From 8e2d11189e14700f721dc0cf17c462352883ef97 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Mon, 19 Dec 2016 11:21:47 +0000
Subject: [PATCH] JAL-2360 amended toAppletParameter() for reproducible
 behaviour

---
 src/jalview/schemes/UserColourScheme.java      |   23 +++++++++++++++++------
 test/jalview/schemes/UserColourSchemeTest.java |    2 +-
 2 files changed, 18 insertions(+), 7 deletions(-)

diff --git a/src/jalview/schemes/UserColourScheme.java b/src/jalview/schemes/UserColourScheme.java
index 7bf02c1..218c285 100755
--- a/src/jalview/schemes/UserColourScheme.java
+++ b/src/jalview/schemes/UserColourScheme.java
@@ -24,9 +24,11 @@ import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
 import jalview.util.ColorUtils;
+import jalview.util.StringUtils;
 
 import java.awt.Color;
 import java.util.ArrayList;
+import java.util.Collections;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
@@ -302,6 +304,9 @@ public class UserColourScheme extends ResidueColourScheme
    */
   public String toAppletParameter()
   {
+    /*
+     * step 1: build a map from colours to the symbol(s) that have the colour
+     */
     Map<Color, List<String>> colours = new HashMap<Color, List<String>>();
 
     for (char symbol = 'A'; symbol <= 'Z'; symbol++)
@@ -331,14 +336,15 @@ public class UserColourScheme extends ResidueColourScheme
         }
       }
     }
-    StringBuilder sb = new StringBuilder();
+
+    /*
+     * step 2: make a list of { A,G,R=12f9d6 } residues/colour specs
+     */
+    List<String> residueColours = new ArrayList<String>();
     for (Entry<Color, List<String>> cols : colours.entrySet())
     {
-      if (sb.length() > 0)
-      {
-        sb.append(";");
-      }
       boolean first = true;
+      StringBuilder sb = new StringBuilder();
       for (String residue : cols.getValue())
       {
         if (!first)
@@ -355,8 +361,13 @@ public class UserColourScheme extends ResidueColourScheme
       String hexString = Integer.toHexString(cols.getKey().getRGB())
               .substring(2);
       sb.append(hexString);
+      residueColours.add(sb.toString());
     }
 
-    return sb.toString();
+    /*
+     * sort and output
+     */
+    Collections.sort(residueColours);
+    return StringUtils.listToDelimitedString(residueColours, ";");
   }
 }
diff --git a/test/jalview/schemes/UserColourSchemeTest.java b/test/jalview/schemes/UserColourSchemeTest.java
index 151462b..497014e 100644
--- a/test/jalview/schemes/UserColourSchemeTest.java
+++ b/test/jalview/schemes/UserColourSchemeTest.java
@@ -78,6 +78,6 @@ public class UserColourSchemeTest
     UserColourScheme cs = new UserColourScheme(
             "E,D=red; K,R,H=0022FF; c=10 , 20,30");
     String param = cs.toAppletParameter();
-    assertEquals("H,K,R=0022ff;c=0a141e;D,E=ff0000", param);
+    assertEquals("D,E=ff0000;H,K,R=0022ff;c=0a141e", param);
   }
 }
-- 
1.7.10.2