From 4cb8a2457311f8f01339eb80430a09b702c8fd62 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Wed, 31 May 2017 16:12:17 +0100
Subject: [PATCH] JAL-2483 JAL-2575 don't sort newly discovered features

---
 .../seqfeatures/FeatureRendererModel.java          |   49 ++------------------
 1 file changed, 4 insertions(+), 45 deletions(-)

diff --git a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
index eb47a80..1af491c 100644
--- a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
+++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
@@ -35,7 +35,6 @@ import java.beans.PropertyChangeListener;
 import java.beans.PropertyChangeSupport;
 import java.util.ArrayList;
 import java.util.Arrays;
-import java.util.Collections;
 import java.util.HashMap;
 import java.util.HashSet;
 import java.util.Hashtable;
@@ -330,48 +329,19 @@ public abstract class FeatureRendererModel implements
         }
       }
     }
-    // <<<<<<< HEAD
-    //
-    // =======
-    // if (minmax == null)
-    // {
-    // minmax = new Hashtable<String, float[][]>();
-    // }
-    //
-    // Set<String> oldGroups = new HashSet<String>(featureGroups.keySet());
-    // >>>>>>> refs/heads/develop
+
     AlignmentI alignment = av.getAlignment();
-    List<String> allfeatures = new ArrayList<String>(); // or HashSet?
+    List<String> allfeatures = new ArrayList<String>();
 
     for (int i = 0; i < alignment.getHeight(); i++)
     {
       SequenceI asq = alignment.getSequenceAt(i);
       for (String group : asq.getFeatures().getFeatureGroups(true))
       {
-        // <<<<<<< HEAD
-        /*
-         * features in null group are always displayed; other groups
-         * keep their current visibility; new groups as 'newMadeVisible'
-         */
         boolean groupDisplayed = true;
         if (group != null)
-        // =======
-        // continue;
-        // }
-        //
-        // int index = 0;
-        // while (index < features.length)
-        // {
-        // String fgrp = features[index].getFeatureGroup();
-        // oldGroups.remove(fgrp);
-        // if (!featuresDisplayed.isRegistered(features[index].getType()))
-        // >>>>>>> refs/heads/develop
         {
-          // <<<<<<< HEAD
           if (featureGroups.containsKey(group))
-          // =======
-          // if (fgrp != null)
-          // >>>>>>> refs/heads/develop
           {
             groupDisplayed = featureGroups.get(group);
           }
@@ -397,11 +367,8 @@ public abstract class FeatureRendererModel implements
       }
     }
 
-    /*
-    //<<<<<<< HEAD
-     * mark any new feature types as visible
-     */
-    Collections.sort(allfeatures, String.CASE_INSENSITIVE_ORDER);
+    // uncomment to add new features in alphebetical order (but JAL-2575)
+    // Collections.sort(allfeatures, String.CASE_INSENSITIVE_ORDER);
     if (newMadeVisible)
     {
       for (String type : allfeatures)
@@ -412,14 +379,6 @@ public abstract class FeatureRendererModel implements
           setOrder(type, 0);
         }
       }
-      // =======
-      // * oldGroups now consists of groups that no longer
-      // * have any feature in them - remove these
-      // */
-      // for (String grp : oldGroups)
-      // {
-      // featureGroups.remove(grp);
-      // >>>>>>> refs/heads/develop
     }
 
     updateRenderOrder(allfeatures);
-- 
1.7.10.2