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 (Cache.log.isDebugEnabled())
+ if (Console.isDebugEnabled())
{
- Cache.log.debug("Command executed: " + cmd);
+ Console.debug("Command executed: " + cmd);
}
}
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;
}