X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FStructureViewer.java;h=5effa1a9c19ef37feb8d4aaaf719887c66ad8106;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=b7767facf7580fd0e26a03ce02c54dfeb2d18dea;hpb=b927b6af7e5654e0df7e2dbaa337322f2b52940f;p=jalview.git

diff --git a/src/jalview/gui/StructureViewer.java b/src/jalview/gui/StructureViewer.java
index b7767fa..5effa1a 100644
--- a/src/jalview/gui/StructureViewer.java
+++ b/src/jalview/gui/StructureViewer.java
@@ -20,14 +20,6 @@
  */
 package jalview.gui;
 
-import jalview.api.structures.JalviewStructureDisplayI;
-import jalview.bin.Cache;
-import jalview.datamodel.PDBEntry;
-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;
@@ -35,6 +27,14 @@ import java.util.List;
 import java.util.Map;
 import java.util.Map.Entry;
 
+import jalview.api.structures.JalviewStructureDisplayI;
+import jalview.bin.Cache;
+import jalview.bin.Console;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.StructureViewerModel;
+import jalview.structure.StructureSelectionManager;
+
 /**
  * A proxy for handling structure viewers, that orchestrates adding selected
  * structures, associated with sequences in Jalview, to an existing viewer, or
@@ -49,9 +49,14 @@ public class StructureViewer
 
   StructureSelectionManager ssm;
 
+  /**
+   * decide if new structures are aligned to existing ones
+   */
+  private boolean superposeAdded = true;
+
   public enum ViewerType
   {
-    JMOL, CHIMERA
+    JMOL, CHIMERA, CHIMERAX, PYMOL
   };
 
   /**
@@ -59,7 +64,8 @@ public class StructureViewer
    * 
    * @param structureSelectionManager
    */
-  public StructureViewer(StructureSelectionManager structureSelectionManager)
+  public StructureViewer(
+          StructureSelectionManager structureSelectionManager)
   {
     ssm = structureSelectionManager;
   }
@@ -85,7 +91,12 @@ 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());
@@ -121,12 +132,13 @@ public class StructureViewer
 
     Map<PDBEntry, SequenceI[]> seqsForPdbs = getSequencesForPdbs(pdbs,
             seqs);
-    PDBEntry[] pdbsForFile = seqsForPdbs.keySet().toArray(
-            new PDBEntry[seqsForPdbs.size()]);
-    SequenceI[][] theSeqs = seqsForPdbs.values().toArray(
-            new SequenceI[seqsForPdbs.size()][]);
+    PDBEntry[] pdbsForFile = seqsForPdbs.keySet()
+            .toArray(new PDBEntry[seqsForPdbs.size()]);
+    SequenceI[][] theSeqs = seqsForPdbs.values()
+            .toArray(new SequenceI[seqsForPdbs.size()][]);
     if (sview != null)
     {
+      sview.setAlignAddedStructures(superposeAdded);
       new Thread(new Runnable()
       {
         @Override
@@ -152,15 +164,25 @@ public class StructureViewer
 
     if (viewerType.equals(ViewerType.JMOL))
     {
-      sview = new AppJmol(ap, pdbsForFile, theSeqs);
+      sview = new AppJmol(ap, superposeAdded, pdbsForFile, theSeqs);
     }
     else if (viewerType.equals(ViewerType.CHIMERA))
     {
-      sview = new ChimeraViewFrame(pdbsForFile, theSeqs, ap);
+      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());
+      Console.error(UNKNOWN_VIEWER_TYPE + getViewerType().toString());
     }
     return sview;
   }
@@ -279,11 +301,14 @@ public class StructureViewer
   {
     if (sview != null)
     {
-      if (!sview.addAlreadyLoadedFile(seqsForPdb, null, ap, pdb.getId()))
+      sview.setAlignAddedStructures(superposeAdded);
+      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();
@@ -295,50 +320,57 @@ 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());
+      Console.error(UNKNOWN_VIEWER_TYPE + getViewerType().toString());
     }
     return sview;
   }
 
   /**
-   * Create a new panel controlling a structure viewer.
+   * Creates a new panel controlling a structure viewer
    * 
    * @param type
-   * @param pdbf
-   * @param id
-   * @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());
+      Console.error(UNKNOWN_VIEWER_TYPE + type.toString());
     }
-    return sview;
+    return viewer;
   }
 
   public boolean isBusy()
@@ -373,4 +405,9 @@ public class StructureViewer
     return sview != null && sview.isVisible();
   }
 
+  public void setSuperpose(boolean alignAddedStructures)
+  {
+    superposeAdded = alignAddedStructures;
+  }
+
 }