DrawableSequence consSequence;\r
Hashtable propHash;\r
int threshold;\r
- Hashtable[] freqs;\r
\r
String name = "";\r
\r
- public Conservation(String name,Hashtable[] freqs,Hashtable propHash, int threshold, Vector sequences, int start, int end) {\r
+ public Conservation(String name,Hashtable propHash, int threshold, Vector sequences, int start, int end) {\r
this.name = name;\r
- this.freqs = freqs;\r
this.propHash = propHash;\r
this.threshold = threshold;\r
this.sequences = sequences;\r
if (sequences.elementAt(j) instanceof Sequence) {\r
Sequence s = (Sequence)sequences.elementAt(j);\r
\r
- if (s.getSequence().length() > i) {\r
+ if (s.getLength() > i) {\r
String res = s.getSequence().substring(i,i+1);\r
\r
if (residueHash.containsKey(res)) {\r
}\r
}\r
\r
- public int countGaps(int j) {\r
+ public int countGaps(int j)\r
+ {\r
int count = 0;\r
\r
- for (int i = 0; i < sequences.size();i++) {\r
- String tmp = ((Sequence)sequences.elementAt(i)).getSequence().substring(j,j+1);\r
- if (tmp.equals(" ") || tmp.equals(".") || tmp.equals("-")) {\r
+ for (int i = 0; i < sequences.size();i++)\r
+ {\r
+ if( j+1 > ((Sequence)sequences.elementAt(i)).getSequence().length())\r
+ { count++; continue;}\r
+\r
+ char c = ((Sequence)sequences.elementAt(i)).getSequence().charAt(j);\r
+ if (jalview.util.Comparison.isGap((c)))\r
count++;\r
- }\r
+\r
}\r
return count;\r
}\r
int totGaps = countGaps(i);\r
float pgaps = (float)totGaps*100/(float)sequences.size();\r
\r
- if (percentageGaps > pgaps) {\r
- Hashtable resultHash = (Hashtable)total.elementAt(i);\r
+ if (percentageGaps > pgaps)\r
+ {\r
+ Hashtable resultHash = (Hashtable)total.elementAt(i-start);\r
\r
//Now find the verdict\r
int count = 0;\r
Enumeration e3 = resultHash.keys();\r
\r
- while (e3.hasMoreElements()) {\r
+ while (e3.hasMoreElements())\r
+ {\r
String type = (String)e3.nextElement();\r
Integer result = (Integer)resultHash.get(type);\r
\r
//Do we want to count +ve conservation or +ve and -ve cons.?\r
\r
- if (consflag) {\r
- if (result.intValue() == 1) {\r
+ if (consflag)\r
+ {\r
+ if (result.intValue() == 1)\r
count++;\r
- }\r
- } else {\r
- if (result.intValue() != -1) {\r
+ }\r
+ else\r
+ {\r
+ if (result.intValue() != -1)\r
count++;\r
- }\r
}\r
}\r
\r
- if (count < 10) {\r
+ if (count < 10)\r
consString = consString + String.valueOf(count);\r
- } else {\r
+ else\r
consString = consString + "*";\r
- }\r
- } else {\r
+\r
+ }\r
+ else\r
+ {\r
consString = consString + "-";\r
}\r
}\r
\r
consSequence = new DrawableSequence(name,consString,start,end);\r
-\r
}\r
\r
public jalview.gui.DrawableSequence getConsSequence() {\r