JAL-1641 added support for exporting sequence features and non auto-generated annotations

[jalview.git] / src / jalview / json / binding / v1 / AlignmentPojo.java

diff --git a/src/jalview/json/binding/v1/AlignmentPojo.java b/src/jalview/json/binding/v1/AlignmentPojo.java
index 4391d80..482da51 100644 (file)
--- a/src/jalview/json/binding/v1/AlignmentPojo.java
+++ b/src/jalview/json/binding/v1/AlignmentPojo.java
@@ -15,6 +15,7 @@ import jalview.schemes.TurnColourScheme;
 import jalview.schemes.ZappoColourScheme;
 
 import java.util.ArrayList;
+import java.util.List;
 
 public class AlignmentPojo
 {
@@ -23,13 +24,17 @@ public class AlignmentPojo
   private String jalviewVersion;
 
   private String webStartUrl;
-  private ArrayList<SequencePojo> seqs = new ArrayList<SequencePojo>();
+
+  private List<SequencePojo> seqs = new ArrayList<SequencePojo>();
+
+  private List<AlignmentAnnotationPojo> alignmentAnnotation = new ArrayList<AlignmentAnnotationPojo>();
 
   public AlignmentPojo()
   {
 
   }
-  public ArrayList<SequencePojo> getSeqs()
+
+  public List<SequencePojo> getSeqs()
   {
     return seqs;
   }
@@ -89,6 +94,16 @@ public class AlignmentPojo
     this.webStartUrl = webStartUrl;
   }
 
+  public List<AlignmentAnnotationPojo> getAlignmentAnnotation()
+  {
+    return alignmentAnnotation;
+  }
+
+  public void setAlignmentAnnotation(List<AlignmentAnnotationPojo> alignmentAnnotation)
+  {
+    this.alignmentAnnotation = alignmentAnnotation;
+  }
+
   public enum JalviewBioJsColorSchemeMapper
   {
     USER_DEFINED("User Defined", "user defined", null), NONE("None", "foo",