Merge branch 'improvement/JAL-3783_upgrade_to_groovy-4' into bug/JAL-4298_java_consol...

[jalview.git] / src / jalview / math / Matrix.java

diff --git a/src/jalview/math/Matrix.java b/src/jalview/math/Matrix.java
index 804421b..ad91464 100755 (executable)
--- a/src/jalview/math/Matrix.java
+++ b/src/jalview/math/Matrix.java
@@ -464,7 +464,7 @@ public class Matrix implements MatrixI
           }
           else
           {
-            // System.out.println("Iteration " + iter);
+            // jalview.bin.Console.outPrintln("Iteration " + iter);
           }
 
           g = (d[l] - d[l - 1]) / (2.0 * e[l - 1]);
@@ -728,7 +728,7 @@ public class Matrix implements MatrixI
           }
           else
           {
-            // System.out.println("Iteration " + iter);
+            // jalview.bin.Console.outPrintln("Iteration " + iter);
           }
 
           g = (d[l] - d[l - 1]) / (2.0 * e[l - 1]);
@@ -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;
+  }
 }