// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
//
// Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
package org.forester.ws.seqdb;
import java.io.BufferedReader;
+import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.InputStreamReader;
import java.io.UnsupportedEncodingException;
import java.net.URLEncoder;
import java.util.ArrayList;
import java.util.List;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
+import java.util.SortedSet;
+import java.util.TreeSet;
+import org.forester.go.GoTerm;
+import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
+import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.PhylogenyNode;
+import org.forester.phylogeny.data.Accession;
+import org.forester.phylogeny.data.Accession.Source;
+import org.forester.phylogeny.data.Annotation;
import org.forester.phylogeny.data.Identifier;
+import org.forester.phylogeny.data.Sequence;
+import org.forester.phylogeny.data.Taxonomy;
+import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
+import org.forester.sequence.MolecularSequence.TYPE;
import org.forester.util.ForesterUtil;
+import org.forester.util.SequenceAccessionTools;
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 final static String BASE_UNIPROT_URL = "http://www.uniprot.org/";
+ public final static int DEFAULT_LINES_TO_RETURN = 4000;
+ public final static String EMBL_DBS_REFSEQ_N = "refseqn";
+ public final static String EMBL_DBS_REFSEQ_P = "refseqp";
+ public final static String EMBL_GENBANK = "http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=GENBANK&style=raw&id=";
+ public final static String EMBL_REFSEQ = "http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=REFSEQ&style=raw&id=";
+ public final static String EMBL_EMBL = "http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=EMBL&style=raw&id=";
+ private final static boolean DEBUG = true;
+ private final static String URL_ENC = "UTF-8";
+ private final static int SLEEP = 200;
+ private static final boolean ALLOW_TO_OVERWRITE_MOL_SEQ = false;
public static List<UniProtTaxonomy> getTaxonomiesFromCommonNameStrict( final String cn,
final int max_taxonomies_return )
- throws IOException {
+ 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>();
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 {
+ 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>();
public static List<UniProtTaxonomy> getTaxonomiesFromTaxonomyCode( final String code,
final int max_taxonomies_return )
- throws IOException {
+ 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 )
+ public static SequenceDatabaseEntry obtainEmblEntry( final Accession acc ) throws IOException {
+ return obtainEmblEntry( acc, DEFAULT_LINES_TO_RETURN );
+ }
+
+ public static SequenceDatabaseEntry obtainEmblEntry( final Accession acc, final int max_lines_to_return )
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 );
+ final List<String> lines = queryEmblDb( acc, max_lines_to_return );
+ return EbiDbEntry.createInstanceFromPlainTextForRefSeq( lines );
+ }
+
+ public static SequenceDatabaseEntry obtainEntry( final String acc_str ) throws IOException {
+ if ( ForesterUtil.isEmpty( acc_str ) ) {
+ throw new IllegalArgumentException( "cannot not extract sequence db accessor from null or empty string" );
}
- else if ( code.equals( "CAPOWC" ) ) {
- return getTaxonomiesFromId( "192875", max_taxonomies_return );
+ final Accession acc = SequenceAccessionTools.parseAccessorFromString( acc_str );
+ if ( acc == null ) {
+ throw new IllegalArgumentException( "could not extract acceptable sequence db accessor from \"" + acc_str
+ + "\"" );
}
- else if ( code.equals( "SPHARC" ) ) {
- return getTaxonomiesFromId( "667725", max_taxonomies_return );
+ if ( acc.getSource().equals( Source.REFSEQ.toString() ) || acc.getSource().equals( Source.EMBL.toString() )
+ || acc.getSource().equals( Source.NCBI.toString() ) ) {
+ return obtainEmblEntry( acc, DEFAULT_LINES_TO_RETURN );
}
- else if ( code.equals( "THETRA" ) ) {
- return getTaxonomiesFromId( "529818", max_taxonomies_return );
+ else if ( acc.getSource().equals( Source.UNIPROT.toString() ) ) {
+ return obtainUniProtEntry( acc.getValue(), DEFAULT_LINES_TO_RETURN );
}
- else if ( code.equals( "CHLVUL" ) ) {
- return getTaxonomiesFromId( "574566", max_taxonomies_return );
+ else {
+ throw new IllegalArgumentException( "don't know how to handle request for source \"" + acc.getSource()
+ + "\"" );
}
- else if ( code.equals( "CITCLE" ) ) {
- return getTaxonomiesFromId( "85681", max_taxonomies_return );
+ }
+
+ public static SequenceDatabaseEntry obtainRefSeqEntryFromEmbl( final Accession acc ) throws IOException {
+ return obtainRefSeqEntryFromEmbl( acc, DEFAULT_LINES_TO_RETURN );
+ }
+
+ public static SequenceDatabaseEntry obtainRefSeqEntryFromEmbl( final Accession acc, final int max_lines_to_return )
+ throws IOException {
+ final List<String> lines = queryEmblDbForRefSeqEntry( acc, max_lines_to_return );
+ return EbiDbEntry.createInstanceFromPlainTextForRefSeq( lines );
+ }
+
+ public final static Accession obtainSeqAccession( final PhylogenyNode node ) {
+ Accession acc = SequenceAccessionTools.obtainFromSeqAccession( node );
+ if ( !isAccessionAcceptable( acc ) ) {
+ acc = SequenceAccessionTools.obtainAccessorFromDataFields( node );
}
- else if ( code.equals( "MYCPOP" ) ) {
- return getTaxonomiesFromId( "85929", max_taxonomies_return );
+ return acc;
+ }
+
+ public final static void obtainSeqInformation( final boolean allow_to_set_taxonomic_data,
+ final int lines_to_return,
+ final SortedSet<String> not_found,
+ final PhylogenyNode node ) throws IOException {
+ final Accession acc = obtainSeqAccession( node );
+ if ( !isAccessionAcceptable( acc ) ) {
+ if ( node.isExternal() || !node.isEmpty() ) {
+ not_found.add( node.toString() );
+ }
}
- else if ( code.equals( "AGABB" ) ) {
- return getTaxonomiesFromId( "597362", max_taxonomies_return );
+ else {
+ addDataFromDbToNode( allow_to_set_taxonomic_data, lines_to_return, not_found, node, acc );
}
- else if ( code.equals( "BAUCOM" ) ) {
- return getTaxonomiesFromId( "430998", max_taxonomies_return );
+ }
+
+ public final static void obtainSeqInformation( final boolean allow_to_set_taxonomic_data,
+ final SortedSet<String> not_found,
+ final PhylogenyNode node ) throws IOException {
+ obtainSeqInformation( allow_to_set_taxonomic_data, DEFAULT_LINES_TO_RETURN, not_found, node );
+ }
+
+ public final static SortedSet<String> obtainSeqInformation( final Phylogeny phy,
+ final boolean ext_nodes_only,
+ final boolean allow_to_set_taxonomic_data,
+ final int lines_to_return ) throws IOException {
+ final SortedSet<String> not_found = new TreeSet<String>();
+ for( final PhylogenyNodeIterator iter = phy.iteratorPostorder(); iter.hasNext(); ) {
+ final PhylogenyNode node = iter.next();
+ if ( node.isExternal() || !ext_nodes_only ) {
+ obtainSeqInformation( allow_to_set_taxonomic_data, lines_to_return, not_found, node );
+ }
}
- else if ( code.equals( "DICSQU" ) ) {
- return getTaxonomiesFromId( "114155", max_taxonomies_return );
+ return not_found;
+ }
+
+ public final static void obtainSeqInformation( final PhylogenyNode node ) throws IOException {
+ obtainSeqInformation( true, DEFAULT_LINES_TO_RETURN, new TreeSet<String>(), node );
+ }
+
+ public static SequenceDatabaseEntry obtainUniProtEntry( final String query ) throws IOException {
+ return obtainUniProtEntry( query, DEFAULT_LINES_TO_RETURN );
+ }
+
+ 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 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 " );
}
- else if ( code.equals( "FOMPIN" ) ) {
- return getTaxonomiesFromId( "40483", max_taxonomies_return );
+ if ( max_lines_to_return < 1 ) {
+ max_lines_to_return = 1;
}
- else if ( code.equals( "HYDMA" ) ) {
- return getTaxonomiesFromId( "6085", max_taxonomies_return );
+ final URL url = new URL( base_url + query );
+ if ( DEBUG ) {
+ System.out.println( "url: " + url.toString() );
}
- else if ( code.equals( "MYCFI" ) ) {
- return getTaxonomiesFromId( "83344", max_taxonomies_return );
+ 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;
+ }
}
- else if ( code.equals( "OIDMAI" ) ) {
- return getTaxonomiesFromId( "78148", max_taxonomies_return );
+ in.close();
+ try {
+ // To prevent accessing online dbs in too quick succession.
+ Thread.sleep( SLEEP );
}
- else if ( code.equals( "OSTRC" ) ) {
- return getTaxonomiesFromId( "385169", max_taxonomies_return );
+ catch ( final InterruptedException e ) {
+ e.printStackTrace();
}
- else if ( code.equals( "POSPL" ) ) {
- return getTaxonomiesFromId( "104341", max_taxonomies_return );
+ return result;
+ }
+
+ public static List<String> queryEmblDb( final Accession acc, final int max_lines_to_return ) throws IOException {
+ final StringBuilder url_sb = new StringBuilder();
+ // url_sb.append( BASE_EMBL_DB_URL );
+ System.out.println( "source: " + acc.getSource() );
+ if ( acc.getSource().equals( Source.NCBI.toString() ) ) {
+ url_sb.append( EMBL_GENBANK );
+ //url_sb.append( '/' );
}
- else if ( code.equals( "SAICOM" ) ) {
- return getTaxonomiesFromId( "5606", max_taxonomies_return );
+ else if ( acc.getSource().equals( Source.REFSEQ.toString() ) ) {
+ url_sb.append( EMBL_REFSEQ );
}
- else if ( code.equals( "SERLA" ) ) {
- return getTaxonomiesFromId( "85982", max_taxonomies_return );
+ else if ( acc.getSource().equals( Source.EMBL.toString() ) ) {
+ url_sb.append( EMBL_EMBL );
}
- else if ( code.equals( "SPORO" ) ) {
- return getTaxonomiesFromId( "40563", max_taxonomies_return );
+ else {
+ throw new IllegalArgumentException( "unable to handle source: " + acc.getSource() );
}
- else if ( code.equals( "ACRALC" ) ) {
- return getTaxonomiesFromId( "398408", max_taxonomies_return );
+ return queryDb( acc.getValue(), max_lines_to_return, url_sb.toString() );
+ }
+
+ public static List<String> queryEmblDbForRefSeqEntry( final Accession id, final int max_lines_to_return )
+ throws IOException {
+ final StringBuilder url_sb = new StringBuilder();
+ url_sb.append( EMBL_REFSEQ );
+ 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 );
+ }
+
+ final static String extractFrom( final String target, final String a ) {
+ final int i_a = target.indexOf( a );
+ return target.substring( i_a + a.length() ).trim();
+ }
+
+ final static String extractFromTo( 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();
+ }
+
+ final static String extractTo( final String target, final String b ) {
+ final int i_b = target.indexOf( b );
+ return target.substring( 0, i_b ).trim();
+ }
+
+ private static void addDataFromDbToNode( final boolean allow_to_set_taxonomic_data,
+ final int lines_to_return,
+ final SortedSet<String> not_found,
+ final PhylogenyNode node,
+ final Accession acc ) throws IOException {
+ SequenceDatabaseEntry db_entry = null;
+ final String query = acc.getValue();
+ if ( acc.getSource().equals( Source.UNIPROT.toString() ) ) {
+ if ( DEBUG ) {
+ System.out.println( "uniprot: " + query );
+ }
+ try {
+ db_entry = obtainUniProtEntry( query, lines_to_return );
+ }
+ catch ( final FileNotFoundException e ) {
+ // Eat this, and move to next.
+ }
}
- else if ( code.equals( "THITER" ) ) {
- return getTaxonomiesFromId( "35720", max_taxonomies_return );
+ else if ( acc.getSource().equals( Source.REFSEQ.toString() ) ) {
+ if ( DEBUG ) {
+ System.out.println( "refseq: " + query );
+ }
+ try {
+ db_entry = obtainRefSeqEntryFromEmbl( new Accession( query ), lines_to_return );
+ }
+ catch ( final FileNotFoundException e ) {
+ // Eat this, and move to next.
+ }
}
- else if ( code.equals( "MYCTHE" ) ) {
- return getTaxonomiesFromId( "78579", max_taxonomies_return );
+ else if ( acc.getSource().equals( Source.EMBL.toString() ) || acc.getSource().equals( Source.NCBI.toString() )
+ || acc.getSource().equals( Source.EMBL.toString() ) ) {
+ if ( DEBUG ) {
+ System.out.println( acc.toString() );
+ }
+ try {
+ db_entry = obtainEmblEntry( acc, lines_to_return );
+ }
+ catch ( final FileNotFoundException e ) {
+ // Eat this, and move to next.
+ }
}
- else if ( code.equals( "CONPUT" ) ) {
- return getTaxonomiesFromId( "80637", max_taxonomies_return );
+ else if ( acc.getSource().equals( Source.GI.toString() ) ) {
+ if ( DEBUG ) {
+ System.out.println( "gi: " + query );
+ }
+ try {
+ db_entry = obtainRefSeqEntryFromEmbl( new Accession( query ), lines_to_return );
+ }
+ catch ( final FileNotFoundException e ) {
+ // Eat this, and move to next.
+ }
}
- else if ( code.equals( "WOLCOC" ) ) {
- return getTaxonomiesFromId( "81056", max_taxonomies_return );
+ if ( ( db_entry != null ) && !db_entry.isEmpty() ) {
+ final Sequence seq = node.getNodeData().isHasSequence() ? node.getNodeData().getSequence() : new Sequence();
+ if ( !ForesterUtil.isEmpty( db_entry.getAccession() ) ) {
+ seq.setAccession( new Accession( db_entry.getAccession(), acc.getSource() ) );
+ }
+ if ( !ForesterUtil.isEmpty( db_entry.getSequenceName() ) ) {
+ seq.setName( db_entry.getSequenceName() );
+ }
+ if ( !ForesterUtil.isEmpty( db_entry.getGeneName() ) ) {
+ seq.setGeneName( db_entry.getGeneName() );
+ }
+ if ( !ForesterUtil.isEmpty( db_entry.getSequenceSymbol() ) ) {
+ try {
+ seq.setSymbol( db_entry.getSequenceSymbol() );
+ }
+ catch ( final PhyloXmlDataFormatException e ) {
+ // Eat this exception.
+ }
+ }
+ if ( ( db_entry.getMolecularSequence() != null )
+ && !ForesterUtil.isEmpty( db_entry.getMolecularSequence().getMolecularSequenceAsString() )
+ && ( ALLOW_TO_OVERWRITE_MOL_SEQ || seq.getMolecularSequence().isEmpty() ) ) {
+ seq.setMolecularSequence( db_entry.getMolecularSequence().getMolecularSequenceAsString() );
+ seq.setMolecularSequenceAligned( false );
+ if ( db_entry.getMolecularSequence().getType() == TYPE.AA ) {
+ seq.setType( "protein" );
+ }
+ else if ( db_entry.getMolecularSequence().getType() == TYPE.DNA ) {
+ seq.setType( "dna" );
+ }
+ else if ( db_entry.getMolecularSequence().getType() == TYPE.RNA ) {
+ seq.setType( "rna" );
+ }
+ }
+ if ( ( db_entry.getGoTerms() != null ) && !db_entry.getGoTerms().isEmpty() ) {
+ for( final GoTerm go : db_entry.getGoTerms() ) {
+ final Annotation ann = new Annotation( go.getGoId().getId() );
+ ann.setDesc( go.getName() );
+ seq.addAnnotation( ann );
+ }
+ }
+ if ( ( db_entry.getCrossReferences() != null ) && !db_entry.getCrossReferences().isEmpty() ) {
+ for( final Accession x : db_entry.getCrossReferences() ) {
+ seq.addCrossReference( x );
+ }
+ }
+ if ( !ForesterUtil.isEmpty( db_entry.getChromosome() ) && !ForesterUtil.isEmpty( db_entry.getMap() ) ) {
+ seq.setLocation( "chr " + db_entry.getChromosome() + ", " + db_entry.getMap() );
+ }
+ else if ( !ForesterUtil.isEmpty( db_entry.getChromosome() ) ) {
+ seq.setLocation( "chr " + db_entry.getChromosome() );
+ }
+ else if ( !ForesterUtil.isEmpty( db_entry.getMap() ) ) {
+ seq.setLocation( db_entry.getMap() );
+ }
+ final Taxonomy tax = node.getNodeData().isHasTaxonomy() ? node.getNodeData().getTaxonomy() : new Taxonomy();
+ if ( !ForesterUtil.isEmpty( db_entry.getTaxonomyScientificName() ) ) {
+ tax.setScientificName( db_entry.getTaxonomyScientificName() );
+ }
+ if ( allow_to_set_taxonomic_data && !ForesterUtil.isEmpty( db_entry.getTaxonomyIdentifier() ) ) {
+ tax.setIdentifier( new Identifier( db_entry.getTaxonomyIdentifier(), "uniprot" ) );
+ }
+ node.getNodeData().setTaxonomy( tax );
+ node.getNodeData().setSequence( seq );
}
- else if ( code.equals( "CLAGRA" ) ) {
- return getTaxonomiesFromId( "27339", max_taxonomies_return );
+ else {
+ if ( node.isExternal() || !node.isEmpty() ) {
+ not_found.add( node.toString() );
+ }
}
- else if ( code.equals( "XANPAR" ) ) {
- return getTaxonomiesFromId( "107463", max_taxonomies_return );
+ try {
+ Thread.sleep( SLEEP );
}
- else if ( code.equals( "HYDPIN" ) ) {
- return getTaxonomiesFromId( "388859", max_taxonomies_return );
+ catch ( final InterruptedException ie ) {
}
- else if ( code.equals( "SERLAC" ) ) {
- return getTaxonomiesFromId( "85982", max_taxonomies_return );
+ }
+
+ private static String encode( final String str ) throws UnsupportedEncodingException {
+ return URLEncoder.encode( str.trim(), URL_ENC );
+ }
+
+ private 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 );
}
- else {
- return null;
+ return null;
+ }
+
+ private static List<UniProtTaxonomy> getTaxonomiesFromScientificName( final String sn,
+ final int max_taxonomies_return )
+ throws IOException {
+ final List<String> result = getTaxonomyStringFromScientificName( sn, max_taxonomies_return );
+ if ( result.size() > 0 ) {
+ return parseUniProtTaxonomy( result );
}
+ return null;
}
private static List<String> getTaxonomyStringFromCommonName( final String cn, final int max_lines_to_return )
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 final static boolean isAccessionAcceptable( final Accession acc ) {
+ return ( !( ( acc == null ) || ForesterUtil.isEmpty( acc.getSource() ) || ForesterUtil.isEmpty( acc.getValue() ) || ( ( acc
+ .getSource().equals( Source.UNIPROT.toString() ) )
+ && ( acc.getSource().toString().equals( Source.EMBL.toString() ) ) && ( acc.getSource().toString()
+ .equals( Source.REFSEQ.toString() ) ) ) ) );
}
private static List<UniProtTaxonomy> parseUniProtTaxonomy( final List<String> result ) throws IOException {
}
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();
- try {
- // To prevent accessing online dbs in too quick succession.
- Thread.sleep( 20 );
- }
- catch ( InterruptedException e ) {
- e.printStackTrace();
- }
- 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 );
- }
}
git://source.jalview.org / jalview.git / blobdiff