From 66d479709f80154ea834491afce7ac894128617e Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Fri, 12 Feb 2016 14:53:02 +0000
Subject: [PATCH] JAL-2008 updates for String[] to List<String> change

---
 src/jalview/analysis/AlignmentSorter.java |   31 ++++++++++++++++++-----------
 1 file changed, 19 insertions(+), 12 deletions(-)

diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index 007d538..5ee4bcb 100755
--- a/src/jalview/analysis/AlignmentSorter.java
+++ b/src/jalview/analysis/AlignmentSorter.java
@@ -32,6 +32,7 @@ import jalview.util.MessageManager;
 import jalview.util.QuickSort;
 
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.List;
 
 /**
@@ -719,12 +720,13 @@ public class AlignmentSorter
           int start, int stop, AlignmentI alignment, String method)
   {
     sortByFeature(featureLabel == null ? null
-            : new String[] { featureLabel }, groupLabel == null ? null
-            : new String[] { groupLabel }, start, stop, alignment, method);
+                    : Arrays.asList(new String[] { featureLabel }),
+            groupLabel == null ? null
+            : Arrays.asList(new String[]{ groupLabel }), start, stop, alignment, method);
   }
 
   private static boolean containsIgnoreCase(final String lab,
-          final String[] labs)
+          final List<String> labs)
   {
     if (labs == null)
     {
@@ -734,9 +736,9 @@ public class AlignmentSorter
     {
       return false;
     }
-    for (int q = 0; q < labs.length; q++)
+    for (String label : labs)
     {
-      if (labs[q] != null && lab.equalsIgnoreCase(labs[q]))
+      if (lab.equalsIgnoreCase(label))
       {
         return true;
       }
@@ -744,8 +746,8 @@ public class AlignmentSorter
     return false;
   }
 
-  public static void sortByFeature(String[] featureLabels,
-          String[] groupLabels, int start, int stop, AlignmentI alignment,
+  public static void sortByFeature(List<String> featureLabels,
+          List<String> groupLabels, int start, int stop, AlignmentI alignment,
           String method)
   {
     if (method != FEATURE_SCORE && method != FEATURE_LABEL
@@ -761,14 +763,19 @@ public class AlignmentSorter
     scoreLabel.append(start + stop + method);
     // This doesn't quite work yet - we'd like to have a canonical ordering that
     // can be preserved from call to call
-    for (int i = 0; featureLabels != null && i < featureLabels.length; i++)
+    if (featureLabels != null)
     {
-      scoreLabel.append(featureLabels[i] == null ? "null"
-              : featureLabels[i]);
+      for (String label : featureLabels)
+      {
+        scoreLabel.append(label);
+      }
     }
-    for (int i = 0; groupLabels != null && i < groupLabels.length; i++)
+    if (groupLabels != null)
     {
-      scoreLabel.append(groupLabels[i] == null ? "null" : groupLabels[i]);
+      for (String label : groupLabels)
+      {
+        scoreLabel.append(label);
+      }
     }
 
     /*
-- 
1.7.10.2