import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
import ext.edu.ucsf.rbvi.strucviz2.StructureManager.ModelType;
import jalview.api.AlignmentViewPanel;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SearchResultMatchI;
import jalview.datamodel.SearchResultsI;
@Override
public boolean isViewerRunning()
{
- return chimeraManager.isChimeraLaunched();
+ return chimeraManager!=null && chimeraManager.isChimeraLaunched();
}
/**
if (getResponse)
{
reply = lastReply;
- if (Cache.log.isDebugEnabled()) {
- Cache.log.debug(
+ if (Console.isDebugEnabled()) {
+ Console.debug(
"Response from command ('" + cmd + "') was:\n" + lastReply);
}
}
+ else
+ {
+ if (Console.isDebugEnabled())
+ {
+ Console.debug("Command executed: " + cmd);
+ }
+ }
return reply;
}
{
return;
}
-
+ if (!found)
+ {
+ // not a valid residue label command, so clear
+ cmd.setLength(0);
+ }
/*
- * unshow the label for the previous residue
+ * prepend with command
+ * to unshow the label for the previous residue
*/
if (lastHighlightCommand != null)
{
- executeCommand(false, null, new StructureCommand("~" + lastHighlightCommand));
+ cmd.insert(0, ";");
+ cmd.insert(0,lastHighlightCommand);
+ cmd.insert(0,"~");
+
}
- if (found)
- {
- executeCommand(false, null, new StructureCommand(command));
+ if (cmd.length()>0) {
+ executeCommand(true, null, new StructureCommand(cmd.toString()));
+ }
+
+ if (found) {
+ this.lastHighlightCommand = command;
}
- this.lastHighlightCommand = command;
}
/**
atomSpecs.add(spec);
} catch (IllegalArgumentException e)
{
- Cache.log.error("Failed to parse atomspec: " + atomSpec);
+ Console.error("Failed to parse atomspec: " + atomSpec);
}
}
return atomSpecs;
spec = parseAtomSpec(atomSpec);
} catch (IllegalArgumentException e)
{
- Cache.log.error("Problem parsing atomspec " + atomSpec);
+ Console.error("Problem parsing atomspec " + atomSpec);
continue;
}