X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FStructureViewer.java;h=6cef66575ed5ac76d6407611360c1a4db32ea981;hb=c4820a850ccb7171fd29206655bc327af7226e6b;hp=360ddf23308fa7f0c221d46d7928a5a8481870f7;hpb=42f4227ed213d422a87d3b22fc9e85d14ffaf53f;p=jalview.git

diff --git a/src/jalview/gui/StructureViewer.java b/src/jalview/gui/StructureViewer.java
index 360ddf2..6cef665 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
@@ -54,6 +54,16 @@ public class StructureViewer
    */
   private boolean superposeAdded = true;
 
+  /**
+   * whether to open structures in their own thread or not
+   */
+  private boolean async = true;
+
+  public void setAsync(boolean b)
+  {
+    async = b;
+  }
+
   public enum ViewerType
   {
     JMOL, CHIMERA, CHIMERAX, PYMOL
@@ -64,7 +74,8 @@ public class StructureViewer
    * 
    * @param structureSelectionManager
    */
-  public StructureViewer(StructureSelectionManager structureSelectionManager)
+  public StructureViewer(
+          StructureSelectionManager structureSelectionManager)
   {
     ssm = structureSelectionManager;
   }
@@ -90,7 +101,12 @@ 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());
@@ -113,6 +129,12 @@ public class StructureViewer
   public JalviewStructureDisplayI viewStructures(PDBEntry[] pdbs,
           SequenceI[] seqs, AlignmentPanel ap)
   {
+    return viewStructures(pdbs, seqs, ap, null);
+  }
+
+  public JalviewStructureDisplayI viewStructures(PDBEntry[] pdbs,
+          SequenceI[] seqs, AlignmentPanel ap, ViewerType viewerType)
+  {
     JalviewStructureDisplayI viewer = onlyOnePdb(pdbs, seqs, ap);
     if (viewer != null)
     {
@@ -122,18 +144,20 @@ public class StructureViewer
       return viewer;
     }
 
-    ViewerType viewerType = getViewerType();
+    if (viewerType == null)
+      viewerType = getViewerType();
 
     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()
+
+      Runnable viewRunnable = new Runnable()
       {
         @Override
         public void run()
@@ -152,7 +176,15 @@ public class StructureViewer
 
           sview.updateTitleAndMenus();
         }
-      }).start();
+      };
+      if (async)
+      {
+        new Thread(viewRunnable).start();
+      }
+      else
+      {
+        viewRunnable.run();
+      }
       return sview;
     }
 
@@ -176,7 +208,7 @@ public class StructureViewer
     }
     else
     {
-      Cache.log.error(UNKNOWN_VIEWER_TYPE + getViewerType().toString());
+      Console.error(UNKNOWN_VIEWER_TYPE + getViewerType().toString());
     }
     return sview;
   }
@@ -290,9 +322,20 @@ public class StructureViewer
 
   JalviewStructureDisplayI sview = null;
 
+  public JalviewStructureDisplayI getJalviewStructureDisplay()
+  {
+    return sview;
+  }
+
   public JalviewStructureDisplayI viewStructures(PDBEntry pdb,
           SequenceI[] seqsForPdb, AlignmentPanel ap)
   {
+    return viewStructures(pdb, seqsForPdb, ap, null);
+  }
+
+  public JalviewStructureDisplayI viewStructures(PDBEntry pdb,
+          SequenceI[] seqsForPdb, AlignmentPanel ap, ViewerType viewerType)
+  {
     if (sview != null)
     {
       sview.setAlignAddedStructures(superposeAdded);
@@ -305,7 +348,8 @@ public class StructureViewer
       sview.raiseViewer();
       return sview;
     }
-    ViewerType viewerType = getViewerType();
+    if (viewerType == null)
+      viewerType = getViewerType();
     if (viewerType.equals(ViewerType.JMOL))
     {
       sview = new AppJmol(pdb, seqsForPdb, null, ap);
@@ -324,48 +368,47 @@ public class StructureViewer
     }
     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()