X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=ce421742f1be8c9910fd1a08bdfd4462fc3a808a;hb=dfa04e77181fccfa6229ffef1591fc9c622d9b39;hp=2ec76a78ec9cf55f604dd07ca09010a5bb6f73ae;hpb=3c0bad69209e65678618327866d569eb3fbd3a71;p=jalview.git

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 2ec76a7..ce42174 100644
--- 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;
 
@@ -1069,6 +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");
     }
@@ -3238,7 +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)
               {
@@ -3268,6 +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());
+                      }
+                    }
                   }
 
                 }
@@ -3467,6 +3488,7 @@ public class Jalview2XML
             view.getHeight());
     af.alignPanel.updateAnnotation(false, true); // recompute any autoannotation
     reorderAutoannotation(af, al, autoAlan);
+    af.alignPanel.alignmentChanged();
     return af;
   }
 
@@ -3715,6 +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);
+              }
+            }
+          }
         }
       }
     }
@@ -3741,11 +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" : ""));
       }