JAL-2422 pull up refactoring in preparation for ChimeraX subclasses

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

diff --git a/src/jalview/gui/ChimeraViewFrame.java b/src/jalview/gui/ChimeraViewFrame.java
index 183b475..22876a4 100644 (file)
--- a/src/jalview/gui/ChimeraViewFrame.java
+++ b/src/jalview/gui/ChimeraViewFrame.java
@@ -20,6 +20,7 @@
  */
 package jalview.gui;
 
+import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureRenderer;
 import jalview.bin.Cache;
 import jalview.datamodel.AlignmentI;
@@ -46,7 +47,6 @@ import java.io.InputStream;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.List;
-import java.util.Random;
 
 import javax.swing.JCheckBoxMenuItem;
 import javax.swing.JInternalFrame;
@@ -65,8 +65,6 @@ public class ChimeraViewFrame extends StructureViewerBase
 {
   private JalviewChimeraBinding jmb;
 
-  private IProgressIndicator progressBar = null;
-
   /*
    * Path to Chimera session file. This is set when an open Jalview/Chimera
    * session is saved, or on restore from a Jalview project (if it holds the
@@ -74,8 +72,6 @@ public class ChimeraViewFrame extends StructureViewerBase
    */
   private String chimeraSessionFile = null;
 
-  private Random random = new Random();
-
   private int myWidth = 500;
 
   private int myHeight = 150;
@@ -203,9 +199,9 @@ public class ChimeraViewFrame extends StructureViewerBase
    */
   protected void createProgressBar()
   {
-    if (progressBar == null)
+    if (getProgressIndicator() == null)
     {
-      progressBar = new ProgressBar(statusPanel, statusBar);
+      setProgressIndicator(new ProgressBar(statusPanel, statusBar));
     }
   }
 
@@ -535,7 +531,7 @@ public class ChimeraViewFrame extends StructureViewerBase
 
             pdb = jmb.getSsm().setMapping(jmb.getSequence()[pos],
                     jmb.getChains()[pos], pe.getFile(), protocol,
-                    progressBar);
+                    getProgressIndicator());
             stashFoundChains(pdb, pe.getFile());
 
           } catch (OutOfMemoryError oomerror)
@@ -570,7 +566,7 @@ public class ChimeraViewFrame extends StructureViewerBase
       }
 
       // refresh the sequence colours for the new structure(s)
-      for (AlignmentPanel ap : _colourwith)
+      for (AlignmentViewPanel ap : _colourwith)
       {
         jmb.updateColours(ap);
       }
@@ -657,40 +653,6 @@ public class ChimeraViewFrame extends StructureViewerBase
     return filePath;
   }
 
-  /**
-   * Convenience method to update the progress bar if there is one. Be sure to
-   * call stopProgressBar with the returned handle to remove the message.
-   * 
-   * @param msg
-   * @param handle
-   */
-  public long startProgressBar(String msg)
-  {
-    // TODO would rather have startProgress/stopProgress as the
-    // IProgressIndicator interface
-    long tm = random.nextLong();
-    if (progressBar != null)
-    {
-      progressBar.setProgressBar(msg, tm);
-    }
-    return tm;
-  }
-
-  /**
-   * End the progress bar with the specified handle, leaving a message (if not
-   * null) on the status bar
-   * 
-   * @param msg
-   * @param handle
-   */
-  public void stopProgressBar(String msg, long handle)
-  {
-    if (progressBar != null)
-    {
-      progressBar.setProgressBar(msg, handle);
-    }
-  }
-
   @Override
   public void eps_actionPerformed(ActionEvent e)
   {
@@ -831,10 +793,4 @@ public class ChimeraViewFrame extends StructureViewerBase
     }
     return reply;
   }
-
-  @Override
-  protected IProgressIndicator getIProgressIndicator()
-  {
-    return progressBar;
-  }
 }