this.av = av;\r
float scores[][] = new float[av.getAlignment().getHeight()][av.getAlignment().getHeight()];\r
double totscore = 0;\r
- int count = av.getSelection().size();\r
+ int count = av.getSelectionGroup().getSize();\r
\r
int acount = 0;\r
for (int i = 1; i < count; i++)\r
for (int j = 0; j < i; j++)\r
{\r
acount++;\r
- AlignSeq as = new AlignSeq(av.getSelection().sequenceAt(i),av.getSelection().sequenceAt(j),"pep");\r
+ AlignSeq as = new AlignSeq(av.getSelectionGroup().getSequenceAt(i),\r
+ av.getSelectionGroup().getSequenceAt(j),"pep");\r
\r
as.calcScoreMatrix();\r
as.traceAlignment();\r
\r
\r
AlignFrame af = new AlignFrame(new Alignment(seq));\r
- int newHeight = seq.length * af.viewport.getCharHeight() + 200;\r
- if(newHeight>500)\r
- newHeight=500;\r
-\r
- Desktop.addInternalFrame(af, "Pairwise Aligned Sequences", 700,newHeight);\r
+ Desktop.addInternalFrame(af, "Pairwise Aligned Sequences",\r
+ AlignFrame.NEW_WINDOW_WIDTH,\r
+ AlignFrame.NEW_WINDOW_HEIGHT);\r
\r
}\r
\r