- // Do we have an id line?\r
- // JBPNote - this code needs to be standardised to EBI/whatever for the\r
- // >dbref/dbref/dbref|refid1|refid2|refid3 'human-readable' style of naming (should it really exist)\r
- if (line.substring(0, 1).equals(">"))\r
- {\r
- if (count != 0)\r
- {\r
- if (sstart != 0)\r
- {\r
- seqs.addElement(new Sequence(id, seq.toString(),\r
- sstart, send));\r
- }\r
- else\r
- {\r
- seqs.addElement(new Sequence(id, seq.toString(), 1,\r
- seq.length()));\r
- }\r
- }\r
-\r
- count++;\r
-\r
- StringTokenizer str = new StringTokenizer(line, " ");\r
-\r
- id = str.nextToken();\r
- id = id.substring(1);\r
-\r
- com.stevesoft.pat.Regex dbId = new com.stevesoft.pat.Regex(\r
- "[A-Za-z-]+/?[A-Za-z-]+\\|(\\w+)\\|(.+)");\r
-\r
- // JBPNote At the moment - we don't get rid of the friendly names but this\r
- // behaviour is probably wrong in the long run.\r
- if (dbId.search(id))\r
- {\r
- String dbid = dbId.stringMatched(1);\r
- String idname = dbId.stringMatched(2);\r
-\r
- if ((idname.length() > 0) &&\r
- (idname.indexOf("_") > -1))\r
- {\r
- id = idname; // use the friendly name - apparently no dbid\r
- }\r
- else if (dbid.length() > 1)\r
- {\r
- id = dbid; // ignore the friendly name - we lose uniprot accession ID otherwise\r
- }\r
- }\r
-\r
- if (id.indexOf("/") > 0)\r
- {\r
- StringTokenizer st = new StringTokenizer(id, "/");\r
+ Annotation[] anots = new Annotation[sb.length()];\r
+ String anotString = sb.toString();\r
+ for (int i = 0; i < sb.length(); i++)\r
+ {\r
+ anots[i] = new Annotation(anotString.substring(i, i + 1),\r
+ null,\r
+ ' ', 0);\r
+ }\r
+ AlignmentAnnotation aa = new AlignmentAnnotation(\r
+ seq.getName().substring(2), seq.getDescription(),\r
+ anots);\r
+\r
+ annotations.addElement(aa);\r
+ }\r
+ }\r
+ else\r
+ {\r
+ annotation = false;\r
+ }\r