+ ////// is the searchString a residue number?\r
+ try\r
+ {\r
+ int res = Integer.parseInt(searchString);\r
+ found = true;\r
+ if (av.getSelectionGroup() == null || av.getSelectionGroup().getSize(false) < 1)\r
+ {\r
+ seq = (Sequence) av.getAlignment().getSequenceAt(0);\r
+ }\r
+ else\r
+ {\r
+ seq = (Sequence) (av.getSelectionGroup().getSequenceAt(0));\r
+ }\r
+\r
+ searchResults.addResult(seq, res, res);\r
+ }\r
+ catch (NumberFormatException ex)\r
+ {\r
+ }\r
+\r
+ ///////////////////////////////////////////////\r
+\r
+ int end = av.alignment.getHeight();\r
+\r
+ SequenceGroup selection = av.getSelectionGroup();\r
+\r
+ if (selection != null)\r
+ {\r
+ if ((selection.getSize(false) < 1) ||\r
+ ((selection.getEndRes() - selection.getStartRes()) < 2))\r
+ {\r
+ selection = null;\r
+ }\r
+ }\r
+\r
+ while (!found && (seqIndex < end))\r
+ {\r
+ seq = (Sequence) av.alignment.getSequenceAt(seqIndex);\r
+\r
+ if ((selection != null) && !selection.getSequences(false).contains(seq))\r
+ {\r
+ seqIndex++;\r
+ resIndex = 0;\r
+\r
+ continue;\r
+ }\r
+\r
+ item = seq.getSequence();\r
+ if(!caseSensitive.isSelected())\r
+ item = item.toUpperCase();\r
+\r
+ if ((selection != null) &&\r
+ (selection.getEndRes() < av.alignment.getWidth()-1))\r
+ {\r
+ item = item.substring(0, selection.getEndRes() + 1);\r
+ }\r
+\r
+ ///Shall we ignore gaps????\r
+ StringBuffer noGapsSB = new StringBuffer();\r
+ int insertCount = 0;\r
+ Vector spaces = new Vector();\r
+\r
+ for (int j = 0; j < item.length(); j++)\r
+ {\r
+ if (!jalview.util.Comparison.isGap(item.charAt(j)))\r
+ {\r
+ noGapsSB.append(item.charAt(j));\r
+ spaces.add(new Integer(insertCount));\r
+ }\r
+ else\r
+ {\r
+ insertCount++;\r
+ }\r
+ }\r
+\r
+ String noGaps = noGapsSB.toString();\r
+\r
+ for (int r = resIndex; r < noGaps.length(); r++)\r
+ {\r
+\r
+ if (regex.searchFrom(noGaps, r))\r
+ {\r
+ resIndex = regex.matchedFrom();\r
+\r
+ if ((selection != null) &&\r
+ ((resIndex +\r
+ Integer.parseInt(spaces.get(resIndex).toString())) < selection.getStartRes()))\r
+ {\r
+ continue;\r
+ }\r
+\r
+\r
+ int sres = seq.findPosition(resIndex +\r
+ Integer.parseInt(spaces.elementAt(resIndex)\r
+ .toString()));\r
+ int eres = seq.findPosition(regex.matchedTo() - 1 +\r
+ Integer.parseInt(spaces.elementAt(regex.matchedTo() -\r
+ 1).toString()));\r
+\r
+ searchResults.addResult(seq, sres, eres);\r
+\r
+ if (!findAll)\r
+ {\r
+ // thats enough, break and display the result\r
+ found = true;\r
+ resIndex++;\r
+\r
+ break;\r
+ }\r
+\r
+ r = resIndex;\r
+ }\r
+ else\r
+ {\r
+ break;\r
+ }\r
+ }\r
+\r
+ if (!found)\r
+ {\r
+ seqIndex++;\r
+ resIndex = 0;\r
+ }\r
+ }\r
+\r
+ Vector idMatch = new Vector();\r
+\r
+ for (int id = 0; id < av.alignment.getHeight(); id++)\r
+ {\r
+ if (regex.search(av.alignment.getSequenceAt(id).getName()))\r
+ {\r
+ idMatch.add(av.alignment.getSequenceAt(id));\r
+ }\r
+ }\r
+\r
+ if ((searchResults.getSize() == 0) && (idMatch.size() > 0))\r
+ {\r
+ ap.idPanel.highlightSearchResults(idMatch);\r
+ }\r
+\r
+\r
+ int resultSize = searchResults.getSize();\r
+\r
+ if (searchResults.getSize() > 0)\r
+ createNewGroup.setEnabled(true);\r
+ else\r
+ searchResults = null;\r
+\r
+ // if allResults is null, this effectively switches displaySearch flag in seqCanvas\r
+ ap.highlightSearchResults(searchResults);\r
+\r
+ if(!findAll && resultSize==0)\r
+ {\r
+ JOptionPane.showInternalMessageDialog(this, "Finished searching",\r
+ null, JOptionPane.INFORMATION_MESSAGE);\r
+ resIndex = 0;\r
+ seqIndex = 0;\r
+ }\r
+\r
+ if (findAll)\r
+ {\r
+ String message = resultSize + " matches found.";\r
+ JOptionPane.showInternalMessageDialog(this, message, null,\r
+ JOptionPane.INFORMATION_MESSAGE);\r
+ }\r
+\r
+ }\r