- public abstract SequenceRenderer getSequenceRenderer(
- AlignmentViewPanel alignment);
-
- // jmol/ssm only
- public void highlightAtom(int atomIndex, int pdbResNum, String chain,
- String pdbfile)
- {
- List<ChimeraModel> cms = chimmaps.get(pdbfile);
- if (cms != null)
- {
- int mdlNum = cms.get(0).getModelNumber();
-
- viewerCommandHistory(false);
- // viewer.stopListening();
- if (resetLastRes.length() > 0)
- {
- eval.setLength(0);
- eval.append(resetLastRes.toString() + ";");
- }
-
- eval.append("display "); // +modelNum
-
- resetLastRes.setLength(0);
- resetLastRes.append("~display ");
- {
- eval.append(" #" + (mdlNum));
- resetLastRes.append(" #" + (mdlNum));
- }
- // complete select string
-
- eval.append(":" + pdbResNum);
- resetLastRes.append(":" + pdbResNum);
- if (!chain.equals(" "))
- {
- eval.append("." + chain);
- resetLastRes.append("." + chain);
- }
-
- viewer.sendChimeraCommand(eval.toString(), false);
- viewerCommandHistory(true);
- // viewer.startListening();
- }
- }
-
- private void log(String message)
- {
- System.err.println("## Chimera log: " + message);
- }
-
- private void viewerCommandHistory(boolean enable)
- {
- // log("(Not yet implemented) History "
- // + ((debug || enable) ? "on" : "off"));
- }
-
- public void loadInline(String string)