X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=ce421742f1be8c9910fd1a08bdfd4462fc3a808a;hb=dfa04e77181fccfa6229ffef1591fc9c622d9b39;hp=40448d21f0ccf25a62bd05e62fd05d9323476168;hpb=b57a02c25e335d033c97f8a6bacd6b54f62bd2b6;p=jalview.git

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 40448d2..ce42174 100644
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -1,19 +1,20 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
+ * 
  * This file is part of Jalview.
- *
+ * 
  * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
+ * modify it under the terms of the GNU General Public License 
  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.gui;
 
@@ -38,7 +39,6 @@ import jalview.schemabinding.version2.*;
 import jalview.schemes.*;
 import jalview.util.Platform;
 import jalview.util.jarInputStreamProvider;
-import jalview.ws.jws2.AAConClient;
 import jalview.ws.jws2.Jws2Discoverer;
 import jalview.ws.jws2.dm.AAConSettings;
 import jalview.ws.jws2.jabaws2.Jws2Instance;
@@ -430,7 +430,7 @@ public class Jalview2XML
     object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel());
 
     object.setCreationDate(new java.util.Date(System.currentTimeMillis()));
-    object.setVersion(jalview.bin.Cache.getProperty("VERSION"));
+    object.setVersion(jalview.bin.Cache.getDefault("VERSION","Development Build"));
 
     jalview.datamodel.AlignmentI jal = av.getAlignment();
 
@@ -1070,6 +1070,8 @@ public class Jalview2XML
 
       ac.setMaxColour(acg.getMaxColour().getRGB());
       ac.setMinColour(acg.getMinColour().getRGB());
+      ac.setPerSequence(acg.isSeqAssociated());
+      ac.setPredefinedColours(acg.isPredefinedColours());
       view.setAnnotationColours(ac);
       view.setBgColour("AnnotationColourGradient");
     }
@@ -1670,6 +1672,8 @@ public class Jalview2XML
 
     try
     {
+      // create list to store references for any new Jmol viewers created
+      newStructureViewers=new Vector<AppJmol>();
       // UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
       // Workaround is to make sure caller implements the JarInputStreamProvider
       // interface
@@ -1677,11 +1681,27 @@ public class Jalview2XML
 
       jarInputStreamProvider jprovider = createjarInputStreamProvider(file);
       af = LoadJalviewAlign(jprovider);
+      
     } catch (MalformedURLException e)
     {
       errorMessage = "Invalid URL format for '" + file + "'";
       reportErrors();
     }
+    finally {
+      try
+      {
+        SwingUtilities.invokeAndWait(new Runnable()
+        {
+          public void run()
+          {
+            setLoadingFinishedForNewStructureViewers();
+          };
+        });
+      } catch (Exception x)
+      {
+
+      }
+    }
     return af;
   }
 
@@ -2969,6 +2989,7 @@ public class Jalview2XML
                       sview = new AppJmol(pdbf, id, sq, alf.alignPanel,
                               useinJmolsuperpos, usetoColourbyseq,
                               jmolColouring, fileloc, rect, vid);
+                      addNewStructureViewer(sview);
                     } catch (OutOfMemoryError ex)
                     {
                       new OOMWarning("restoring structure view for PDB id "
@@ -3038,6 +3059,27 @@ public class Jalview2XML
     // and finally return.
     return af;
   }
+  Vector<AppJmol> newStructureViewers=null;
+  protected void addNewStructureViewer(AppJmol sview)
+  {
+    if (newStructureViewers!=null)
+    {
+      sview.jmb.setFinishedLoadingFromArchive(false);
+      newStructureViewers.add(sview);
+    }
+  }
+  protected void setLoadingFinishedForNewStructureViewers()
+  {
+    if (newStructureViewers!=null)
+    {
+      for (AppJmol sview:newStructureViewers)
+      {
+        sview.jmb.setFinishedLoadingFromArchive(true);
+      }
+      newStructureViewers.clear();
+      newStructureViewers=null;
+    }
+  }
 
   AlignFrame loadViewport(String file, JSeq[] JSEQ, Vector hiddenSeqs,
           Alignment al, JalviewModelSequence jms, Viewport view,
@@ -3199,7 +3241,14 @@ public class Jalview2XML
                                 .getAnnotationColours().getColourScheme()),
                         view.getAnnotationColours().getAboveThreshold());
               }
-
+              if (view.getAnnotationColours().hasPerSequence())
+              {
+                ((AnnotationColourGradient)cs).setSeqAssociated(view.getAnnotationColours().isPerSequence());
+              }
+              if (view.getAnnotationColours().hasPredefinedColours())
+              {
+                ((AnnotationColourGradient)cs).setPredefinedColours(view.getAnnotationColours().isPredefinedColours());
+              }
               // Also use these settings for all the groups
               if (al.getGroups() != null)
               {
@@ -3229,6 +3278,17 @@ public class Jalview2XML
                             .getAlignment().getAlignmentAnnotation()[i],
                             sg.cs, view.getAnnotationColours()
                                     .getAboveThreshold());
+                    if (cs instanceof AnnotationColourGradient) 
+                    {
+                      if (view.getAnnotationColours().hasPerSequence())
+                      { 
+                        ((AnnotationColourGradient)cs).setSeqAssociated(view.getAnnotationColours().isPerSequence());
+                      }
+                      if (view.getAnnotationColours().hasPredefinedColours())
+                      {
+                        ((AnnotationColourGradient)cs).setPredefinedColours(view.getAnnotationColours().isPredefinedColours());
+                      }
+                    }
                   }
 
                 }
@@ -3428,6 +3488,7 @@ public class Jalview2XML
             view.getHeight());
     af.alignPanel.updateAnnotation(false, true); // recompute any autoannotation
     reorderAutoannotation(af, al, autoAlan);
+    af.alignPanel.alignmentChanged();
     return af;
   }
 
@@ -3676,6 +3737,20 @@ public class Jalview2XML
         if (sq != dsq)
         { // make this dataset sequence sq's dataset sequence
           sq.setDatasetSequence(dsq);
+          // and update the current dataset alignment
+          if (ds==null) {
+            if (dseqs!=null) {
+              if (!dseqs.contains(dsq))
+              {
+                dseqs.add(dsq);
+              }
+            } else {
+              if (ds.findIndex(dsq)<0)
+              {
+                ds.addSequence(dsq);
+              }
+            }
+          }
         }
       }
     }
@@ -3702,11 +3777,11 @@ public class Jalview2XML
            * sb.append(newres.substring(newres.length() - sq.getEnd() -
            * dsq.getEnd())); dsq.setEnd(sq.getEnd()); }
            */
-          dsq.setSequence(sb.toString());
+          dsq.setSequence(newres);
         }
         // TODO: merges will never happen if we 'know' we have the real dataset
         // sequence - this should be detected when id==dssid
-        System.err.println("DEBUG Notice:  Merged dataset sequence"); // ("
+        System.err.println("DEBUG Notice:  Merged dataset sequence (if you see this often, post at http://issues.jalview.org/browse/JAL-1474)"); // ("
         // + (pre ? "prepended" : "") + " "
         // + (post ? "appended" : ""));
       }