JAL-1781 annotation.sequenceRef now sequence id not name, incrementing

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

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 4c5ea17..322fd54 100755 (executable)
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -20,10 +20,6 @@
  */
 package jalview.datamodel;
 
-import jalview.analysis.Rna;
-import jalview.analysis.SecStrConsensus.SimpleBP;
-import jalview.analysis.WUSSParseException;
-
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Collections;
@@ -32,6 +28,10 @@ import java.util.Iterator;
 import java.util.Map;
 import java.util.Map.Entry;
 
+import jalview.analysis.Rna;
+import jalview.analysis.SecStrConsensus.SimpleBP;
+import jalview.analysis.WUSSParseException;
+
 /**
  * DOCUMENT ME!
  * 
@@ -40,6 +40,8 @@ import java.util.Map.Entry;
  */
 public class AlignmentAnnotation
 {
+  private static final String ANNOTATION_ID_PREFIX = "ann";
+
   /*
    * Identifers for different types of profile data
    */
@@ -49,6 +51,8 @@ public class AlignmentAnnotation
 
   public static final int CDNA_PROFILE = 2;
 
+  private static long counter = 0;
+
   /**
    * If true, this annotations is calculated every edit, eg consensus, quality
    * or conservation graphs
@@ -282,6 +286,7 @@ public class AlignmentAnnotation
   public AlignmentAnnotation(String label, String description,
           Annotation[] annotations)
   {
+    setAnnotationId();
     // always editable?
     editable = true;
     this.label = label;
@@ -458,8 +463,6 @@ public class AlignmentAnnotation
         _updateRnaSecStr(new AnnotCharSequence());
       }
     }
-
-    annotationId = this.hashCode() + "";
   }
 
   /**
@@ -565,6 +568,7 @@ public class AlignmentAnnotation
   public AlignmentAnnotation(String label, String description,
           Annotation[] annotations, float min, float max, int graphType)
   {
+    setAnnotationId();
     // graphs are not editable
     editable = graphType == 0;
 
@@ -664,6 +668,7 @@ public class AlignmentAnnotation
    */
   public AlignmentAnnotation(AlignmentAnnotation annotation)
   {
+    setAnnotationId();
     this.label = new String(annotation.label);
     if (annotation.description != null)
     {
@@ -1382,4 +1387,18 @@ public class AlignmentAnnotation
     return sequenceMapping == null ? null : sequenceMapping.get(position);
 
   }
+
+  /**
+   * Set the id to "ann" followed by a counter that increments so as to be
+   * unique for the lifetime of the JVM
+   */
+  protected final void setAnnotationId()
+  {
+    this.annotationId = ANNOTATION_ID_PREFIX + Long.toString(nextId());
+  }
+
+  protected static synchronized long nextId()
+  {
+    return counter++;
+  }
 }