Saves structures

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index da807d4..3c8d31a 100755 (executable)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -28,6 +28,7 @@ import javax.swing.*;
 import org.exolab.castor.xml.*;
 import jalview.schemabinding.version2.*;
 import jalview.schemes.*;
+import jalview.structure.StructureSelectionManager;
 
 /**
  * DOCUMENT ME!
@@ -334,6 +335,37 @@ public class Jalview2XML
           pdb.setId(entry.getId());
           pdb.setType(entry.getType());
 
+          AppJMol jmol;
+          //This must have been loaded, is it still visible?
+          JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+          for (int f = frames.length - 1; f > -1; f--)
+          {
+            if (frames[f] instanceof AppJMol)
+            {
+              jmol = (AppJMol) frames[f];
+              if (!jmol.pdbentry.getId().equals(entry.getId()))
+                continue;
+
+              StructureState state = new StructureState();
+              state.setVisible(true);
+              state.setXpos(jmol.getX());
+              state.setYpos(jmol.getY());
+              state.setWidth(jmol.getWidth());
+              state.setHeight(jmol.getHeight());
+
+              state.setContent(jmol.viewer.getStateInfo().replaceAll("\n", ""));
+
+              for (int s = 0; s < jmol.sequence.length; s++)
+              {
+                if (jal.findIndex(jmol.sequence[s]) > -1)
+                {
+                  pdb.addStructureState(state);
+                }
+              }
+            }
+          }
+
+
           if (entry.getFile() != null)
           {
             pdb.setFile(entry.getFile());
@@ -363,8 +395,9 @@ public class Jalview2XML
               }
               catch (Exception ex)
               {
-                ex.printStackTrace();
+                  ex.printStackTrace();
               }
+
             }
           }
 
@@ -604,6 +637,8 @@ public class Jalview2XML
     view.setViewName(av.viewName);
     view.setGatheredViews(av.gatherViewsHere);
 
+
+
     if (ap.av.explodedPosition != null)
     {
       view.setXpos(av.explodedPosition.x);
@@ -893,7 +928,7 @@ public class Jalview2XML
     seqRefIds = new Hashtable();
     viewportsAdded = new Hashtable();
 
-    Vector gatherToThisFrame = new Vector();
+    Hashtable gatherToThisFrame = new Hashtable();
 
     try
     {
@@ -937,7 +972,7 @@ public class Jalview2XML
           af = LoadFromObject(object, file, true);
           if (af.viewport.gatherViewsHere)
           {
-            gatherToThisFrame.add(af);
+            gatherToThisFrame.put(af.viewport.getSequenceSetId(), af);
           }
           entryCount++;
         }
@@ -998,10 +1033,11 @@ public class Jalview2XML
       Desktop.instance.stopLoading();
     }
 
-    for (int i = 0; i < gatherToThisFrame.size(); i++)
+    Enumeration en = gatherToThisFrame.elements();
+    while(en.hasMoreElements())
     {
       Desktop.instance.gatherViews(
-          (AlignFrame) gatherToThisFrame.elementAt(i));
+          (AlignFrame) en.nextElement());
     }
 
     return af;
@@ -1062,7 +1098,7 @@ public class Jalview2XML
 
   AlignFrame LoadFromObject(JalviewModel object,
                             String file,
-                            boolean loadTrees)
+                            boolean loadTreesAndStructures)
   {
     SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
     Sequence[] vamsasSeq = vamsasSet.getSequence();
@@ -1133,6 +1169,7 @@ public class Jalview2XML
 
 
     Hashtable pdbloaded = new Hashtable();
+
     if (!multipleView)
     {
       for (int i = 0; i < vamsasSeq.length; i++)
@@ -1166,6 +1203,7 @@ public class Jalview2XML
             al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
           }
         }
+
         if (JSEQ[i].getPdbidsCount() > 0)
         {
           Pdbids[] ids = JSEQ[i].getPdbids();
@@ -1179,9 +1217,7 @@ public class Jalview2XML
             {
               if (!pdbloaded.containsKey(ids[p].getFile()))
               {
-                String tmppdb = loadPDBFile(file, ids[p].getId());
-                entry.setFile(tmppdb);
-                pdbloaded.put(ids[p].getId(), tmppdb);
+                entry.setFile(loadPDBFile(file, ids[p].getId()));
               }
               else
               {
@@ -1693,7 +1729,7 @@ public class Jalview2XML
 
     //LOAD TREES
     ///////////////////////////////////////
-    if (loadTrees && jms.getTreeCount() > 0)
+    if (loadTreesAndStructures && jms.getTreeCount() > 0)
     {
       try
       {
@@ -1740,7 +1776,67 @@ public class Jalview2XML
       {
         ex.printStackTrace();
       }
+    }
+
+    ////LOAD STRUCTURES
+    if(loadTreesAndStructures)
+    {
+      for (int i = 0; i < JSEQ.length; i++)
+      {
+        if (JSEQ[i].getPdbidsCount() > 0)
+        {
+          Pdbids[] ids = JSEQ[i].getPdbids();
+          for (int p = 0; p < ids.length; p++)
+          {
+            for (int s = 0; s < ids[p].getStructureStateCount(); s++)
+            {
+              jalview.datamodel.PDBEntry jpdb = new jalview.datamodel.PDBEntry();
+
+              jpdb.setFile(loadPDBFile(ids[p].getFile(), ids[p].getId()));
+              jpdb.setId(ids[p].getId());
+
+              int x = ids[p].getStructureState(s).getXpos();
+              int y = ids[p].getStructureState(s).getYpos();
+              int width = ids[p].getStructureState(s).getWidth();
+              int height = ids[p].getStructureState(s).getHeight();
+
+              java.awt.Component comp = Desktop.desktop.getComponentAt(x, y);
+
+              String pdbFile = loadPDBFile(file, ids[p].getId());
+
+              jalview.datamodel.SequenceI[] seq = new jalview.datamodel.SequenceI[]
+                  {
+                  al.getSequenceAt(i)};
+
+              if (comp == null ||
+                  (comp.getWidth() != width && comp.getHeight() != height))
+              {
+                String state = ids[p].getStructureState(s).getContent();
 
+                StringBuffer newFileLoc = new StringBuffer(state.substring(0,
+                    state.indexOf("\"", state.indexOf("load")) + 1));
+
+                newFileLoc.append(jpdb.getFile());
+                newFileLoc.append(state.substring(
+                    state.indexOf("\"", state.indexOf("load \"") + 6)));
+
+                new AppJMol(pdbFile,
+                            ids[p].getId(),
+                            seq,
+                            af.alignPanel,
+                            newFileLoc.toString(),
+                            new java.awt.Rectangle(x, y, width, height));
+
+              }
+              else
+              {
+                StructureSelectionManager.getStructureSelectionManager()
+                    .setMapping(seq, pdbFile, jalview.io.AppletFormatAdapter.FILE);
+              }
+            }
+          }
+        }
+      }
     }
 
     return af;