X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fmath%2FRotatableMatrix.java;h=eff8dea1ee72d3c9c7d8359a07229c0fdd810bc1;hb=def10fb2252c67e8256ec1fddc6605e34d760c63;hp=ba903703c5f2c1a97370e5ede301651f2132d0b4;hpb=174230b4233d9ce80f94527768d2cd2f76da11ab;p=jalview.git

diff --git a/src/jalview/math/RotatableMatrix.java b/src/jalview/math/RotatableMatrix.java
index ba90370..eff8dea 100755
--- a/src/jalview/math/RotatableMatrix.java
+++ b/src/jalview/math/RotatableMatrix.java
@@ -1,24 +1,23 @@
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with this program; if not, write to the Free Software
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
-*/
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.math;
 
-
 /**
  * DOCUMENT ME!
  *
@@ -27,306 +26,306 @@ package jalview.math;
  */
 public class RotatableMatrix
 {
-    float[][] matrix;
-    float[] temp;
-    float[][] rot;
-
-    /**
-     * Creates a new RotatableMatrix object.
-     *
-     * @param rows DOCUMENT ME!
-     * @param cols DOCUMENT ME!
-     */
-    public RotatableMatrix(int rows, int cols)
-    {
-        matrix = new float[rows][cols];
-
-        temp = new float[3];
-
-        rot = new float[3][3];
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param i DOCUMENT ME!
-     * @param j DOCUMENT ME!
-     * @param value DOCUMENT ME!
-     */
-    public void addElement(int i, int j, float value)
-    {
-        matrix[i][j] = value;
-    }
-
-    /**
-     * DOCUMENT ME!
-     */
-    public void print()
+  float[][] matrix;
+  float[] temp;
+  float[][] rot;
+
+  /**
+   * Creates a new RotatableMatrix object.
+   *
+   * @param rows DOCUMENT ME!
+   * @param cols DOCUMENT ME!
+   */
+  public RotatableMatrix(int rows, int cols)
+  {
+    matrix = new float[rows][cols];
+
+    temp = new float[3];
+
+    rot = new float[3][3];
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param i DOCUMENT ME!
+   * @param j DOCUMENT ME!
+   * @param value DOCUMENT ME!
+   */
+  public void addElement(int i, int j, float value)
+  {
+    matrix[i][j] = value;
+  }
+
+  /**
+   * DOCUMENT ME!
+   */
+  public void print()
+  {
+    System.out.println(matrix[0][0] + " " + matrix[0][1] + " " +
+                       matrix[0][2]);
+
+    System.out.println(matrix[1][0] + " " + matrix[1][1] + " " +
+                       matrix[1][2]);
+
+    System.out.println(matrix[2][0] + " " + matrix[2][1] + " " +
+                       matrix[2][2]);
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param degrees DOCUMENT ME!
+   * @param axis DOCUMENT ME!
+   */
+  public void rotate(float degrees, char axis)
+  {
+    float costheta = (float) Math.cos( (degrees * Math.PI) / (float) 180.0);
+
+    float sintheta = (float) Math.sin( (degrees * Math.PI) / (float) 180.0);
+
+    if (axis == 'z')
     {
-        System.out.println(matrix[0][0] + " " + matrix[0][1] + " " +
-            matrix[0][2]);
-
-        System.out.println(matrix[1][0] + " " + matrix[1][1] + " " +
-            matrix[1][2]);
-
-        System.out.println(matrix[2][0] + " " + matrix[2][1] + " " +
-            matrix[2][2]);
-    }
+      rot[0][0] = (float) costheta;
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param degrees DOCUMENT ME!
-     * @param axis DOCUMENT ME!
-     */
-    public void rotate(float degrees, char axis)
-    {
-        float costheta = (float) Math.cos((degrees * Math.PI) / (float) 180.0);
+      rot[0][1] = (float) - sintheta;
 
-        float sintheta = (float) Math.sin((degrees * Math.PI) / (float) 180.0);
+      rot[0][2] = (float) 0.0;
 
-        if (axis == 'z')
-        {
-            rot[0][0] = (float) costheta;
+      rot[1][0] = (float) sintheta;
 
-            rot[0][1] = (float) -sintheta;
+      rot[1][1] = (float) costheta;
 
-            rot[0][2] = (float) 0.0;
+      rot[1][2] = (float) 0.0;
 
-            rot[1][0] = (float) sintheta;
+      rot[2][0] = (float) 0.0;
 
-            rot[1][1] = (float) costheta;
+      rot[2][1] = (float) 0.0;
 
-            rot[1][2] = (float) 0.0;
+      rot[2][2] = (float) 1.0;
 
-            rot[2][0] = (float) 0.0;
+      preMultiply(rot);
+    }
 
-            rot[2][1] = (float) 0.0;
+    if (axis == 'x')
+    {
+      rot[0][0] = (float) 1.0;
 
-            rot[2][2] = (float) 1.0;
+      rot[0][1] = (float) 0.0;
 
-            preMultiply(rot);
-        }
+      rot[0][2] = (float) 0.0;
 
-        if (axis == 'x')
-        {
-            rot[0][0] = (float) 1.0;
+      rot[1][0] = (float) 0.0;
 
-            rot[0][1] = (float) 0.0;
+      rot[1][1] = (float) costheta;
 
-            rot[0][2] = (float) 0.0;
+      rot[1][2] = (float) sintheta;
 
-            rot[1][0] = (float) 0.0;
+      rot[2][0] = (float) 0.0;
 
-            rot[1][1] = (float) costheta;
+      rot[2][1] = (float) - sintheta;
 
-            rot[1][2] = (float) sintheta;
+      rot[2][2] = (float) costheta;
 
-            rot[2][0] = (float) 0.0;
+      preMultiply(rot);
+    }
 
-            rot[2][1] = (float) -sintheta;
+    if (axis == 'y')
+    {
+      rot[0][0] = (float) costheta;
 
-            rot[2][2] = (float) costheta;
+      rot[0][1] = (float) 0.0;
 
-            preMultiply(rot);
-        }
+      rot[0][2] = (float) - sintheta;
 
-        if (axis == 'y')
-        {
-            rot[0][0] = (float) costheta;
+      rot[1][0] = (float) 0.0;
 
-            rot[0][1] = (float) 0.0;
+      rot[1][1] = (float) 1.0;
 
-            rot[0][2] = (float) -sintheta;
+      rot[1][2] = (float) 0.0;
 
-            rot[1][0] = (float) 0.0;
+      rot[2][0] = (float) sintheta;
 
-            rot[1][1] = (float) 1.0;
+      rot[2][1] = (float) 0.0;
 
-            rot[1][2] = (float) 0.0;
+      rot[2][2] = (float) costheta;
 
-            rot[2][0] = (float) sintheta;
+      preMultiply(rot);
+    }
+  }
 
-            rot[2][1] = (float) 0.0;
+  /**
+   * DOCUMENT ME!
+   *
+   * @param vect DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public float[] vectorMultiply(float[] vect)
+  {
+    temp[0] = vect[0];
 
-            rot[2][2] = (float) costheta;
+    temp[1] = vect[1];
 
-            preMultiply(rot);
-        }
-    }
+    temp[2] = vect[2];
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param vect DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public float[] vectorMultiply(float[] vect)
+    for (int i = 0; i < 3; i++)
     {
-        temp[0] = vect[0];
-
-        temp[1] = vect[1];
+      temp[i] = (matrix[i][0] * vect[0]) + (matrix[i][1] * vect[1]) +
+          (matrix[i][2] * vect[2]);
+    }
 
-        temp[2] = vect[2];
+    vect[0] = temp[0];
 
-        for (int i = 0; i < 3; i++)
-        {
-            temp[i] = (matrix[i][0] * vect[0]) + (matrix[i][1] * vect[1]) +
-                (matrix[i][2] * vect[2]);
-        }
+    vect[1] = temp[1];
 
-        vect[0] = temp[0];
+    vect[2] = temp[2];
 
-        vect[1] = temp[1];
+    return vect;
+  }
 
-        vect[2] = temp[2];
+  /**
+   * DOCUMENT ME!
+   *
+   * @param mat DOCUMENT ME!
+   */
+  public void preMultiply(float[][] mat)
+  {
+    float[][] tmp = new float[3][3];
 
-        return vect;
+    for (int i = 0; i < 3; i++)
+    {
+      for (int j = 0; j < 3; j++)
+      {
+        tmp[i][j] = (mat[i][0] * matrix[0][j]) +
+            (mat[i][1] * matrix[1][j]) + (mat[i][2] * matrix[2][j]);
+      }
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param mat DOCUMENT ME!
-     */
-    public void preMultiply(float[][] mat)
+    for (int i = 0; i < 3; i++)
     {
-        float[][] tmp = new float[3][3];
-
-        for (int i = 0; i < 3; i++)
-        {
-            for (int j = 0; j < 3; j++)
-            {
-                tmp[i][j] = (mat[i][0] * matrix[0][j]) +
-                    (mat[i][1] * matrix[1][j]) + (mat[i][2] * matrix[2][j]);
-            }
-        }
-
-        for (int i = 0; i < 3; i++)
-        {
-            for (int j = 0; j < 3; j++)
-            {
-                matrix[i][j] = tmp[i][j];
-            }
-        }
+      for (int j = 0; j < 3; j++)
+      {
+        matrix[i][j] = tmp[i][j];
+      }
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param mat DOCUMENT ME!
-     */
-    public void postMultiply(float[][] mat)
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param mat DOCUMENT ME!
+   */
+  public void postMultiply(float[][] mat)
+  {
+    float[][] tmp = new float[3][3];
+
+    for (int i = 0; i < 3; i++)
     {
-        float[][] tmp = new float[3][3];
-
-        for (int i = 0; i < 3; i++)
-        {
-            for (int j = 0; j < 3; j++)
-            {
-                tmp[i][j] = (matrix[i][0] * mat[0][j]) +
-                    (matrix[i][1] * mat[1][j]) + (matrix[i][2] * mat[2][j]);
-            }
-        }
-
-        for (int i = 0; i < 3; i++)
-        {
-            for (int j = 0; j < 3; j++)
-            {
-                matrix[i][j] = tmp[i][j];
-            }
-        }
+      for (int j = 0; j < 3; j++)
+      {
+        tmp[i][j] = (matrix[i][0] * mat[0][j]) +
+            (matrix[i][1] * mat[1][j]) + (matrix[i][2] * mat[2][j]);
+      }
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param args DOCUMENT ME!
-     */
-    public static void main(String[] args)
+    for (int i = 0; i < 3; i++)
     {
-        RotatableMatrix m = new RotatableMatrix(3, 3);
+      for (int j = 0; j < 3; j++)
+      {
+        matrix[i][j] = tmp[i][j];
+      }
+    }
+  }
 
-        m.addElement(0, 0, 1);
+  /**
+   * DOCUMENT ME!
+   *
+   * @param args DOCUMENT ME!
+   */
+  public static void main(String[] args)
+  {
+    RotatableMatrix m = new RotatableMatrix(3, 3);
 
-        m.addElement(0, 1, 0);
+    m.addElement(0, 0, 1);
 
-        m.addElement(0, 2, 0);
+    m.addElement(0, 1, 0);
 
-        m.addElement(1, 0, 0);
+    m.addElement(0, 2, 0);
 
-        m.addElement(1, 1, 2);
+    m.addElement(1, 0, 0);
 
-        m.addElement(1, 2, 0);
+    m.addElement(1, 1, 2);
 
-        m.addElement(2, 0, 0);
+    m.addElement(1, 2, 0);
 
-        m.addElement(2, 1, 0);
+    m.addElement(2, 0, 0);
 
-        m.addElement(2, 2, 1);
+    m.addElement(2, 1, 0);
 
-        m.print();
+    m.addElement(2, 2, 1);
 
-        RotatableMatrix n = new RotatableMatrix(3, 3);
+    m.print();
 
-        n.addElement(0, 0, 2);
+    RotatableMatrix n = new RotatableMatrix(3, 3);
 
-        n.addElement(0, 1, 1);
+    n.addElement(0, 0, 2);
 
-        n.addElement(0, 2, 1);
+    n.addElement(0, 1, 1);
 
-        n.addElement(1, 0, 2);
+    n.addElement(0, 2, 1);
 
-        n.addElement(1, 1, 1);
+    n.addElement(1, 0, 2);
 
-        n.addElement(1, 2, 1);
+    n.addElement(1, 1, 1);
 
-        n.addElement(2, 0, 2);
+    n.addElement(1, 2, 1);
 
-        n.addElement(2, 1, 1);
+    n.addElement(2, 0, 2);
 
-        n.addElement(2, 2, 1);
+    n.addElement(2, 1, 1);
 
-        n.print();
+    n.addElement(2, 2, 1);
 
-        //m.postMultiply(n.matrix);
-        //m.print();
-        //     m.rotate(45,'z',new RotatableMatrix(3,3));
-        float[] vect = new float[3];
+    n.print();
 
-        vect[0] = 2;
+    //m.postMultiply(n.matrix);
+    //m.print();
+    //     m.rotate(45,'z',new RotatableMatrix(3,3));
+    float[] vect = new float[3];
 
-        vect[1] = 4;
+    vect[0] = 2;
 
-        vect[2] = 6;
+    vect[1] = 4;
 
-        vect = m.vectorMultiply(vect);
+    vect[2] = 6;
 
-        System.out.println(vect[0] + " " + vect[1] + " " + vect[2]);
-    }
+    vect = m.vectorMultiply(vect);
 
-    /**
-     * DOCUMENT ME!
-     */
-    public void setIdentity()
-    {
-        matrix[0][0] = (float) 1.0;
+    System.out.println(vect[0] + " " + vect[1] + " " + vect[2]);
+  }
 
-        matrix[1][1] = (float) 1.0;
+  /**
+   * DOCUMENT ME!
+   */
+  public void setIdentity()
+  {
+    matrix[0][0] = (float) 1.0;
 
-        matrix[2][2] = (float) 1.0;
+    matrix[1][1] = (float) 1.0;
 
-        matrix[0][1] = (float) 0.0;
+    matrix[2][2] = (float) 1.0;
 
-        matrix[0][2] = (float) 0.0;
+    matrix[0][1] = (float) 0.0;
 
-        matrix[1][0] = (float) 0.0;
+    matrix[0][2] = (float) 0.0;
 
-        matrix[1][2] = (float) 0.0;
+    matrix[1][0] = (float) 0.0;
 
-        matrix[2][0] = (float) 0.0;
+    matrix[1][2] = (float) 0.0;
 
-        matrix[2][1] = (float) 0.0;
-    }
+    matrix[2][0] = (float) 0.0;
+
+    matrix[2][1] = (float) 0.0;
+  }
 }