From: kiramt <k.mourao@dundee.ac.uk>
Date: Mon, 13 Nov 2017 07:54:56 +0000 (+0000)
Subject: JAL-2759 Converted getHiddenBoundaryLeft/Right to use cursor
X-Git-Tag: Release_2_10_4~55^2~1^2~73
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=aee4f1ed59e360cfee845b480d6d85550b7e6d82;p=jalview.git

JAL-2759 Converted getHiddenBoundaryLeft/Right to use cursor
---

diff --git a/src/jalview/datamodel/HiddenColumns.java b/src/jalview/datamodel/HiddenColumns.java
index dd1e1b3..084ea55 100644
--- a/src/jalview/datamodel/HiddenColumns.java
+++ b/src/jalview/datamodel/HiddenColumns.java
@@ -267,17 +267,6 @@ public class HiddenColumns
       if (hiddenColumns != null)
       {
         result += cursor.getHiddenOffset(column);
-
-
-        /*Iterator<int[]> it = hiddenColumns.iterator();
-        while (it.hasNext())
-        {
-          int[] region = it.next();
-          if (result >= region[0])
-          {
-            result += region[1] - region[0] + 1;
-          }
-        }*/
       }
 
       return result;
@@ -404,7 +393,8 @@ public class HiddenColumns
    * hidden columns. In otherwords, the next hidden column.
    * 
    * @param alPos
-   *          the (visible) alignmentPosition to find the next hidden column for
+   *          the absolute (visible) alignmentPosition to find the next hidden
+   *          column for
    */
   public int getHiddenBoundaryRight(int alPos)
   {
@@ -413,14 +403,22 @@ public class HiddenColumns
       LOCK.readLock().lock();
       if (hiddenColumns != null)
       {
-        Iterator<int[]> it = hiddenColumns.iterator();
-        while (it.hasNext())
+        int index = cursor.findRegionForColumn(alPos);
+        if (index < hiddenColumns.size())
         {
-          int[] region = it.next();
+          int[] region = hiddenColumns.get(index);
           if (alPos < region[0])
           {
             return region[0];
           }
+          else if ((alPos <= region[1])
+                  && (index + 1 < hiddenColumns.size()))
+          {
+            // alPos is within a hidden region, return the next one
+            // if there is one
+            region = hiddenColumns.get(index + 1);
+            return region[0];
+          }
         }
       }
       return alPos;
@@ -435,8 +433,8 @@ public class HiddenColumns
    * hidden columns. In otherwords, the previous hidden column.
    * 
    * @param alPos
-   *          the (visible) alignmentPosition to find the previous hidden column
-   *          for
+   *          the absolute (visible) alignmentPosition to find the previous
+   *          hidden column for
    */
   public int getHiddenBoundaryLeft(int alPos)
   {
@@ -444,17 +442,16 @@ public class HiddenColumns
     {
       LOCK.readLock().lock();
 
-      Iterator<int[]> it = new ReverseRegionsIterator(0, alPos,
-              hiddenColumns);
-      while (it.hasNext())
+      if (hiddenColumns != null)
       {
-        int[] region = it.next();
-        if (alPos > region[1])
+        int index = cursor.findRegionForColumn(alPos);
+
+        if (index > 0)
         {
+          int[] region = hiddenColumns.get(index - 1);
           return region[1];
         }
       }
-
       return alPos;
     } finally
     {
@@ -1289,18 +1286,25 @@ public class HiddenColumns
       int adjres = adjustForHiddenColumns(res);
 
       int[] reveal = null;
-      Iterator<int[]> it = new RegionsIterator(adjres - 2,
-              adjres + 2, hiddenColumns, cursor);
-      while (it.hasNext())
+
+      if (hiddenColumns != null)
       {
-        int[] region = it.next();
-        if (adjres + 1 == region[0] || adjres - 1 == region[1])
+        int regionindex = cursor.findRegionForColumn(adjres - 1);
+        if (hiddenColumns.get(regionindex)[1] == adjres - 1)
         {
-          reveal = region;
-          break;
+          reveal = hiddenColumns.get(regionindex);
+        }
+        else
+        {
+          regionindex = cursor.findRegionForColumn(adjres + 1);
+          if (hiddenColumns.get(regionindex)[0] == adjres + 1)
+          {
+            reveal = hiddenColumns.get(regionindex);
+          }
         }
       }
       return reveal;
+
     } finally
     {
       LOCK.readLock().unlock();
diff --git a/src/jalview/datamodel/HiddenColumnsCursor.java b/src/jalview/datamodel/HiddenColumnsCursor.java
index 7fa96c1..7be6cca 100644
--- a/src/jalview/datamodel/HiddenColumnsCursor.java
+++ b/src/jalview/datamodel/HiddenColumnsCursor.java
@@ -99,8 +99,9 @@ public class HiddenColumnsCursor
     }
 
     if ((hiddenColumns.get(index)[0] <= column)
-            && (hiddenColumns.get(index)[1] >= column))
+            && hiddenColumns.get(index)[1] >= column)
     {
+      // column is in the current region
       // we hit the jackpot
       // don't need to move index
     }
@@ -109,26 +110,25 @@ public class HiddenColumnsCursor
       index = 0;
       hiddenCount = 0;
     }
-    /*else if (column > lastColumn)
-    {
-      index = hiddenColumns.size();
-      // TODO resolve here - need full hidden count
-    }*/
+    // column is after current region
     else if (column > hiddenColumns.get(index)[1]) // includes if column >
                                                    // lastColumn
     {
       // iterate from where we are now, if we're lucky we'll be close by
       // (but still better than iterating from 0)
+      // stop when we find the region *before* column
+      // i.e. the next region starts after column or if not, ends after column
       while ((index < hiddenColumns.size())
-              && (hiddenColumns.get(index)[0] <= column))
+              && (column > hiddenColumns.get(index)[1]))
       {
         int[] region = hiddenColumns.get(index);
         hiddenCount += region[1] - region[0] + 1;
         index++;
       }
-
     }
-    else // (column < hiddenColumns.get(regionIndex)[0])
+
+    // column is before current region
+    else if (column < hiddenColumns.get(index)[0])
     {
       while ((index > 0) && (hiddenColumns.get(index)[1] > column))
       {
diff --git a/src/jalview/datamodel/RegionsIterator.java b/src/jalview/datamodel/RegionsIterator.java
index d1251f8..bafc288 100644
--- a/src/jalview/datamodel/RegionsIterator.java
+++ b/src/jalview/datamodel/RegionsIterator.java
@@ -41,13 +41,6 @@ public class RegionsIterator implements Iterator<int[]>
     {
       currentPosition = cursor.findRegionForColumn(start);
 
-      // iterate until a region overlaps with [start,end]
-      /*      currentPosition = 0;
-      while ((currentPosition < hiddenColumns.size())
-              && (hiddenColumns.get(currentPosition)[1] < start))
-      {
-        currentPosition++;
-      }*/
       if (currentPosition < hiddenColumns.size())
       {
         nextRegion = hiddenColumns.get(currentPosition);