X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2Fanalysis%2FScoreModelI.java;h=7f138cd0eb2bdd5a4c9df3ffc59f162c237bfd9a;hb=b6d4e801a1e2a9a81b44f457ce7e7673e5ad646e;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..7f138cd 100644
--- a/src/jalview/api/analysis/ScoreModelI.java
+++ b/src/jalview/api/analysis/ScoreModelI.java
@@ -1,5 +1,9 @@
 package jalview.api.analysis;
 
+import jalview.api.AlignmentViewPanel;
+import jalview.datamodel.AlignmentView;
+import jalview.math.MatrixI;
+
 public interface ScoreModelI
 {
   /**
@@ -12,6 +16,15 @@ 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 +40,40 @@ 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);
 }