- public void colourBySequence(Sequence seq) {\r
-\r
-// for (int i = 0; i < bonds.size(); i++) {\r
-// Bond tmp = (Bond)bonds.elementAt(i);\r
-// try {\r
-//\r
-// if (tmp.at1.resNumber >= (offset + seq.pdbstart - 1) && tmp.at1.resNumber <= (offset + seq.pdbend - 1)) {\r
-//\r
-// int pos = seq.seqtart() + (tmp.at1.resNumber - seq.pdbstart - offset) ;\r
-// int index = seq.findIndex(pos);\r
-//\r
-// tmp.startCol = (Color)seq.getResidueBoxColour(index);\r
-//\r
-// } else {\r
-// tmp.startCol = Color.gray;\r
-// }\r
-//\r
-// if (tmp.at2.resNumber >= (offset + seq.pdbstart -1) && tmp.at2.resNumber <= (seq.pdbend+offset-1)) {\r
-//\r
-// int pos = seq.seqstart + (tmp.at2.resNumber - seq.pdbstart-offset);\r
-// int index = seq.findIndex(pos);\r
-//\r
-// tmp.endCol = (Color)seq.getResidueBoxColour(index);\r
-//\r
-// } else {\r
-// tmp.endCol = Color.gray;\r
-// }\r
-// } catch (Exception e) {\r
-// tmp.startCol = Color.lightGray;\r
-// tmp.endCol = Color.lightGray;\r
-// }\r
-// }\r
+ public void colourBySequence(jalview.gui.AlignViewport av, Sequence seq) {\r
+jalview.gui.SequenceRenderer sr = new jalview.gui.SequenceRenderer(av);\r
+\r
+\r
+ for (int i = 0; i < bonds.size(); i++) {\r
+ Bond tmp = (Bond)bonds.elementAt(i);\r
+ try {\r
+\r
+ if (tmp.at1.resNumber >= (offset + pdbstart - 1) && tmp.at1.resNumber <= (offset + pdbend - 1)) {\r
+\r
+ int pos = seqstart + (tmp.at1.resNumber - pdbstart - offset) ;\r
+ int index = seq.findIndex(pos);\r
+\r
+\r
+ tmp.startCol = sr.getResidueBoxColour(av.getGlobalColourScheme(), seq, index);\r
+\r
+ } else {\r
+ tmp.startCol = Color.gray;\r
+ }\r
+\r
+ if (tmp.at2.resNumber >= (offset + pdbstart -1) && tmp.at2.resNumber <= (pdbend+offset-1)) {\r
+\r
+ int pos = seqstart + (tmp.at2.resNumber - pdbstart-offset);\r
+ int index = seq.findIndex(pos);\r
+\r
+ tmp.endCol = sr.getResidueBoxColour(av.getGlobalColourScheme(), seq, index);\r
+\r
+ } else {\r
+ tmp.endCol = Color.gray;\r
+ }\r
+ } catch (Exception e) {\r
+ tmp.startCol = Color.lightGray;\r
+ tmp.endCol = Color.lightGray;\r
+ }\r
+ }\r