g.setFont(av.getFont());\r
double charWidth = av.getCharWidth();\r
int charHeight = av.getCharHeight();\r
+ RendererI sr = av.getRenderer();\r
\r
- // Vector pid = av.calcNewConsensus();\r
\r
- RendererI sr = av.getRenderer();\r
+ /*Vector pid = av.getConsensus(false);\r
\r
-/* Vector tmpseq = new Vector();\r
+ Vector tmpseq = new Vector();\r
\r
- for (int i = 0; i < av.getAlignment().getHeight(); i++) {\r
- if (!av.getSelection().contains(av.getAlignment().getSequenceAt(i))) {\r
+ for (int i = 0; i < av.getAlignment().getHeight(); i++)\r
+ if (!av.getSelection().contains(av.getAlignment().getSequenceAt(i)))\r
tmpseq.addElement(av.getAlignment().getSequenceAt(i));\r
- }\r
- }\r
\r
- if (sr instanceof SequenceRenderer) {\r
+\r
+\r
+ if (sr instanceof SequenceRenderer)\r
pid = AAFrequency.calculate(tmpseq,x1,x2);\r
\r
- } else if (sr instanceof GraphRenderer) {\r
+ else if (sr instanceof GraphRenderer)\r
pid = AAFrequency.calculatePID(av.getAlignment().getSequenceAt(0),\r
av.getAlignment().getSequences(),\r
av.getPIDWindow(),x1,x2);\r
\r
- }*/\r
+*/\r
\r
if (y2 > starty && y1 < av.getEndSeq()) {\r
\r
for (int i = y1 ; i < y2 ;i++) {\r
\r
RendererI r = sr;\r
-\r
- /* if (av.getSelection().contains(av.getAlignment().getSequenceAt(i))) {\r
+/*\r
+ if (av.getSelection().contains(av.getAlignment().getSequenceAt(i))) {\r
r = fr;\r
System.out.println("use feature renderer");\r
- // } else if ( i == 0) {\r
- // r = br;\r
+ } else if ( i == 0) {\r
+ // r = br;\r
} else if (av.getAlignment().getSequenceAt(i).getName().equals("CpG")) {\r
r = cgr;\r
System.out.println("cg renderer");\r
- }*/\r
+ }\r
+*/\r
\r
r.drawSequence(g,cs,av.getAlignment().getSequenceAt(i),\r
x1,\r