-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-\r
-package jalview.math;\r
-\r
-\r
-\r
-public class RotatableMatrix {\r
-\r
- float matrix[][];\r
-\r
- float[] temp;\r
-\r
- float[][] rot;\r
-\r
-\r
-\r
- public RotatableMatrix(int rows, int cols) {\r
-\r
- matrix = new float[rows][cols];\r
-\r
- temp = new float[3];\r
-\r
- rot = new float[3][3];\r
-\r
- }\r
-\r
-\r
-\r
- public void addElement(int i, int j, float value) {\r
-\r
- matrix[i][j] = value;\r
-\r
- }\r
-\r
-\r
-\r
- public void print() {\r
-\r
- System.out.println(matrix[0][0] + " " + matrix[0][1] + " " + matrix[0][2]);\r
-\r
- System.out.println(matrix[1][0] + " " + matrix[1][1] + " " + matrix[1][2]);\r
-\r
- System.out.println(matrix[2][0] + " " + matrix[2][1] + " " + matrix[2][2]);\r
-\r
- }\r
-\r
-\r
-\r
- public void rotate (float degrees, char axis) {\r
-\r
-\r
-\r
- float costheta = (float)Math.cos(degrees*Math.PI/(float)180.0);\r
-\r
- float sintheta = (float)Math.sin(degrees*Math.PI/(float)180.0);\r
-\r
-\r
-\r
- if (axis == 'z') {\r
-\r
-\r
-\r
- rot[0][0] = (float)costheta;\r
-\r
- rot[0][1] = (float)-sintheta;\r
-\r
- rot[0][2] = (float)0.0;\r
-\r
-\r
-\r
- rot[1][0] = (float)sintheta;\r
-\r
- rot[1][1] = (float)costheta;\r
-\r
- rot[1][2] = (float)0.0;\r
-\r
-\r
-\r
- rot[2][0] = (float)0.0;\r
-\r
- rot[2][1] = (float)0.0;\r
-\r
- rot[2][2] = (float)1.0;\r
-\r
-\r
-\r
- preMultiply(rot);\r
-\r
- }\r
-\r
- if (axis == 'x') {\r
-\r
- rot[0][0] = (float)1.0;\r
-\r
- rot[0][1] = (float)0.0;\r
-\r
- rot[0][2] = (float)0.0;\r
-\r
-\r
-\r
- rot[1][0] = (float)0.0;\r
-\r
- rot[1][1] = (float)costheta;\r
-\r
- rot[1][2] = (float)sintheta;\r
-\r
-\r
-\r
- rot[2][0] = (float)0.0;\r
-\r
- rot[2][1] = (float)-sintheta;\r
-\r
- rot[2][2] = (float)costheta;\r
-\r
-\r
-\r
- preMultiply(rot);\r
-\r
-\r
-\r
- }\r
-\r
- if (axis == 'y') {\r
-\r
- rot[0][0] = (float)costheta;\r
-\r
- rot[0][1] = (float)0.0;\r
-\r
- rot[0][2] = (float)-sintheta;\r
-\r
-\r
-\r
- rot[1][0] = (float)0.0;\r
-\r
- rot[1][1] = (float)1.0;\r
-\r
- rot[1][2] = (float)0.0;\r
-\r
-\r
-\r
- rot[2][0] = (float)sintheta;\r
-\r
- rot[2][1] = (float)0.0;\r
-\r
- rot[2][2] = (float)costheta;\r
-\r
-\r
-\r
- preMultiply(rot);\r
-\r
-\r
-\r
- }\r
-\r
-\r
-\r
- }\r
-\r
-\r
-\r
- public float[] vectorMultiply(float[] vect) {\r
-\r
- temp[0] = vect[0];\r
-\r
- temp[1] = vect[1];\r
-\r
- temp[2] = vect[2];\r
-\r
-\r
-\r
- for (int i = 0; i < 3; i++) {\r
-\r
- temp[i] = matrix[i][0]*vect[0] + matrix[i][1]*vect[1] + matrix[i][2]*vect[2];\r
-\r
- }\r
-\r
-\r
-\r
- vect[0] = temp[0];\r
-\r
- vect[1] = temp[1];\r
-\r
- vect[2] = temp[2];\r
-\r
-\r
-\r
- return vect;\r
-\r
- }\r
-\r
-\r
-\r
- public void preMultiply(float mat[][]) {\r
-\r
- float tmp[][] = new float[3][3];\r
-\r
-\r
-\r
- for (int i = 0; i < 3 ; i++) {\r
-\r
- for (int j = 0; j < 3; j++ ) {\r
-\r
- tmp[i][j] = mat[i][0]*matrix[0][j] +\r
-\r
- mat[i][1]*matrix[1][j] +\r
-\r
- mat[i][2]*matrix[2][j];\r
-\r
- }\r
-\r
- }\r
-\r
-\r
-\r
- for (int i = 0; i < 3 ; i++) {\r
-\r
- for (int j = 0; j < 3; j++ ) {\r
-\r
- matrix[i][j] = tmp[i][j];\r
-\r
- }\r
-\r
- }\r
-\r
- }\r
-\r
-\r
-\r
- public void postMultiply(float mat[][]) {\r
-\r
- float tmp[][] = new float[3][3];\r
-\r
-\r
-\r
- for (int i = 0; i < 3 ; i++) {\r
-\r
- for (int j = 0; j < 3; j++ ) {\r
-\r
- tmp[i][j] = matrix[i][0]*mat[0][j] +\r
-\r
- matrix[i][1]*mat[1][j] +\r
-\r
- matrix[i][2]*mat[2][j];\r
-\r
- }\r
-\r
- }\r
-\r
-\r
-\r
- for (int i = 0; i < 3 ; i++) {\r
-\r
- for (int j = 0; j < 3; j++ ) {\r
-\r
- matrix[i][j] = tmp[i][j];\r
-\r
- }\r
-\r
- }\r
-\r
- }\r
-\r
-\r
-\r
- public static void main(String[] args) {\r
-\r
-\r
-\r
- RotatableMatrix m = new RotatableMatrix(3,3);\r
-\r
- m.addElement(0,0,1);\r
-\r
- m.addElement(0,1,0);\r
-\r
- m.addElement(0,2,0);\r
-\r
- m.addElement(1,0,0);\r
-\r
- m.addElement(1,1,2);\r
-\r
- m.addElement(1,2,0);\r
-\r
- m.addElement(2,0,0);\r
-\r
- m.addElement(2,1,0);\r
-\r
- m.addElement(2,2,1);\r
-\r
-\r
-\r
- m.print();\r
-\r
-\r
-\r
- RotatableMatrix n = new RotatableMatrix(3,3);\r
-\r
- n.addElement(0,0,2);\r
-\r
- n.addElement(0,1,1);\r
-\r
- n.addElement(0,2,1);\r
-\r
- n.addElement(1,0,2);\r
-\r
- n.addElement(1,1,1);\r
-\r
- n.addElement(1,2,1);\r
-\r
- n.addElement(2,0,2);\r
-\r
- n.addElement(2,1,1);\r
-\r
- n.addElement(2,2,1);\r
-\r
-\r
-\r
- n.print();\r
-\r
-\r
-\r
- //m.postMultiply(n.matrix);\r
-\r
- //m.print();\r
-\r
- // m.rotate(45,'z',new RotatableMatrix(3,3));\r
-\r
-\r
-\r
- float vect[] = new float[3];\r
-\r
- vect[0] = 2;\r
-\r
- vect[1] = 4;\r
-\r
- vect[2] = 6;\r
-\r
-\r
-\r
- vect = m.vectorMultiply(vect);\r
-\r
- System.out.println(vect[0] + " " + vect[1] + " " + vect[2]);\r
-\r
-\r
-\r
- }\r
-\r
- public void setIdentity() {\r
-\r
- matrix[0][0] = (float)1.0;\r
-\r
- matrix[1][1] = (float)1.0;\r
-\r
- matrix[2][2] = (float)1.0;\r
-\r
- matrix[0][1] = (float)0.0;\r
-\r
- matrix[0][2] = (float)0.0;\r
-\r
- matrix[1][0] = (float)0.0;\r
-\r
- matrix[1][2] = (float) 0.0;\r
-\r
- matrix[2][0] = (float)0.0;\r
-\r
- matrix[2][1] = (float)0.0;\r
-\r
- }\r
-\r
-}\r
-\r
-\r
-\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview 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 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.math;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+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()
+ {
+ 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')
+ {
+ rot[0][0] = (float) costheta;
+
+ rot[0][1] = (float) -sintheta;
+
+ rot[0][2] = (float) 0.0;
+
+ rot[1][0] = (float) sintheta;
+
+ rot[1][1] = (float) costheta;
+
+ rot[1][2] = (float) 0.0;
+
+ rot[2][0] = (float) 0.0;
+
+ rot[2][1] = (float) 0.0;
+
+ rot[2][2] = (float) 1.0;
+
+ preMultiply(rot);
+ }
+
+ if (axis == 'x')
+ {
+ rot[0][0] = (float) 1.0;
+
+ rot[0][1] = (float) 0.0;
+
+ rot[0][2] = (float) 0.0;
+
+ rot[1][0] = (float) 0.0;
+
+ rot[1][1] = (float) costheta;
+
+ rot[1][2] = (float) sintheta;
+
+ rot[2][0] = (float) 0.0;
+
+ rot[2][1] = (float) -sintheta;
+
+ rot[2][2] = (float) costheta;
+
+ preMultiply(rot);
+ }
+
+ if (axis == 'y')
+ {
+ rot[0][0] = (float) costheta;
+
+ rot[0][1] = (float) 0.0;
+
+ rot[0][2] = (float) -sintheta;
+
+ rot[1][0] = (float) 0.0;
+
+ rot[1][1] = (float) 1.0;
+
+ rot[1][2] = (float) 0.0;
+
+ rot[2][0] = (float) sintheta;
+
+ rot[2][1] = (float) 0.0;
+
+ rot[2][2] = (float) costheta;
+
+ preMultiply(rot);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param vect
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public float[] vectorMultiply(float[] vect)
+ {
+ temp[0] = vect[0];
+
+ temp[1] = vect[1];
+
+ temp[2] = vect[2];
+
+ 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[0] = temp[0];
+
+ vect[1] = temp[1];
+
+ vect[2] = temp[2];
+
+ return vect;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param mat
+ * DOCUMENT ME!
+ */
+ public void preMultiply(float[][] mat)
+ {
+ 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];
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param mat
+ * DOCUMENT ME!
+ */
+ public void postMultiply(float[][] mat)
+ {
+ 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];
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args
+ * DOCUMENT ME!
+ */
+ public static void main(String[] args)
+ {
+ RotatableMatrix m = new RotatableMatrix(3, 3);
+
+ m.addElement(0, 0, 1);
+
+ m.addElement(0, 1, 0);
+
+ m.addElement(0, 2, 0);
+
+ m.addElement(1, 0, 0);
+
+ m.addElement(1, 1, 2);
+
+ m.addElement(1, 2, 0);
+
+ m.addElement(2, 0, 0);
+
+ m.addElement(2, 1, 0);
+
+ m.addElement(2, 2, 1);
+
+ m.print();
+
+ RotatableMatrix n = new RotatableMatrix(3, 3);
+
+ n.addElement(0, 0, 2);
+
+ n.addElement(0, 1, 1);
+
+ n.addElement(0, 2, 1);
+
+ n.addElement(1, 0, 2);
+
+ n.addElement(1, 1, 1);
+
+ n.addElement(1, 2, 1);
+
+ n.addElement(2, 0, 2);
+
+ n.addElement(2, 1, 1);
+
+ n.addElement(2, 2, 1);
+
+ n.print();
+
+ // m.postMultiply(n.matrix);
+ // m.print();
+ // m.rotate(45,'z',new RotatableMatrix(3,3));
+ float[] vect = new float[3];
+
+ vect[0] = 2;
+
+ vect[1] = 4;
+
+ vect[2] = 6;
+
+ vect = m.vectorMultiply(vect);
+
+ System.out.println(vect[0] + " " + vect[1] + " " + vect[2]);
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void setIdentity()
+ {
+ matrix[0][0] = (float) 1.0;
+
+ matrix[1][1] = (float) 1.0;
+
+ matrix[2][2] = (float) 1.0;
+
+ matrix[0][1] = (float) 0.0;
+
+ matrix[0][2] = (float) 0.0;
+
+ matrix[1][0] = (float) 0.0;
+
+ matrix[1][2] = (float) 0.0;
+
+ matrix[2][0] = (float) 0.0;
+
+ matrix[2][1] = (float) 0.0;
+ }
+}
git://source.jalview.org / jalview.git / blobdiff