X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FMCMatrix.java;h=2effba666e674aa03434a4940c38df9d29411993;hb=ba0bffb2a7cda833ff1dd2691f756294402b48cd;hp=4994573a0a83ec06bf2a7b624b434267e15c25d2;hpb=9b22c11a0e12a9320e41eca2cbcbe30f81eb1cb4;p=jalview.git

diff --git a/src/MCview/MCMatrix.java b/src/MCview/MCMatrix.java
index 4994573..2effba6 100755
--- a/src/MCview/MCMatrix.java
+++ b/src/MCview/MCMatrix.java
@@ -1,143 +1,161 @@
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2005 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 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]);
-  }
-
-  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];
+    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];
     }
 
-    vect[0] = temp[0];
-    vect[1] = temp[1];
-    vect[2] = temp[2];
+    public void addElement(int i, int j, float value) {
+        matrix[i][j] = value;
+    }
 
-    return vect;
-  }
+    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]);
+    }
 
-  public void preMultiply(float mat[][]) {
-    float tmp[][]  = new float[3][3];
+    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);
+    }
 
-    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];
-      }
+    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);
     }
 
-    for (int i = 0; i < 3 ; i++) {
-      for (int j = 0; j < 3; j++ ) {
-        matrix[i][j] = tmp[i][j];
-      }
+    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 void postMultiply(float mat[][]) {
-    float tmp[][]  = new float[3][3];
+    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]);
+        }
 
-    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];
-      }
+        vect[0] = temp[0];
+        vect[1] = temp[1];
+        vect[2] = temp[2];
+
+        return vect;
     }
 
-    for (int i = 0; i < 3 ; i++) {
-      for (int j = 0; j < 3; j++ ) {
-        matrix[i][j] = tmp[i][j];
-      }
+    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 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;
-  }
-}
 
+    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;
+    }
+}