JAL-2403 JAL-1483 changes to ScoreModelI hierarchy and signatures to

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

diff --git a/src/jalview/api/analysis/SimilarityScoreModelI.java b/src/jalview/api/analysis/SimilarityScoreModelI.java
new file mode 100644 (file)
index 0000000..96208a3
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+++ b/src/jalview/api/analysis/SimilarityScoreModelI.java
@@ -0,0 +1,24 @@
+package jalview.api.analysis;
+
+import jalview.datamodel.AlignmentView;
+import jalview.math.MatrixI;
+
+/**
+ * A class that provides a method to compute similarity scores of pairs of
+ * sequences
+ * 
+ * @author gmcarstairs
+ *
+ */
+public interface SimilarityScoreModelI extends ScoreModelI
+{
+  /**
+   * 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
+   * 
+   * @param seqData
+   * @return
+   */
+  MatrixI findSimilarities(AlignmentView seqData);
+}