import jalview.api.FeatureRenderer;
import jalview.api.FeatureSettingsModelI;
import jalview.api.SequenceRenderer;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.gui.AppJmol;
private String jmolScript(String script)
{
- Cache.log.debug(">>Jmol>> " + script);
- String s = jmolViewer.evalStringQuiet(script); // scriptWait(script); BH
- Cache.log.debug("<<Jmol<< " + s);
+ return jmolScript(script, false);
+ }
+
+ private String jmolScript(String script, boolean useScriptWait)
+ {
+ Console.debug(">>Jmol>> " + script);
+ String s;
+ if (useScriptWait)
+ {
+ s = jmolViewer.scriptWait(script);
+ }
+ else
+ {
+ s = jmolViewer.evalStringQuiet(script); // scriptWait(script); BH
+ }
+ Console.debug("<<Jmol<< " + s);
return s;
}
{
if (atoms != null)
{
+ boolean useScriptWait = atoms.size() > 1;
if (resetLastRes.length() > 0)
{
- jmolScript(resetLastRes.toString());
+ jmolScript(resetLastRes.toString(), useScriptWait);
resetLastRes.setLength(0);
}
for (AtomSpec atom : atoms)
{
highlightAtom(atom.getAtomIndex(), atom.getPdbResNum(),
- atom.getChain(), atom.getPdbFile());
+ atom.getChain(), atom.getPdbFile(), useScriptWait);
}
+ // Highlight distances between atoms with a 'measure' command - not yet
+ // working
+ // if (atoms.size() >= 2)
+ // {
+ // StringBuilder sb = new StringBuilder();
+ // for (int a = 0; a < atoms.size(); a++)
+ // {
+ // AtomSpec speca = atoms.get(a);
+ // String a_model = getModelIdForFile(speca.getPdbFile());
+ // for (int b = a + 1; b < atoms.size(); b++)
+ // {
+ // AtomSpec specb = atoms.get(b);
+ // String b_model = getModelIdForFile(speca.getPdbFile());
+ // sb.append("measure ALL (" + speca.getAtomIndex() + " and */"
+ // + a_model + ") (" + specb.getAtomIndex() + " and */"
+ // + b_model + ");");
+ // }
+ // }
+ // jmolHistory(false, useScriptWait);
+ // jmolScript(sb.toString(), useScriptWait);
+ // jmolHistory(true, useScriptWait);
+ // }
+
}
+
}
// jmol/ssm only
public void highlightAtom(int atomIndex, int pdbResNum, String chain,
- String pdbfile)
+ String pdbfile, boolean useScriptWait)
{
String modelId = getModelIdForFile(pdbfile);
if (modelId.isEmpty())
return;
}
- jmolHistory(false);
+ jmolHistory(false, useScriptWait);
StringBuilder selection = new StringBuilder(32);
StringBuilder cmd = new StringBuilder(64);
resetLastRes.append(selection).append(";wireframe 0;").append(selection)
.append(" and not hetero; spacefill 0;");
- jmolScript(cmd.toString());
- jmolHistory(true);
+ jmolScript(cmd.toString(), useScriptWait);
+ jmolHistory(true, useScriptWait);
}
private boolean debug = true;
private void jmolHistory(boolean enable)
{
- jmolScript("History " + ((debug || enable) ? "on" : "off"));
+ jmolHistory(enable, false);
+ }
+
+ private void jmolHistory(boolean enable, boolean useScriptWait)
+ {
+ jmolScript("History " + ((debug || enable) ? "on" : "off"),
+ useScriptWait);
}
public void loadInline(String string)