Merge branch 'develop' into features/JAL-250_hideredundantseqs

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

diff --git a/src/jalview/api/analysis/PairwiseScoreModelI.java b/src/jalview/api/analysis/PairwiseScoreModelI.java
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+++ b/src/jalview/api/analysis/PairwiseScoreModelI.java
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+/*
+ * 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;
+
+/**
+ * An interface that describes classes that can compute similarity (aka
+ * substitution) scores for pairs of residues
+ */
+public interface PairwiseScoreModelI
+{
+  /**
+   * Answers a similarity score between two sequence characters (for
+   * substitution of the first by the second). Typically the highest scores are
+   * for identity, and the lowest for substitution of a residue by one with very
+   * different properties.
+   * 
+   * @param c
+   * @param d
+   * @return
+   */
+  abstract public float getPairwiseScore(char c, char d);
+  // TODO make this static when Java 8
+
+}