// 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;
-
- synchronized private static String encode( final String str ) throws UnsupportedEncodingException {
+ public enum Db {
+ UNKNOWN, UNIPROT;
+ }
+ public final static String BASE_URL = "http://www.uniprot.org/";
+ 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
+ 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]?" );
+ private final static boolean DEBUG = false;
+
+ 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 )
+ /**
+ * Return 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" ) ) {
* 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!
return null;
}
- synchronized private static List<String> getTaxonomyStringFromCommonName( final String cn,
- final int max_lines_to_return )
+ 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> hack( 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 ) ) {
return taxonomies;
}
- synchronized public static List<String> queryUniprot( final String query, int max_lines_to_return )
- throws IOException {
+ public static List<String> queryUniprot( final String query, int max_lines_to_return ) throws IOException {
if ( ForesterUtil.isEmpty( query ) ) {
throw new IllegalArgumentException( "illegal attempt to use empty query " );
}
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 );
+ }
}
git://source.jalview.org / jalview.git / blobdiff