JAL-2944 expose UI update methods in api

[jalview.git] / src / jalview / gui / StructureViewerBase.java

diff --git a/src/jalview/gui/StructureViewerBase.java b/src/jalview/gui/StructureViewerBase.java
index 93d675a..3e06724 100644 (file)
--- a/src/jalview/gui/StructureViewerBase.java
+++ b/src/jalview/gui/StructureViewerBase.java
@@ -20,6 +20,7 @@
  */
 package jalview.gui;
 
+import jalview.api.AlignmentViewPanel;
 import jalview.bin.Cache;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
@@ -402,8 +403,15 @@ public abstract class StructureViewerBase extends GStructureViewer
     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
@@ -416,41 +424,23 @@ public abstract class StructureViewerBase extends GStructureViewer
    * @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;
   }
 
   /**
@@ -462,9 +452,12 @@ public abstract class StructureViewerBase extends GStructureViewer
    * @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
@@ -521,8 +514,9 @@ public abstract class StructureViewerBase extends GStructureViewer
    * @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()
@@ -533,23 +527,8 @@ public abstract class StructureViewerBase extends GStructureViewer
       /*
        * 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;
   }
@@ -997,6 +976,7 @@ public abstract class StructureViewerBase extends GStructureViewer
   /**
    * Configures the title and menu items of the viewer panel.
    */
+  @Override
   public void updateTitleAndMenus()
   {
     AAStructureBindingModel binding = getBinding();