*/
package jalview.gui;
+import jalview.api.AlignmentViewPanel;
import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
protected boolean alignAddedStructures = false;
- protected boolean _started = false;
+ protected volatile boolean _started = false;
- protected boolean addingStructures = false;
+ protected volatile boolean addingStructures = false;
protected Thread worker = null;
* used to determine if the final sequence/structure mapping has been
* determined
*/
- protected boolean seqColoursApplied = false;
+ protected volatile boolean seqColoursApplied = false;
/**
* Default constructor
return getBinding().hasPdbId(pdbId);
}
- protected abstract List<StructureViewerBase> getViewersFor(
- AlignmentPanel alp);
+ /**
+ * Returns a list of any viewer of the instantiated type. The list is
+ * restricted to those linked to the given alignment panel if it is not null.
+ */
+ protected List<StructureViewerBase> getViewersFor(AlignmentPanel alp)
+ {
+ return Desktop.instance.getStructureViewers(alp, this.getClass());
+ }
+
/**
* Check for any existing views involving this alignment and give user the
* @param pdbId
* @return true if user adds to a view, or cancels entirely, else false
*/
- protected boolean addToExistingViewer(PDBEntry pdbentry, SequenceI[] seq,
- String[] chains, final AlignmentPanel apanel, String pdbId)
+ @Override
+ public boolean addToExistingViewer(PDBEntry pdbentry, SequenceI[] seq,
+ String[] chains, final AlignmentViewPanel apanel, String pdbId)
{
- for (StructureViewerBase view : getViewersFor(apanel))
- {
- // TODO: highlight the view somehow
- /*
- * JAL-1742 exclude view with this structure already mapped (don't offer
- * to align chain B to chain A of the same structure)
- */
- if (view.hasPdbId(pdbId))
- {
- continue;
- }
- int option = chooseAlignStructureToViewer(pdbId, view);
- if (option == JvOptionPane.CANCEL_OPTION)
- {
- return true;
- }
- else if (option == JvOptionPane.YES_OPTION)
- {
- view.useAlignmentPanelForSuperposition(apanel);
- view.addStructure(pdbentry, seq, chains, true, apanel.alignFrame);
- return true;
- }
- else
- {
- // NO_OPTION - offer the next viewer if any
- }
- }
-
/*
- * nothing offered and selected
+ * JAL-1742 exclude view with this structure already mapped (don't offer
+ * to align chain B to chain A of the same structure)
*/
- return false;
+ if (hasPdbId(pdbId))
+ {
+ return false;
+ }
+ AlignmentPanel ap = (AlignmentPanel) apanel; // Implementation error if this
+ // cast fails
+ useAlignmentPanelForSuperposition(ap);
+ addStructure(pdbentry, seq, chains, true, ap.alignFrame);
+ return true;
}
/**
* @param apanel
* @param pdbFilename
*/
- protected void addSequenceMappingsToStructure(SequenceI[] seq,
- String[] chains, final AlignmentPanel apanel, String pdbFilename)
+ public void addSequenceMappingsToStructure(SequenceI[] seq,
+ String[] chains, final AlignmentViewPanel alpanel,
+ String pdbFilename)
{
+ AlignmentPanel apanel = (AlignmentPanel) alpanel;
+
// TODO : Fix multiple seq to one chain issue here.
/*
* create the mappings
* @param pdbId
* @return true if the user chooses to add to a viewer, or to cancel entirely
*/
- protected boolean addAlreadyLoadedFile(SequenceI[] seq, String[] chains,
- final AlignmentPanel apanel, String pdbId)
+ @Override
+ public boolean addAlreadyLoadedFile(SequenceI[] seq, String[] chains,
+ final AlignmentViewPanel apanel, String pdbId)
{
boolean finished = false;
String alreadyMapped = apanel.getStructureSelectionManager()
/*
* the PDB file is already loaded
*/
- int option = JvOptionPane.showInternalConfirmDialog(Desktop.desktop,
- MessageManager.formatMessage(
- "label.pdb_entry_is_already_displayed", new Object[]
- { pdbId }),
- MessageManager.formatMessage(
- "label.map_sequences_to_visible_window", new Object[]
- { pdbId }),
- JvOptionPane.YES_NO_CANCEL_OPTION);
- if (option == JvOptionPane.CANCEL_OPTION)
- {
- finished = true;
- }
- else if (option == JvOptionPane.YES_OPTION)
- {
- addSequenceMappingsToStructure(seq, chains, apanel, alreadyMapped);
- finished = true;
- }
+ addSequenceMappingsToStructure(seq, chains, apanel, alreadyMapped);
+ finished = true;
}
return finished;
}
/**
* Configures the title and menu items of the viewer panel.
*/
+ @Override
public void updateTitleAndMenus()
{
AAStructureBindingModel binding = getBinding();
}
if (getBinding() == null)
{
+ if (_aps == null || _aps.size() == 0)
+ {
+ // viewer has been closed, but we did at some point run.
+ return true;
+ }
return false;
}
String[] pdbids = getBinding().getStructureFiles();