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

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

diff --git a/src/jalview/api/analysis/PairwiseScoreModelI.java b/src/jalview/api/analysis/PairwiseScoreModelI.java
new file mode 100644 (file)
index 0000000..ecada36
--- /dev/null
+++ b/src/jalview/api/analysis/PairwiseScoreModelI.java
@@ -0,0 +1,22 @@
+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
+
+}