniProtTaxonomy>();
for( final String line : result ) {
if ( ForesterUtil.isEmpty( line ) ) {
// 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 ) {
return taxonomies;
}
- synchronized public static List<String> queryUniprot( final String query, int max_lines_to_return )
+ public static List<String> 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<String> queryUniprot( final String query, final int max_lines_to_return ) throws IOException {
+ return queryDb( query, max_lines_to_return, BASE_URL );
+ }
+
+ public static List<String> 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 " );
if ( max_lines_to_return < 1 ) {
max_lines_to_return = 1;
}
- final URL url = new URL( BASE_URL + query );
+ final URL url = new URL( base_url + query );
if ( DEBUG ) {
System.out.println( "url: " + url.toString() );
}
String line;
final List<String> result = new ArrayList<String>();
while ( ( line = in.readLine() ) != null ) {
+ if ( DEBUG ) {
+ System.out.println( line );
+ }
result.add( line );
if ( result.size() > max_lines_to_return ) {
break;
in.close();
return result;
}
+
+ public static SequenceDatabaseEntry obtainUniProtEntry( final String query, final int max_lines_to_return )
+ throws IOException {
+ final List<String> lines = queryUniprot( "uniprot/" + query + ".txt", max_lines_to_return );
+ return UniProtEntry.createInstanceFromPlainText( lines );
+ }
+
+ public static SequenceDatabaseEntry obtainEmblEntry( final String query, final int max_lines_to_return )
+ throws IOException {
+ final List<String> lines = queryEmblDb( query, max_lines_to_return );
+ return EbiDbEntry.createInstanceFromPlainText( lines );
+ }
}
git://source.jalview.org / jalview.git / blobdiff