X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2Fanalysis%2FSimilarityParamsI.java;h=8d83a17278e8d5ac442f92e1783564720b5efcdd;hb=e1dbbc5edc07f65706eeb1dda9f4c9bcdee9d3a5;hp=9ec215120f07dc6dd50ee4b99e958488a152774f;hpb=a4015623cfd1057095d5d54043de462d9163af4b;p=jalview.git

diff --git a/src/jalview/api/analysis/SimilarityParamsI.java b/src/jalview/api/analysis/SimilarityParamsI.java
index 9ec2151..8d83a17 100644
--- a/src/jalview/api/analysis/SimilarityParamsI.java
+++ b/src/jalview/api/analysis/SimilarityParamsI.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.api.analysis;
 
 /**
@@ -19,17 +39,19 @@ public interface SimilarityParamsI
    * 
    * @return
    */
+  // TODO is this specific to a PID score only?
+  // score matrix will compute whatever is configured for gap-residue
   boolean matchGaps();
 
   /**
-   * Answers true if the demoninator (normalisation factor) of the score count
-   * includes gap-residue positions, false if it only includes residue-residue
-   * aligned positions. Gap-gap positions are included if this and
-   * includeGappedColumns both answer true.
+   * Answers true if gaps are included in the calculation. This may affect the
+   * calculated score, the denominator (normalisation factor) of the score, or
+   * both. Gap-gap positions are included if this and includeGappedColumns both
+   * answer true.
    * 
    * @return
    */
-  boolean denominatorIncludesGaps();
+  boolean includeGaps();
 
   /**
    * Answers true if only the shortest sequence length is used to divide the