JAL-2759 Convert reveal to use cursor

diff --git a/src/jalview/datamodel/HiddenColumns.java b/src/jalview/datamodel/HiddenColumns.java
index 8a67741..050603e 100644 (file)
--- a/src/jalview/datamodel/HiddenColumns.java
+++ b/src/jalview/datamodel/HiddenColumns.java
@@ -289,55 +289,9 @@ public class HiddenColumns
   {
     try
     {
-      /*    LOCK.readLock().lock();
-      int result = hiddenColumn;
-      int[] region = null;
-      if (hiddenColumns != null)
-      {
-        Iterator<int[]> it = new RegionsIterator(0, hiddenColumn,
-                hiddenColumns, cursor);
-        while (it.hasNext())
-        {
-          region = it.next();
-          if (hiddenColumn > region[1])
-          {
-            result -= region[1] + 1 - region[0];
-          }
-        }
-      
-        if (region != null && hiddenColumn >= region[0]
-                && hiddenColumn <= region[1])
-        {
-          // Here the hidden column is within a region, so
-          // we want to return the position of region[0]-1, adjusted for any
-          // earlier hidden columns.
-          // Calculate the difference between the actual hidden col position
-          // and region[0]-1, and then subtract from result to convert result
-          // from the adjusted hiddenColumn value to the adjusted region[0]-1
-          // value.
-      
-          // However, if the region begins at 0 we cannot return region[0]-1
-          // just return 0
-          if (region[0] == 0)
-          {
-            return 0;
-          }
-          else
-          {
-            return result - (hiddenColumn - region[0] + 1);
-          }
-        }
-      }
-      return result; // return the shifted position after removing hidden
-                     // columns.
-        } finally
-        {
-      LOCK.readLock().unlock();
-        }*/
-
       LOCK.readLock().lock();
       int result = hiddenColumn;
-      // int[] region = null;
+
       if (hiddenColumns != null)
       {
         int index = cursor.findRegionForColumn(hiddenColumn);
@@ -367,7 +321,6 @@ public class HiddenColumns
           }
         }
       }
-      System.out.println(hiddenColumn + " " + result);
       return result; // return the shifted position after removing hidden
                      // columns.
     } finally
@@ -989,31 +942,32 @@ public class HiddenColumns
     try
     {
       LOCK.writeLock().lock();
-      Iterator<int[]> it = new RegionsIterator(start, start, hiddenColumns,
-              cursor);
-      while (it.hasNext())
+
+      if (hiddenColumns != null)
       {
-        int[] region = it.next();
-        if (start == region[0])
+        int regionIndex = cursor.findRegionForColumn(start);
+
+        if (regionIndex != -1 && regionIndex != hiddenColumns.size())
         {
-          for (int j = region[0]; j < region[1] + 1; j++)
+          // regionIndex is the region which either contains start
+          // or lies to the right of start
+          int[] region = hiddenColumns.get(regionIndex);
+          if (start == region[0])
           {
-            sel.addElement(j);
+            for (int j = region[0]; j < region[1] + 1; j++)
+            {
+              sel.addElement(j);
+            }
+            hiddenColumns.remove(regionIndex);
+
+            if (hiddenColumns.isEmpty())
+            {
+              hiddenColumns = null;
+            }
+            cursor.updateForDeletedRegion(hiddenColumns);
           }
-          it.remove();
-          break;
-        }
-        else if (start < region[0])
-        {
-          break; // passed all possible matching regions
         }
       }
-
-      if (hiddenColumns.size() == 0)
-      {
-        hiddenColumns = null;
-      }
-      cursor.resetCursor(hiddenColumns);
     } finally
     {
       LOCK.writeLock().unlock();
@@ -1330,14 +1284,16 @@ public class HiddenColumns
       if (hiddenColumns != null)
       {
         int regionindex = cursor.findRegionForColumn(adjres - 1);
-        if (hiddenColumns.get(regionindex)[1] == adjres - 1)
+        if (regionindex < hiddenColumns.size()
+                && hiddenColumns.get(regionindex)[1] == adjres - 1)
         {
           reveal = hiddenColumns.get(regionindex);
         }
         else
         {
           regionindex = cursor.findRegionForColumn(adjres + 1);
-          if (hiddenColumns.get(regionindex)[0] == adjres + 1)
+          if (regionindex < hiddenColumns.size()
+                  && hiddenColumns.get(regionindex)[0] == adjres + 1)
           {
             reveal = hiddenColumns.get(regionindex);
           }

diff --git a/src/jalview/datamodel/HiddenColumnsCursor.java b/src/jalview/datamodel/HiddenColumnsCursor.java
index b40afdf..2d579b0 100644 (file)
--- a/src/jalview/datamodel/HiddenColumnsCursor.java
+++ b/src/jalview/datamodel/HiddenColumnsCursor.java
@@ -43,22 +43,15 @@ public class HiddenColumnsCursor
   /**
    * Set the cursor to a position
    * 
-   * @param first
-   *          absolute position of first hidden column
-   * @param last
-   *          absolute position of last hidden column
-   * @param index
-   *          index of last visited region
-   * @param hiddenCount
-   *          number of hidden columns before last visited region
+   * @param hiddenCols
    */
   protected void resetCursor(List<int[]> hiddenCols)
   {
     synchronized (this)
     {
+      hiddenColumns = hiddenCols;
       if ((hiddenCols != null) && (!hiddenCols.isEmpty()))
       {
-        hiddenColumns = hiddenCols;
         firstColumn = hiddenColumns.get(0)[0];
         regionIndex = 0;
         hiddenSoFar = 0;
@@ -66,6 +59,31 @@ public class HiddenColumnsCursor
     }
   }
 
+  /**
+   * Delete the region the cursor is currently at. Avoids having to reset the
+   * cursor just because we deleted a region.
+   *
+   * @param hiddenCols
+   */
+  protected void updateForDeletedRegion(List<int[]> hiddenCols)
+  {
+
+    if ((hiddenCols != null) && (!hiddenCols.isEmpty()))
+    {
+      // if there is a region to the right of the current region,
+      // nothing changes; otherwise
+      // we deleted the last region (index=hiddenCols.size()-1)
+      // or the index was at the end of the alignment (index=hiddenCols.size())
+      if (regionIndex >= hiddenColumns.size() - 1)
+      {
+        // deleted last region, index is now end of alignment
+        regionIndex = hiddenCols.size();
+      }
+    }
+
+    hiddenColumns = hiddenCols;
+  }
+
   protected void updateCursor(int index, int hiddenCount)
   {
     synchronized (this)

diff --git a/test/jalview/datamodel/HiddenColumnsTest.java b/test/jalview/datamodel/HiddenColumnsTest.java
index 320a199..fbeaa71 100644 (file)
--- a/test/jalview/datamodel/HiddenColumnsTest.java
+++ b/test/jalview/datamodel/HiddenColumnsTest.java
@@ -774,6 +774,9 @@ public class HiddenColumnsTest
     result = hc.getRegionWithEdgeAtRes(8);
     assertEquals(14, result[0]);
     assertEquals(15, result[1]);
+
+    result = hc.getRegionWithEdgeAtRes(16);
+    assertNull(result);
   }
 
   @Test(groups = "Functional")