--- /dev/null
+
+package org.forester.ws.seqdb;
+
+
+public class DatabaseTools {
+
+
+ static String extract( final String target, final String a, final String b ) {
+ final int i_a = target.indexOf( a );
+ final int i_b = target.indexOf( b );
+ if ( ( i_a < 0 ) || ( i_b < i_a ) ) {
+ throw new IllegalArgumentException( "attempt to extract from [" + target + "] between [" + a + "] and ["
+ + b + "]" );
+ }
+ return target.substring( i_a + a.length(), i_b ).trim();
+ }
+
+ static String extract( final String target, final String a ) {
+ final int i_a = target.indexOf( a );
+ return target.substring( i_a + a.length() ).trim();
+ }
+}
--- /dev/null
+// $Id:
+// forester -- software libraries and applications
+// for genomics and evolutionary biology research.
+//
+// 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
+// version 2.1 of the License, or (at your option) any later version.
+//
+// This library is distributed in the hope that it will be useful,
+// 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
+//
+// Contact: phylosoft @ gmail . com
+// WWW: www.phylosoft.org/forester
+
+package org.forester.ws.seqdb;
+
+import java.util.List;
+
+import org.forester.util.ForesterUtil;
+
+public final class EbiDbEntry implements SequenceDatabaseEntry {
+
+ //http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/emb/AAR37336/
+ private String _pa;
+ private String _de;
+ private String _os;
+ private String _tax_id;
+ private String _symbol;
+ private String _provider;
+
+ private EbiDbEntry() {
+ }
+
+ @Override
+ public Object clone() throws CloneNotSupportedException {
+ throw new CloneNotSupportedException();
+ }
+
+
+ public static SequenceDatabaseEntry createInstanceFromPlainTextForRefSeq( final List<String> lines ) {
+ final EbiDbEntry e = new EbiDbEntry();
+ for( final String line : lines ) {
+ // System.out.println( "-" + line );
+ if ( line.startsWith( "ACCESSION" ) ) {
+ e.setPA( DatabaseTools.extract( line, "ACCESSION" ) );
+ }
+ else if ( line.startsWith( "DEFINITION" ) ) {
+ if ( line.indexOf( "[" ) > 0 ) {
+ e.setDe( DatabaseTools.extract( line, "DEFINITION", "[" ) );
+ }
+ else {
+ e.setDe( DatabaseTools.extract( line, "DEFINITION" ) );
+ }
+
+
+ }
+
+ else if ( line.startsWith( "SOURCE" ) ) {
+ if ( line.indexOf( "(" ) > 0 ) {
+ e.setOs( DatabaseTools.extract( line, "SOURCE", "(" ) );
+ }
+ else {
+ e.setOs( DatabaseTools.extract( line, "SOURCE" ) );
+ }
+ }
+
+ }
+ return e;
+ }
+
+
+
+ public static SequenceDatabaseEntry createInstanceFromPlainText( final List<String> lines ) {
+ final EbiDbEntry e = new EbiDbEntry();
+ for( final String line : lines ) {
+
+ if ( line.startsWith( "PA" ) ) {
+ e.setPA( DatabaseTools.extract( line, "PA" ) );
+ }
+ else if ( line.startsWith( "DE" ) ) {
+ // if ( ( line.indexOf( "RecName:" ) > 0 ) && ( line.indexOf( "Full=" ) > 0 ) ) {
+ e.setDe( DatabaseTools.extract( line, "DE" ) );
+ //}
+ }
+ // else if ( line.startsWith( "GN" ) ) {
+ // if ( ( line.indexOf( "Name=" ) > 0 ) ) {
+ // e.setSymbol( extract( line, "Name=", ";" ) );
+ // }
+ // }
+ else if ( line.startsWith( "OS" ) ) {
+ if ( line.indexOf( "(" ) > 0 ) {
+ e.setOs( DatabaseTools.extract( line, "OS", "(" ) );
+ }
+ else {
+ e.setOs( DatabaseTools.extract( line, "OS" ) );
+ }
+ }
+ else if ( line.startsWith( "OX" ) ) {
+ if ( line.indexOf( "NCBI_TaxID=" ) > 0 ) {
+ e.setTaxId( DatabaseTools.extract( line, "NCBI_TaxID=", ";" ) );
+ }
+ }
+ }
+ return e;
+ }
+
+ @Override
+ public String getAccession() {
+ return _pa;
+ }
+
+ private void setPA( final String pa ) {
+ if ( _pa == null ) {
+ _pa = pa;
+ }
+ }
+
+ @Override
+ public String getSequenceName() {
+ return _de;
+ }
+
+ private void setDe( final String rec_name ) {
+ if ( _de == null ) {
+ _de = rec_name;
+ }
+ }
+
+ @Override
+ public String getTaxonomyScientificName() {
+ return _os;
+ }
+
+ private void setOs( final String os ) {
+ if ( _os == null ) {
+ _os = os;
+ }
+ }
+
+ @Override
+ public String getTaxonomyIdentifier() {
+ return _tax_id;
+ }
+
+ private void setTaxId( final String tax_id ) {
+ if ( _tax_id == null ) {
+ _tax_id = tax_id;
+ }
+ }
+
+ @Override
+ public String getSequenceSymbol() {
+ return _symbol;
+ }
+
+ private void setSymbol( final String symbol ) {
+ if ( _symbol == null ) {
+ _symbol = symbol;
+ }
+ }
+
+ @Override
+ public boolean isEmpty() {
+ return ( ForesterUtil.isEmpty( getAccession() ) && ForesterUtil.isEmpty( getSequenceName() )
+ && ForesterUtil.isEmpty( getTaxonomyScientificName() )
+ && ForesterUtil.isEmpty( getTaxonomyIdentifier() ) && ForesterUtil.isEmpty( getSequenceSymbol() ) );
+ }
+
+ @Override
+ public String getProvider() {
+ return _provider;
+ }
+
+ public void setProvider( final String provider ) {
+ _provider = provider;
+ }
+}
--- /dev/null
+// $Id:
+// forester -- software libraries and applications
+// for genomics and evolutionary biology research.
+//
+// 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
+// version 2.1 of the License, or (at your option) any later version.
+//
+// This library is distributed in the hope that it will be useful,
+// 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
+//
+// Contact: phylosoft @ gmail . com
+// WWW: www.phylosoft.org/forester
+
+package org.forester.ws.seqdb;
+
+public interface SequenceDatabaseEntry {
+
+ public boolean isEmpty();
+
+ public String getAccession();
+
+ public String getProvider();
+
+ public String getSequenceName();
+
+ public String getTaxonomyScientificName();
+
+ public String getTaxonomyIdentifier();
+
+ public String getSequenceSymbol();
+}
\ No newline at end of file
--- /dev/null
+// $Id:
+// forester -- software libraries and applications
+// for genomics and evolutionary biology research.
+//
+// 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
+// version 2.1 of the License, or (at your option) any later version.
+//
+// This library is distributed in the hope that it will be useful,
+// 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
+//
+// Contact: phylosoft @ gmail . com
+// WWW: www.phylosoft.org/forester
+
+package org.forester.ws.seqdb;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.io.UnsupportedEncodingException;
+import java.net.URL;
+import java.net.URLConnection;
+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.phylogeny.data.Identifier;
+import org.forester.util.ForesterUtil;
+
+public final class SequenceDbWsTools {
+
+ 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_UNIPROT_URL = "http://www.uniprot.org/";
+ public final static String BASE_EMBL_DB_URL = "http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/";
+ public final static String EMBL_DBS_EMBL = "embl";
+ public final static String EMBL_DBS_REFSEQ_P = "refseqp";
+ public final static String EMBL_DBS_REFSEQ_N = "refseqn";
+
+ 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;
+
+ private static String encode( final String str ) throws UnsupportedEncodingException {
+ return URLEncoder.encode( str.trim(), URL_ENC );
+ }
+
+ /**
+ * 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 parseUniProtTaxonomy( result );
+ }
+ return null;
+ }
+
+ 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 ) ) {
+ final List<UniProtTaxonomy> filtered_taxonomies = new ArrayList<UniProtTaxonomy>();
+ for( final UniProtTaxonomy taxonomy : taxonomies ) {
+ if ( taxonomy.getCommonName().equalsIgnoreCase( cn ) ) {
+ filtered_taxonomies.add( taxonomy );
+ }
+ }
+ return filtered_taxonomies;
+ }
+ return null;
+ }
+
+ 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 parseUniProtTaxonomy( result );
+ }
+ return null;
+ }
+
+ public static List<UniProtTaxonomy> getTaxonomiesFromScientificName( final String sn,
+ final int max_taxonomies_return )
+ throws IOException {
+ // Hack! Craniata? ..
+ if ( sn.equals( "Drosophila" ) ) {
+ return uniProtTaxonomyToList( UniProtTaxonomy.DROSOPHILA_GENUS );
+ }
+ else if ( sn.equals( "Xenopus" ) ) {
+ 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 );
+ }
+ return null;
+ }
+
+ /**
+ * Does not return "sub-types".
+ * For example, for "Mus musculus" only returns "Mus musculus"
+ * and not "Mus musculus", "Mus musculus bactrianus", ...
+ *
+ */
+ 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 ) ) {
+ final List<UniProtTaxonomy> filtered_taxonomies = new ArrayList<UniProtTaxonomy>();
+ for( final UniProtTaxonomy taxonomy : taxonomies ) {
+ if ( taxonomy.getScientificName().equalsIgnoreCase( sn ) ) {
+ filtered_taxonomies.add( taxonomy );
+ }
+ }
+ return filtered_taxonomies;
+ }
+ return null;
+ }
+
+ public static List<UniProtTaxonomy> getTaxonomiesFromTaxonomyCode( final String code,
+ final int max_taxonomies_return )
+ throws IOException {
+ 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 parseUniProtTaxonomy( result );
+ }
+ return null;
+ }
+
+ 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 if ( code.equals( "HYDPIN" ) ) {
+ return getTaxonomiesFromId( "388859", max_taxonomies_return );
+ }
+ else if ( code.equals( "SERLAC" ) ) {
+ return getTaxonomiesFromId( "85982", 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 );
+ }
+
+ 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 );
+ }
+
+ 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 );
+ }
+
+ 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 );
+ }
+
+ private static List<UniProtTaxonomy> uniProtTaxonomyToList( final UniProtTaxonomy tax ) {
+ final List<UniProtTaxonomy> l = new ArrayList<UniProtTaxonomy>();
+ l.add( tax );
+ return l;
+ }
+
+ 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" ) ) {
+ 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 ) {
+ taxonomies.add( new UniProtTaxonomy( line ) );
+ }
+ }
+ }
+ return taxonomies;
+ }
+
+ public static List<String> queryEmblDb( final Identifier id, final int max_lines_to_return ) throws IOException {
+
+ StringBuilder url_sb = new StringBuilder();
+ url_sb.append( BASE_EMBL_DB_URL );
+
+ if ( ForesterUtil.isEmpty( id.getProvider() ) || id.getProvider().equalsIgnoreCase( Identifier.NCBI ) ) {
+
+ url_sb.append( SequenceDbWsTools.EMBL_DBS_EMBL );
+ url_sb.append( '/');
+ }
+ else if ( id.getProvider().equalsIgnoreCase( Identifier.REFSEQ ) ) {
+ if ( id.getValue().toUpperCase().indexOf( 'P' ) == 1 ) {
+
+ url_sb.append( SequenceDbWsTools.EMBL_DBS_REFSEQ_P );
+ url_sb.append( '/');
+ }
+ else {
+
+ url_sb.append( SequenceDbWsTools.EMBL_DBS_REFSEQ_N );
+ url_sb.append( '/');
+ }
+ }
+ return queryDb( id.getValue(), max_lines_to_return, url_sb.toString() );
+ }
+
+ public static List<String> queryUniprot( final String query, final int max_lines_to_return ) throws IOException {
+ return queryDb( query, max_lines_to_return, BASE_UNIPROT_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 );
+ if ( DEBUG ) {
+ System.out.println( "url: " + url.toString() );
+ }
+ final URLConnection urlc = url.openConnection();
+ final BufferedReader in = new BufferedReader( new InputStreamReader( urlc.getInputStream() ) );
+ 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 obtainRefSeqEntryFromEmbl( final Identifier id, final int max_lines_to_return )
+ throws IOException {
+ final List<String> lines = queryEmblDb( id, max_lines_to_return );
+ return EbiDbEntry.createInstanceFromPlainTextForRefSeq( lines );
+ }
+
+ public static SequenceDatabaseEntry obtainEmblEntry( final Identifier id, final int max_lines_to_return )
+ throws IOException {
+ final List<String> lines = queryEmblDb( id , max_lines_to_return );
+ return EbiDbEntry.createInstanceFromPlainText( lines );
+ }
+}
--- /dev/null
+// $Id:
+// forester -- software libraries and applications
+// for genomics and evolutionary biology research.
+//
+// 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
+// version 2.1 of the License, or (at your option) any later version.
+//
+// This library is distributed in the hope that it will be useful,
+// 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
+//
+// Contact: phylosoft @ gmail . com
+// WWW: www.phylosoft.org/forester
+
+package org.forester.ws.seqdb;
+
+import java.util.List;
+
+import org.forester.util.ForesterUtil;
+
+public final class UniProtEntry implements SequenceDatabaseEntry {
+
+ private String _ac;
+ private String _rec_name;
+ private String _os_scientific_name;
+ private String _tax_id;
+ private String _symbol;
+
+ private UniProtEntry() {
+ }
+
+ @Override
+ public Object clone() throws CloneNotSupportedException {
+ throw new CloneNotSupportedException();
+ }
+
+ public static SequenceDatabaseEntry createInstanceFromPlainText( final List<String> lines ) {
+ final UniProtEntry e = new UniProtEntry();
+ for( final String line : lines ) {
+ if ( line.startsWith( "AC" ) ) {
+ e.setAc( DatabaseTools.extract( line, "AC", ";" ) );
+ }
+ else if ( line.startsWith( "DE" ) ) {
+ if ( ( line.indexOf( "RecName:" ) > 0 ) && ( line.indexOf( "Full=" ) > 0 ) ) {
+ e.setRecName( DatabaseTools.extract( line, "Full=", ";" ) );
+ }
+ }
+ else if ( line.startsWith( "GN" ) ) {
+ if ( ( line.indexOf( "Name=" ) > 0 ) ) {
+ e.setSymbol( DatabaseTools.extract( line, "Name=", ";" ) );
+ }
+ }
+ else if ( line.startsWith( "OS" ) ) {
+ if ( line.indexOf( "(" ) > 0 ) {
+ e.setOsScientificName( DatabaseTools.extract( line, "OS", "(" ) );
+ }
+ else {
+ e.setOsScientificName( DatabaseTools.extract( line, "OS", "." ) );
+ }
+ }
+ else if ( line.startsWith( "OX" ) ) {
+ if ( line.indexOf( "NCBI_TaxID=" ) > 0 ) {
+ e.setTaxId( DatabaseTools.extract( line, "NCBI_TaxID=", ";" ) );
+ }
+ }
+ }
+ return e;
+ }
+
+ @Override
+ public String getAccession() {
+ return _ac;
+ }
+
+ private void setAc( final String ac ) {
+ if ( _ac == null ) {
+ _ac = ac;
+ }
+ }
+
+ @Override
+ public String getSequenceName() {
+ return _rec_name;
+ }
+
+ private void setRecName( final String rec_name ) {
+ if ( _rec_name == null ) {
+ _rec_name = rec_name;
+ }
+ }
+
+ @Override
+ public String getTaxonomyScientificName() {
+ return _os_scientific_name;
+ }
+
+ private void setOsScientificName( final String os_scientific_name ) {
+ if ( _os_scientific_name == null ) {
+ _os_scientific_name = os_scientific_name;
+ }
+ }
+
+ @Override
+ public String getTaxonomyIdentifier() {
+ return _tax_id;
+ }
+
+ private void setTaxId( final String tax_id ) {
+ if ( _tax_id == null ) {
+ _tax_id = tax_id;
+ }
+ }
+
+ @Override
+ public String getSequenceSymbol() {
+ return _symbol;
+ }
+
+ private void setSymbol( final String symbol ) {
+ if ( _symbol == null ) {
+ _symbol = symbol;
+ }
+ }
+
+ @Override
+ public boolean isEmpty() {
+ return ( ForesterUtil.isEmpty( getAccession() ) && ForesterUtil.isEmpty( getSequenceName() )
+ && ForesterUtil.isEmpty( getTaxonomyScientificName() )
+ && ForesterUtil.isEmpty( getTaxonomyIdentifier() ) && ForesterUtil.isEmpty( getSequenceSymbol() ) );
+ }
+
+ @Override
+ public String getProvider() {
+ return "uniprot";
+ }
+}
--- /dev/null
+// $Id:
+// forester -- software libraries and applications
+// for genomics and evolutionary biology research.
+//
+// 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
+// version 2.1 of the License, or (at your option) any later version.
+//
+// This library is distributed in the hope that it will be useful,
+// 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
+//
+// Contact: phylosoft @ gmail . com
+// WWW: www.phylosoft.org/forester
+
+package org.forester.ws.seqdb;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.forester.util.ForesterUtil;
+
+public final class UniProtTaxonomy {
+
+ private static final String ARCHAEA = "Archaea";
+ private static final String BACTERIA = "Bacteria";
+ private static final String EUKARYOTA = "Eukaryota";
+ private final List<String> _lineage;
+ private final String _code;
+ private final String _scientific_name;
+ private final String _common_name;
+ private final String _synonym;
+ private final String _rank;
+ private final String _id;
+ public final static String CELLULAR_ORGANISMS = "cellular organisms";
+ public final static String VIRUSES = "Viruses";
+ public final static UniProtTaxonomy DROSOPHILA_GENUS = new UniProtTaxonomy( new String[] {
+ CELLULAR_ORGANISMS, EUKARYOTA, "Metazoa", "Arthropoda", "Hexapoda", "Insecta", "Pterygota", "Neoptera",
+ "Endopterygota", "Diptera", "Brachycera", "Muscomorpha", "Ephydroidea", "Drosophilidae", "Drosophila" },
+ "",
+ "fruit flies",
+ "Drosophila",
+ "",
+ "genus",
+ "7215" );
+ public final static UniProtTaxonomy XENOPUS_GENUS = new UniProtTaxonomy( new String[] {
+ CELLULAR_ORGANISMS, EUKARYOTA, "Metazoa", "Chordata", "Craniata", "Vertebrata", "Euteleostomi", "Amphibia",
+ "Batrachia", "Anura", "Mesobatrachia", "Pipoidea", "Pipidae", "Xenopodinae", "Xenopus" },
+ "",
+ "",
+ "Xenopus",
+ "",
+ "genus",
+ "8353" );
+ public final static UniProtTaxonomy CAPITELLA_TELATA_SPECIES = new UniProtTaxonomy( new String[] {
+ CELLULAR_ORGANISMS, EUKARYOTA, "Metazoa", "Annelida", "Polychaeta", "Scolecida", "Capitellida",
+ "Capitellidae", "Capitella", "Capitella teleta" },
+ "",
+ "",
+ "Capitella teleta",
+ "Capitella sp. I",
+ "species",
+ "283909" );
+
+ // public final static UniProtTaxonomy NUCLEARIIDAE_AND_FONTICULA = new UniProtTaxonomy( new String[] {
+ // CELLULAR_ORGANISMS, EUKARYOTA, "Nucleariidae and Fonticula group" }, "", "", "", "", "", "1001604" );
+ public UniProtTaxonomy( final String line ) {
+ final String[] items = line.split( "\t" );
+ if ( items.length < 5 ) {
+ throw new IllegalArgumentException( "cannot parse uniprot taxonomy from: " + line );
+ }
+ _id = items[ 0 ].trim();
+ _code = items[ 1 ].trim();
+ _scientific_name = items[ 2 ].trim();
+ _common_name = items[ 3 ].trim();
+ _synonym = items[ 4 ].trim();
+ if ( items.length > 6 ) {
+ _rank = items[ 7 ].trim();
+ }
+ else {
+ _rank = "";
+ }
+ String[] lin = null;
+ if ( items.length > 8 ) {
+ lin = items[ 8 ].split( "; " );
+ }
+ _lineage = new ArrayList<String>();
+ if ( ( lin != null ) && ( lin.length > 0 ) ) {
+ final List<String> temp = new ArrayList<String>();
+ for( final String t : lin ) {
+ if ( !ForesterUtil.isEmpty( t ) ) {
+ temp.add( t.trim() );
+ }
+ }
+ for( int i = 0; i < temp.size(); ++i ) {
+ if ( ( i == 0 )
+ && ( temp.get( i ).equalsIgnoreCase( EUKARYOTA ) || temp.get( i ).equalsIgnoreCase( BACTERIA ) || temp
+ .get( i ).equalsIgnoreCase( ARCHAEA ) ) ) {
+ _lineage.add( CELLULAR_ORGANISMS );
+ }
+ _lineage.add( temp.get( i ) );
+ }
+ }
+ if ( _lineage.isEmpty()
+ && ( _scientific_name.equalsIgnoreCase( EUKARYOTA ) || _scientific_name.equalsIgnoreCase( BACTERIA ) || _scientific_name
+ .equalsIgnoreCase( ARCHAEA ) ) ) {
+ _lineage.add( CELLULAR_ORGANISMS );
+ }
+ _lineage.add( _scientific_name );
+ if ( _lineage.isEmpty() ) {
+ throw new IllegalArgumentException( "lineage in a UniProt Taxonomy can not be empty\n: " + line );
+ }
+ }
+
+ public UniProtTaxonomy( final List<String> lineage,
+ final String code,
+ final String common_name,
+ final String scientific_name,
+ final String synonym,
+ final String rank,
+ final String id ) {
+ _lineage = lineage;
+ _code = code;
+ _scientific_name = scientific_name;
+ _common_name = common_name;
+ _synonym = synonym;
+ _rank = rank;
+ _id = id;
+ if ( ( _lineage != null ) && !_lineage.get( _lineage.size() - 1 ).equalsIgnoreCase( _scientific_name ) ) {
+ _lineage.add( _scientific_name );
+ }
+ }
+
+ public UniProtTaxonomy( final String[] lineage,
+ final String code,
+ final String common_name,
+ final String scientific_name,
+ final String synonym,
+ final String rank,
+ final String id ) {
+ _lineage = new ArrayList<String>();
+ if ( lineage != null ) {
+ for( final String l : lineage ) {
+ _lineage.add( l );
+ }
+ }
+ _code = code;
+ _scientific_name = scientific_name;
+ _common_name = common_name;
+ _synonym = synonym;
+ _rank = rank;
+ _id = id;
+ if ( ( _lineage != null ) && !_lineage.get( _lineage.size() - 1 ).equalsIgnoreCase( _scientific_name ) ) {
+ _lineage.add( _scientific_name );
+ }
+ }
+
+ /**
+ * Creates deep copy for all fields, except lineage.
+ *
+ * @return
+ */
+ public UniProtTaxonomy copy() {
+ return new UniProtTaxonomy( getLineage(),
+ getCode() != null ? new String( getCode() ) : null,
+ getCommonName() != null ? new String( getCommonName() ) : null,
+ getScientificName() != null ? new String( getScientificName() ) : null,
+ getSynonym() != null ? new String( getSynonym() ) : null,
+ getRank() != null ? new String( getRank() ) : null,
+ getId() != null ? new String( getId() ) : null );
+ }
+
+ public String getCode() {
+ return _code;
+ }
+
+ public String getCommonName() {
+ return _common_name;
+ }
+
+ public String getId() {
+ return _id;
+ }
+
+ public List<String> getLineage() {
+ return _lineage;
+ }
+
+ public String getRank() {
+ return _rank;
+ }
+
+ public String getScientificName() {
+ return _scientific_name;
+ }
+
+ public String getSynonym() {
+ return _synonym;
+ }
+}
git://source.jalview.org / jalview.git / commitdiff