Merge branch 'develop' into feature/JAL-3416_update_to_flatlaf_3.1.1_with_unpacked_na...

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 35125fa..2365fd2 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -59,7 +59,6 @@ import java.util.Hashtable;
 import java.util.List;
 import java.util.Locale;
 import java.util.Vector;
-import java.util.concurrent.Callable;
 
 import javax.swing.ButtonGroup;
 import javax.swing.JCheckBoxMenuItem;
@@ -151,10 +150,12 @@ import jalview.util.HttpUtils;
 import jalview.util.ImageMaker.TYPE;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
+import jalview.util.imagemaker.BitmapImageSizing;
 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;
@@ -980,14 +981,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public void setProgressBar(String message, long id)
   {
-    progressBar.setProgressBar(message, id);
+    if (!Platform.isHeadless() && progressBar != null)
+      progressBar.setProgressBar(message, id);
   }
 
   @Override
   public void registerHandler(final long id,
           final IProgressIndicatorHandler handler)
   {
-    progressBar.registerHandler(id, handler);
+    if (progressBar != null)
+      progressBar.registerHandler(id, handler);
   }
 
   /**
@@ -997,7 +1000,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public boolean operationInProgress()
   {
-    return progressBar.operationInProgress();
+    return progressBar == null ? false : progressBar.operationInProgress();
   }
 
   /**
@@ -1275,11 +1278,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
 
     AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
-    Callable<Void> cancelAction = () -> {
+    Runnable cancelAction = () -> {
       lastSaveSuccessful = false;
-      return null;
     };
-    Callable<Void> outputAction = () -> {
+    Runnable outputAction = () -> {
       // todo defer this to inside formatSequences (or later)
       AlignmentExportData exportData = viewport.getAlignExportData(options);
       String output = new FormatAdapter(alignPanel, options)
@@ -1357,7 +1359,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           AlignFrame.this.getViewport().setSavedUpToDate(true);
         }
       }
-      return null;
     };
 
     /*
@@ -1375,7 +1376,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       try
       {
-        outputAction.call();
+        outputAction.run();
       } catch (Exception e)
       {
         // TODO Auto-generated catch block
@@ -1397,7 +1398,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     FileFormatI fileFormat = FileFormats.getInstance()
             .forName(fileFormatName);
     AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
-    Callable<Void> outputAction = () -> {
+    Runnable outputAction = () -> {
       // todo defer this to inside formatSequences (or later)
       AlignmentExportData exportData = viewport.getAlignExportData(options);
       CutAndPasteTransfer cap = new CutAndPasteTransfer();
@@ -1419,7 +1420,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                 oom);
         cap.dispose();
       }
-      return null;
     };
 
     /*
@@ -1436,7 +1436,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       try
       {
-        outputAction.call();
+        outputAction.run();
       } catch (Exception e)
       {
         e.printStackTrace();
@@ -1478,7 +1478,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public void createPNG(File f)
   {
-    alignPanel.makeAlignmentImage(TYPE.PNG, f);
+    createPNG(f, null, BitmapImageSizing.nullBitmapImageSizing());
+  }
+
+  public void createPNG(File f, String renderer, BitmapImageSizing userBis)
+  {
+    alignPanel.makeAlignmentImage(TYPE.PNG, f, renderer, userBis);
   }
 
   /**
@@ -1490,7 +1495,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public void createEPS(File f)
   {
-    alignPanel.makeAlignmentImage(TYPE.EPS, f);
+    createEPS(f, null);
+  }
+
+  public void createEPS(File f, String renderer)
+  {
+    alignPanel.makeAlignmentImage(TYPE.EPS, f, renderer);
   }
 
   /**
@@ -1502,7 +1512,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public void createSVG(File f)
   {
-    alignPanel.makeAlignmentImage(TYPE.SVG, f);
+    createSVG(f, null);
+  }
+
+  public void createSVG(File f, String renderer)
+  {
+    alignPanel.makeAlignmentImage(TYPE.SVG, f, renderer);
   }
 
   @Override
@@ -1552,7 +1567,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       String choice = chooser.getSelectedFile().getPath();
       Cache.setProperty("LAST_DIRECTORY", choice);
       loadJalviewDataFile(chooser.getSelectedFile(), null, null, null);
-      return null;
     });
 
     chooser.showOpenDialog(this);
@@ -2474,7 +2488,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       return;
     }
 
-    Callable okAction = () -> {
+    Runnable okAction = () -> {
       SequenceI[] cut = sg.getSequences()
               .toArray(new SequenceI[sg.getSize()]);
 
@@ -2498,7 +2512,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         {
         }
       }
-      return null;
     };
 
     /*
@@ -2524,7 +2537,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       try
       {
-        okAction.call();
+        okAction.run();
       } catch (Exception e)
       {
         e.printStackTrace();
@@ -2634,6 +2647,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     viewport.invertColumnSelection();
     alignPanel.paintAlignment(true, false);
+    PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
     viewport.sendSelection();
   }
 
@@ -2914,6 +2928,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       viewport.setGatherViewsHere(true);
     }
     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
+
     return newap;
   }
 
@@ -3429,29 +3444,34 @@ 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(),
-            true, true);
+    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 +3480,7 @@ 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 +3489,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
 
     alignPanel.setOverviewPanel(overview);
+    alignPanel.setOverviewTitle(this);
+
+    return overview;
   }
 
   @Override
@@ -4106,7 +4129,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                         .getString("label.possible_problem_with_tree_file"),
                 JvOptionPane.WARNING_MESSAGE);
       }
-      return null;
     });
     chooser.showOpenDialog(this);
   }
@@ -4172,6 +4194,56 @@ 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 +5032,19 @@ 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);
@@ -5624,7 +5708,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    *          update non-sequence-related annotations
    */
   @Override
-  protected void setAnnotationsVisibility(boolean visible,
+  public void setAnnotationsVisibility(boolean visible,
           boolean forSequences, boolean forAlignment)
   {
     AlignmentAnnotation[] anns = alignPanel.getAlignment()
@@ -5890,7 +5974,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       Cache.setProperty("LAST_DIRECTORY", choice);
       SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
       new VCFLoader(choice).loadVCF(seqs, us);
-      return null;
     });
     chooser.showOpenDialog(null);
 
@@ -5909,6 +5992,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     return lastFeatureSettingsBounds;
   }
+
 }
 
 class PrintThread extends Thread