X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2Fanalysis%2FScoreModelI.java;h=275cd92829ce79921ef2d73141ad7e0cd7de0c0b;hb=8f992e8f0ecac1cfb85903ee8dce8f3dbf73d323;hp=9a633f0b629c8fda920172034546e6ba3a7d950b;hpb=582493a5b56d3e01d901c6da9906685c31a32abb;p=jalview.git

diff --git a/src/jalview/api/analysis/ScoreModelI.java b/src/jalview/api/analysis/ScoreModelI.java
index 9a633f0..275cd92 100644
--- a/src/jalview/api/analysis/ScoreModelI.java
+++ b/src/jalview/api/analysis/ScoreModelI.java
@@ -1,5 +1,29 @@
+/*
+ * 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.api.AlignmentViewPanel;
+import jalview.datamodel.AlignmentView;
+import jalview.math.MatrixI;
+
 public interface ScoreModelI
 {
   /**
@@ -12,6 +36,15 @@ public interface ScoreModelI
   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)
    * 
@@ -27,4 +60,41 @@ public interface ScoreModelI
    */
   boolean isProtein();
 
+  // TODO getName, isDNA, isProtein can be static methods in Java 8
+
+  /**
+   * Returns a distance score for the given sequence regions, that is, a matrix
+   * whose value [i][j] is the distance of sequence i from sequence j by some
+   * measure. The options parameter provides configuration choices for how the
+   * similarity score is calculated.
+   * 
+   * @param seqData
+   * @param options
+   * @return
+   */
+
+  MatrixI findDistances(AlignmentView seqData, SimilarityParamsI options);
+
+  /**
+   * Returns a similarity score for the given sequence regions, that is, a
+   * matrix whose value [i][j] is the similarity of sequence i to sequence j by
+   * some measure. The options parameter provides configuration choices for how
+   * the similarity score is calculated.
+   * 
+   * @param seqData
+   * @param options
+   * @return
+   */
+  MatrixI findSimilarities(AlignmentView seqData,
+          SimilarityParamsI options);
+
+  /**
+   * Returns a score model object configured for the given alignment view.
+   * Depending on the score model, this may just be a singleton instance, or a
+   * new instance configured with data from the view.
+   * 
+   * @param avp
+   * @return
+   */
+  ScoreModelI getInstance(AlignmentViewPanel avp);
 }