\r
String consString = "";\r
\r
- DrawableSequence consSequence;\r
+ Sequence consSequence;\r
Hashtable propHash;\r
int threshold;\r
\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
+ for (int i = 0; i < sequences.size();i++)\r
+ {\r
if( j+1 > ((Sequence)sequences.elementAt(i)).getSequence().length())\r
{ count++; continue;}\r
\r
- String tmp = ((Sequence)sequences.elementAt(i)).getSequence().substring(j,j+1);\r
- if (tmp.equals(" ") || tmp.equals(".") || tmp.equals("-")) {\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
}\r
}\r
\r
- consSequence = new DrawableSequence(name,consString,start,end);\r
+ consSequence = new Sequence(name,consString,start,end);\r
}\r
\r
- public jalview.gui.DrawableSequence getConsSequence() {\r
+ public Sequence getConsSequence() {\r
return consSequence;\r
}\r
\r