From 7c5c70f4bbe69a722dd6e8bd269d7d01e1089034 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Tue, 21 Feb 2017 10:13:06 +0000
Subject: [PATCH] JAL-2416 more validation in ScoreMatrix constructor

---
 src/jalview/analysis/scoremodels/ScoreMatrix.java  |   29 +++++++++-
 .../analysis/scoremodels/ScoreMatrixTest.java      |   61 +++++++++++++++++++-
 2 files changed, 88 insertions(+), 2 deletions(-)

diff --git a/src/jalview/analysis/scoremodels/ScoreMatrix.java b/src/jalview/analysis/scoremodels/ScoreMatrix.java
index 51d8276..eb94817 100644
--- a/src/jalview/analysis/scoremodels/ScoreMatrix.java
+++ b/src/jalview/analysis/scoremodels/ScoreMatrix.java
@@ -58,7 +58,9 @@ public class ScoreMatrix implements PairwiseScoreModelI
   private boolean peptide;
 
   /**
-   * Constructor
+   * Constructor given a name, symbol alphabet, and matrix of scores for pairs
+   * of symbols. The matrix should be square and of the same size as the
+   * alphabet, for example 20x20 for a 20 symbol alphabet.
    * 
    * @param name
    *          Unique, human readable name for the matrix
@@ -69,6 +71,20 @@ public class ScoreMatrix implements PairwiseScoreModelI
    */
   public ScoreMatrix(String name, char[] alphabet, float[][] matrix)
   {
+    if (alphabet.length != matrix.length)
+    {
+      throw new IllegalArgumentException(
+              "score matrix size must match alphabet size");
+    }
+    for (float[] row : matrix)
+    {
+      if (row.length != alphabet.length)
+      {
+        throw new IllegalArgumentException(
+                "score matrix size must be square");
+      }
+    }
+
     this.matrix = matrix;
     this.name = name;
     this.symbols = alphabet;
@@ -265,4 +281,15 @@ public class ScoreMatrix implements PairwiseScoreModelI
     }
     return sb.toString();
   }
+
+  /**
+   * Answers the number of symbols coded for (also equal to the number of rows
+   * and columns of the score matrix)
+   * 
+   * @return
+   */
+  public int getSize()
+  {
+    return symbols.length;
+  }
 }
diff --git a/test/jalview/analysis/scoremodels/ScoreMatrixTest.java b/test/jalview/analysis/scoremodels/ScoreMatrixTest.java
index fcc0bc3..0a9dd25 100644
--- a/test/jalview/analysis/scoremodels/ScoreMatrixTest.java
+++ b/test/jalview/analysis/scoremodels/ScoreMatrixTest.java
@@ -1,12 +1,64 @@
 package jalview.analysis.scoremodels;
-
 import static org.testng.Assert.assertEquals;
+import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
 
 import org.testng.annotations.Test;
 
 public class ScoreMatrixTest
 {
   @Test(groups = "Functional")
+  public void testConstructor()
+  {
+    // note score matrix does not have to be symmetric (though it should be!)
+    float[][] scores = new float[3][];
+    scores[0] = new float[] { 1f, 2f, 3f };
+    scores[1] = new float[] { 4f, 5f, 6f };
+    scores[2] = new float[] { 7f, 8f, 9f };
+    ScoreMatrix sm = new ScoreMatrix("Test", "ABC".toCharArray(), scores);
+    assertEquals(sm.getSize(), 3);
+    assertArrayEquals(scores, sm.getMatrix());
+    assertEquals(sm.getPairwiseScore('A', 'a'), 1f);
+    assertEquals(sm.getPairwiseScore('b', 'c'), 6f);
+    assertEquals(sm.getPairwiseScore('c', 'b'), 8f);
+    assertEquals(sm.getPairwiseScore('A', 'D'), 0f);
+    assertEquals(sm.getMatrixIndex('c'), 2);
+    assertEquals(sm.getMatrixIndex(' '), -1);
+  }
+
+  @Test(
+    groups = "Functional",
+    expectedExceptions = { IllegalArgumentException.class })
+  public void testConstructor_matrixTooSmall()
+  {
+    float[][] scores = new float[2][];
+    scores[0] = new float[] { 1f, 2f };
+    scores[1] = new float[] { 3f, 4f };
+    new ScoreMatrix("Test", "ABC".toCharArray(), scores);
+  }
+
+  @Test(
+    groups = "Functional",
+    expectedExceptions = { IllegalArgumentException.class })
+  public void testConstructor_matrixTooBig()
+  {
+    float[][] scores = new float[2][];
+    scores[0] = new float[] { 1f, 2f };
+    scores[1] = new float[] { 3f, 4f };
+    new ScoreMatrix("Test", "A".toCharArray(), scores);
+  }
+
+  @Test(
+    groups = "Functional",
+    expectedExceptions = { IllegalArgumentException.class })
+  public void testConstructor_matrixNotSquare()
+  {
+    float[][] scores = new float[2][];
+    scores[0] = new float[] { 1f, 2f };
+    scores[1] = new float[] { 3f };
+    new ScoreMatrix("Test", "AB".toCharArray(), scores);
+  }
+
+  @Test(groups = "Functional")
   public void testBuildSymbolIndex()
   {
     short[] index = ScoreMatrix.buildSymbolIndex("AX-. yxYp".toCharArray());
@@ -75,4 +127,11 @@ public class ScoreMatrixTest
     assertEquals(sm.getMatrixIndex('?'), -1);
     assertEquals(sm.getMatrixIndex((char) 128), -1);
   }
+
+  @Test(groups = "Functional")
+  public void testGetSize()
+  {
+    ScoreMatrix sm = ScoreModels.getInstance().getBlosum62();
+    assertEquals(sm.getMatrix().length, sm.getSize());
+  }
 }
-- 
1.7.10.2