-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2007 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
-package jalview.math;\r
-\r
-/**\r
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-public class RotatableMatrix\r
-{\r
- float[][] matrix;\r
- float[] temp;\r
- float[][] rot;\r
-\r
- /**\r
- * Creates a new RotatableMatrix object.\r
- *\r
- * @param rows DOCUMENT ME!\r
- * @param cols DOCUMENT ME!\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
- * DOCUMENT ME!\r
- *\r
- * @param i DOCUMENT ME!\r
- * @param j DOCUMENT ME!\r
- * @param value DOCUMENT ME!\r
- */\r
- public void addElement(int i, int j, float value)\r
- {\r
- matrix[i][j] = value;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- */\r
- public void print()\r
- {\r
- System.out.println(matrix[0][0] + " " + matrix[0][1] + " " +\r
- matrix[0][2]);\r
-\r
- System.out.println(matrix[1][0] + " " + matrix[1][1] + " " +\r
- matrix[1][2]);\r
-\r
- System.out.println(matrix[2][0] + " " + matrix[2][1] + " " +\r
- matrix[2][2]);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param degrees DOCUMENT ME!\r
- * @param axis DOCUMENT ME!\r
- */\r
- public void rotate(float degrees, char axis)\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
- if (axis == 'z')\r
- {\r
- rot[0][0] = (float) costheta;\r
-\r
- rot[0][1] = (float) - sintheta;\r
-\r
- rot[0][2] = (float) 0.0;\r
-\r
- rot[1][0] = (float) sintheta;\r
-\r
- rot[1][1] = (float) costheta;\r
-\r
- rot[1][2] = (float) 0.0;\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
- preMultiply(rot);\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
- rot[1][0] = (float) 0.0;\r
-\r
- rot[1][1] = (float) costheta;\r
-\r
- rot[1][2] = (float) sintheta;\r
-\r
- rot[2][0] = (float) 0.0;\r
-\r
- rot[2][1] = (float) - sintheta;\r
-\r
- rot[2][2] = (float) costheta;\r
-\r
- preMultiply(rot);\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
- rot[1][0] = (float) 0.0;\r
-\r
- rot[1][1] = (float) 1.0;\r
-\r
- rot[1][2] = (float) 0.0;\r
-\r
- rot[2][0] = (float) sintheta;\r
-\r
- rot[2][1] = (float) 0.0;\r
-\r
- rot[2][2] = (float) costheta;\r
-\r
- preMultiply(rot);\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param vect DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\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
- for (int i = 0; i < 3; i++)\r
- {\r
- temp[i] = (matrix[i][0] * vect[0]) + (matrix[i][1] * vect[1]) +\r
- (matrix[i][2] * vect[2]);\r
- }\r
-\r
- vect[0] = temp[0];\r
-\r
- vect[1] = temp[1];\r
-\r
- vect[2] = temp[2];\r
-\r
- return vect;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param mat DOCUMENT ME!\r
- */\r
- public void preMultiply(float[][] mat)\r
- {\r
- float[][] tmp = new float[3][3];\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
- (mat[i][1] * matrix[1][j]) + (mat[i][2] * matrix[2][j]);\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
- * DOCUMENT ME!\r
- *\r
- * @param mat DOCUMENT ME!\r
- */\r
- public void postMultiply(float[][] mat)\r
- {\r
- float[][] tmp = new float[3][3];\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
- (matrix[i][1] * mat[1][j]) + (matrix[i][2] * mat[2][j]);\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
- * DOCUMENT ME!\r
- *\r
- * @param args DOCUMENT ME!\r
- */\r
- public static void main(String[] args)\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
- m.print();\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
- n.print();\r
-\r
- //m.postMultiply(n.matrix);\r
- //m.print();\r
- // m.rotate(45,'z',new RotatableMatrix(3,3));\r
- float[] vect = new float[3];\r
-\r
- vect[0] = 2;\r
-\r
- vect[1] = 4;\r
-\r
- vect[2] = 6;\r
-\r
- vect = m.vectorMultiply(vect);\r
-\r
- System.out.println(vect[0] + " " + vect[1] + " " + vect[2]);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\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
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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;
+
+import jalview.datamodel.Point;
+
+import java.io.PrintStream;
+import java.util.HashMap;
+import java.util.Map;
+
+/**
+ * Model for a 3x3 matrix which provides methods for rotation in 3-D space
+ */
+public class RotatableMatrix
+{
+ private static final int DIMS = 3;
+
+ /*
+ * cache the most used rotations: +/- 1, 2, 3, 4 degrees around x or y axis
+ */
+ private static Map<Axis, Map<Float, float[][]>> cachedRotations;
+
+ static
+ {
+ cachedRotations = new HashMap<>();
+ for (Axis axis : Axis.values())
+ {
+ HashMap<Float, float[][]> map = new HashMap<>();
+ cachedRotations.put(axis, map);
+ for (int deg = 1; deg < 5; deg++)
+ {
+ float[][] rotation = getRotation(deg, axis);
+ map.put(Float.valueOf(deg), rotation);
+ rotation = getRotation(-deg, axis);
+ map.put(Float.valueOf(-deg), rotation);
+ }
+ }
+ }
+
+ public enum Axis
+ {
+ X, Y, Z
+ }
+
+ float[][] matrix;
+
+ /**
+ * Constructor creates a new identity matrix (all values zero except for 1 on
+ * the diagonal)
+ */
+ public RotatableMatrix()
+ {
+ matrix = new float[DIMS][DIMS];
+ for (int j = 0; j < DIMS; j++)
+ {
+ matrix[j][j] = 1f;
+ }
+ }
+
+ /**
+ * Sets the value at position (i, j) of the matrix
+ *
+ * @param i
+ * @param j
+ * @param value
+ */
+ public void setValue(int i, int j, float value)
+ {
+ matrix[i][j] = value;
+ }
+
+ /**
+ * Answers the value at position (i, j) of the matrix
+ *
+ * @param i
+ * @param j
+ * @return
+ */
+ public float getValue(int i, int j)
+ {
+ return matrix[i][j];
+ }
+
+ /**
+ * Prints the matrix in rows of space-delimited values
+ */
+ public void print(PrintStream ps)
+ {
+ ps.println(matrix[0][0] + " " + matrix[0][1] + " " + matrix[0][2]);
+ ps.println(matrix[1][0] + " " + matrix[1][1] + " " + matrix[1][2]);
+ ps.println(matrix[2][0] + " " + matrix[2][1] + " " + matrix[2][2]);
+ }
+
+ /**
+ * Rotates the matrix through the specified number of degrees around the
+ * specified axis
+ *
+ * @param degrees
+ * @param axis
+ */
+ public void rotate(float degrees, Axis axis)
+ {
+ float[][] rot = getRotation(degrees, axis);
+
+ preMultiply(rot);
+ }
+
+ /**
+ * Answers a matrix which, when it pre-multiplies another matrix, applies a
+ * rotation of the specified number of degrees around the specified axis
+ *
+ * @param degrees
+ * @param axis
+ * @return
+ * @see https://en.wikipedia.org/wiki/Rotation_matrix#Basic_rotations
+ */
+ protected static float[][] getRotation(float degrees, Axis axis)
+ {
+ Float floatValue = Float.valueOf(degrees);
+ if (cachedRotations.get(axis).containsKey(floatValue))
+ {
+ // jalview.bin.Console.outPrintln("getRotation from cache: " + (int) degrees);
+ return cachedRotations.get(axis).get(floatValue);
+ }
+
+ float costheta = (float) Math.cos(degrees * Math.PI / 180f);
+
+ float sintheta = (float) Math.sin(degrees * Math.PI / 180f);
+
+ float[][] rot = new float[DIMS][DIMS];
+
+ switch (axis)
+ {
+ case X:
+ rot[0][0] = 1f;
+ rot[1][1] = costheta;
+ rot[1][2] = sintheta;
+ rot[2][1] = -sintheta;
+ rot[2][2] = costheta;
+ break;
+ case Y:
+ rot[0][0] = costheta;
+ rot[0][2] = -sintheta;
+ rot[1][1] = 1f;
+ rot[2][0] = sintheta;
+ rot[2][2] = costheta;
+ break;
+ case Z:
+ rot[0][0] = costheta;
+ rot[0][1] = -sintheta;
+ rot[1][0] = sintheta;
+ rot[1][1] = costheta;
+ rot[2][2] = 1f;
+ break;
+ }
+ return rot;
+ }
+
+ /**
+ * Answers a new array of float values which is the result of pre-multiplying
+ * this matrix by the given vector. Each value of the result is the dot
+ * product of the vector with one column of this matrix. The matrix and input
+ * vector are not modified.
+ *
+ * @param vect
+ *
+ * @return
+ */
+ public float[] vectorMultiply(float[] vect)
+ {
+ float[] result = new float[DIMS];
+
+ for (int i = 0; i < DIMS; i++)
+ {
+ result[i] = (matrix[i][0] * vect[0]) + (matrix[i][1] * vect[1])
+ + (matrix[i][2] * vect[2]);
+ }
+
+ return result;
+ }
+
+ /**
+ * Performs pre-multiplication of this matrix by the given one. Value (i, j)
+ * of the result is the dot product of the i'th row of <code>mat</code> with
+ * the j'th column of this matrix.
+ *
+ * @param mat
+ */
+ public void preMultiply(float[][] mat)
+ {
+ float[][] tmp = new float[DIMS][DIMS];
+
+ for (int i = 0; i < DIMS; i++)
+ {
+ for (int j = 0; j < DIMS; j++)
+ {
+ tmp[i][j] = (mat[i][0] * matrix[0][j]) + (mat[i][1] * matrix[1][j])
+ + (mat[i][2] * matrix[2][j]);
+ }
+ }
+
+ matrix = tmp;
+ }
+
+ /**
+ * Performs post-multiplication of this matrix by the given one. Value (i, j)
+ * of the result is the dot product of the i'th row of this matrix with the
+ * j'th column of <code>mat</code>.
+ *
+ * @param mat
+ */
+ public void postMultiply(float[][] mat)
+ {
+ float[][] tmp = new float[DIMS][DIMS];
+
+ for (int i = 0; i < DIMS; i++)
+ {
+ for (int j = 0; j < DIMS; j++)
+ {
+ tmp[i][j] = (matrix[i][0] * mat[0][j]) + (matrix[i][1] * mat[1][j])
+ + (matrix[i][2] * mat[2][j]);
+ }
+ }
+
+ matrix = tmp;
+ }
+
+ /**
+ * Performs a vector multiplication whose result is the Point representing the
+ * input point's value vector post-multiplied by this matrix.
+ *
+ * @param coord
+ * @return
+ */
+ public Point vectorMultiply(Point coord)
+ {
+ float[] v = vectorMultiply(new float[] { coord.x, coord.y, coord.z });
+ return new Point(v[0], v[1], v[2]);
+ }
+}
git://source.jalview.org / jalview.git / blobdiff