- 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();
+ }