JAL-1641 Re-implemented lost changes after sequenceFeature refactor

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

diff --git a/src/jalview/json/binding/v1/BioJsAlignmentPojo.java b/src/jalview/json/binding/v1/AlignmentPojo.java
similarity index 82%
rename from src/jalview/json/binding/v1/BioJsAlignmentPojo.java
rename to src/jalview/json/binding/v1/AlignmentPojo.java
index 8e8747f..48c477d 100644 (file)
--- a/src/jalview/json/binding/v1/BioJsAlignmentPojo.java
+++ b/src/jalview/json/binding/v1/AlignmentPojo.java
@@ -15,26 +15,33 @@ import jalview.schemes.TurnColourScheme;
 import jalview.schemes.ZappoColourScheme;
 
 import java.util.ArrayList;
+import java.util.List;
 
-public class BioJsAlignmentPojo
+public class AlignmentPojo
 {
   private String globalColorScheme = "none";
 
   private String jalviewVersion;
 
   private String webStartUrl;
-  private ArrayList<BioJsSeqPojo> seqs = new ArrayList<BioJsSeqPojo>();
 
-  public BioJsAlignmentPojo()
+  private List<SequencePojo> seqs = new ArrayList<SequencePojo>();
+
+  private List<AlignmentAnnotationPojo> alignmentAnnotation = new ArrayList<AlignmentAnnotationPojo>();
+
+  private List<SequenceGrpPojo> sequenceGroups = new ArrayList<SequenceGrpPojo>();
+
+  public AlignmentPojo()
   {
 
   }
-  public ArrayList<BioJsSeqPojo> getSeqs()
+
+  public List<SequencePojo> getSeqs()
   {
     return seqs;
   }
 
-  public void setSeqs(ArrayList<BioJsSeqPojo> seqs)
+  public void setSeqs(ArrayList<SequencePojo> seqs)
   {
     this.seqs = seqs;
   }
@@ -89,6 +96,26 @@ public class BioJsAlignmentPojo
     this.webStartUrl = webStartUrl;
   }
 
+  public List<AlignmentAnnotationPojo> getAlignmentAnnotation()
+  {
+    return alignmentAnnotation;
+  }
+
+  public void setAlignmentAnnotation(List<AlignmentAnnotationPojo> alignmentAnnotation)
+  {
+    this.alignmentAnnotation = alignmentAnnotation;
+  }
+
+  public List<SequenceGrpPojo> getSequenceGroups()
+  {
+    return sequenceGroups;
+  }
+
+  public void setSequenceGroups(List<SequenceGrpPojo> sequenceGroups)
+  {
+    this.sequenceGroups = sequenceGroups;
+  }
+
   public enum JalviewBioJsColorSchemeMapper
   {
     USER_DEFINED("User Defined", "user defined", null), NONE("None", "foo",