X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fjalview%2Fapi%2Fanalysis%2FPairwiseScoreModelI.java;fp=src%2Fjalview%2Fapi%2Fanalysis%2FPairwiseScoreModelI.java;h=ecada36ef3c3be8668b2124b499a3c93a1d28b9d;hp=0000000000000000000000000000000000000000;hb=773ac00a0ac2eb882e993e567a650ee4d7df3dda;hpb=651ed4273f899e80f4931bed82714355e16fd837

diff --git a/src/jalview/api/analysis/PairwiseScoreModelI.java b/src/jalview/api/analysis/PairwiseScoreModelI.java
new file mode 100644
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+++ b/src/jalview/api/analysis/PairwiseScoreModelI.java
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+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
+
+}