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 ); if ( DEBUG ) { System.out.println( "source: " + acc.getSource() ); } if ( acc.getSource().equals( Source.NCBI.toString() ) ) { url_sb.append( EMBL_GENBANK ); //url_sb.append( '/' ); } else if ( acc.getSource().equals( Source.REFSEQ.toString() ) ) { url_sb.append( EMBL_REFSEQ ); } else if ( acc.getSource().equals( Source.EMBL.toString() ) ) { url_sb.append( EMBL_EMBL ); } else { throw new IllegalArgumentException( "unable to handle source: " + acc.getSource() ); } return queryDb( acc.getValue(), max_lines_to_return, url_sb.toString() ); }
SequenceDatabaseEntry db_entry = null; final String query = acc.getValue(); if ( acc.getSource().equals( Source.UNIPROT.toString() ) ) { if ( DEBUG ) { System.out.println( "uniprot: " + query ); else if ( acc.getSource().equals( Source.REFSEQ.toString() ) ) { if ( DEBUG ) { System.out.println( "refseq: " + query ); 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() ); else if ( acc.getSource().equals( Source.GI.toString() ) ) { if ( DEBUG ) { System.out.println( "gi: " + query );
n.setName( "NP_001025424" ); Accession acc = SequenceDbWsTools.obtainSeqAccession( n ); if ( ( acc == null ) || !acc.getSource().equals( Source.REFSEQ.toString() ) || !acc.getValue().equals( "NP_001025424" ) ) { return false; if ( ( acc == null ) || !acc.getSource().equals( Source.REFSEQ.toString() ) || !acc.getValue().equals( "NP_001025424" ) ) { return false; if ( ( acc == null ) || !acc.getSource().equals( Source.REFSEQ.toString() ) || !acc.getValue().equals( "NP_001025424" ) ) { return false; if ( ( acc == null ) || !acc.getSource().equals( Source.REFSEQ.toString() ) || !acc.getValue().equals( "NM_001030253" ) ) { return false; if ( ( acc == null ) || !acc.getSource().equals( Source.UNIPROT.toString() ) || !acc.getValue().equals( "BCL2_HUMAN" ) ) { System.out.println( acc.toString() ); if ( ( acc == null ) || !acc.getSource().equals( Source.UNIPROT.toString() ) || !acc.getValue().equals( "P10415" ) ) { System.out.println( acc.toString() ); if ( ( acc == null ) || !acc.getSource().equals( Source.UNIPROT.toString() ) || !acc.getValue().equals( "P10415" ) ) { System.out.println( acc.toString() );
return false; if ( !n1.getNodeData().getSequence().getAccession().getSource().equals( Source.REFSEQ.toString() ) ) { return false; return false; if ( !n2.getNodeData().getSequence().getAccession().getSource().equals( Source.REFSEQ.toString() ) ) { return false; return false; if ( !n3.getNodeData().getSequence().getAccession().getSource().equals( Source.REFSEQ.toString() ) ) { return false;
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" ); } final Accession acc = SequenceAccessionTools.parseAccessorFromString( acc_str ); if ( acc == null ) { throw new IllegalArgumentException( "could not extract acceptable sequence db accessor from \"" + acc_str + "\"" ); } 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 ( acc.getSource().equals( Source.UNIPROT.toString() ) ) { return obtainUniProtEntry( acc.getValue(), DEFAULT_LINES_TO_RETURN ); } else { throw new IllegalArgumentException( "don't know how to handle request for source \"" + acc.getSource() + "\"" ); } }
public Accession( final String value, final Source source ) { _value = value; _source = source.toString(); _comment = ""; _source_value = source + value; }
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() ) ) ) ) ); }