From fa5b03518dd51a47066670e6782ca81c792b6a29 Mon Sep 17 00:00:00 2001
From: kiramt <k.mourao@dundee.ac.uk>
Date: Wed, 4 Oct 2017 16:11:59 +0100
Subject: [PATCH] JAL-2674 Adjustments to hideColumns

---
 src/jalview/datamodel/HiddenColumns.java |  107 ++++++++++++++++--------------
 1 file changed, 56 insertions(+), 51 deletions(-)

diff --git a/src/jalview/datamodel/HiddenColumns.java b/src/jalview/datamodel/HiddenColumns.java
index b9e67ef..cd3183f 100644
--- a/src/jalview/datamodel/HiddenColumns.java
+++ b/src/jalview/datamodel/HiddenColumns.java
@@ -526,66 +526,71 @@ public class HiddenColumns
       }
 
       /*
-       * traverse existing hidden ranges and insert / amend / append as
-       * appropriate
+       * new range follows everything else; check first to avoid looping over whole hiddenColumns collection
        */
-      for (int i = 0; i < hiddenColumns.size(); i++)
+      if (hiddenColumns.isEmpty()
+              || start > hiddenColumns.get(hiddenColumns.size() - 1)[1])
       {
-        int[] region = hiddenColumns.get(i);
-
-        if (end < region[0] - 1)
-        {
-          /*
-           * insert discontiguous preceding range
-           */
-          hiddenColumns.add(i, new int[] { start, end });
-          return;
-        }
-
-        if (end <= region[1])
+        hiddenColumns.add(new int[] { start, end });
+      }
+      else
+      {
+        /*
+         * traverse existing hidden ranges and insert / amend / append as
+         * appropriate
+         */
+        boolean added = false;
+        for (int i = 0; !added && i < hiddenColumns.size(); i++)
         {
-          /*
-           * new range overlaps existing, or is contiguous preceding it - adjust
-           * start column
-           */
-          region[0] = Math.min(region[0], start);
-          return;
-        }
+          int[] region = hiddenColumns.get(i);
 
-        if (start <= region[1] + 1)
-        {
-          /*
-           * new range overlaps existing, or is contiguous following it - adjust
-           * start and end columns
-           */
-          region[0] = Math.min(region[0], start);
-          region[1] = Math.max(region[1], end);
-
-          /*
-           * also update or remove any subsequent ranges 
-           * that are overlapped
-           */
-          while (i < hiddenColumns.size() - 1)
+          if (end < region[0] - 1)
           {
-            int[] nextRegion = hiddenColumns.get(i + 1);
-            if (nextRegion[0] > end + 1)
+            /*
+             * insert discontiguous preceding range
+             */
+            hiddenColumns.add(i, new int[] { start, end });
+            added = true;
+          }
+          else if (end <= region[1])
+          {
+            /*
+             * new range overlaps existing, or is contiguous preceding it - adjust
+             * start column
+             */
+            region[0] = Math.min(region[0], start);
+            added = true;
+          }
+          else if (start <= region[1] + 1)
+          {
+            /*
+             * new range overlaps existing, or is contiguous following it - adjust
+             * start and end columns
+             */
+            region[0] = Math.min(region[0], start);
+            region[1] = Math.max(region[1], end);
+
+            /*
+             * also update or remove any subsequent ranges 
+             * that are overlapped
+             */
+            while (i < hiddenColumns.size() - 1)
             {
-              /*
-               * gap to next hidden range - no more to update
-               */
-              break;
+              int[] nextRegion = hiddenColumns.get(i + 1);
+              if (nextRegion[0] > end + 1)
+              {
+                /*
+                 * gap to next hidden range - no more to update
+                 */
+                break;
+              }
+              region[1] = Math.max(nextRegion[1], end);
+              hiddenColumns.remove(i + 1);
             }
-            region[1] = Math.max(nextRegion[1], end);
-            hiddenColumns.remove(i + 1);
+            added = true;
           }
-          return;
-        }
+        } // for
       }
-
-      /*
-       * remaining case is that the new range follows everything else
-       */
-      hiddenColumns.add(new int[] { start, end });
     } finally
     {
       if (!wasAlreadyLocked)
-- 
1.7.10.2