Merge branch 'develop' into features/JAL-2393customMatrices

[jalview.git] / src / jalview / api / analysis / ScoreModelI.java

diff --git a/src/jalview/api/analysis/ScoreModelI.java b/src/jalview/api/analysis/ScoreModelI.java
index 31a1c32..7352a71 100644 (file)
--- a/src/jalview/api/analysis/ScoreModelI.java
+++ b/src/jalview/api/analysis/ScoreModelI.java
@@ -1,36 +1,40 @@
-/*
- * 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;
 
-import jalview.datamodel.AlignmentView;
-
 public interface ScoreModelI
 {
-
-  float[][] findDistances(AlignmentView seqData);
-
+  /**
+   * Answers a name for the score model, suitable for display in menus. Names
+   * should be unique across score models in use.
+   * 
+   * @return
+   * @see jalview.analysis.scoremodels.ScoreModels#forName(String)
+   */
   String getName();
 
+  /**
+   * Answers an informative description of the model, suitable for use in
+   * tooltips. Descriptions may be internationalised, and need not be unique
+   * (but should be).
+   * 
+   * @return
+   */
+  String getDescription();
+
+  /**
+   * Answers true if this model is applicable for nucleotide data (so should be
+   * shown in menus in that context)
+   * 
+   * @return
+   */
   boolean isDNA();
 
+  /**
+   * Answers true if this model is applicable for peptide data (so should be
+   * shown in menus in that context)
+   * 
+   * @return
+   */
   boolean isProtein();
 
+  // TODO getName, isDNA, isProtein can be static methods in Java 8
 }