From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 18 Apr 2007 12:01:33 +0000 (+0000)
Subject: Check values not null in copy constructor
X-Git-Tag: Release_2_3~227
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=ff37fec79b0304a4a9a67bbb512c7d2b120f6f34;p=jalview.git

Check values not null in copy constructor
---

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 8e6d50d..f43529d 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -189,6 +189,8 @@ public class AlignmentAnnotation
                              int graphType)
   {
     // graphs are not editable
+    editable = graphType==0;
+
     this.label = label;
     this.description = description;
     this.annotations = annotations;
@@ -209,7 +211,7 @@ public class AlignmentAnnotation
     float min = graphMin;
     float max = graphMax;
     boolean drawValues = true;
-    
+
     if (min == max)
     {
       min = 999999999;
@@ -253,16 +255,17 @@ public class AlignmentAnnotation
       }
     }
   }
-  
+
   /**
    * Copy constructor
-   * creates a new independent annotation row with the same associated sequenceRef 
+   * creates a new independent annotation row with the same associated sequenceRef
    * @param annotation
    */
   public AlignmentAnnotation(AlignmentAnnotation annotation)
   {
     this.label = new String(annotation.label);
-    this.description = new String(annotation.description);
+    if (annotation.description != null)
+      this.description = new String(annotation.description);
     this.graphMin = annotation.graphMin;
     this.graphMax = annotation.graphMax;
     this.graph = annotation.graph;
@@ -294,7 +297,7 @@ public class AlignmentAnnotation
           while (pos.hasMoreElements()) {
             Integer p = (Integer) pos.nextElement();
             Annotation a = (Annotation) sequenceMapping.get(p);
-            sequenceMapping.put(p, annotations[anvec.indexOf(a)]); 
+            sequenceMapping.put(p, annotations[anvec.indexOf(a)]);
           }
           anvec.removeAllElements();
         } else {
@@ -407,7 +410,7 @@ public class AlignmentAnnotation
   {
     if (sequenceRef==null)
       return;
-    
+
     int a = 0, aSize = sequenceRef.getLength();
 
     if (aSize == 0)
@@ -451,7 +454,7 @@ public class AlignmentAnnotation
     ann = null;
     return j;
   }
-  
+
   /**
    * Associate this annotion with the aligned residues of a particular sequence.
    * sequenceMapping will be updated in the following way:
@@ -467,7 +470,7 @@ public class AlignmentAnnotation
         if (sequenceRef!=sequenceI && !sequenceRef.equals(sequenceI)) {
           // throw away old mapping and reconstruct.
           sequenceRef=null;
-          if (sequenceMapping!=null) 
+          if (sequenceMapping!=null)
           {
             sequenceMapping=null;
             // compactAnnotationArray();