Merge commit 'alpha/update_2_12_for_2_11_2_series_merge^2' into HEAD

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

diff --git a/src/jalview/gui/StructureViewer.java b/src/jalview/gui/StructureViewer.java
index 19e0a22..4db6140 100644 (file)
--- a/src/jalview/gui/StructureViewer.java
+++ b/src/jalview/gui/StructureViewer.java
@@ -20,6 +20,12 @@
  */
 package jalview.gui;
 
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
 import jalview.api.structures.JalviewStructureDisplayI;
 import jalview.bin.Cache;
 import jalview.datamodel.PDBEntry;
@@ -27,13 +33,6 @@ import jalview.datamodel.SequenceI;
 import jalview.datamodel.StructureViewerModel;
 import jalview.structure.StructureSelectionManager;
 
-import java.awt.Rectangle;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
 
 /**
  * A proxy for handling structure viewers, that orchestrates adding selected
@@ -45,6 +44,16 @@ import java.util.Map.Entry;
  */
 public class StructureViewer
 {
+  
+  static
+  {
+    Platform.loadStaticResource("core/core_jvjmol.z.js",
+            "org.jmol.viewer.Viewer");
+  }
+
+
+  
+  
   private static final String UNKNOWN_VIEWER_TYPE = "Unknown structure viewer type ";
 
   StructureSelectionManager ssm;
@@ -56,7 +65,7 @@ public class StructureViewer
 
   public enum ViewerType
   {
-    JMOL, CHIMERA
+    JMOL, CHIMERA, CHIMERAX, PYMOL
   };
 
   /**
@@ -81,6 +90,7 @@ public class StructureViewer
     return sv;
   }
 
+  
   @Override
   public String toString()
   {
@@ -90,7 +100,11 @@ public class StructureViewer
     }
     return "New View";
   }
-  public ViewerType getViewerType()
+  /**
+   * 
+   * @return ViewerType for currently configured structure viewer 
+   */
+  public static ViewerType getViewerType()
   {
     String viewType = Cache.getDefault(Preferences.STRUCTURE_DISPLAY,
             ViewerType.JMOL.name());
@@ -165,6 +179,15 @@ public class StructureViewer
       sview = new ChimeraViewFrame(pdbsForFile, superposeAdded, theSeqs,
               ap);
     }
+    else if (viewerType.equals(ViewerType.CHIMERAX))
+    {
+      sview = new ChimeraXViewFrame(pdbsForFile, superposeAdded, theSeqs,
+              ap);
+    }
+    else if (viewerType.equals(ViewerType.PYMOL))
+    {
+      sview = new PymolViewer(pdbsForFile, superposeAdded, theSeqs, ap);
+    }
     else
     {
       Cache.log.error(UNKNOWN_VIEWER_TYPE + getViewerType().toString());
@@ -287,11 +310,13 @@ public class StructureViewer
     if (sview != null)
     {
       sview.setAlignAddedStructures(superposeAdded);
-      if (!sview.addAlreadyLoadedFile(seqsForPdb, null, ap, pdb.getId()))
+      String pdbId = pdb.getId();
+      if (!sview.addAlreadyLoadedFile(seqsForPdb, null, ap, pdbId))
       {
-        sview.addToExistingViewer(pdb, seqsForPdb, null, ap, pdb.getId());
+        sview.addToExistingViewer(pdb, seqsForPdb, null, ap, pdbId);
       }
       sview.updateTitleAndMenus();
+      sview.raiseViewer();
       return sview;
     }
     ViewerType viewerType = getViewerType();
@@ -303,6 +328,14 @@ public class StructureViewer
     {
       sview = new ChimeraViewFrame(pdb, seqsForPdb, null, ap);
     }
+    else if (viewerType.equals(ViewerType.CHIMERAX))
+    {
+      sview = new ChimeraXViewFrame(pdb, seqsForPdb, null, ap);
+    }
+    else if (viewerType.equals(ViewerType.PYMOL))
+    {
+      sview = new PymolViewer(pdb, seqsForPdb, null, ap);
+    }
     else
     {
       Cache.log.error(UNKNOWN_VIEWER_TYPE + getViewerType().toString());
@@ -311,7 +344,7 @@ public class StructureViewer
   }
 
   /**
-   * Create a new panel controlling a structure viewer.
+   * Creates a new panel controlling a structure viewer
    * 
    * @param type
    * @param pdbf
@@ -319,34 +352,37 @@ public class StructureViewer
    * @param sq
    * @param alignPanel
    * @param viewerData
-   * @param fileloc
-   * @param rect
+   * @param sessionFile
    * @param vid
    * @return
    */
-  public JalviewStructureDisplayI createView(ViewerType type, String[] pdbf,
-          String[] id, SequenceI[][] sq, AlignmentPanel alignPanel,
-          StructureViewerModel viewerData, String fileloc, Rectangle rect,
-          String vid)
+  public static JalviewStructureDisplayI createView(ViewerType type,
+          AlignmentPanel alignPanel, StructureViewerModel viewerData,
+          String sessionFile, String vid)
   {
-    final boolean useinViewerSuperpos = viewerData.isAlignWithPanel();
-    final boolean usetoColourbyseq = viewerData.isColourWithAlignPanel();
-    final boolean viewerColouring = viewerData.isColourByViewer();
+    JalviewStructureDisplayI viewer = null;
 
     switch (type)
     {
     case JMOL:
-      sview = new AppJmol(pdbf, id, sq, alignPanel, usetoColourbyseq,
-              useinViewerSuperpos, viewerColouring, fileloc, rect, vid);
+      viewer = new AppJmol(viewerData, alignPanel, sessionFile, vid);
+      // todo or construct and then openSession(sessionFile)?
       break;
     case CHIMERA:
-      Cache.log.error(
-              "Unsupported structure viewer type " + type.toString());
+      viewer = new ChimeraViewFrame(viewerData, alignPanel, sessionFile,
+              vid);
+      break;
+    case CHIMERAX:
+      viewer = new ChimeraXViewFrame(viewerData, alignPanel, sessionFile,
+              vid);
+      break;
+    case PYMOL:
+      viewer = new PymolViewer(viewerData, alignPanel, sessionFile, vid);
       break;
     default:
       Cache.log.error(UNKNOWN_VIEWER_TYPE + type.toString());
     }
-    return sview;
+    return viewer;
   }
 
   public boolean isBusy()