JAL-2380 code tidy after review

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

diff --git a/src/jalview/math/Matrix.java b/src/jalview/math/Matrix.java
index 28b9d67..647fc3a 100755 (executable)
--- a/src/jalview/math/Matrix.java
+++ b/src/jalview/math/Matrix.java
@@ -26,22 +26,23 @@ import jalview.util.MessageManager;
 import java.io.PrintStream;
 
 /**
- * DOCUMENT ME!
- * 
- * @author $author$
- * @version $Revision$
+ * A class to model rectangular matrices of double values and operations on them
  */
 public class Matrix
 {
-  /**
-   * SMJSPUBLIC
+  /*
+   * the cell values in row-major order
    */
   public double[][] value;
 
-  /** DOCUMENT ME!! */
+  /*
+   * the number of rows
+   */
   public int rows;
 
-  /** DOCUMENT ME!! */
+  /*
+   * the number of columns
+   */
   public int cols;
 
   /** DOCUMENT ME!! */
@@ -60,10 +61,10 @@ public class Matrix
    * Creates a new Matrix object. For example
    * 
    * <pre>
-   *   new Matrix(new double[][] {{2, 3}, {4, 5}, 2, 2)
+   *   new Matrix(new double[][] {{2, 3, 4}, {5, 6, 7})
    * constructs
-   *   (2 3)
-   *   (4 5)
+   *   (2 3 4)
+   *   (5 6 7)
    * </pre>
    * 
    * Note that ragged arrays (with not all rows, or columns, of the same
@@ -72,13 +73,11 @@ public class Matrix
    * 
    * @param values
    *          the matrix values in row-major order
-   * @param rows
-   * @param cols
    */
-  public Matrix(double[][] values, int rows, int cols)
+  public Matrix(double[][] values)
   {
-    this.rows = rows;
-    this.cols = cols;
+    this.rows = values.length;
+    this.cols = this.rows == 0 ? 0 : values[0].length;
     this.value = values;
   }
 
@@ -99,7 +98,7 @@ public class Matrix
       }
     }
 
-    return new Matrix(out, cols, rows);
+    return new Matrix(out);
   }
 
   /**
@@ -155,7 +154,7 @@ public class Matrix
       }
     }
 
-    return new Matrix(tmp, in.rows, this.cols);
+    return new Matrix(tmp);
   }
 
   /**
@@ -218,13 +217,9 @@ public class Matrix
     for (int i = 0; i < rows; i++)
     {
       System.arraycopy(value[i], 0, newmat[i], 0, value[i].length);
-      // for (int j = 0; j < cols; j++)
-      // {
-      // newmat[i][j] = value[i][j];
-      // }
     }
 
-    return new Matrix(newmat, rows, cols);
+    return new Matrix(newmat);
   }
 
   /**