X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmol.java;h=ff9b0a7126dbfa2fbccd6271235101d362872200;hb=ba263c975bd8a9740aa1fe105acaad16418e0ae1;hp=4e6ab8340cd46442b8f2aa76daaefa81f3c48951;hpb=f59ae49cdd2bb8f6721424ea6ce167e8245e7d15;p=jalview.git

diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index 4e6ab83..ff9b0a7 100644
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -84,41 +84,8 @@ public class AppJmol extends StructureViewerBase
 
   RenderPanel renderPanel;
 
-  Vector atomsPicked = new Vector();
-
   private boolean addingStructures = false;
 
-  /**
-   * 
-   * @param file
-   * @param id
-   * @param seq
-   * @param ap
-   * @param loadStatus
-   * @param bounds
-   * @deprecated defaults to AppJmol(String[] files, ... , viewid);
-   */
-  @Deprecated
-  public AppJmol(String file, String id, SequenceI[] seq,
-          AlignmentPanel ap, String loadStatus, Rectangle bounds)
-  {
-    this(file, id, seq, ap, loadStatus, bounds, null);
-  }
-
-  /**
-   * @deprecated
-   */
-  @Deprecated
-  public AppJmol(String file, String id, SequenceI[] seq,
-          AlignmentPanel ap, String loadStatus, Rectangle bounds,
-          String viewid)
-  {
-    this(new String[]
-    { file }, new String[]
-    { id }, new SequenceI[][]
-    { seq }, ap, true, true, false, loadStatus, bounds, viewid);
-  }
-
   ViewSelectionMenu seqColourBy;
 
   /**
@@ -901,8 +868,7 @@ public class AppJmol extends StructureViewerBase
 
     if (im.getGraphics() != null)
     {
-      Rectangle rect = new Rectangle(width, height);
-      jmb.viewer.renderScreenImage(im.getGraphics(), rect.getSize(), rect);
+      jmb.viewer.renderScreenImage(im.getGraphics(), width, height);
       im.writeImage();
     }
   }
@@ -1079,15 +1045,12 @@ public class AppJmol extends StructureViewerBase
   {
     final Dimension currentSize = new Dimension();
 
-    final Rectangle rectClip = new Rectangle();
-
     @Override
     public void paintComponent(Graphics g)
     {
       getSize(currentSize);
-      g.getClipBounds(rectClip);
 
-      if (jmb.fileLoadingError != null)
+      if (jmb != null && jmb.fileLoadingError != null)
       {
         g.setColor(Color.black);
         g.fillRect(0, 0, currentSize.width, currentSize.height);
@@ -1124,7 +1087,8 @@ public class AppJmol extends StructureViewerBase
       }
       else
       {
-        jmb.viewer.renderScreenImage(g, currentSize, rectClip);
+        jmb.viewer.renderScreenImage(g, currentSize.width,
+                currentSize.height);
       }
     }
   }