From 71cf7645b3b66be24a155fd39a0f0e98c9ec1430 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 21 Nov 2019 10:43:21 +0000
Subject: [PATCH] JAL-3081 test and fix for preserve annotation order on New
 View

---
 src/jalview/project/Jalview2XML.java       |   18 +++++++++---------
 test/jalview/project/Jalview2xmlTests.java |   22 ++++++++++++++++++++++
 2 files changed, 31 insertions(+), 9 deletions(-)

diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java
index eaabd47..b58b01c 100644
--- a/src/jalview/project/Jalview2XML.java
+++ b/src/jalview/project/Jalview2XML.java
@@ -199,14 +199,14 @@ import javax.xml.stream.XMLInputFactory;
 import javax.xml.stream.XMLStreamReader;
 
 /**
- * Write out the current jalview desktop state as a Jalview XML stream.
- * 
- * Note: the vamsas objects referred to here are primitive versions of the
- * VAMSAS project schema elements - they are not the same and most likely never
- * will be :)
- * 
- * @author $author$
- * @version $Revision: 1.134 $
+ * Provides methods to read in or write out the Jalview desktop state as a
+ * Jalview XML model, as one or more entries in a .jar archive. The jar file may
+ * include additional data file entries, such as
+ * <ul>
+ * <li>PDB structure data files</li>
+ * <li>session state for one or more Jmol, Chimera or Varna structure
+ * viewers</li>
+ * </ul>
  */
 public class Jalview2XML
 {
@@ -3674,7 +3674,7 @@ public class Jalview2XML
           }
 
           al.addAnnotation(jda);
-
+          addedAnnotation.add(jda);
           continue;
         }
         // Construct new annotation from model.
diff --git a/test/jalview/project/Jalview2xmlTests.java b/test/jalview/project/Jalview2xmlTests.java
index 57cade5..3e7279c 100644
--- a/test/jalview/project/Jalview2xmlTests.java
+++ b/test/jalview/project/Jalview2xmlTests.java
@@ -1267,6 +1267,28 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     assertFalse(anns[3].visible);
 
     /*
+     * make a new view of the alignment (uses project save/load code)
+     * and verify annotations are ordered the same
+     */
+    AlignmentPanel newPanel = af.newView("new", true);
+    AlignmentAnnotation[] newAnns = newPanel.getAlignment()
+            .getAlignmentAnnotation();
+    assertEquals(newAnns.length, 4);
+    assertEquals(newAnns[0].label, "Occupancy");
+    assertEquals(newAnns[1].label, "hello");
+    assertEquals(newAnns[2].label, "Conservation");
+    assertEquals(newAnns[3].label, "world");
+    assertEquals(newAnns[0].graphHeight, 60);
+    assertEquals(newAnns[1].graphHeight, 70);
+    assertEquals(newAnns[2].graphHeight, 80);
+    assertEquals(newAnns[3].graphHeight, 90);
+    assertFalse(newAnns[0].visible);
+    assertTrue(newAnns[1].visible);
+    assertTrue(newAnns[2].visible);
+    assertFalse(newAnns[3].visible);
+    newPanel.closePanel();
+
+    /*
      * reload the project with Preferences set to not create Occupancy;
      * this should still appear, as it is in the saved project
      */
-- 
1.7.10.2