JAL-3081 more efficient algorithm for annotation ordering by sequence

[jalview.git] / src / jalview / analysis / AlignmentUtils.java

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index 0dfd383..f1e9551 100644 (file)
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -228,30 +228,6 @@ public class AlignmentUtils
   }
 
   /**
-   * Returns the index (zero-based position) of a sequence in an alignment, or
-   * -1 if not found.
-   * 
-   * @param al
-   * @param seq
-   * @return
-   */
-  public static int getSequenceIndex(AlignmentI al, SequenceI seq)
-  {
-    int result = -1;
-    int pos = 0;
-    for (SequenceI alSeq : al.getSequences())
-    {
-      if (alSeq == seq)
-      {
-        result = pos;
-        break;
-      }
-      pos++;
-    }
-    return result;
-  }
-
-  /**
    * Returns a map of lists of sequences in the alignment, keyed by sequence
    * name. For use in mapping between different alignment views of the same
    * sequences.