-\r
- if ((tmp.at1.resNumber >= ((offset + pdbstart) - 1)) &&\r
- (tmp.at1.resNumber <= ((offset + pdbend) - 1)))\r
- {\r
- int pos = seqstart +\r
- (tmp.at1.resNumber - pdbstart - offset);\r
-\r
-\r
- int index = sequence.findIndex(pos);\r
-\r
- tmp.startCol = sr.findSequenceColour(Color.gray, sequence, index);\r
-\r
- tmp.startCol = fr.findFeatureColour(tmp.startCol, sequence, index);\r
-\r
- } else\r
- {\r
- tmp.startCol = Color.gray;\r
- }\r
-\r
- if ((tmp.at2.resNumber >= ((offset + pdbstart) - 1)) &&\r
- (tmp.at2.resNumber <= ((pdbend + offset) - 1))) {\r
- int pos = seqstart +\r
- (tmp.at2.resNumber - pdbstart - offset);\r
- int index = sequence.findIndex(pos);\r
-\r
- tmp.endCol = sr.findSequenceColour(Color.gray, sequence, index);\r
- tmp.endCol = fr.findFeatureColour( tmp.endCol, sequence, index);\r
- }\r
- else\r
- {\r
- tmp.endCol = Color.gray;\r
- }\r
- }\r
- }\r
-\r
- public void setChainColours() {\r
- for (int i = 0; i < bonds.size(); i++) {\r
- Bond tmp = (Bond) bonds.elementAt(i);\r
-\r
- try {\r
- tmp.startCol = (Color) ResidueProperties.getChainColours().get(id);\r
- tmp.endCol = (Color) ResidueProperties.getChainColours().get(id);\r
- } catch (Exception e) {\r
- tmp.startCol = Color.lightGray;\r
- tmp.endCol = Color.lightGray;\r
- }\r