JAL-1517 fix copyright for 2.8.2

[jalview.git] / src / jalview / datamodel / Alignment.java

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 1553710..62de7e8 100755 (executable)
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -1,19 +1,22 @@
 /*
- * 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 2.8.2)
+ * 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 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * 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 
  * 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/>.
+ * 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.datamodel;
 
@@ -370,7 +373,7 @@ public class Alignment implements AlignmentI
             return;
           }
         }
-
+        sg.setContext(this);
         groups.add(sg);
       }
     }
@@ -445,6 +448,9 @@ public class Alignment implements AlignmentI
       {
         removeAnnotationForGroup(null);
       }
+      for (SequenceGroup sg:groups) {
+        sg.setContext(null);
+      }
       groups.clear();
     }
   }
@@ -459,6 +465,7 @@ public class Alignment implements AlignmentI
       {
         removeAnnotationForGroup(g);
         groups.remove(g);
+        g.setContext(null);
       }
     }
   }
@@ -1479,5 +1486,32 @@ public class Alignment implements AlignmentI
 
     }
   }
+ @Override
+ public void validateAnnotation(AlignmentAnnotation alignmentAnnotation)
+ {
+   alignmentAnnotation.validateRangeAndDisplay();
+   if (isNucleotide() && alignmentAnnotation.isValidStruc())
+   {
+     hasRNAStructure = true;
+   }
+ }
+ @Override
+public int getEndRes()
+{
+  return getWidth()-1;
+}@Override
+public int getStartRes()
+{
+  return 0;
+}
 
+/* In the case of AlignmentI - returns the dataset for the alignment, if set
+ * (non-Javadoc)
+ * @see jalview.datamodel.AnnotatedCollectionI#getContext()
+ */
+@Override
+public AnnotatedCollectionI getContext()
+{
+  return dataset;
+}
 }