X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fmath%2FMatrix.java;h=b22bf4e1d27558fc09c6e59e64a45733f12d75cf;hb=refs%2Ftags%2FRelease_2_11_1_4;hp=804421b066f98165f71361beb0cba62ccfdb63ec;hpb=e8b765f24913520d23f4526d815587853094b3f4;p=jalview.git

diff --git a/src/jalview/math/Matrix.java b/src/jalview/math/Matrix.java
index 804421b..b22bf4e 100755
--- a/src/jalview/math/Matrix.java
+++ b/src/jalview/math/Matrix.java
@@ -972,4 +972,54 @@ public class Matrix implements MatrixI
       }
     }
   }
+
+  @Override
+  public void setD(double[] v)
+  {
+    d = v;
+  }
+
+  @Override
+  public void setE(double[] v)
+  {
+    e = v;
+  }
+
+  public double getTotal()
+  {
+    double d = 0d;
+    for (int i = 0; i < this.height(); i++)
+    {
+      for (int j = 0; j < this.width(); j++)
+      {
+        d += value[i][j];
+      }
+    }
+    return d;
+  }
+
+  /**
+   * {@inheritDoc}
+   */
+  @Override
+  public boolean equals(MatrixI m2, double delta)
+  {
+    if (m2 == null || this.height() != m2.height()
+            || this.width() != m2.width())
+    {
+      return false;
+    }
+    for (int i = 0; i < this.height(); i++)
+    {
+      for (int j = 0; j < this.width(); j++)
+      {
+        double diff = this.getValue(i, j) - m2.getValue(i, j);
+        if (Math.abs(diff) > delta)
+        {
+          return false;
+        }
+      }
+    }
+    return true;
+  }
 }