JAL-1641 cherry-picked changes into develop compatible branch

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

diff --git a/src/jalview/json/binding/v1/BioJsSeqPojo.java b/src/jalview/json/binding/v1/SequencePojo.java
similarity index 59%
rename from src/jalview/json/binding/v1/BioJsSeqPojo.java
rename to src/jalview/json/binding/v1/SequencePojo.java
index bac8601..232cefb 100644 (file)
--- a/src/jalview/json/binding/v1/BioJsSeqPojo.java
+++ b/src/jalview/json/binding/v1/SequencePojo.java
@@ -1,9 +1,8 @@
 package jalview.json.binding.v1;
 
-import java.util.ArrayList;
 
 
-public class BioJsSeqPojo
+public class SequencePojo
 {
   private String seq;
 
@@ -11,17 +10,20 @@ public class BioJsSeqPojo
 
   private String id;
 
+  private int order;
+
   private int start;
 
   private int end;
 
-  private ArrayList<BioJsFeaturePojo> features = new ArrayList<BioJsFeaturePojo>();
+  // private ArrayList<SequenceFeaturesPojo> features = new
+  // ArrayList<SequenceFeaturesPojo>();
 
-  public BioJsSeqPojo()
+  public SequencePojo()
   {
   }
 
-  public BioJsSeqPojo(int start, int end, String id, String name, String seq)
+  public SequencePojo(int start, int end, String id, String name, String seq)
   {
     this.id = id;
     this.name = name;
@@ -78,13 +80,23 @@ public class BioJsSeqPojo
     this.end = end;
   }
 
-  public ArrayList<BioJsFeaturePojo> getFeatures()
+  // public ArrayList<SequenceFeaturesPojo> getFeatures()
+  // {
+  // return features;
+  // }
+  //
+  // public void setFeatures(ArrayList<SequenceFeaturesPojo> features)
+  // {
+  // this.features = features;
+  // }
+
+  public int getOrder()
   {
-    return features;
+    return order;
   }
 
-  public void setFeatures(ArrayList<BioJsFeaturePojo> features)
+  public void setOrder(int order)
   {
-    this.features = features;
+    this.order = order;
   }
 }