import jalview.structure.StructureCommandsBase;
import jalview.structure.StructureMapping;
import jalview.structure.StructureSelectionManager;
-import jalview.structure.StructureCommandsI.AtomSpecType;
import jalview.util.Comparison;
import jalview.util.Platform;
.append("|");
sb.append(getAtomSpec(refAtoms, AtomSpecType.RESIDUE_ONLY))
.append(getCommandSeparator()).append("cartoons");
+ return Arrays.asList(new StructureCommand(sb.toString()));
+ }
+ @Override
+ public List<StructureCommandI> centerViewOn(List<AtomSpecModel> residues)
+ {
+ StringBuilder sb = new StringBuilder(64);
+ sb.append("center ");
+ for (AtomSpecModel ranges : residues)
+ {
+ if (sb.length() > 9)
+ {
+ sb.append(" or ");
+ }
+ sb.append(getAtomSpec(ranges, AtomSpecType.RESIDUE_ONLY));
+ }
return Arrays.asList(new StructureCommand(sb.toString()));
}
/*
* https://chemapps.stolaf.edu/jmol/docs/#writemodel
*/
- return new StructureCommand("write STATE \"" + filepath + "\"");
+ StructureCommand sc = new StructureCommand(
+ "write STATE \"" + filepath + "\"");
+ sc.setWaitNeeded(true);
+ return sc;
}
@Override
"load FILES \"" + Platform.escapeBackslashes(file) + "\"");
}
+ @Override
+ public StructureCommandI restoreSession(String filePath)
+ {
+ return new StructureCommand("restore STATE \""
+ + Platform.escapeBackslashes(filePath) + "\"");
+ }
+
+ @Override
+ public List<StructureCommandI> showHetatms(List<String> toShow)
+ {
+ // always clear the current hetero cpk display
+
+ StringBuilder sb = new StringBuilder();
+ sb.append("select hetero; cpk off;");
+
+ if (toShow != null && !toShow.isEmpty())
+ {
+ // select what was requested
+ sb.append("select ");
+ boolean or = false;
+ for (String k : toShow)
+ {
+ sb.append(or ? " or " : " ");
+ sb.append(k);
+ or = true;
+ }
+ // and show as
+ sb.append("; cpk;");
+ }
+
+ return Arrays.asList(new StructureCommand(sb.toString()));
+ }
+
/**
* Obsolete method, only referenced from
* jalview.javascript.MouseOverStructureListener