JAL-1474 note about buggy 'merge sequence' operation pointing to relevant issue

[jalview.git] / src / jalview / gui / Jalview2XML.java

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 41dd71d..8bbf735 100644 (file)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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.
  * 
@@ -14,6 +14,7 @@
  * 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");
     }
@@ -1679,12 +1681,27 @@ public class Jalview2XML
 
       jarInputStreamProvider jprovider = createjarInputStreamProvider(file);
       af = LoadJalviewAlign(jprovider);
-      setLoadingFinishedForNewStructureViewers();
+      
     } 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;
   }
 
@@ -3224,7 +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)
               {
@@ -3254,6 +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());
+                      }
+                    }
                   }
 
                 }
@@ -3453,6 +3488,7 @@ public class Jalview2XML
             view.getHeight());
     af.alignPanel.updateAnnotation(false, true); // recompute any autoannotation
     reorderAutoannotation(af, al, autoAlan);
+    af.alignPanel.alignmentChanged();
     return af;
   }
 
@@ -3731,7 +3767,7 @@ public class Jalview2XML
         }
         // 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" : ""));
       }