JAL-1596 refactoring to allow unit tests to start and shut down Chimera
[jalview.git] / src / jalview / gui / AppJmol.java
index 55288d0..04235be 100644 (file)
@@ -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.
  * 
  */
 package jalview.gui;
 
-import jalview.bin.Cache;
-import jalview.datamodel.Alignment;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.ColumnSelection;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SequenceI;
-import jalview.io.AppletFormatAdapter;
-import jalview.io.JalviewFileChooser;
-import jalview.io.JalviewFileView;
-import jalview.schemes.BuriedColourScheme;
-import jalview.schemes.ColourSchemeI;
-import jalview.schemes.HelixColourScheme;
-import jalview.schemes.HydrophobicColourScheme;
-import jalview.schemes.PurinePyrimidineColourScheme;
-import jalview.schemes.StrandColourScheme;
-import jalview.schemes.TaylorColourScheme;
-import jalview.schemes.TurnColourScheme;
-import jalview.schemes.ZappoColourScheme;
-import jalview.structures.models.AAStructureBindingModel;
-import jalview.util.MessageManager;
-import jalview.util.Platform;
-
 import java.awt.BorderLayout;
 import java.awt.Color;
 import java.awt.Dimension;
@@ -73,6 +51,28 @@ import javax.swing.event.InternalFrameEvent;
 import javax.swing.event.MenuEvent;
 import javax.swing.event.MenuListener;
 
+import jalview.bin.Cache;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.io.AppletFormatAdapter;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
+import jalview.schemes.BuriedColourScheme;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.HelixColourScheme;
+import jalview.schemes.HydrophobicColourScheme;
+import jalview.schemes.PurinePyrimidineColourScheme;
+import jalview.schemes.StrandColourScheme;
+import jalview.schemes.TaylorColourScheme;
+import jalview.schemes.TurnColourScheme;
+import jalview.schemes.ZappoColourScheme;
+import jalview.structures.models.AAStructureBindingModel;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+
 public class AppJmol extends StructureViewerBase
 {
   AppJmolBinding jmb;
@@ -147,9 +147,7 @@ public class AppJmol extends StructureViewerBase
     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
@@ -169,7 +167,7 @@ public class AppJmol extends StructureViewerBase
       seqColour.setSelected(false);
       viewerColour.setSelected(true);
     }
-    if (usetoColour)
+    else if (usetoColour)
     {
       useAlignmentPanelForColourbyseq(ap);
       jmb.setColourBySequence(true);
@@ -186,7 +184,7 @@ public class AppJmol extends StructureViewerBase
     {
       public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
       {
-        closeViewer();
+        closeViewer(false);
       }
     });
     initJmol(loadStatus); // pdbentry, seq, JBPCHECK!
@@ -408,7 +406,7 @@ public class AppJmol extends StructureViewerBase
     {
       public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
       {
-        closeViewer();
+        closeViewer(false);
       }
     });
 
@@ -427,118 +425,6 @@ public class AppJmol extends StructureViewerBase
     openNewJmol(ap, pe, seqs);
   }
 
-  public AlignmentPanel[] getAllAlignmentPanels()
-  {
-    AlignmentPanel[] t;
-    AlignmentPanel[] 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 (getAlignmentPanel() == null)
-    {
-      setAlignmentPanel(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 (getAlignmentPanel() == nap)
-      {
-        setAlignmentPanel(null);
-        for (AlignmentPanel aps : getAllAlignmentPanels())
-        {
-          if (aps != nap)
-          {
-            setAlignmentPanel(aps);
-            break;
-          }
-        }
-      }
-    } catch (Exception ex)
-    {
-    }
-    if (getAlignmentPanel() != null)
-    {
-      buildActionMenu();
-    }
-  }
-
-  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);
-    getBinding().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.
    */
@@ -716,8 +602,9 @@ public class AppJmol extends StructureViewerBase
     jmb.centerViewer(toshow);
   }
 
-  public void closeViewer()
+  public void closeViewer(boolean closeExternalViewer)
   {
+    // JMol does not use an external viewer
     jmb.closeViewer();
     setAlignmentPanel(null);
     _aps.clear();
@@ -1052,7 +939,7 @@ public class AppJmol extends StructureViewerBase
       // 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);
       }
     }
   }