From e8b765f24913520d23f4526d815587853094b3f4 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Tue, 1 May 2018 12:20:54 +0100
Subject: [PATCH] JAL-1767 include d and e vectors in Matrix.copy()

---
 src/jalview/math/Matrix.java      |   13 ++++++++++++-
 test/jalview/math/MatrixTest.java |   14 ++++++++++++++
 2 files changed, 26 insertions(+), 1 deletion(-)

diff --git a/src/jalview/math/Matrix.java b/src/jalview/math/Matrix.java
index b910a7e..804421b 100755
--- a/src/jalview/math/Matrix.java
+++ b/src/jalview/math/Matrix.java
@@ -24,6 +24,7 @@ import jalview.util.Format;
 import jalview.util.MessageManager;
 
 import java.io.PrintStream;
+import java.util.Arrays;
 
 /**
  * A class to model rectangular matrices of double values and operations on them
@@ -215,7 +216,17 @@ public class Matrix implements MatrixI
       System.arraycopy(value[i], 0, newmat[i], 0, value[i].length);
     }
 
-    return new Matrix(newmat);
+    Matrix m = new Matrix(newmat);
+    if (this.d != null)
+    {
+      m.d = Arrays.copyOf(this.d, this.d.length);
+    }
+    if (this.e != null)
+    {
+      m.e = Arrays.copyOf(this.e, this.e.length);
+    }
+
+    return m;
   }
 
   /**
diff --git a/test/jalview/math/MatrixTest.java b/test/jalview/math/MatrixTest.java
index 97ded5a..6e9c0f1 100644
--- a/test/jalview/math/MatrixTest.java
+++ b/test/jalview/math/MatrixTest.java
@@ -188,9 +188,23 @@ public class MatrixTest
       }
     }
     Matrix m1 = new Matrix(in);
+
     Matrix m2 = (Matrix) m1.copy();
     assertNotSame(m1, m2);
     assertTrue(matrixEquals(m1, m2));
+    assertNull(m2.d);
+    assertNull(m2.e);
+
+    /*
+     * now add d and e vectors and recopy
+     */
+    m1.d = Arrays.copyOf(in[2], in[2].length);
+    m1.e = Arrays.copyOf(in[4], in[4].length);
+    m2 = (Matrix) m1.copy();
+    assertNotSame(m2.d, m1.d);
+    assertNotSame(m2.e, m1.e);
+    assertEquals(m2.d, m1.d);
+    assertEquals(m2.e, m1.e);
   }
 
   /**
-- 
1.7.10.2