JAL-1988 JAL-3416 Using the flatlaf-extras About, Preferences and Quit handler system...

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

diff --git a/src/jalview/gui/StructureViewer.java b/src/jalview/gui/StructureViewer.java
index 79d3836..7b1864b 100644 (file)
--- 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 +27,13 @@ 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;
+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
@@ -56,7 +55,7 @@ public class StructureViewer
 
   public enum ViewerType
   {
-    JMOL, CHIMERA, CHIMERAX
+    JMOL, CHIMERA, CHIMERAX, PYMOL
   };
 
   /**
@@ -81,6 +80,7 @@ public class StructureViewer
     return sv;
   }
 
+  
   @Override
   public String toString()
   {
@@ -90,7 +90,11 @@ 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());
@@ -170,6 +174,10 @@ public class StructureViewer
       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());
@@ -314,6 +322,10 @@ public class StructureViewer
     {
       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());
@@ -322,44 +334,44 @@ public class StructureViewer
   }
 
   /**
-   * 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());
     }
-    return sview;
+    return viewer;
   }
 
+
   public boolean isBusy()
   {
     if (sview != null)