X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmol.java;h=b28b81cf0a96e612d72a37611d9fa7e8638c5afb;hb=9811278f9e18ee6cb88470dbae98da046734a0af;hp=aff40e4e9983d2b2e057034f8e56a7e6b513ae40;hpb=75db7abd6c89a9465861dc7604faca4893c52101;p=jalview.git

diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index aff40e4..b28b81c 100644
--- 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;
@@ -44,7 +45,6 @@ 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;
@@ -58,7 +58,7 @@ public class AppJmol extends StructureViewerBase
 
   private static final String SPACE = " ";
 
-  private static final String BACKSLASH = "\"";
+  private static final String QUOTE = "\"";
 
   AppJmolBinding jmb;
 
@@ -162,8 +162,9 @@ 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 +175,14 @@ 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 +191,9 @@ 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();
@@ -234,41 +214,21 @@ 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);
   }
 
-  /**
-   * Returns a list of any Jmol viewers. The list is restricted to those linked
-   * to the given alignment panel if it is not null.
-   */
-  @Override
-  protected List<StructureViewerBase> getViewersFor(AlignmentPanel apanel)
-  {
-    List<StructureViewerBase> result = new ArrayList<StructureViewerBase>();
-    JInternalFrame[] frames = Desktop.instance.getAllFrames();
-
-    for (JInternalFrame frame : frames)
-    {
-      if (frame instanceof AppJmol)
-      {
-        if (apanel == null
-                || ((StructureViewerBase) frame).isLinkedWith(apanel))
-        {
-          result.add((StructureViewerBase) frame);
-        }
-      }
-    }
-    return result;
-  }
 
   void initJmol(String command)
   {
@@ -300,12 +260,10 @@ public class AppJmol extends StructureViewerBase
     jmb.setFinishedInit(true);
   }
 
-  boolean allChainsSelected = false;
-
   @Override
   void showSelectedChains()
   {
-    Vector<String> toshow = new Vector<String>();
+    Vector<String> toshow = new Vector<>();
     for (int i = 0; i < chainMenu.getItemCount(); i++)
     {
       if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
@@ -368,8 +326,8 @@ public class AppJmol extends StructureViewerBase
     StringBuilder fileList = new StringBuilder();
     for (String s : files)
     {
-      fileList.append(SPACE).append(BACKSLASH)
-              .append(Platform.escapeString(s)).append(BACKSLASH);
+      fileList.append(SPACE).append(QUOTE)
+              .append(Platform.escapeBackslashes(s)).append(QUOTE);
     }
     String filesString = fileList.toString();
 
@@ -439,12 +397,12 @@ public class AppJmol extends StructureViewerBase
     }
 
     // refresh the sequence colours for the new structure(s)
-    for (AlignmentPanel ap : _colourwith)
+    for (AlignmentViewPanel avp : _colourwith)
     {
-      jmb.updateColours(ap);
+      jmb.updateColours(avp);
     }
     // do superposition if asked to
-    if (Cache.getDefault("AUTOSUPERIMPOSE", true) && alignAddedStructures)
+    if (alignAddedStructures)
     {
       alignAddedStructures();
     }
@@ -478,7 +436,7 @@ public class AppJmol extends StructureViewerBase
         }
       }
     });
-    alignAddedStructures = false;
+
   }
 
   /**
@@ -494,7 +452,7 @@ public class AppJmol extends StructureViewerBase
     // todo - record which pdbids were successfully imported.
     StringBuilder errormsgs = new StringBuilder();
 
-    List<String> files = new ArrayList<String>();
+    List<String> files = new ArrayList<>();
     String pdbid = "";
     try
     {
@@ -507,6 +465,7 @@ 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();
@@ -557,7 +516,7 @@ public class AppJmol extends StructureViewerBase
             addingStructures = true; // already files loaded.
             for (int c = 0; c < filesInViewer.length; c++)
             {
-              if (filesInViewer[c].equals(file))
+              if (Platform.pathEquals(filesInViewer[c], file))
               {
                 file = null;
                 break;