JAL-4134 propagate column selection changes in tree and alignment views

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 35125fa..2d02e79 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -155,6 +155,7 @@ import jalview.viewmodel.AlignmentViewport;
 import jalview.viewmodel.ViewportRanges;
 import jalview.ws.DBRefFetcher;
 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
+import jalview.ws.datamodel.alphafold.PAEContactMatrix;
 import jalview.ws.jws1.Discoverer;
 import jalview.ws.jws2.Jws2Discoverer;
 import jalview.ws.jws2.jabaws2.Jws2Instance;
@@ -980,7 +981,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public void setProgressBar(String message, long id)
   {
-    progressBar.setProgressBar(message, id);
+    if (!Platform.isHeadless())
+      progressBar.setProgressBar(message, id);
   }
 
   @Override
@@ -2634,6 +2636,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     viewport.invertColumnSelection();
     alignPanel.paintAlignment(true, false);
+    PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
     viewport.sendSelection();
   }
 
@@ -2914,6 +2917,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       viewport.setGatherViewsHere(true);
     }
     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
+
     return newap;
   }
 
@@ -3429,29 +3433,33 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   /**
-   * DOCUMENT ME!
+   * Opens an Overview panel for the alignment, unless one is open already
    * 
    * @param e
-   *          DOCUMENT ME!
    */
   @Override
   public void overviewMenuItem_actionPerformed(ActionEvent e)
   {
+    boolean showHiddenRegions = Cache.getDefault(Preferences.SHOW_OV_HIDDEN_AT_START,
+                false);
+    openOverviewPanel(showHiddenRegions);
+  }
+
+  public OverviewPanel openOverviewPanel(boolean showHidden)
+  {
     if (alignPanel.overviewPanel != null)
     {
-      return;
+      return alignPanel.overviewPanel;
     }
-
     JInternalFrame frame = new JInternalFrame();
-    final OverviewPanel overview = new OverviewPanel(alignPanel);
+    final OverviewPanel overview = new OverviewPanel(alignPanel, frame, showHidden);
     frame.setContentPane(overview);
-    Desktop.addInternalFrame(frame, MessageManager
-            .formatMessage("label.overview_params", new Object[]
-            { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
+    Desktop.addInternalFrame(frame, "", true, frame.getWidth(), frame.getHeight(),
             true, true);
     frame.setFrameIcon(null);
     frame.pack();
     frame.setLayer(JLayeredPane.PALETTE_LAYER);
+    final AlignmentPanel thePanel = this.alignPanel; 
     frame.addInternalFrameListener(
             new javax.swing.event.InternalFrameAdapter()
             {
@@ -3460,7 +3468,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                       javax.swing.event.InternalFrameEvent evt)
               {
                 overview.dispose();
-                alignPanel.setOverviewPanel(null);
+                thePanel.setOverviewPanel(null);
               }
             });
     if (getKeyListeners().length > 0)
@@ -3469,6 +3477,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
 
     alignPanel.setOverviewPanel(overview);
+    alignPanel.setOverviewTitle(this);
+    
+    return overview;
   }
 
   @Override
@@ -4122,6 +4133,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     return showNewickTree(nf, treeTitle, null, w, h, x, y);
   }
 
+
   /**
    * Add a treeviewer for the tree extracted from a Newick file object to the
    * current alignment view
@@ -4172,6 +4184,56 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     return tp;
   }
 
+
+  public void showContactMapTree(AlignmentAnnotation aa,
+          PAEContactMatrix cm)
+  {
+    int x = 4, y = 5;
+    int w = 400, h = 500;
+    
+    try
+    {
+      NewickFile fin = new NewickFile(
+              new FileParse(cm.getNewick(), DataSourceType.PASTE));
+      String title = "PAE Matrix Tree for "
+              + cm.getReferenceSeq().getDisplayId(false);
+
+      showColumnWiseTree(fin, aa, title, w,h, x,y);
+    } catch (Throwable xx)
+    {
+      Console.error("Unexpected exception showing tree for contact matrix",
+              xx);
+    }
+  }
+  public TreePanel showColumnWiseTree(NewickFile nf, AlignmentAnnotation aa, String treeTitle,
+           int w, int h, int x, int y)
+  {
+      try
+      {
+        nf.parse();
+        if (nf.getTree() == null)
+        {
+          return null;
+        }
+        TreePanel tp = new TreePanel(alignPanel, nf, aa, title);
+
+        tp.setSize(w, h);
+
+        if (x > 0 && y > 0)
+        {
+          tp.setLocation(x, y);
+        }
+
+        Desktop.addInternalFrame(tp, title, w, h);
+        return tp;
+      } catch (Throwable xx)
+      {
+        Console.error("Unexpected exception showing tree for contact matrix",
+                xx);
+      }
+      return null;
+  }
+  
   private boolean buildingMenu = false;
 
   /**
@@ -4960,7 +5022,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     if (index > -1)
     {
+      /*
+       * update current Overview window title (if there is one)
+       * to add view name "Original" if necessary
+       */
+      alignPanel.setOverviewTitle(this);
+      
+      /*
+       * switch panels and set Overview title (if there is one
+       * because it was opened automatically)
+       */
       alignPanel = alignPanels.get(index);
+      alignPanel.setOverviewTitle(this);
+
       viewport = alignPanel.av;
       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
       setMenusFromViewport(viewport);
@@ -5909,6 +5983,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     return lastFeatureSettingsBounds;
   }
+
 }
 
 class PrintThread extends Thread