- Hashtable residueHash = new Hashtable();\r
- int maxCount = 0;\r
- String maxResidue = "-";\r
- int nongap = 0;\r
-\r
- for (int j = 0; j < sequences.size(); j++)\r
- {\r
- if (sequences.elementAt(j) instanceof Sequence)\r
- {\r
- Sequence s = (Sequence) sequences.elementAt(j);\r
-\r
- if (s.getSequence().length() > i)\r
- {\r
- String res = s.getSequence().charAt(i) + "";\r
-\r
- if (!jalview.util.Comparison.isGap(res.charAt(0)))\r
- {\r
- nongap++;\r
- }\r
- else\r
- {\r
- res = "-"; // we always use this for gaps in the property vectors\r
- }\r
-\r
- if (residueHash.containsKey(res))\r
- {\r
- int count = ((Integer) residueHash.get(res)).intValue();\r
- count++;\r
-\r
- if (!jalview.util.Comparison.isGap(res.charAt(0)) &&\r
- (count >= maxCount))\r
- {\r
- if (count > maxCount)\r
- {\r
- maxResidue = res;\r
- }\r
- else if (maxResidue.indexOf(res) == -1)\r
- {\r
- maxResidue += res;\r
- }\r
-\r
- maxCount = count;\r
- }\r
-\r
- residueHash.put(res, new Integer(count));\r
- }\r
- else\r
- {\r
- residueHash.put(res, new Integer(1));\r
- }\r
- }\r
- else\r
- {\r
- if (residueHash.containsKey("-"))\r
- {\r
- int count = ((Integer) residueHash.get("-")).intValue();\r
- count++;\r
- residueHash.put("-", new Integer(count));\r
- }\r
- else\r
- {\r
- residueHash.put("-", new Integer(1));\r
- }\r
- }\r
- }\r
- }\r
-\r
- residueHash.put("maxCount", new Integer(maxCount));\r
-\r
- if (maxCount < 0)\r
- {\r
- System.out.println("asasa " + maxCount);\r
- }\r
-\r
- residueHash.put("maxResidue", maxResidue);\r
- residueHash.put("size", new Integer(sequences.size()));\r
- residueHash.put("nongap", new Integer(nongap));\r
- result.addElement(residueHash);\r