X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FMCMatrix.java;h=e3ba289280f78423c9ead0f6bd4ec649306509f5;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=9eba8869655270cb914fe168f038c071d526c33d;hpb=dd74fc4938723fe5ec48d4e5fdcfbe58ac42a48d;p=jalview.git diff --git a/src/MCview/MCMatrix.java b/src/MCview/MCMatrix.java index 9eba886..e3ba289 100755 --- a/src/MCview/MCMatrix.java +++ b/src/MCview/MCMatrix.java @@ -1,171 +1,177 @@ -/* - * 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 MCview; - -public class MCMatrix -{ - float[][] matrix; - float[][] tmp; - float mycos; - float mysin; - float myconst = (float) (Math.PI / 180); - - public MCMatrix(int rows, int cols) - { - matrix = new float[rows][cols]; - tmp = new float[rows][cols]; - } - - public void addElement(int i, int j, float value) - { - matrix[i][j] = value; - } - - public void rotatex(float degrees) - { - mycos = (float) (Math.cos(degrees * myconst)); - mysin = (float) (Math.sin(degrees * myconst)); - - tmp[0][0] = 1; - tmp[0][1] = 0; - tmp[0][2] = 0; - tmp[1][0] = 0; - tmp[1][1] = mycos; - tmp[1][2] = mysin; - tmp[2][0] = 0; - tmp[2][1] = -mysin; - tmp[2][2] = mycos; - preMultiply(tmp); - } - - public void rotatez(float degrees) - { - mycos = (float) (Math.cos(degrees * myconst)); - mysin = (float) (Math.sin(degrees * myconst)); - - tmp[0][0] = mycos; - tmp[0][1] = -mysin; - tmp[0][2] = 0; - tmp[1][0] = mysin; - tmp[1][1] = mycos; - tmp[1][2] = 0; - tmp[2][0] = 0; - tmp[2][1] = 0; - tmp[2][2] = 1; - - preMultiply(tmp); - } - - public void rotatey(float degrees) - { - mycos = (float) (Math.cos(degrees * myconst)); - mysin = (float) (Math.sin(degrees * myconst)); - - tmp[0][0] = mycos; - tmp[0][1] = 0; - tmp[0][2] = -mysin; - tmp[1][0] = 0; - tmp[1][1] = 1; - tmp[1][2] = 0; - tmp[2][0] = mysin; - tmp[2][1] = 0; - tmp[2][2] = mycos; - - preMultiply(tmp); - } - - public float[] vectorMultiply(float[] vect) - { - float[] temp = new float[3]; - - temp[0] = vect[0]; - temp[1] = vect[1]; - temp[2] = vect[2]; - - for (int i = 0; i < 3; i++) - { - temp[i] = ( (float) matrix[i][0] * vect[0]) + - ( (float) matrix[i][1] * vect[1]) + - ( (float) matrix[i][2] * vect[2]); - } - - vect[0] = temp[0]; - vect[1] = temp[1]; - vect[2] = temp[2]; - - return vect; - } - - 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]; - } - } - } - - 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]; - } - } - } - - public void setIdentity() - { - matrix[0][0] = 1; - matrix[1][1] = 1; - matrix[2][2] = 1; - matrix[0][1] = 0; - matrix[0][2] = 0; - matrix[1][0] = 0; - matrix[1][2] = 0; - matrix[2][0] = 0; - matrix[2][1] = 0; - } -} +/* + * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ +package MCview; + +public class MCMatrix +{ + float[][] matrix; + + float[][] tmp; + + float mycos; + + float mysin; + + float myconst = (float) (Math.PI / 180); + + public MCMatrix(int rows, int cols) + { + matrix = new float[rows][cols]; + tmp = new float[rows][cols]; + } + + public void addElement(int i, int j, float value) + { + matrix[i][j] = value; + } + + public void rotatex(float degrees) + { + mycos = (float) (Math.cos(degrees * myconst)); + mysin = (float) (Math.sin(degrees * myconst)); + + tmp[0][0] = 1; + tmp[0][1] = 0; + tmp[0][2] = 0; + tmp[1][0] = 0; + tmp[1][1] = mycos; + tmp[1][2] = mysin; + tmp[2][0] = 0; + tmp[2][1] = -mysin; + tmp[2][2] = mycos; + preMultiply(tmp); + } + + public void rotatez(float degrees) + { + mycos = (float) (Math.cos(degrees * myconst)); + mysin = (float) (Math.sin(degrees * myconst)); + + tmp[0][0] = mycos; + tmp[0][1] = -mysin; + tmp[0][2] = 0; + tmp[1][0] = mysin; + tmp[1][1] = mycos; + tmp[1][2] = 0; + tmp[2][0] = 0; + tmp[2][1] = 0; + tmp[2][2] = 1; + + preMultiply(tmp); + } + + public void rotatey(float degrees) + { + mycos = (float) (Math.cos(degrees * myconst)); + mysin = (float) (Math.sin(degrees * myconst)); + + tmp[0][0] = mycos; + tmp[0][1] = 0; + tmp[0][2] = -mysin; + tmp[1][0] = 0; + tmp[1][1] = 1; + tmp[1][2] = 0; + tmp[2][0] = mysin; + tmp[2][1] = 0; + tmp[2][2] = mycos; + + preMultiply(tmp); + } + + public float[] vectorMultiply(float[] vect) + { + float[] temp = new float[3]; + + temp[0] = vect[0]; + temp[1] = vect[1]; + temp[2] = vect[2]; + + for (int i = 0; i < 3; i++) + { + temp[i] = ((float) matrix[i][0] * vect[0]) + + ((float) matrix[i][1] * vect[1]) + + ((float) matrix[i][2] * vect[2]); + } + + vect[0] = temp[0]; + vect[1] = temp[1]; + vect[2] = temp[2]; + + return vect; + } + + 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]; + } + } + } + + 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]; + } + } + } + + public void setIdentity() + { + matrix[0][0] = 1; + matrix[1][1] = 1; + matrix[2][2] = 1; + matrix[0][1] = 0; + matrix[0][2] = 0; + matrix[1][0] = 0; + matrix[1][2] = 0; + matrix[2][0] = 0; + matrix[2][1] = 0; + } +}