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;
public final class SequenceDbWsTools {
- public final static String BASE_EMBL_DB_URL = "http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/";
- public final static String BASE_UNIPROT_URL = "http://www.uniprot.org/";
- public final static String EMBL_DBS_EMBL = "embl";
- public final static String EMBL_DBS_REFSEQ_N = "refseqn";
- public final static String EMBL_DBS_REFSEQ_P = "refseqp";
- private final static boolean DEBUG = true;
- private final static String URL_ENC = "UTF-8";
+ public final static String EMBL_REFSEQ = "http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=REFSEQ&style=raw&id=";
+ public final static String EMBL_GENBANK = "http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=GENBANK&style=raw&id=";
+ public final static String BASE_UNIPROT_URL = "http://www.uniprot.org/";
+ //public final static String EMBL_DBS_EMBL = "embl";
+ public final static String EMBL_DBS_REFSEQ_N = "refseqn";
+ public final static String EMBL_DBS_REFSEQ_P = "refseqp";
+ private final static boolean DEBUG = true;
+ private final static String URL_ENC = "UTF-8";
+ public final static int DEFAULT_LINES_TO_RETURN = 4000;
+
+ 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();
+ }
public static List<UniProtTaxonomy> getTaxonomiesFromCommonNameStrict( final String cn,
final int max_taxonomies_return )
return null;
}
- public static SequenceDatabaseEntry obtainEmblEntry( final Accession id, final int max_lines_to_return )
+ public static SequenceDatabaseEntry obtainEmblEntry( final Accession acc, final int max_lines_to_return )
throws IOException {
- final List<String> lines = queryEmblDb( id, max_lines_to_return );
- return EbiDbEntry.createInstanceFromPlainText( lines );
+ final List<String> lines = queryEmblDb( acc, max_lines_to_return );
+ return EbiDbEntry.createInstanceFromPlainTextForRefSeq( lines );
}
- public final static Accession obtainFromSeqAccession( final PhylogenyNode node ) {
+ public static SequenceDatabaseEntry obtainEmblEntry( final Accession acc ) throws IOException {
+ return obtainEmblEntry( acc, DEFAULT_LINES_TO_RETURN );
+ }
+
+ public final static Accession obtainSeqAccession( final PhylogenyNode node ) {
Accession acc = SequenceAccessionTools.obtainFromSeqAccession( node );
if ( !isAccessionAcceptable( acc ) ) {
acc = SequenceAccessionTools.obtainAccessorFromDataFields( node );
return acc;
}
- public static SequenceDatabaseEntry obtainRefSeqEntryFromEmbl( final Accession id, final int max_lines_to_return )
+ public static SequenceDatabaseEntry obtainRefSeqEntryFromEmbl( final Accession acc, final int max_lines_to_return )
throws IOException {
- final List<String> lines = queryEmblDb( id, max_lines_to_return );
+ final List<String> lines = queryEmblDbForRefSeqEntry( acc, max_lines_to_return );
return EbiDbEntry.createInstanceFromPlainTextForRefSeq( lines );
}
+ public static SequenceDatabaseEntry obtainRefSeqEntryFromEmbl( final Accession acc ) throws IOException {
+ return obtainRefSeqEntryFromEmbl( acc, DEFAULT_LINES_TO_RETURN );
+ }
+
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 = obtainFromSeqAccession( node );
+ final Accession acc = obtainSeqAccession( node );
if ( !isAccessionAcceptable( acc ) ) {
if ( node.isExternal() || !node.isEmpty() ) {
not_found.add( node.toString() );
}
}
+ 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 void obtainSeqInformation( final PhylogenyNode node ) throws IOException {
+ obtainSeqInformation( true, DEFAULT_LINES_TO_RETURN, new TreeSet<String>(), node );
+ }
+
public final static SortedSet<String> obtainSeqInformation( final Phylogeny phy,
final boolean ext_nodes_only,
final boolean allow_to_set_taxonomic_data,
return UniProtEntry.createInstanceFromPlainText( lines );
}
+ public static SequenceDatabaseEntry obtainUniProtEntry( final String query ) throws IOException {
+ return obtainUniProtEntry( query, DEFAULT_LINES_TO_RETURN );
+ }
+
public static List<String> queryDb( final String query, int max_lines_to_return, final String base_url )
throws IOException {
if ( ForesterUtil.isEmpty( query ) ) {
return result;
}
+ 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> queryEmblDb( final Accession 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.getSource() ) || ( id.getSource() == Accession.NCBI ) ) {
- url_sb.append( SequenceDbWsTools.EMBL_DBS_EMBL );
- url_sb.append( '/' );
+ // url_sb.append( BASE_EMBL_DB_URL );
+ if ( id.getSource().equals( Source.NCBI.toString() ) ) {
+ url_sb.append( EMBL_GENBANK );
+ //url_sb.append( '/' );
}
- else if ( id.getSource() == Accession.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( '/' );
- }
+ else if ( id.getSource().equals( Source.REFSEQ.toString() ) ) {
+ url_sb.append( EMBL_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( '/' );
+ // }
+ }
+ else {
+ throw new IllegalArgumentException( "unable to handle source: " + id.getSource() );
}
return queryDb( id.getValue(), max_lines_to_return, url_sb.toString() );
}
final Accession acc ) throws IOException {
SequenceDatabaseEntry db_entry = null;
final String query = acc.getValue();
- if ( acc.getSource() == Accession.UNIPROT ) {
+ if ( acc.getSource().equals( Source.UNIPROT.toString() ) ) {
if ( DEBUG ) {
System.out.println( "uniprot: " + query );
}
// Eat this, and move to next.
}
}
- else if ( acc.getSource() == Accession.EMBL ) {
+ else if ( acc.getSource().equals( Source.EMBL.toString() ) ) {
if ( DEBUG ) {
System.out.println( "embl: " + query );
}
// Eat this, and move to next.
}
}
- else if ( acc.getSource() == Accession.REFSEQ ) {
+ else if ( acc.getSource().equals( Source.REFSEQ.toString() ) ) {
if ( DEBUG ) {
System.out.println( "refseq: " + query );
}
private final static boolean isAccessionAcceptable( final Accession acc ) {
return ( !( ( acc == null ) || ForesterUtil.isEmpty( acc.getSource() ) || ForesterUtil.isEmpty( acc.getValue() ) || ( ( acc
- .getSource() != Accession.UNIPROT ) && ( acc.getSource() != Accession.EMBL ) && ( acc.getSource() != Accession.REFSEQ ) ) ) );
+ .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 {