X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignmentSorter.java;h=cc4c46930ebce044e4178c5b2a56e69ab32c8dca;hb=45715055c536e1c31020b8ab7ce30b2e28f3aafd;hp=e9fb3355a40aac50059a6674e1723b18db7d0791;hpb=f4e78f8f0fa25050e2f164d93cf81d8bea69e4e7;p=jalview.git

diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index e9fb335..cc4c469 100755
--- a/src/jalview/analysis/AlignmentSorter.java
+++ b/src/jalview/analysis/AlignmentSorter.java
@@ -33,7 +33,6 @@ import jalview.util.MessageManager;
 import jalview.util.QuickSort;
 
 import java.util.ArrayList;
-import java.util.Arrays;
 import java.util.List;
 
 /**
@@ -703,6 +702,26 @@ public class AlignmentSorter
     return false;
   }
 
+  /**
+   * Sort sequences by feature score or density, optionally restricted by
+   * feature types, feature groups, or alignment start/end positions.
+   * <p>
+   * If the sort is repeated for the same combination of types and groups, sort
+   * order is reversed.
+   * 
+   * @param featureLabels
+   *          a list of feature types to include (or null for all)
+   * @param groupLabels
+   *          a list of feature groups to include (or null for all)
+   * @param start
+   *          start column position to include (base zero)
+   * @param stop
+   *          end column position to include (base zero)
+   * @param alignment
+   *          the alignment to be sorted
+   * @param method
+   *          either "average_score" or "density" ("text" not yet implemented)
+   */
   public static void sortByFeature(List<String> featureLabels,
           List<String> groupLabels, int start, int stop,
           AlignmentI alignment, String method)