X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FStructureViewer.java;h=0c8354be1fb797b74a39aec11df69672b737e9d5;hb=797a5cffdb1e932a419094a828ad3ccf4c3e5568;hp=f37df711d8f0b3462f3a8ad113ddb3a1b125cf1b;hpb=e07d62e6efbd954164c27e15eee49f57aa2e1b4c;p=jalview.git

diff --git a/src/jalview/gui/StructureViewer.java b/src/jalview/gui/StructureViewer.java
index f37df71..0c8354b 100644
--- a/src/jalview/gui/StructureViewer.java
+++ b/src/jalview/gui/StructureViewer.java
@@ -49,6 +49,11 @@ public class StructureViewer
 
   StructureSelectionManager ssm;
 
+  /**
+   * decide if new structures are aligned to existing ones
+   */
+  private boolean superposeAdded = true;
+
   public enum ViewerType
   {
     JMOL, CHIMERA
@@ -64,6 +69,27 @@ public class StructureViewer
     ssm = structureSelectionManager;
   }
 
+  /**
+   * Factory to create a proxy for modifying existing structure viewer
+   * 
+   */
+  public static StructureViewer reconfigure(
+          JalviewStructureDisplayI display)
+  {
+    StructureViewer sv = new StructureViewer(display.getBinding().getSsm());
+    sv.sview = display;
+    return sv;
+  }
+
+  @Override
+  public String toString()
+  {
+    if (sview != null)
+    {
+      return sview.toString();
+    }
+    return "New View";
+  }
   public ViewerType getViewerType()
   {
     String viewType = Cache.getDefault(Preferences.STRUCTURE_DISPLAY,
@@ -104,14 +130,40 @@ public class StructureViewer
             new PDBEntry[seqsForPdbs.size()]);
     SequenceI[][] theSeqs = seqsForPdbs.values().toArray(
             new SequenceI[seqsForPdbs.size()][]);
+    if (sview != null)
+    {
+      sview.setAlignAddedStructures(superposeAdded);
+      new Thread(new Runnable()
+      {
+        @Override
+        public void run()
+        {
+
+          for (int pdbep = 0; pdbep < pdbsForFile.length; pdbep++)
+          {
+            PDBEntry pdb = pdbsForFile[pdbep];
+            if (!sview.addAlreadyLoadedFile(theSeqs[pdbep], null, ap,
+                    pdb.getId()))
+            {
+              sview.addToExistingViewer(pdb, theSeqs[pdbep], null, ap,
+                      pdb.getId());
+            }
+          }
+
+          sview.updateTitleAndMenus();
+        }
+      }).start();
+      return sview;
+    }
 
     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
     {
@@ -232,6 +284,18 @@ public class StructureViewer
   public JalviewStructureDisplayI viewStructures(PDBEntry pdb,
           SequenceI[] seqsForPdb, AlignmentPanel ap)
   {
+    if (sview != null)
+    {
+      sview.setAlignAddedStructures(superposeAdded);
+      String pdbId = pdb.getId();
+      if (!sview.addAlreadyLoadedFile(seqsForPdb, null, ap, pdbId))
+      {
+        sview.addToExistingViewer(pdb, seqsForPdb, null, ap, pdbId);
+      }
+      sview.updateTitleAndMenus();
+      sview.raiseViewer();
+      return sview;
+    }
     ViewerType viewerType = getViewerType();
     if (viewerType.equals(ViewerType.JMOL))
     {
@@ -299,4 +363,29 @@ public class StructureViewer
     return false;
   }
 
+  /**
+   * 
+   * @param pDBid
+   * @return true if view is already showing PDBid
+   */
+  public boolean hasPdbId(String pDBid)
+  {
+    if (sview == null)
+    {
+      return false;
+    }
+
+    return sview.getBinding().hasPdbId(pDBid);
+  }
+
+  public boolean isVisible()
+  {
+    return sview != null && sview.isVisible();
+  }
+
+  public void setSuperpose(boolean alignAddedStructures)
+  {
+    superposeAdded = alignAddedStructures;
+  }
+
 }