JAL-3446 reorganized JalviewJSApp (accidentally put that in jalview/api)

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 6eb2dfe..f74eb32 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -167,6 +167,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
 {
 
+  public static int frameCount;
+  
   public static final int DEFAULT_WIDTH = 700;
 
   public static final int DEFAULT_HEIGHT = 500;
@@ -194,6 +196,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   File fileObject;
 
+  private int id;
+
   /**
    * Creates a new AlignFrame object with specific width and height.
    * 
@@ -288,6 +292,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
           int height, String sequenceSetId, String viewId)
   {
+    
+    id = (++frameCount);
+    
     setSize(width, height);
 
     if (al.getDataset() == null)
@@ -553,7 +560,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         {
 
         case 27: // escape key
-          deselectAllSequenceMenuItem_actionPerformed(null);
+          alignPanel.deselectAllSequences();
 
           break;
 
@@ -2486,18 +2493,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
   {
-    SequenceGroup sg = new SequenceGroup(
-            viewport.getAlignment().getSequences());
-
-    sg.setEndRes(viewport.getAlignment().getWidth() - 1);
-    viewport.setSelectionGroup(sg);
-    viewport.isSelectionGroupChanged(true);
-    viewport.sendSelection();
-    // JAL-2034 - should delegate to
-    // alignPanel to decide if overview needs
-    // updating.
-    alignPanel.paintAlignment(false, false);
-    PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
+    alignPanel.selectAllSequences();
   }
 
   /**
@@ -2509,21 +2505,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
   {
-    if (viewport.cursorMode)
-    {
-      alignPanel.getSeqPanel().keyboardNo1 = null;
-      alignPanel.getSeqPanel().keyboardNo2 = null;
-    }
-    viewport.setSelectionGroup(null);
-    viewport.getColumnSelection().clear();
-    viewport.setSelectionGroup(null);
-    alignPanel.getIdPanel().getIdCanvas().searchResults = null;
-    // JAL-2034 - should delegate to
-    // alignPanel to decide if overview needs
-    // updating.
-    alignPanel.paintAlignment(false, false);
-    PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
-    viewport.sendSelection();
+    alignPanel.deselectAllSequences();
   }
 
   /**
@@ -2539,7 +2521,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     if (sg == null)
     {
-      selectAllSequenceMenuItem_actionPerformed(null);
+      alignPanel.selectAllSequences();
 
       return;
     }
@@ -3375,7 +3357,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     // BH 2019.07.26 we allow for an embedded
     // undecorated overview with defined size
-    frame.setName(Jalview.getAppID("overview"));
+    frame.setName(Platform.getAppID("overview"));
     //
     Dimension dim = Platform.getDimIfEmbedded(frame, -1, -1);
     if (dim != null && dim.width == 0)
@@ -3400,8 +3382,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             "resize") != "none");
     Desktop.addInternalFrame(frame, MessageManager
             .formatMessage("label.overview_params", new Object[]
-            { this.getTitle() }), true, dim.width, dim.height, resizable,
-            true);
+            { this.getTitle() }), Desktop.FRAME_MAKE_VISIBLE, dim.width, dim.height, resizable,
+            Desktop.FRAME_ALLOW_ANY_SIZE);
     frame.pack();
     frame.setLayer(JLayeredPane.PALETTE_LAYER);
     frame.addInternalFrameListener(
@@ -5948,6 +5930,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     alignPanel.getSeqPanel().selection(sel, csel, hidden, null);
   }
 
+  
+  public int getID()
+  {
+    return id;
+  }
+
 }
 
 class PrintThread extends Thread