From: Nomi H. <no...@us...> - 2004-06-30 00:02:08
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Update of /cvsroot/gmod/apollo/src/java/apollo/dataadapter/genbank In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv22327 Modified Files: PublicDbFeature.java Log Message: don't strip out stuff before the : for more tags. (why would we ever want to do this, anyway?) Index: PublicDbFeature.java =================================================================== RCS file: /cvsroot/gmod/apollo/src/java/apollo/dataadapter/genbank/PublicDbFeature.java,v retrieving revision 1.5 retrieving revision 1.6 diff -C2 -d -r1.5 -r1.6 *** PublicDbFeature.java 22 Jun 2004 05:30:41 -0000 1.5 --- PublicDbFeature.java 30 Jun 2004 00:01:59 -0000 1.6 *************** *** 33,36 **** --- 33,37 ---- this.type = str.substring(0, index); this.location.append(str.substring(index).trim()); + // System.out.println("getFeatureType: this.location = " + location); // DEL } return this.type; *************** *** 175,186 **** !tag.equals("note") && !tag.equals("gene") && ! !tag.equals("method")) { if (!tag.equals("db_xref")) { tag = value.substring(0, index); String tmp = value.substring(index + ":".length()); ! System.out.println ("Changing " + tag + " from " + ! value + " to " + tmp); value = tmp; ! } else { db_tag = value.substring(0, index); db_value = value.substring(index + ":".length()); --- 176,193 ---- !tag.equals("note") && !tag.equals("gene") && ! !tag.equals("method") && ! !tag.equals("date") && ! !tag.endsWith("synonym") && ! !tag.equals("product") && ! !tag.equals("prot_desc")) { if (!tag.equals("db_xref")) { + // Why do we want to do this? I see lots of cases where we *don't* + // want to, but I don't see when we'd ever want to. --NH tag = value.substring(0, index); String tmp = value.substring(index + ":".length()); ! System.out.println ("setTagValue: changing tag " + tag + " from " + ! value + " to " + tmp); // DEL value = tmp; ! } else { // db_xref db_tag = value.substring(0, index); db_value = value.substring(index + ":".length()); *************** *** 282,285 **** --- 289,293 ---- **/ private void parseLocations(String location_str, Vector locs) { + System.out.println("parseLocations: location str = " + location_str); // DEL if (location_str != null && !location_str.equals("")) { String operation_str = null; *************** *** 326,329 **** --- 334,338 ---- else if (!Character.isDigit(location_str.charAt(0))) { if (location_str.charAt(0) == '<') { + // System.out.println("location_str starts with <; extend5prime = true"); // DEL extend5prime = true; parseLocations(location_str.substring(1), locs); *************** *** 341,344 **** --- 350,354 ---- } else { + // System.out.println("In else--parsing location_str: " + location_str); // DEL index_start = 0; index_end = indexOfNextNonDigit(location_str, index_start); *************** *** 358,361 **** --- 368,372 ---- index_start = ++index_end; if (location_str.charAt(index_start) == '>') { + // System.out.println("location_str has embedded >: " + location_str); // DEL extend3prime = true; index_start++; |