X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjson%2Fbinding%2Fbiojson%2Fv1%2FAlignmentAnnotationPojo.java;h=673b09db26f639a7b3b45384f0fa1c2937d563e7;hb=3587df3dbcbd892eedd41a42d9f4e02a8b1e96ce;hp=6b9cf42228ed6d93b6a414233dbb40965172e3fb;hpb=4d7f98a6dd54d9863ba449ec79dcd95d25ed863d;p=jalview.git

diff --git a/src/jalview/json/binding/biojson/v1/AlignmentAnnotationPojo.java b/src/jalview/json/binding/biojson/v1/AlignmentAnnotationPojo.java
index 6b9cf42..673b09d 100644
--- a/src/jalview/json/binding/biojson/v1/AlignmentAnnotationPojo.java
+++ b/src/jalview/json/binding/biojson/v1/AlignmentAnnotationPojo.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.
+ *  
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.json.binding.biojson.v1;
 
 import java.util.ArrayList;
@@ -10,17 +30,42 @@ public class AlignmentAnnotationPojo
 
   @Attributes(
     required = false,
-    description = "Label for the Alignment Annotation")
+    description = "Label for the alignment annotation")
   private String label;
 
   @Attributes(
     required = false,
-    description = "Description for the Alignment Annotation")
+    description = "Description for the alignment annotation")
   private String description;
 
   @Attributes(required = false)
   private List<AnnotationPojo> annotations = new ArrayList<AnnotationPojo>();
 
+  @Attributes(
+    required = false,
+    enums =
+    { "0", "1", "2" },
+    description = "Determines the rendering for the annotation<br><ul><li>0 - No graph</li><li>1 - Bar Graph</li><li>2 - Line graph</li></ul>")
+  private int graphType;
+
+  @Attributes(
+    required = false,
+    description = "Reference to the sequence in the alignment<br> if per-sequence annotation")
+  private String sequenceRef;
+
+  @Attributes(
+    required = false,
+    description = "Stores display settings for an annotation")
+  private AnnotationDisplaySettingPojo annotationSettings;
+
+  @Attributes(required = false, description = "Score of the annotation")
+  private double score;
+
+  @Attributes(
+    required = false,
+    description = "The annotation generation source")
+  private String calcId;
+
   public String getLabel()
   {
     return label;
@@ -51,4 +96,55 @@ public class AlignmentAnnotationPojo
     this.annotations = annotations;
   }
 
+  public String getSequenceRef()
+  {
+    return sequenceRef;
+  }
+
+  public void setSequenceRef(String sequenceRef)
+  {
+    this.sequenceRef = sequenceRef;
+  }
+
+  public int getGraphType()
+  {
+    return graphType;
+  }
+
+  public void setGraphType(int graphType)
+  {
+    this.graphType = graphType;
+  }
+
+  public AnnotationDisplaySettingPojo getAnnotationSettings()
+  {
+    return annotationSettings;
+  }
+
+  public void setAnnotationSettings(
+          AnnotationDisplaySettingPojo annotationSettings)
+  {
+    this.annotationSettings = annotationSettings;
+  }
+
+  public double getScore()
+  {
+    return score;
+  }
+
+  public void setScore(double score)
+  {
+    this.score = score;
+  }
+
+  public String getCalcId()
+  {
+    return calcId;
+  }
+
+  public void setCalcId(String calcId)
+  {
+    this.calcId = calcId;
+  }
+
 }