- addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,\r
- HistoryItem.HIDE));\r
-\r
- //This is to maintain viewport position on first residue\r
- //of first sequence\r
- SequenceI seq = viewport.alignment.getSequenceAt(0);\r
- int startRes = seq.findPosition(viewport.startRes);\r
-\r
- SequenceI current;\r
- int jSize;\r
-\r
- Vector seqs=null;\r
-\r
- int start=0, end = viewport.alignment.getWidth();\r
-\r
- if (viewport.getSelectionGroup() != null\r
- && viewport.getSelectionGroup().getSequences(false) != null\r
- && viewport.getSelectionGroup().getSize(false)>0)\r
- {\r
- seqs = viewport.getSelectionGroup().getSequences(true);\r
- start = viewport.getSelectionGroup().getStartRes();\r
- end = viewport.getSelectionGroup().getEndRes()+1;\r
- }\r
- else\r
- seqs = viewport.alignment.getSequences();\r
-\r
- for (int i = 0; i < seqs.size(); i++)\r
- {\r
- current = (SequenceI) seqs.elementAt(i);\r
- jSize = current.getLength();\r
-\r
- // Removing a range is much quicker than removing gaps\r
- // one by one for long sequences\r
- int j = start;\r
- int rangeStart=-1, rangeEnd=-1;\r
-\r
- do\r
- {\r
- if (jalview.util.Comparison.isGap(current.getCharAt(j)))\r
- {\r
- if(rangeStart==-1)\r
- {\r
- rangeStart = j;\r
- rangeEnd = j+1;\r
- }\r
- else\r
- {\r
- rangeEnd++;\r
- }\r
- j++;\r
- }\r
- else\r
- {\r
- if(rangeStart>-1)\r
- {\r
- current.deleteChars(rangeStart, rangeEnd);\r
- j-=rangeEnd-rangeStart;\r
- jSize-=rangeEnd-rangeStart;\r
- rangeStart = -1;\r
- rangeEnd = -1;\r
- }\r
- else\r
- j++;\r
- }\r
- }\r
- while (j < end && j < jSize);\r
- if(rangeStart>-1)\r
- {\r
- current.deleteChars(rangeStart, rangeEnd);\r
- }\r
- }\r
- viewport.setStartRes(seq.findIndex(startRes)-1);\r
- viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r