X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmol.java;h=86ab5367d197acffa2338e1395e6827bf79d9980;hb=ad15cff29620f960119f80176f1fd443da9f6763;hp=90d3b153c190c99fd9e8c008c96071ae0c195f75;hpb=c66902a9536b10a5477b58aaf7c2d75772890a5d;p=jalview.git

diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index 90d3b15..86ab536 100644
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -26,11 +26,9 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
-import jalview.gui.ViewSelectionMenu.ViewSetProvider;
 import jalview.io.AppletFormatAdapter;
 import jalview.io.JalviewFileChooser;
 import jalview.io.JalviewFileView;
-import jalview.jbgui.GStructureViewer;
 import jalview.schemes.BuriedColourScheme;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.HelixColourScheme;
@@ -46,7 +44,6 @@ import jalview.util.Platform;
 
 import java.awt.BorderLayout;
 import java.awt.Color;
-import java.awt.Component;
 import java.awt.Dimension;
 import java.awt.Font;
 import java.awt.Graphics;
@@ -76,9 +73,7 @@ import javax.swing.event.InternalFrameEvent;
 import javax.swing.event.MenuEvent;
 import javax.swing.event.MenuListener;
 
-public class AppJmol extends GStructureViewer implements Runnable,
-        ViewSetProvider
-
+public class AppJmol extends StructureViewerBase
 {
   AppJmolBinding jmb;
 
@@ -88,8 +83,6 @@ public class AppJmol extends GStructureViewer implements Runnable,
 
   RenderPanel renderPanel;
 
-  AlignmentPanel ap;
-
   Vector atomsPicked = new Vector();
 
   private boolean addingStructures = false;
@@ -154,9 +147,7 @@ public class AppJmol extends GStructureViewer implements Runnable,
     PDBEntry[] pdbentrys = new PDBEntry[files.length];
     for (int i = 0; i < pdbentrys.length; i++)
     {
-      PDBEntry pdbentry = new PDBEntry();
-      pdbentry.setFile(files[i]);
-      pdbentry.setId(ids[i]);
+      PDBEntry pdbentry = new PDBEntry(files[i], ids[i]);
       pdbentrys[i] = pdbentry;
     }
     // / TODO: check if protocol is needed to be set, and if chains are
@@ -176,7 +167,7 @@ public class AppJmol extends GStructureViewer implements Runnable,
       seqColour.setSelected(false);
       viewerColour.setSelected(true);
     }
-    if (usetoColour)
+    else if (usetoColour)
     {
       useAlignmentPanelForColourbyseq(ap);
       jmb.setColourBySequence(true);
@@ -339,7 +330,7 @@ public class AppJmol extends GStructureViewer implements Runnable,
                 topJmol.addAlignmentPanel(ap);
                 // add it to the set used for colouring
                 topJmol.useAlignmentPanelForColourbyseq(ap);
-                topJmol.buildJmolActionMenu();
+                topJmol.buildActionMenu();
                 ap.getStructureSelectionManager()
                         .sequenceColoursChanged(ap);
                 break;
@@ -434,117 +425,6 @@ public class AppJmol extends GStructureViewer implements Runnable,
     openNewJmol(ap, pe, seqs);
   }
 
-  public AlignmentPanel[] getAllAlignmentPanels()
-  {
-    AlignmentPanel[] t, list = new AlignmentPanel[0];
-    for (String setid : _aps)
-    {
-      AlignmentPanel[] panels = PaintRefresher.getAssociatedPanels(setid);
-      if (panels != null)
-      {
-        t = new AlignmentPanel[list.length + panels.length];
-        System.arraycopy(list, 0, t, 0, list.length);
-        System.arraycopy(panels, 0, t, list.length, panels.length);
-        list = t;
-      }
-    }
-
-    return list;
-  }
-
-  /**
-   * set the primary alignmentPanel reference and add another alignPanel to the
-   * list of ones to use for colouring and aligning
-   * 
-   * @param nap
-   */
-  public void addAlignmentPanel(AlignmentPanel nap)
-  {
-    if (ap == null)
-    {
-      ap = nap;
-    }
-    if (!_aps.contains(nap.av.getSequenceSetId()))
-    {
-      _aps.add(nap.av.getSequenceSetId());
-    }
-  }
-
-  /**
-   * remove any references held to the given alignment panel
-   * 
-   * @param nap
-   */
-  public void removeAlignmentPanel(AlignmentPanel nap)
-  {
-    try
-    {
-      _alignwith.remove(nap);
-      _colourwith.remove(nap);
-      if (ap == nap)
-      {
-        ap = null;
-        for (AlignmentPanel aps : getAllAlignmentPanels())
-        {
-          if (aps != nap)
-          {
-            ap = aps;
-            break;
-          }
-        }
-      }
-    } catch (Exception ex)
-    {
-    }
-    if (ap != null)
-    {
-      buildJmolActionMenu();
-    }
-  }
-
-  public void useAlignmentPanelForSuperposition(AlignmentPanel nap)
-  {
-    addAlignmentPanel(nap);
-    if (!_alignwith.contains(nap))
-    {
-      _alignwith.add(nap);
-    }
-  }
-
-  public void excludeAlignmentPanelForSuperposition(AlignmentPanel nap)
-  {
-    if (_alignwith.contains(nap))
-    {
-      _alignwith.remove(nap);
-    }
-  }
-
-  public void useAlignmentPanelForColourbyseq(AlignmentPanel nap,
-          boolean enableColourBySeq)
-  {
-    useAlignmentPanelForColourbyseq(nap);
-    jmb.setColourBySequence(enableColourBySeq);
-    seqColour.setSelected(enableColourBySeq);
-    viewerColour.setSelected(!enableColourBySeq);
-  }
-
-  public void useAlignmentPanelForColourbyseq(AlignmentPanel nap)
-  {
-    addAlignmentPanel(nap);
-    if (!_colourwith.contains(nap))
-    {
-      _colourwith.add(nap);
-    }
-  }
-
-  public void excludeAlignmentPanelForColourbyseq(AlignmentPanel nap)
-  {
-    if (_colourwith.contains(nap))
-    {
-      _colourwith.remove(nap);
-    }
-  }
-
   /**
    * pdb retrieval thread.
    */
@@ -615,7 +495,7 @@ public class AppJmol extends GStructureViewer implements Runnable,
     {
       if (frame instanceof AppJmol)
       {
-        if (((GStructureViewer) frame).isLinkedWith(apanel))
+        if (((StructureViewerBase) frame).isLinkedWith(apanel))
         {
           result.addElement(frame);
         }
@@ -725,7 +605,7 @@ public class AppJmol extends GStructureViewer implements Runnable,
   public void closeViewer()
   {
     jmb.closeViewer();
-    ap = null;
+    setAlignmentPanel(null);
     _aps.clear();
     _alignwith.clear();
     _colourwith.clear();
@@ -1049,16 +929,16 @@ public class AppJmol extends GStructureViewer implements Runnable,
     {
       if (!jmb.isLoadingFromArchive())
       {
-        if (_colourwith.size() == 0 && ap != null)
+        if (_colourwith.size() == 0 && getAlignmentPanel() != null)
         {
           // Make the currently displayed alignment panel the associated view
-          _colourwith.add(ap.alignFrame.alignPanel);
+          _colourwith.add(getAlignmentPanel().alignFrame.alignPanel);
         }
       }
       // Set the colour using the current view for the associated alignframe
       for (AlignmentPanel ap : _colourwith)
       {
-        jmb.colourBySequence(ap.av.showSequenceFeatures, ap);
+        jmb.colourBySequence(ap.av.isShowSequenceFeatures(), ap);
       }
     }
   }
@@ -1268,27 +1148,6 @@ public class AppJmol extends GStructureViewer implements Runnable,
     }
   }
 
-  protected void buildJmolActionMenu()
-  {
-    if (_alignwith == null)
-    {
-      _alignwith = new Vector<AlignmentPanel>();
-    }
-    if (_alignwith.size() == 0 && ap != null)
-    {
-      _alignwith.add(ap);
-    }
-    ;
-    for (Component c : viewerActionMenu.getMenuComponents())
-    {
-      if (c != alignStructs)
-      {
-        viewerActionMenu.remove((JMenuItem) c);
-      }
-    }
-    final ItemListener handler;
-  }
-
   /*
    * (non-Javadoc)
    * 
@@ -1304,14 +1163,14 @@ public class AppJmol extends GStructureViewer implements Runnable,
 
   private void alignStructs_withAllAlignPanels()
   {
-    if (ap == null)
+    if (getAlignmentPanel() == null)
     {
       return;
     }
     ;
     if (_alignwith.size() == 0)
     {
-      _alignwith.add(ap);
+      _alignwith.add(getAlignmentPanel());
     }
     ;
     try
@@ -1363,7 +1222,7 @@ public class AppJmol extends GStructureViewer implements Runnable,
         return ap;
       }
     }
-    return ap;
+    return getAlignmentPanel();
   }
 
   @Override