import jalview.structure.AtomSpec;
import jalview.structure.StructureListener;
import jalview.structure.StructureMapping;
-import jalview.structure.StructureMappingcommandSet;
import jalview.structure.StructureSelectionManager;
import jalview.util.HttpUtils;
"" + (atom.getPdbResNum()), "" + atom.getAtomIndex() });
} catch (Exception ex)
{
- System.err.println("Couldn't execute callback with " + _listenerfn
- + " for atomSpec: " + atom);
+ jalview.bin.Console.errPrintln("Couldn't execute callback with "
+ + _listenerfn + " for atomSpec: " + atom);
ex.printStackTrace();
}
}
if (JalviewLite.debug)
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
this.getClass().getName() + " modelSet[0]: " + modelSet[0]);
ssm.reportMapping();
}
}
// if (jvlite.debug)
// {
- // System.err.println("Mapped '" + modelSet[m] + "' to "
+ // jalview.bin.Console.errPrintln("Mapped '" + modelSet[m] + "' to "
// + sequence[m].length + " sequences.");
// }
}
// Form a colour command from the given alignment panel for each distinct
// structure
- ArrayList<String[]> ccomands = new ArrayList<String[]>();
- ArrayList<String> pdbfn = new ArrayList<String>();
- StructureMappingcommandSet[] colcommands = JmolCommands
- .getColourBySequenceCommand(ssm, modelSet, sequence, sr,
- (AlignmentViewPanel) source);
+ ArrayList<String[]> ccomands = new ArrayList<>();
+ ArrayList<String> pdbfn = new ArrayList<>();
+ String[] colcommands = new JmolCommands().colourBySequence(ssm,
+ modelSet, sequence, sr, (AlignmentViewPanel) source);
if (colcommands == null)
{
return;
}
int sz = 0;
- for (jalview.structure.StructureMappingcommandSet ccset : colcommands)
+ // for (jalview.structure.StructureMappingcommandSet ccset : colcommands)
+ for (String command : colcommands)
{
- sz += ccset.commands.length;
- ccomands.add(ccset.commands);
- pdbfn.add(ccset.mapping);
+ // sz += ccset.commands.length;
+ // ccomands.add(command); // ccset.commands);
+ // pdbfn.add(ccset.mapping);
}
String mclass, mhandle;
executeJavascriptFunction(true, _listenerfn, st);
} catch (Exception ex)
{
- System.err.println("Couldn't execute callback with " + _listenerfn
- + " using args { " + st[0] + ", " + st[1] + ", " + st[2]
- + "," + st[3] + "}"); // + ","+st[4]+"\n");
+ jalview.bin.Console.errPrintln("Couldn't execute callback with "
+ + _listenerfn + " using args { " + st[0] + ", " + st[1]
+ + ", " + st[2] + "," + st[3] + "}"); // + ","+st[4]+"\n");
ex.printStackTrace();
}
* executeJavascriptFunction( false, _listenerfn, st = new String[] {
* "colourstruct", "" + ((jalview.appletgui.AlignmentPanel) source).av
* .getViewId(), handle, "" }); } catch (Exception ex) {
- * System.err.println("Couldn't execute callback with " + _listenerfn +
+ * jalview.bin.Console.errPrintln("Couldn't execute callback with " + _listenerfn +
* " using args { " + st[0] + ", " + st[1] + ", " + st[2] + "," + st[3] +
* "\n"); ex.printStackTrace();
*