X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FHiddenSequences.java;h=6950c287bff121b99312c260559dc447ccf45f22;hb=6d6c9b65d01adbdd8b624bea6a766165e4497bb6;hp=8ca3c5abdc9fe5286914ae8803c3a897efe1dcad;hpb=a457753abc62fe63774215de98f74f5c6aeb10d4;p=jalview.git

diff --git a/src/jalview/datamodel/HiddenSequences.java b/src/jalview/datamodel/HiddenSequences.java
index 8ca3c5a..6950c28 100755
--- a/src/jalview/datamodel/HiddenSequences.java
+++ b/src/jalview/datamodel/HiddenSequences.java
@@ -154,8 +154,8 @@ public class HiddenSequences
       hiddenSequences = new SequenceI[alignment.getHeight()];
     }
 
-    int alignmentIndex = alignment.findIndex(sequence);
-    alignmentIndex = adjustForHiddenSeqs(alignmentIndex);
+    int absAlignmentIndex = alignment.findIndex(sequence);
+    int alignmentIndex = adjustForHiddenSeqs(absAlignmentIndex);
 
     if (hiddenSequences[alignmentIndex] != null)
     {
@@ -164,7 +164,7 @@ public class HiddenSequences
 
     hiddenSequences[alignmentIndex] = sequence;
 
-    alignment.deleteSequence(sequence);
+    alignment.deleteHiddenSequence(absAlignmentIndex);
   }
 
   public List<SequenceI> showAll(
@@ -246,6 +246,12 @@ public class HiddenSequences
     return hiddenSequences == null ? null : hiddenSequences[alignmentIndex];
   }
 
+  /**
+   * Convert absolute alignment index to visible alignment index
+   * 
+   * @param alignmentIndex
+   * @return
+   */
   public int findIndexWithoutHiddenSeqs(int alignmentIndex)
   {
     if (hiddenSequences == null)
@@ -254,8 +260,14 @@ public class HiddenSequences
     }
     int index = 0;
     int hiddenSeqs = 0;
+    int diff = 0;
     if (hiddenSequences.length <= alignmentIndex)
     {
+      // if the alignmentIndex runs past the end of hidden sequences
+      // and therefore actually past the end of the alignment
+      // store the difference to add back on at the end, so that behaviour
+      // is consistent with hidden columns behaviour (used by overview panel)
+      diff = alignmentIndex - hiddenSequences.length + 1;
       alignmentIndex = hiddenSequences.length - 1;
     }
 
@@ -268,9 +280,50 @@ public class HiddenSequences
       index++;
     }
 
-    return (alignmentIndex - hiddenSeqs);
+    return (alignmentIndex - hiddenSeqs + diff);
   }
 
+  /**
+   * 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 subtractVisibleRows(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
+   * @return
+   */
   public int adjustForHiddenSeqs(int alignmentIndex)
   {
     if (hiddenSequences == null)
@@ -296,6 +349,7 @@ public class HiddenSequences
    * makes a copy of the alignment with hidden sequences included. Using the
    * copy for anything other than simple output is not recommended. Note - this
    * method DOES NOT USE THE AlignmentI COPY CONSTRUCTOR!
+   * 
    * @return
    */
   public AlignmentI getFullAlignment()