JAL-1759 unused field / methods removed

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

diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index 86ab536..ff9b0a7 100644 (file)
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -26,6 +26,7 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
+import jalview.gui.StructureViewer.ViewerType;
 import jalview.io.AppletFormatAdapter;
 import jalview.io.JalviewFileChooser;
 import jalview.io.JalviewFileView;
@@ -83,41 +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;
 
   /**
@@ -147,7 +115,9 @@ public class AppJmol extends StructureViewerBase
     PDBEntry[] pdbentrys = new PDBEntry[files.length];
     for (int i = 0; i < pdbentrys.length; i++)
     {
-      PDBEntry pdbentry = new PDBEntry(files[i], ids[i]);
+      // PDBEntry pdbentry = new PDBEntry(files[i], ids[i]);
+      PDBEntry pdbentry = new PDBEntry(ids[i], null, PDBEntry.Type.PDB,
+              files[i]);
       pdbentrys[i] = pdbentry;
     }
     // / TODO: check if protocol is needed to be set, and if chains are
@@ -182,9 +152,10 @@ public class AppJmol extends StructureViewerBase
 
     this.addInternalFrameListener(new InternalFrameAdapter()
     {
+      @Override
       public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
       {
-        closeViewer();
+        closeViewer(false);
       }
     });
     initJmol(loadStatus); // pdbentry, seq, JBPCHECK!
@@ -404,9 +375,10 @@ public class AppJmol extends StructureViewerBase
     }
     this.addInternalFrameListener(new InternalFrameAdapter()
     {
+      @Override
       public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
       {
-        closeViewer();
+        closeViewer(false);
       }
     });
 
@@ -524,7 +496,7 @@ public class AppJmol extends StructureViewerBase
     ;
     jmb.allocateViewer(renderPanel, true, "", null, null, "", scriptWindow,
             null);
-    jmb.newJmolPopup(true, "Jmol", true);
+    jmb.newJmolPopup("Jmol");
     if (command == null)
     {
       command = "";
@@ -602,8 +574,9 @@ 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();
@@ -646,9 +619,7 @@ public class AppJmol extends StructureViewerBase
           }
           try
           {
-            pdbseq = pdbclient.getSequenceRecords(pdbid = jmb.getPdbEntry(
-                    pi)
-                    .getId());
+            pdbseq = pdbclient.getSequenceRecords(pdbid);
           } catch (OutOfMemoryError oomerror)
           {
             new OOMWarning("Retrieving PDB id " + pdbid, oomerror);
@@ -665,8 +636,8 @@ public class AppJmol extends StructureViewerBase
           {
             // just transfer the file name from the first sequence's first
             // PDBEntry
-            file = new File(((PDBEntry) pdbseq.getSequenceAt(0).getPDBId()
-                    .elementAt(0)).getFile()).getAbsolutePath();
+            file = new File(pdbseq.getSequenceAt(0).getPDBId()
+                    .elementAt(0).getFile()).getAbsolutePath();
             jmb.getPdbEntry(pi).setFile(file);
 
             files.append(" \"" + Platform.escapeString(file) + "\"");
@@ -841,11 +812,7 @@ public class AppJmol extends StructureViewerBase
     jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
     try
     {
-      for (int pdbe = 0; pdbe < jmb.getPdbCount(); pdbe++)
-      {
-        cap.appendText(jmb.printMapping(jmb.getPdbEntry(pdbe).getFile()));
-        cap.appendText("\n");
-      }
+      cap.appendText(jmb.printMappings());
     } catch (OutOfMemoryError e)
     {
       new OOMWarning(
@@ -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();
     }
   }
@@ -1079,14 +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);
@@ -1123,7 +1087,8 @@ public class AppJmol extends StructureViewerBase
       }
       else
       {
-        jmb.viewer.renderScreenImage(g, currentSize, rectClip);
+        jmb.viewer.renderScreenImage(g, currentSize.width,
+                currentSize.height);
       }
     }
   }
@@ -1237,4 +1202,10 @@ public class AppJmol extends StructureViewerBase
     return jmb == null ? null : jmb.viewer.getStateInfo();
   }
 
+  @Override
+  public ViewerType getViewerType()
+  {
+    return ViewerType.JMOL;
+  }
+
 }