From 86f56c7a53d72066544ff74c893188d304598bec Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Tue, 21 Feb 2017 17:01:37 +0000
Subject: [PATCH] JAL-2416 ScoreMatrix.getMatrix() returns a defensive copy to
 keep the class invariant

---
 src/jalview/analysis/scoremodels/ScoreMatrix.java  |   31 +++++++++++++++++---
 .../analysis/scoremodels/ScoreMatrixTest.java      |   25 ++++++++++++++++
 2 files changed, 52 insertions(+), 4 deletions(-)

diff --git a/src/jalview/analysis/scoremodels/ScoreMatrix.java b/src/jalview/analysis/scoremodels/ScoreMatrix.java
index 13ce6a8..9da28eb 100644
--- a/src/jalview/analysis/scoremodels/ScoreMatrix.java
+++ b/src/jalview/analysis/scoremodels/ScoreMatrix.java
@@ -60,6 +60,8 @@ public class ScoreMatrix implements PairwiseScoreModelI
    */
   private boolean peptide;
 
+  private boolean symmetric;
+
   /**
    * 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
@@ -161,16 +163,22 @@ public class ScoreMatrix implements PairwiseScoreModelI
   }
 
   /**
-   * Returns the score matrix as used in getPairwiseScore. If using this matrix
-   * directly, callers <em>must</em> also call <code>getMatrixIndex</code> in
-   * order to get the matrix index for each character (symbol).
+   * Returns a copy of the score matrix as used in getPairwiseScore. If using
+   * this matrix directly, callers <em>must</em> also call
+   * <code>getMatrixIndex</code> in order to get the matrix index for each
+   * character (symbol).
    * 
    * @return
    * @see #getMatrixIndex(char)
    */
   public float[][] getMatrix()
   {
-    return matrix;
+    float[][] v = new float[matrix.length][matrix.length];
+    for (int i = 0; i < matrix.length; i++)
+    {
+      v[i] = Arrays.copyOf(matrix[i], matrix[i].length);
+    }
+    return v;
   }
 
   /**
@@ -383,4 +391,19 @@ public class ScoreMatrix implements PairwiseScoreModelI
     }
     return false;
   }
+
+  public boolean isSymmetric()
+  {
+    return symmetric;
+  }
+
+  /**
+   * Returns the alphabet the matrix scores for, as a string of characters
+   * 
+   * @return
+   */
+  public String getSymbols()
+  {
+    return new String(symbols);
+  }
 }
diff --git a/test/jalview/analysis/scoremodels/ScoreMatrixTest.java b/test/jalview/analysis/scoremodels/ScoreMatrixTest.java
index 002084d..ae5ad5d 100644
--- a/test/jalview/analysis/scoremodels/ScoreMatrixTest.java
+++ b/test/jalview/analysis/scoremodels/ScoreMatrixTest.java
@@ -2,6 +2,7 @@ package jalview.analysis.scoremodels;
 
 import static org.testng.Assert.assertEquals;
 import static org.testng.Assert.assertNotNull;
+import static org.testng.Assert.assertNotSame;
 import static org.testng.Assert.assertTrue;
 import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
 
@@ -12,6 +13,7 @@ import jalview.math.MatrixI;
 
 import java.io.IOException;
 import java.net.MalformedURLException;
+import java.util.Arrays;
 
 import org.testng.annotations.Test;
 
@@ -121,6 +123,19 @@ public class ScoreMatrixTest
   }
 
   @Test(groups = "Functional")
+  public void testGetMatrix()
+  {
+    ScoreMatrix sm = ScoreModels.getInstance().getBlosum62();
+    float[][] m = sm.getMatrix();
+    assertEquals(m.length, sm.getSize());
+    assertEquals(m[2][4], -3f);
+    // verify a defensive copy is returned
+    float[][] m2 = sm.getMatrix();
+    assertNotSame(m, m2);
+    assertTrue(Arrays.deepEquals(m, m2));
+  }
+
+  @Test(groups = "Functional")
   public void testGetMatrixIndex()
   {
     ScoreMatrix sm = ScoreModels.getInstance().getBlosum62();
@@ -219,4 +234,14 @@ public class ScoreMatrixTest
     assertNotNull(sm2);
     assertTrue(sm2.equals(sm));
   }
+
+  @Test(groups = "Functional")
+  public void testEauals()
+  {
+    ScoreMatrix sm = ScoreModels.getInstance().getBlosum62();
+    ScoreMatrix sm2 = new ScoreMatrix(sm.getName(), sm.getSymbols()
+            .toCharArray(), sm.getMatrix());
+    assertTrue(sm.equals(sm2));
+    assertEquals(sm.hashCode(), sm2.hashCode());
+  }
 }
-- 
1.7.10.2