- int n = 0;\r
- SequenceI seq2;\r
- while (n < align.getHeight())\r
- {\r
- //This loop enables multiple sequences with the same\r
- //id to have features added and seq limits updated\r
- seq2 = align.getSequenceAt(n);\r
- if (seq2.getName().equals(idmatch))\r
- {\r
- nonGapped = AlignSeq.extractGaps("-. ", seq2.getSequence());\r
-\r
- absStart = sequence.getSequence().indexOf(nonGapped);\r
- absEnd = absStart + nonGapped.toString().length() - 1;\r
-\r
- // This is the Viewd alignment sequences\r
- // No need to tell the user of the dataset updates\r
- if ( (seq2.getStart() != absStart+sequence.getStart())\r
- || (seq2.getEnd() != absEnd+sequence.getStart()))\r
- {\r
- sbuffer.append("Updated: " + seq2.getName() + " " +\r
- seq2.getStart() + "/" + seq2.getEnd() +\r
- " to " + (absStart + sequence.getStart()) + "/" +\r
- (absEnd + sequence.getStart()) + "\n");\r
-\r
- seq2.setStart(absStart + sequence.getStart());\r
- seq2.setEnd(absEnd + sequence.getStart());\r
- }\r
- }\r