X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FStructureViewer.java;h=0c8354be1fb797b74a39aec11df69672b737e9d5;hb=8dadf27423ca69874dc6a3c9d416974ba5ae767f;hp=b1426136edfd8e591c8d8ab4de61204c7db78301;hpb=771d1758a42abc6e3e330dd6c5117734acf0067f;p=jalview.git

diff --git a/src/jalview/gui/StructureViewer.java b/src/jalview/gui/StructureViewer.java
index b142613..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()][]);
-    JalviewStructureDisplayI sview = null;
+    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
     {
@@ -154,6 +206,10 @@ public class StructureViewer
       PDBEntry pdb = pdbs[i];
       SequenceI seq = seqs[i];
       String pdbFile = pdb.getFile();
+      if (pdbFile == null || pdbFile.length() == 0)
+      {
+        pdbFile = pdb.getId();
+      }
       if (!pdbsSeen.containsKey(pdbFile))
       {
         pdbsSeen.put(pdbFile, pdb);
@@ -199,7 +255,7 @@ public class StructureViewer
   private JalviewStructureDisplayI onlyOnePdb(PDBEntry[] pdbs,
           SequenceI[] seqsForPdbs, AlignmentPanel ap)
   {
-    List<SequenceI> seqs = new ArrayList<SequenceI>();
+    List<SequenceI> seqs = new ArrayList<>();
     if (pdbs == null || pdbs.length == 0)
     {
       return null;
@@ -223,11 +279,24 @@ public class StructureViewer
             ap);
   }
 
+  JalviewStructureDisplayI sview = null;
+
   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();
-    JalviewStructureDisplayI sview = null;
     if (viewerType.equals(ViewerType.JMOL))
     {
       sview = new AppJmol(pdb, seqsForPdb, null, ap);
@@ -266,7 +335,6 @@ public class StructureViewer
     final boolean usetoColourbyseq = viewerData.isColourWithAlignPanel();
     final boolean viewerColouring = viewerData.isColourByViewer();
 
-    JalviewStructureDisplayI sview = null;
     switch (type)
     {
     case JMOL:
@@ -283,4 +351,41 @@ public class StructureViewer
     return sview;
   }
 
+  public boolean isBusy()
+  {
+    if (sview != null)
+    {
+      if (!sview.hasMapping())
+      {
+        return true;
+      }
+    }
+    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;
+  }
+
 }