JAL-2944 tidies for review comments

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

diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index af25653..dae54a5 100644 (file)
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -44,7 +44,6 @@ import java.util.List;
 import java.util.Vector;
 
 import javax.swing.JCheckBoxMenuItem;
-import javax.swing.JInternalFrame;
 import javax.swing.JPanel;
 import javax.swing.JSplitPane;
 import javax.swing.SwingUtilities;
@@ -162,8 +161,9 @@ public class AppJmol extends StructureViewerBase
   {
     return progressBar;
   }
+  
   /**
-   * add a single PDB structure to a new or existing Jmol view
+   * display a single PDB structure in a new Jmol view
    * 
    * @param pdbentry
    * @param seq
@@ -174,33 +174,14 @@ public class AppJmol extends StructureViewerBase
           final AlignmentPanel ap)
   {
     progressBar = ap.alignFrame;
-    String pdbId = pdbentry.getId();
 
-    /*
-     * If the PDB file is already loaded, the user may just choose to add to an
-     * existing viewer (or cancel)
-     */
-    if (addAlreadyLoadedFile(seq, chains, ap, pdbId))
-    {
-      return;
-    }
-
-    /*
-     * Check if there are other Jmol views involving this alignment and prompt
-     * user about adding this molecule to one of them
-     */
-    if (addToExistingViewer(pdbentry, seq, chains, ap, pdbId))
-    {
-      return;
-    }
-
-    /*
-     * If the options above are declined or do not apply, open a new viewer
-     */
-    openNewJmol(ap, new PDBEntry[] { pdbentry }, new SequenceI[][] { seq });
+    openNewJmol(ap, alignAddedStructures, new PDBEntry[] { pdbentry },
+            new SequenceI[][]
+            { seq });
   }
 
-  private void openNewJmol(AlignmentPanel ap, PDBEntry[] pdbentrys,
+  private void openNewJmol(AlignmentPanel ap, boolean alignAdded,
+          PDBEntry[] pdbentrys,
           SequenceI[][] seqs)
   {
     progressBar = ap.alignFrame;
@@ -209,11 +190,9 @@ public class AppJmol extends StructureViewerBase
     addAlignmentPanel(ap);
     useAlignmentPanelForColourbyseq(ap);
 
-    if (pdbentrys.length > 1)
-    {
-      alignAddedStructures = true;
-      useAlignmentPanelForSuperposition(ap);
-    }
+    alignAddedStructures = alignAdded;
+    useAlignmentPanelForSuperposition(ap);
+
     jmb.setColourBySequence(true);
     setSize(400, 400); // probably should be a configurable/dynamic default here
     initMenus();
@@ -234,16 +213,19 @@ public class AppJmol extends StructureViewerBase
   }
 
   /**
-   * create a new Jmol containing several structures superimposed using the
-   * given alignPanel.
+   * create a new Jmol containing several structures optionally superimposed
+   * using the given alignPanel.
    * 
    * @param ap
+   * @param alignAdded
+   *          - true to superimpose
    * @param pe
    * @param seqs
    */
-  public AppJmol(AlignmentPanel ap, PDBEntry[] pe, SequenceI[][] seqs)
+  public AppJmol(AlignmentPanel ap, boolean alignAdded, PDBEntry[] pe,
+          SequenceI[][] seqs)
   {
-    openNewJmol(ap, pe, seqs);
+    openNewJmol(ap, alignAdded, pe, seqs);
   }
 
 
@@ -277,8 +259,6 @@ public class AppJmol extends StructureViewerBase
     jmb.setFinishedInit(true);
   }
 
-  boolean allChainsSelected = false;
-
   @Override
   void showSelectedChains()
   {
@@ -421,7 +401,7 @@ public class AppJmol extends StructureViewerBase
       jmb.updateColours(ap);
     }
     // do superposition if asked to
-    if (Cache.getDefault("AUTOSUPERIMPOSE", true) && alignAddedStructures)
+    if (alignAddedStructures)
     {
       alignAddedStructures();
     }
@@ -455,7 +435,7 @@ public class AppJmol extends StructureViewerBase
         }
       }
     });
-    alignAddedStructures = false;
+
   }
 
   /**
@@ -484,6 +464,7 @@ public class AppJmol extends StructureViewerBase
         String file = jmb.getPdbEntry(pi).getFile();
         if (file == null)
         {
+          // todo: extract block as method and pull up (also ChimeraViewFrame)
           // retrieve the pdb and store it locally
           AlignmentI pdbseq = null;
           pdbid = jmb.getPdbEntry(pi).getId();