+++ /dev/null
-
-package org.forester.ws.uniprot;
-
-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.uniprot;
-
-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.uniprot;
-
-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.uniprot;
-
-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 {
- final 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.uniprot;
-
-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.uniprot;
-
-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