JAL-2944 remove modal prompt logic and expose methods for adding structure data to...

diff --git a/src/jalview/api/structures/JalviewStructureDisplayI.java b/src/jalview/api/structures/JalviewStructureDisplayI.java
index b4612cf..69d08fa 100644 (file)
--- a/src/jalview/api/structures/JalviewStructureDisplayI.java
+++ b/src/jalview/api/structures/JalviewStructureDisplayI.java
@@ -20,6 +20,9 @@
  */
 package jalview.api.structures;
 
+import jalview.api.AlignmentViewPanel;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
 import jalview.schemes.ColourSchemeI;
 import jalview.structures.models.AAStructureBindingModel;
 
@@ -69,4 +72,12 @@ public interface JalviewStructureDisplayI
    */
   boolean hasMapping();
 
+  // construction method - move to another interface ?
+  boolean addAlreadyLoadedFile(SequenceI[] seq, String[] chains,
+          AlignmentViewPanel apanel, String pdbId);
+
+  // construction method - move to another interface ?
+  boolean addToExistingViewer(PDBEntry pdbentry, SequenceI[] seq,
+          String[] chains, AlignmentViewPanel apanel, String pdbId);
+
 }

diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index af25653..29f02d6 100644 (file)
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -44,7 +44,6 @@ import java.util.List;
 import java.util.Vector;
 
 import javax.swing.JCheckBoxMenuItem;
-import javax.swing.JInternalFrame;
 import javax.swing.JPanel;
 import javax.swing.JSplitPane;
 import javax.swing.SwingUtilities;
@@ -162,8 +161,9 @@ public class AppJmol extends StructureViewerBase
   {
     return progressBar;
   }
+  
   /**
-   * add a single PDB structure to a new or existing Jmol view
+   * display a single PDB structure in a new Jmol view
    * 
    * @param pdbentry
    * @param seq
@@ -174,29 +174,7 @@ public class AppJmol extends StructureViewerBase
           final AlignmentPanel ap)
   {
     progressBar = ap.alignFrame;
-    String pdbId = pdbentry.getId();
 
-    /*
-     * If the PDB file is already loaded, the user may just choose to add to an
-     * existing viewer (or cancel)
-     */
-    if (addAlreadyLoadedFile(seq, chains, ap, pdbId))
-    {
-      return;
-    }
-
-    /*
-     * Check if there are other Jmol views involving this alignment and prompt
-     * user about adding this molecule to one of them
-     */
-    if (addToExistingViewer(pdbentry, seq, chains, ap, pdbId))
-    {
-      return;
-    }
-
-    /*
-     * If the options above are declined or do not apply, open a new viewer
-     */
     openNewJmol(ap, new PDBEntry[] { pdbentry }, new SequenceI[][] { seq });
   }
 
@@ -209,11 +187,9 @@ public class AppJmol extends StructureViewerBase
     addAlignmentPanel(ap);
     useAlignmentPanelForColourbyseq(ap);
 
-    if (pdbentrys.length > 1)
-    {
-      alignAddedStructures = true;
+    alignAddedStructures = true;
       useAlignmentPanelForSuperposition(ap);
-    }
+
     jmb.setColourBySequence(true);
     setSize(400, 400); // probably should be a configurable/dynamic default here
     initMenus();

diff --git a/src/jalview/gui/ChimeraViewFrame.java b/src/jalview/gui/ChimeraViewFrame.java
index 87512f5..c595d9d 100644 (file)
--- a/src/jalview/gui/ChimeraViewFrame.java
+++ b/src/jalview/gui/ChimeraViewFrame.java
@@ -202,7 +202,7 @@ public class ChimeraViewFrame extends StructureViewerBase
   }
 
   /**
-   * add a single PDB structure to a new or existing Chimera view
+   * open a single PDB structure in a new Chimera view
    * 
    * @param pdbentry
    * @param seq
@@ -213,30 +213,7 @@ public class ChimeraViewFrame extends StructureViewerBase
           String[] chains, final AlignmentPanel ap)
   {
     this();
-    String pdbId = pdbentry.getId();
 
-    /*
-     * If the PDB file is already loaded, the user may just choose to add to an
-     * existing viewer (or cancel)
-     */
-    if (addAlreadyLoadedFile(seq, chains, ap, pdbId))
-    {
-      return;
-    }
-
-    /*
-     * Check if there are other Chimera views involving this alignment and give
-     * user the option to add and align this molecule to one of them (or cancel)
-     */
-    if (addToExistingViewer(pdbentry, seq, chains, ap, pdbId))
-    {
-      return;
-    }
-
-    /*
-     * If the options above are declined or do not apply, show the structure in
-     * a new viewer
-     */
     openNewChimera(ap, new PDBEntry[] { pdbentry },
             new SequenceI[][]
             { seq });

diff --git a/src/jalview/gui/StructureViewerBase.java b/src/jalview/gui/StructureViewerBase.java
index 0b45417..e084417 100644 (file)
--- a/src/jalview/gui/StructureViewerBase.java
+++ b/src/jalview/gui/StructureViewerBase.java
@@ -424,41 +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;
   }
 
   /**
@@ -470,9 +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
@@ -529,8 +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()
@@ -541,23 +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;
   }