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 {
- 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;
+ 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 = false;
+ 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 )
* 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 )
public static SequenceDatabaseEntry obtainEmblEntry( final Accession acc, final int max_lines_to_return )
throws IOException {
final List<String> lines = queryEmblDb( acc, max_lines_to_return );
- return EbiDbEntry.createInstanceFromPlainTextForRefSeq( lines );
+ return EbiDbEntry.createInstance( lines );
}
public static SequenceDatabaseEntry obtainEntry( final String acc_str ) throws IOException {
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 );
+ return EbiDbEntry.createInstance( lines );
}
public final static Accession obtainSeqAccession( final PhylogenyNode node ) {
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 );
+ return UniProtEntry.createInstance( lines );
}
public static List<String> queryDb( final String query, int max_lines_to_return, final String base_url )
}
in.close();
try {
- // To prevent accessing online dbs in too quick succession.
+ // To prevent accessing online dbs in too quick succession.
Thread.sleep( SLEEP );
}
catch ( final InterruptedException e ) {
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 ( DEBUG ) {
+ System.out.println( "source: " + acc.getSource() );
+ }
if ( acc.getSource().equals( Source.NCBI.toString() ) ) {
url_sb.append( EMBL_GENBANK );
//url_sb.append( '/' );
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 "";
}
return target.substring( i_a + a.length(), i_b ).trim();
}
// 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() );