-\r
- residueHash.put("maxCount",new Integer(maxCount));\r
- if(maxCount<0)\r
- System.out.println("asasa "+maxCount);\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
- }\r
-\r
- return result;\r
- }\r
-\r
- public static Vector calculatePID(SequenceI refseq,Vector sequences,int window,int start,int end) {\r
-\r
- Vector result = new Vector();\r
-\r
- boolean init = true;\r
-\r
-\r
- Vector prev = null;\r
-\r
- for (int i = start;i <= end; i++) {\r
- Vector values = new Vector();\r
-\r
- result.addElement(values);\r
-\r
- // If start < window/2 then set value to zero.\r
-\r
- if (i< window/2 || i >= refseq.getSequence().length()-window/2) {\r
- for (int j = 0; j < sequences.size(); j++) {\r
- values.addElement(new Integer(0));\r
- }\r
- } else if (init == true) {\r
- init = false;\r
-\r
- int winstart = i-window/2;\r
- int winend = i+window/2;\r
-\r
- if (window%2 != 0) {\r
- winend++;\r
- }\r
-\r
- for (int j = 0; j < sequences.size(); j++) {\r
- values.addElement(new Integer(0));\r
- }\r
-\r
- for (int k = winstart; k <= winend; k++) {\r
- String refchar = refseq.getSequence().substring(k,k+1);\r
- if (jalview.util.Comparison.isGap(refchar.charAt(0)))\r
- refchar="-";\r
- else {\r
- for (int j = 0; j < sequences.size(); j++) {\r
-\r
- Sequence s = (Sequence)sequences.elementAt(j);\r
-\r
- if (s.getSequence().length() > k) {\r
-\r
- String res = s.getSequence().substring(k,k+1); // no gapchar test needed\r
-\r
- if (res.equals(refchar)) {\r
- int val = ((Integer)values.elementAt(j)).intValue();\r
- val++;\r
- values.setElementAt(new Integer(val),j);\r
- }\r
- }\r
- }\r
- }\r
-\r
- }\r
-\r
- prev = values;\r
- } else {\r
- int winstart = i-window/2;\r
- int winend = i+window/2;\r
-\r
- if (window%2 != 0) {\r
- winend++;\r
- }\r
- // We need to take the previous set of values\r
- // subtract the pid at winstart-1\r
- // and add the pid at winend;\r
-\r
- String pre_refchar = refseq.getSequence().substring(winstart-1,winstart);\r
- String pos_refchar = "-";\r
-\r
- if (refseq.getSequence().length() > winend) {\r
- pos_refchar = refseq.getSequence().substring(winend,winend+1);\r
- }\r
-\r
- for (int j = 0; j < sequences.size(); j++) {\r
- // First copy the pid value from i-1\r
-\r
- int val = ((Integer)prev.elementAt(j)).intValue();\r
-\r
- Sequence s = (Sequence)sequences.elementAt(j);\r
-\r
- String pre_char = s.getSequence().substring(winstart-1,winstart);\r
-\r
- String pos_char = "-";\r
-\r
- if (s.getSequence().length() > winend) {\r
- pos_char = s.getSequence().substring(winend,winend+1);\r
- }\r
-\r
- // Now substract 1 if the chars at winstart-1 match\r
-\r
- if (jalview.util.Comparison.isGap(pre_refchar.charAt(0)) == false\r
- && pre_char.equals(pre_refchar)) {\r
- val--;\r
- }\r
-\r
- if (jalview.util.Comparison.isGap(pos_refchar.charAt(0)) == false\r
- && pos_char.equals(pos_refchar)) {\r
- val++;\r
- }\r
-\r
- values.addElement(new Integer(val));\r
-\r
-\r
- }\r
- prev = values;\r
- }\r
- }\r
-\r
- return result;\r