From 51f05d7903402a5dec8e915fbe5e49ce913d069a Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Tue, 22 Dec 2015 08:58:50 +0000
Subject: [PATCH] JAL-653 hold AlignedCodonFrame collections as list rather
 than set

---
 src/jalview/gui/Jalview2XML.java                     |    2 +-
 src/jalview/io/VamsasAppDatastore.java               |    5 ++---
 src/jalview/structure/StructureSelectionManager.java |   17 ++++++++++-------
 src/jalview/ws/AWSThread.java                        |    4 +++-
 4 files changed, 16 insertions(+), 12 deletions(-)

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 7258b63..96abf81 100644
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -880,7 +880,7 @@ public class Jalview2XML
     // SAVE MAPPINGS
     if (jal.getCodonFrames() != null)
     {
-      Set<AlignedCodonFrame> jac = jal.getCodonFrames();
+      List<AlignedCodonFrame> jac = jal.getCodonFrames();
       for (AlignedCodonFrame acf : jac)
       {
         AlcodonFrame alc = new AlcodonFrame();
diff --git a/src/jalview/io/VamsasAppDatastore.java b/src/jalview/io/VamsasAppDatastore.java
index a093ebe..2c35547 100644
--- a/src/jalview/io/VamsasAppDatastore.java
+++ b/src/jalview/io/VamsasAppDatastore.java
@@ -43,7 +43,6 @@ import java.util.Hashtable;
 import java.util.IdentityHashMap;
 import java.util.Iterator;
 import java.util.List;
-import java.util.Set;
 import java.util.Vector;
 import java.util.jar.JarInputStream;
 import java.util.jar.JarOutputStream;
@@ -1433,7 +1432,7 @@ public class VamsasAppDatastore
         // to the align frames.
         boolean gathered = false;
         String newviewid = null;
-        Set<AlignedCodonFrame> mappings = av.getAlignment()
+        List<AlignedCodonFrame> mappings = av.getAlignment()
                 .getCodonFrames();
         for (int i = 0; i < views.length; i++)
         {
@@ -2732,7 +2731,7 @@ public class VamsasAppDatastore
 
       }
       // Store any sequence mappings.
-      Set<AlignedCodonFrame> cframes = av.getAlignment().getCodonFrames();
+      List<AlignedCodonFrame> cframes = av.getAlignment().getCodonFrames();
       if (cframes != null)
       {
         for (AlignedCodonFrame acf : cframes)
diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 26b7d48..b497824 100644
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -43,10 +43,8 @@ import java.util.Collections;
 import java.util.Enumeration;
 import java.util.HashMap;
 import java.util.IdentityHashMap;
-import java.util.LinkedHashSet;
 import java.util.List;
 import java.util.Map;
-import java.util.Set;
 import java.util.Vector;
 
 import MCview.Atom;
@@ -70,7 +68,7 @@ public class StructureSelectionManager
   /*
    * Set of any registered mappings between (dataset) sequences.
    */
-  public Set<AlignedCodonFrame> seqmappings = new LinkedHashSet<AlignedCodonFrame>();
+  private List<AlignedCodonFrame> seqmappings = new ArrayList<AlignedCodonFrame>();
 
   private List<CommandListener> commandListeners = new ArrayList<CommandListener>();
 
@@ -929,13 +927,13 @@ public class StructureSelectionManager
   /**
    * Add each of the given codonFrames to the stored set, if not aready present.
    * 
-   * @param set
+   * @param mappings
    */
-  public void registerMappings(Set<AlignedCodonFrame> set)
+  public void registerMappings(List<AlignedCodonFrame> mappings)
   {
-    if (set != null)
+    if (mappings != null)
     {
-      for (AlignedCodonFrame acf : set)
+      for (AlignedCodonFrame acf : mappings)
       {
         registerMapping(acf);
       }
@@ -1147,4 +1145,9 @@ public class StructureSelectionManager
     }
     return null;
   }
+
+  public List<AlignedCodonFrame> getSequenceMappings()
+  {
+    return seqmappings;
+  }
 }
diff --git a/src/jalview/ws/AWSThread.java b/src/jalview/ws/AWSThread.java
index fe28d6c..b158448 100644
--- a/src/jalview/ws/AWSThread.java
+++ b/src/jalview/ws/AWSThread.java
@@ -32,6 +32,7 @@ import jalview.util.MessageManager;
 import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
 
 import java.util.LinkedHashSet;
+import java.util.List;
 import java.util.Set;
 
 public abstract class AWSThread extends Thread
@@ -98,6 +99,7 @@ public abstract class AWSThread extends Thread
   /**
    * generic web service job/subjob poll loop
    */
+  @Override
   public void run()
   {
     JobStateSummary jstate = null;
@@ -378,7 +380,7 @@ public abstract class AWSThread extends Thread
     WsUrl = wsurl2;
     if (alframe != null)
     {
-      Set<AlignedCodonFrame> cf = alframe.getViewport().getAlignment()
+      List<AlignedCodonFrame> cf = alframe.getViewport().getAlignment()
               .getCodonFrames();
       if (cf != null)
       {
-- 
1.7.10.2