JAL-2429 Fix to ColumnSelection::findColumnPosition

diff --git a/src/jalview/datamodel/ColumnSelection.java b/src/jalview/datamodel/ColumnSelection.java
index 98a7fe2..7459033 100644 (file)
--- a/src/jalview/datamodel/ColumnSelection.java
+++ b/src/jalview/datamodel/ColumnSelection.java
@@ -690,8 +690,8 @@ public class ColumnSelection
    * left-most visible column will always be returned.
    * 
    * @param hiddenColumn
-   *          int
-   * @return int
+   *          the column index in the full alignment including hidden columns
+   * @return the position of the column in the visible alignment
    */
   public int findColumnPosition(int hiddenColumn)
   {
@@ -708,9 +708,17 @@ public class ColumnSelection
           result -= region[1] + 1 - region[0];
         }
       } while ((hiddenColumn > region[1]) && (index < hiddenColumns.size()));
-      if (hiddenColumn > region[0] && hiddenColumn < region[1])
-      {
-        return region[0] + hiddenColumn - result;
+
+      if (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
+
+         return result - (hiddenColumn - region[0] + 1);
       }
     }
     return result; // return the shifted position after removing hidden columns.

diff --git a/test/jalview/datamodel/ColumnSelectionTest.java b/test/jalview/datamodel/ColumnSelectionTest.java
index 1d819c9..63d5e56 100644 (file)
--- a/test/jalview/datamodel/ColumnSelectionTest.java
+++ b/test/jalview/datamodel/ColumnSelectionTest.java
@@ -105,9 +105,31 @@ public class ColumnSelectionTest
     cs.hideColumns(4, 4);
     assertEquals(4, cs.findColumnPosition(5));
 
+    // hiding column 4 moves column 4 to position 3
+    assertEquals(3, cs.findColumnPosition(4));
+
     // hiding columns 1 and 2 moves column 5 to column 2
     cs.hideColumns(1, 2);
     assertEquals(2, cs.findColumnPosition(5));
+
+    // check with > 1 hidden column regions
+    // where some columns are in the hidden regions
+    ColumnSelection cs2 = new ColumnSelection();
+    cs2.hideColumns(5, 10);
+    cs2.hideColumns(20, 27);
+    cs2.hideColumns(40, 44);
+
+    // hiding columns 5-10 and 20-27 moves column 8 to column 4
+    assertEquals(4, cs2.findColumnPosition(8));
+
+    // and moves column 24 to 13
+    assertEquals(13, cs2.findColumnPosition(24));
+
+    // and moves column 28 to 14
+    assertEquals(14, cs2.findColumnPosition(28));
+
+    // and moves column 40 to 25
+    assertEquals(25, cs2.findColumnPosition(40));
   }
 
   /**