X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fproject%2FJalview2XML.java;h=cadc25316bf76411604cf6976b3a4f7d474bd0ea;hb=595a9e25db7f4f24c17de84656d7d5391a3d104d;hp=0291a0a31d0389533454420eff8bdb2b8f977b32;hpb=0031ee4b6a42ad328e417cb65c7a840183e62e87;p=jalview.git

diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java
index 0291a0a..cadc253 100644
--- a/src/jalview/project/Jalview2XML.java
+++ b/src/jalview/project/Jalview2XML.java
@@ -2862,12 +2862,16 @@ public class Jalview2XML
     IdentityHashMap<AlignmentI, AlignmentI> importedDatasets = new IdentityHashMap<>();
     Map<String, AlignFrame> gatherToThisFrame = new HashMap<>();
     final String file = jprovider.getFilename();
+
+    List<AlignFrame> alignFrames = new ArrayList<>();
+
     try
     {
       JarInputStream jin = null;
       JarEntry jarentry = null;
       int entryCount = 1;
 
+
       // Look for all the entry names ending with ".xml"
       // This includes all panels and at least one frame.
 //      Platform.timeCheck(null, Platform.TIME_MARK);
@@ -2879,9 +2883,14 @@ public class Jalview2XML
           jarentry = jin.getNextJarEntry();
         }
         String name = (jarentry == null ? null : jarentry.getName());
+
+//        System.out.println("Jalview2XML opening " + name);
         if (name != null && name.endsWith(".xml"))
         {
 
+          // DataSet for.... is read last.
+          
+          
           // The question here is what to do with the two
           // .xml files in the jvp file.
           // Some number of them, "...Dataset for...", will be the
@@ -2911,8 +2920,14 @@ public class Jalview2XML
             _af = loadFromObject(model, file, true, jprovider);
 //            Platform.timeCheck("Jalview2XML.loadFromObject",
             // Platform.TIME_MARK);
+
+            if (_af != null)
+            {
+              alignFrames.add(_af);
+            }
             if (_af != null && model.getViewport().size() > 0)
             {
+
               // That is, this is one of the AlignmentPanel models
               if (af == null)
               {
@@ -2979,6 +2994,13 @@ public class Jalview2XML
       errorMessage = "Out of memory loading jalview XML file";
       System.err.println("Out of memory whilst loading jalview XML file");
       e.printStackTrace();
+    } finally
+    {
+      for (AlignFrame alf : alignFrames)
+      {
+        alf.alignPanel.setHoldRepaint(false);
+      }
+
     }
 
     /*
@@ -2998,7 +3020,7 @@ public class Jalview2XML
     {
       if (ds.getCodonFrames() != null)
       {
-        Desktop.getInstance().getStructureSelectionManager()
+        Desktop.getStructureSelectionManager()
                 .registerMappings(ds.getCodonFrames());
       }
     }
@@ -3519,7 +3541,7 @@ public class Jalview2XML
       // now, for 2.10 projects, this is also done if the xml doc includes
       // dataset sequences not actually present in any particular view.
       //
-      Platform.timeCheck("J2XML features0", Platform.TIME_MARK);
+//      Platform.timeCheck("J2XML features0", Platform.TIME_RESET);
       for (int i = 0; i < vamsasSeqs.size(); i++)
       {
         JSeq jseq = jseqs.get(i);
@@ -3574,11 +3596,11 @@ public class Jalview2XML
             }
 
             // adds feature to datasequence's feature set (since Jalview 2.10)
+//            Platform.timeCheck(null, Platform.TIME_SET);
             al.getSequenceAt(i).addSequenceFeature(sf);
+//            Platform.timeCheck(null, Platform.TIME_MARK);
           }
         }
-        Platform.timeCheck("J2XML features done", Platform.TIME_MARK);
-
         if (vamsasSeqs.get(i).getDBRef().size() > 0)
         {
           // adds dbrefs to datasequence's set (since Jalview 2.10)
@@ -3636,7 +3658,7 @@ public class Jalview2XML
             {
               entry.setProperty(prop.getName(), prop.getValue());
             }
-            Desktop.getInstance().getStructureSelectionManager()
+            Desktop.getStructureSelectionManager()
                     .registerPDBEntry(entry);
             // adds PDBEntry to datasequence's set (since Jalview 2.10)
             if (al.getSequenceAt(i).getDatasetSequence() != null)
@@ -3649,7 +3671,10 @@ public class Jalview2XML
             }
           }
         }
+
       }
+
+//      Platform.timeCheck("features done", Platform.TIME_GET);
 //      Platform.timeCheck("Jalview2XML.loadFromObject-endmultiview",
 //              Platform.TIME_MARK);
     } // end !multipleview
@@ -4180,6 +4205,8 @@ public class Jalview2XML
       });
     }
     // and finally return.
+    // but do not set holdRepaint true just yet, because this could be the
+    // initial frame with just its dataset.
     return af;
   }
 
@@ -4976,7 +5003,7 @@ public class Jalview2XML
   {
     AlignFrame af = null;
     af = new AlignFrame(al, safeInt(view.getWidth()),
-            safeInt(view.getHeight()), uniqueSeqSetId, viewId) 
+            safeInt(view.getHeight()), uniqueSeqSetId, viewId)
 //    {
 //    	
 //    	@Override
@@ -4988,7 +5015,7 @@ public class Jalview2XML
 //    	
 //    }
     ;
-
+    af.alignPanel.setHoldRepaint(true);
     af.setFileName(file, FileFormat.Jalview);
 
     final AlignViewport viewport = af.getViewport();
@@ -5676,8 +5703,8 @@ public class Jalview2XML
       SequenceI[] dsseqs = new SequenceI[dseqs.size()];
       dseqs.copyInto(dsseqs);
       ds = new jalview.datamodel.Alignment(dsseqs);
-      debug("Created new dataset " + vamsasSet.getDatasetId()
-              + " for alignment " + System.identityHashCode(al));
+//      debug("Jalview2XML Created new dataset " + vamsasSet.getDatasetId()
+//              + " for alignment " + System.identityHashCode(al));
       addDatasetRef(vamsasSet.getDatasetId(), ds);
     }
     // set the dataset for the newly imported alignment.
@@ -6091,14 +6118,7 @@ public class Jalview2XML
     AlignFrame af = loadFromObject(jm, null, false, null);
     af.getAlignPanels().clear();
     af.closeMenuItem_actionPerformed(true);
-
-    /*
-     * if(ap.av.getAlignment().getAlignmentAnnotation()!=null) { for(int i=0;
-     * i<ap.av.getAlignment().getAlignmentAnnotation().length; i++) {
-     * if(!ap.av.getAlignment().getAlignmentAnnotation()[i].autoCalculated) {
-     * af.alignPanel.av.getAlignment().getAlignmentAnnotation()[i] =
-     * ap.av.getAlignment().getAlignmentAnnotation()[i]; } } }
-     */
+    af.alignPanel.setHoldRepaint(false);
 
     return af.alignPanel;
   }