UNKNOWN, UNIPROT;
}
public final static String BASE_URL = "http://www.uniprot.org/";
-
public final static String BASE_EMBL_DB_URL = "http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/embl/";
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-zA-Z0-9]?([A-NR-ZOPQ]\\d[A-Z0-9]{3}\\d)[^a-zA-Z0-9]?" );
+ .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 null;
}
}
-
-
public static List<UniProtTaxonomy> getTaxonomiesFromCommonName( final String cn, final int max_taxonomies_return )
throws IOException {
else if ( sn.equals( "Xenopus" ) ) {
return hack( 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 );
// Ignore empty lines.
}
else if ( line.startsWith( "Taxon" ) ) {
- //TODO next the check format FIXME
+ 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 ) {
return taxonomies;
}
-
- public static List<String> queryEmblDb( final String query, int max_lines_to_return ) throws IOException {
- return queryDb( query,
- max_lines_to_return,
- BASE_EMBL_DB_URL ) ;
+ public static List<String> queryEmblDb( final String query, final int max_lines_to_return ) throws IOException {
+ return queryDb( query, max_lines_to_return, BASE_EMBL_DB_URL );
}
-
-
-
- public static List<String> queryUniprot( final String query, int max_lines_to_return ) throws IOException {
- return queryDb( query,
- max_lines_to_return,
- BASE_URL ) ;
-
-
+
+ public static List<String> queryUniprot( final String query, final int max_lines_to_return ) throws IOException {
+ return queryDb( query, max_lines_to_return, BASE_URL );
}
- public static List<String> queryDb( final String query,
- int max_lines_to_return,
- final String base_url ) throws IOException {
+ 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 " );
}
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 obtainEmblEntry( String query, int max_lines_to_return ) throws IOException {
- final List<String> lines = queryEmblDb( "query", max_lines_to_return );
+ public static SequenceDatabaseEntry obtainEmblEntry( final String query, final int max_lines_to_return )
+ throws IOException {
+ final List<String> lines = queryEmblDb( query, max_lines_to_return );
return EbiDbEntry.createInstanceFromPlainText( lines );
}
}