From 5c9623b7296d1b1be7ca242c531489262630c477 Mon Sep 17 00:00:00 2001
From: tcofoegbu <tcnofoegbu@dundee.ac.uk>
Date: Wed, 20 May 2015 10:39:39 +0100
Subject: [PATCH] JAL-1739 added svid - serial version id to hold version info
 for all the json objects

---
 .../json/binding/v1/AlignmentAnnotationPojo.java   |    8 ++++++++
 src/jalview/json/binding/v1/AlignmentPojo.java     |    7 ++++++-
 src/jalview/json/binding/v1/AnnotationPojo.java    |    1 +
 .../json/binding/v1/JalviewSettingsPojo.java       |    8 ++++++++
 .../json/binding/v1/SequenceFeaturesPojo.java      |    7 +++++++
 src/jalview/json/binding/v1/SequenceGrpPojo.java   |    8 ++++++++
 src/jalview/json/binding/v1/SequencePojo.java      |   20 ++++++++------------
 7 files changed, 46 insertions(+), 13 deletions(-)

diff --git a/src/jalview/json/binding/v1/AlignmentAnnotationPojo.java b/src/jalview/json/binding/v1/AlignmentAnnotationPojo.java
index 17fe2a7..32c433b 100644
--- a/src/jalview/json/binding/v1/AlignmentAnnotationPojo.java
+++ b/src/jalview/json/binding/v1/AlignmentAnnotationPojo.java
@@ -5,6 +5,8 @@ import java.util.List;
 
 public class AlignmentAnnotationPojo
 {
+  private String svid = "1.0";
+
   private String label;
 
   private String description;
@@ -40,4 +42,10 @@ public class AlignmentAnnotationPojo
   {
     this.annotations = annotations;
   }
+
+  public String getSvid()
+  {
+    return svid;
+  }
+
 }
diff --git a/src/jalview/json/binding/v1/AlignmentPojo.java b/src/jalview/json/binding/v1/AlignmentPojo.java
index ccf55a4..b3189c0 100644
--- a/src/jalview/json/binding/v1/AlignmentPojo.java
+++ b/src/jalview/json/binding/v1/AlignmentPojo.java
@@ -5,6 +5,8 @@ import java.util.List;
 
 public class AlignmentPojo
 {
+  private String svid = "1.0";
+
   private List<SequencePojo> seqs = new ArrayList<SequencePojo>();
 
   private List<AlignmentAnnotationPojo> alignAnnotation = new ArrayList<AlignmentAnnotationPojo>();
@@ -70,5 +72,8 @@ public class AlignmentPojo
     this.seqFeatures = seqFeatures;
   }
 
-
+  public String getSvid()
+  {
+    return svid;
+  }
 }
diff --git a/src/jalview/json/binding/v1/AnnotationPojo.java b/src/jalview/json/binding/v1/AnnotationPojo.java
index 2e5aac4..41eae82 100644
--- a/src/jalview/json/binding/v1/AnnotationPojo.java
+++ b/src/jalview/json/binding/v1/AnnotationPojo.java
@@ -51,4 +51,5 @@ public class AnnotationPojo
   {
     this.value = value;
   }
+
 }
diff --git a/src/jalview/json/binding/v1/JalviewSettingsPojo.java b/src/jalview/json/binding/v1/JalviewSettingsPojo.java
index 3cc8824..595234c 100644
--- a/src/jalview/json/binding/v1/JalviewSettingsPojo.java
+++ b/src/jalview/json/binding/v1/JalviewSettingsPojo.java
@@ -16,6 +16,8 @@ import jalview.schemes.ZappoColourScheme;
 
 public class JalviewSettingsPojo
 {
+  private String svid = "1.0";
+
   private String globalColorScheme = "none";
 
   private String jalviewVersion;
@@ -147,4 +149,10 @@ public class JalviewSettingsPojo
     }
 
   }
+
+  public String getSvid()
+  {
+    return svid;
+  }
+
 }
diff --git a/src/jalview/json/binding/v1/SequenceFeaturesPojo.java b/src/jalview/json/binding/v1/SequenceFeaturesPojo.java
index c69d811..f55be46 100644
--- a/src/jalview/json/binding/v1/SequenceFeaturesPojo.java
+++ b/src/jalview/json/binding/v1/SequenceFeaturesPojo.java
@@ -5,6 +5,7 @@ import java.util.Vector;
 
 public class SequenceFeaturesPojo
 {
+  private String svid = "1.0";
 
   private int xstart;
 
@@ -134,4 +135,10 @@ public class SequenceFeaturesPojo
   {
     this.sequenceRef = sequenceRef;
   }
+
+  public String getSvid()
+  {
+    return svid;
+  }
+
 }
diff --git a/src/jalview/json/binding/v1/SequenceGrpPojo.java b/src/jalview/json/binding/v1/SequenceGrpPojo.java
index bb0e724..f19f8ba 100644
--- a/src/jalview/json/binding/v1/SequenceGrpPojo.java
+++ b/src/jalview/json/binding/v1/SequenceGrpPojo.java
@@ -4,6 +4,8 @@ import java.util.ArrayList;
 
 public class SequenceGrpPojo
 {
+  private String svid = "1.0";
+
   private String colourScheme;
 
   private String groupName;
@@ -123,4 +125,10 @@ public class SequenceGrpPojo
   {
     this.seqsHash = seqsHash;
   }
+
+  public String getSvid()
+  {
+    return svid;
+  }
+
 }
diff --git a/src/jalview/json/binding/v1/SequencePojo.java b/src/jalview/json/binding/v1/SequencePojo.java
index 232cefb..d96da2a 100644
--- a/src/jalview/json/binding/v1/SequencePojo.java
+++ b/src/jalview/json/binding/v1/SequencePojo.java
@@ -4,6 +4,8 @@ package jalview.json.binding.v1;
 
 public class SequencePojo
 {
+  private String svid = "1.0";
+
   private String seq;
 
   private String name;
@@ -16,8 +18,6 @@ public class SequencePojo
 
   private int end;
 
-  // private ArrayList<SequenceFeaturesPojo> features = new
-  // ArrayList<SequenceFeaturesPojo>();
 
   public SequencePojo()
   {
@@ -80,16 +80,6 @@ public class SequencePojo
     this.end = end;
   }
 
-  // public ArrayList<SequenceFeaturesPojo> getFeatures()
-  // {
-  // return features;
-  // }
-  //
-  // public void setFeatures(ArrayList<SequenceFeaturesPojo> features)
-  // {
-  // this.features = features;
-  // }
-
   public int getOrder()
   {
     return order;
@@ -99,4 +89,10 @@ public class SequencePojo
   {
     this.order = order;
   }
+
+  public String getSvid()
+  {
+    return svid;
+  }
+
 }
-- 
1.7.10.2