*/
package jalview.ext.rbvi.chimera;
-import java.awt.Color;
-import java.net.BindException;
-import java.util.ArrayList;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-
-import ext.edu.ucsf.rbvi.strucviz2.ChimeraManager;
-import ext.edu.ucsf.rbvi.strucviz2.ChimeraModel;
-import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
-import ext.edu.ucsf.rbvi.strucviz2.StructureManager.ModelType;
-
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureRenderer;
import jalview.api.SequenceRenderer;
import jalview.structures.models.AAStructureBindingModel;
import jalview.util.MessageManager;
+import java.awt.Color;
+import java.net.BindException;
+import java.util.ArrayList;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+
+import ext.edu.ucsf.rbvi.strucviz2.ChimeraManager;
+import ext.edu.ucsf.rbvi.strucviz2.ChimeraModel;
+import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
+import ext.edu.ucsf.rbvi.strucviz2.StructureManager.ModelType;
+
public abstract class JalviewChimeraBinding extends AAStructureBindingModel
{
// Chimera clause to exclude alternate locations in atom selection
*/
private boolean loadingFinished = true;
- /*
- * state flag used to check if the Chimera viewer's paint method can be called
- */
- private boolean finishedInit = false;
-
public String fileLoadingError;
/*
*/
public void sendChimeraCommand(final String command, boolean logResponse)
{
+ if (viewer == null)
+ {
+ // ? thread running after viewer shut down
+ return;
+ }
viewerCommandHistory(false);
if (lastCommand == null || !lastCommand.equals(command))
{
}
StringBuilder atomSpecs = new StringBuilder();
boolean first = true;
+
for (AtomSpec atom : atoms)
{
int pdbResNum = atom.getPdbResNum();
List<ChimeraModel> cms = chimeraMaps.get(pdbfile);
if (cms != null && !cms.isEmpty())
{
- /*
- * Formatting as #0:34.A,#1:33.A doesn't work as desired, so instead we
- * concatenate multiple 'show' commands
- */
- atomSpecs.append(first ? "" : ";show ");
+ atomSpecs.append(first ? "" : ",");
first = false;
- atomSpecs.append("#" + cms.get(0).getModelNumber());
+ atomSpecs.append(cms.get(0).getModelNumber());
atomSpecs.append(":" + pdbResNum);
if (!chain.equals(" "))
{
viewerCommandHistory(false);
if (atomSpec.length() > 0)
{
- command.append("show ").append(atomSpec);
+ command.append("show #").append(atomSpec);
viewer.sendChimeraCommand(command.toString(), false);
}
viewerCommandHistory(true);
*/
public abstract void refreshGUI();
+ @Override
public void setLoadingFromArchive(boolean loadingFromArchive)
{
this.loadingFromArchive = loadingFromArchive;
* @return true if Chimeral is still restoring state or loading is still going
* on (see setFinsihedLoadingFromArchive)
*/
+ @Override
public boolean isLoadingFromArchive()
{
return loadingFromArchive && !loadingFinished;
*
* @param finishedLoading
*/
+ @Override
public void setFinishedLoadingFromArchive(boolean finishedLoading)
{
loadingFinished = finishedLoading;
return true;
}
- public boolean isFinishedInit()
- {
- return finishedInit;
- }
-
- public void setFinishedInit(boolean finishedInit)
- {
- this.finishedInit = finishedInit;
- }
-
/**
* Returns a list of chains mapped in this viewer. Note this list is not
* currently scoped per structure.