JAL-2422 pull up refactoring in preparation for ChimeraX subclasses

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

diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index e9c5416..83ec177 100644 (file)
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -20,6 +20,7 @@
  */
 package jalview.gui;
 
+import jalview.api.AlignmentViewPanel;
 import jalview.bin.Cache;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.PDBEntry;
@@ -154,14 +155,6 @@ public class AppJmol extends StructureViewerBase
             .getString("label.let_jmol_manage_structure_colours"));
   }
 
-  IProgressIndicator progressBar = null;
-
-  @Override
-  protected IProgressIndicator getIProgressIndicator()
-  {
-    return progressBar;
-  }
-  
   /**
    * display a single PDB structure in a new Jmol view
    * 
@@ -173,7 +166,7 @@ public class AppJmol extends StructureViewerBase
   public AppJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
           final AlignmentPanel ap)
   {
-    progressBar = ap.alignFrame;
+    setProgressIndicator(ap.alignFrame);
 
     openNewJmol(ap, alignAddedStructures, new PDBEntry[] { pdbentry },
             new SequenceI[][]
@@ -184,7 +177,7 @@ public class AppJmol extends StructureViewerBase
           PDBEntry[] pdbentrys,
           SequenceI[][] seqs)
   {
-    progressBar = ap.alignFrame;
+    setProgressIndicator(ap.alignFrame);
     jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(),
             pdbentrys, seqs, null);
     addAlignmentPanel(ap);
@@ -396,7 +389,7 @@ public class AppJmol extends StructureViewerBase
     }
 
     // refresh the sequence colours for the new structure(s)
-    for (AlignmentPanel ap : _colourwith)
+    for (AlignmentViewPanel ap : _colourwith)
     {
       jmb.updateColours(ap);
     }
@@ -418,7 +411,7 @@ public class AppJmol extends StructureViewerBase
       @Override
       public void run()
       {
-        if (jmb.viewer.isScriptExecuting())
+        if (jmb.jmolViewer.isScriptExecuting())
         {
           SwingUtilities.invokeLater(this);
           try
@@ -469,12 +462,9 @@ public class AppJmol extends StructureViewerBase
           AlignmentI pdbseq = null;
           pdbid = jmb.getPdbEntry(pi).getId();
           long hdl = pdbid.hashCode() - System.currentTimeMillis();
-          if (progressBar != null)
-          {
-            progressBar.setProgressBar(MessageManager
-                    .formatMessage("status.fetching_pdb", new String[]
-                    { pdbid }), hdl);
-          }
+          setProgressMessage(MessageManager
+                  .formatMessage("status.fetching_pdb", new String[]
+                  { pdbid }), hdl);
           try
           {
             pdbseq = pdbclient.getSequenceRecords(pdbid);
@@ -487,12 +477,8 @@ public class AppJmol extends StructureViewerBase
             errormsgs.append("'").append(pdbid).append("'");
           } finally
           {
-            if (progressBar != null)
-            {
-              progressBar.setProgressBar(
-                      MessageManager.getString("label.state_completed"),
-                      hdl);
-            }
+            setProgressMessage(
+                    MessageManager.getString("label.state_completed"), hdl);
           }
           if (pdbseq != null)
           {
@@ -590,7 +576,7 @@ public class AppJmol extends StructureViewerBase
 
     if (im.getGraphics() != null)
     {
-      jmb.viewer.renderScreenImage(im.getGraphics(), width, height);
+      jmb.jmolViewer.renderScreenImage(im.getGraphics(), width, height);
       im.writeImage();
     }
   }
@@ -608,9 +594,9 @@ public class AppJmol extends StructureViewerBase
     }
   }
 
+  @Override
   public void showConsole(boolean showConsole)
   {
-
     if (showConsole)
     {
       if (splitPane == null)
@@ -676,7 +662,7 @@ public class AppJmol extends StructureViewerBase
           }
         }
       }
-      else if (jmb == null || jmb.viewer == null || !jmb.isFinishedInit())
+      else if (jmb == null || jmb.jmolViewer == null || !jmb.isFinishedInit())
       {
         g.setColor(Color.black);
         g.fillRect(0, 0, currentSize.width, currentSize.height);
@@ -687,7 +673,7 @@ public class AppJmol extends StructureViewerBase
       }
       else
       {
-        jmb.viewer.renderScreenImage(g, currentSize.width,
+        jmb.jmolViewer.renderScreenImage(g, currentSize.width,
                 currentSize.height);
       }
     }
@@ -702,7 +688,7 @@ public class AppJmol extends StructureViewerBase
   @Override
   public String getStateInfo()
   {
-    return jmb == null ? null : jmb.viewer.getStateInfo();
+    return jmb == null ? null : jmb.jmolViewer.getStateInfo();
   }
 
   @Override