JAL-2674 testing

[jalview.git] / src / jalview / datamodel / HiddenColumns.java

diff --git a/src/jalview/datamodel/HiddenColumns.java b/src/jalview/datamodel/HiddenColumns.java
index f8a7f0c..839cee2 100644 (file)
--- a/src/jalview/datamodel/HiddenColumns.java
+++ b/src/jalview/datamodel/HiddenColumns.java
@@ -1641,14 +1641,14 @@ public class HiddenColumns
 
     private List<int[]> localHidden = new ArrayList<>();
 
-    private int lasthiddenregion;
+    private int nexthiddenregion;
 
     VisibleColsIterator(int firstcol, int lastcol, boolean useCopy)
     {
       last = lastcol;
       current = firstcol;
       next = firstcol;
-      lasthiddenregion = -1;
+      nexthiddenregion = 0;
 
       try
       {
@@ -1663,7 +1663,7 @@ public class HiddenColumns
         {
           int i = 0;
           for (i = 0; i < hiddenColumns.size()
-                  && (current < hiddenColumns.get(i)[0]); ++i)
+                  && (current <= hiddenColumns.get(i)[0]); ++i)
           {
             if (current >= hiddenColumns.get(i)[0]
                     && current <= hiddenColumns.get(i)[1])
@@ -1671,13 +1671,12 @@ public class HiddenColumns
               // current is hidden, move to right
               current = hiddenColumns.get(i)[1] + 1;
               next = current;
+              nexthiddenregion = i + 1;
             }
           }
 
-          lasthiddenregion = i - 1;
-
           for (i = hiddenColumns.size() - 1; i >= 0
-                  && (last > hiddenColumns.get(i)[1]); --i)
+                  && (last >= hiddenColumns.get(i)[1]); --i)
           {
             if (last >= hiddenColumns.get(i)[0]
                     && last <= hiddenColumns.get(i)[1])
@@ -1688,7 +1687,7 @@ public class HiddenColumns
           }
 
           // make a local copy of the bit we need
-          i = lasthiddenregion + 1;
+          i = nexthiddenregion;
           while (i < hiddenColumns.size()
                   && hiddenColumns.get(i)[0] <= last)
           {
@@ -1697,7 +1696,6 @@ public class HiddenColumns
             localHidden.add(region);
             i++;
           }
-          lasthiddenregion = -1;
         }
       } finally
       {
@@ -1723,20 +1721,20 @@ public class HiddenColumns
       }
       current = next;
       if ((localHidden != null)
-              && (lasthiddenregion + 1 < localHidden.size()))
+              && (nexthiddenregion < localHidden.size()))
       {
         // still some more hidden regions
-        if (next + 1 < localHidden.get(lasthiddenregion + 1)[0])
+        if (next + 1 < localHidden.get(nexthiddenregion)[0])
         {
           // next+1 is still before the next hidden region
           next++;
         }
-        else if ((next + 1 >= localHidden.get(lasthiddenregion + 1)[0])
-                && (next + 1 <= localHidden.get(lasthiddenregion + 1)[1]))
+        else if ((next + 1 >= localHidden.get(nexthiddenregion)[0])
+                && (next + 1 <= localHidden.get(nexthiddenregion)[1]))
         {
           // next + 1 is in the next hidden region
-          next = localHidden.get(lasthiddenregion + 1)[1] + 1;
-          lasthiddenregion++;
+          next = localHidden.get(nexthiddenregion)[1] + 1;
+          nexthiddenregion++;
         }
       }
       else
@@ -1949,7 +1947,6 @@ public class HiddenColumns
           int blockEnd = end;
           int hiddenSoFar = 0;
           int visSoFar = 0;
-          int maxVisible = end - start;
           endsAtHidden = false;
 
           // iterate until a region begins within (start,end]
@@ -1985,9 +1982,9 @@ public class HiddenColumns
 
             i++;
           }
-          if (visSoFar < maxVisible)
+          if (visSoFar < end - start)
           {
-            blockEnd = blockStart + maxVisible - visSoFar;
+            blockEnd = blockStart + end - start - visSoFar;
             int[] contig = new int[] { blockStart, blockEnd };
             vcontigs.add(contig);