JAL-2388 New hidden cols/seqs functions to support overview panel

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

diff --git a/src/jalview/datamodel/HiddenSequences.java b/src/jalview/datamodel/HiddenSequences.java
index aca0be6..9c02f29 100755 (executable)
--- a/src/jalview/datamodel/HiddenSequences.java
+++ b/src/jalview/datamodel/HiddenSequences.java
@@ -278,6 +278,41 @@ public class HiddenSequences
   }
 
   /**
+   * Find the visible row which is a given visible number of rows above another
+   * visible row. i.e. for a startRow x, the row which is distance 1 away will
+   * be row x-1.
+   * 
+   * @param visibleDistance
+   *          the number of visible rows to offset by
+   * @param startRow
+   *          the row to start from
+   * @return the position of the row in the visible alignment
+   */
+  public int findIndexNAboveRow(int visibleDistance, int startRow)
+  {
+    // walk upwards through the alignment
+    // count all the non-null sequences until we have visibleDistance counted
+    // then return the next visible sequence
+    if (hiddenSequences == null)
+    {
+      return startRow - visibleDistance;
+    }
+
+    int index = startRow;
+    int count = 0;
+    while ((index > -1) && (count < visibleDistance))
+    {
+      if (hiddenSequences[index] == null)
+      {
+        // count visible sequences
+        count++;
+      }
+      index--;
+    }
+    return index;
+  }
+
+  /**
    * Convert alignment index from visible alignment to absolute alignment
    * 
    * @param alignmentIndex