X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FMCMatrix.java;h=298fcc4c5a38ae961b0fc31ab466baed6072f8cd;hb=a45774ee31d9f35d4eff46d54d7deab719afb092;hp=4994573a0a83ec06bf2a7b624b434267e15c25d2;hpb=9b22c11a0e12a9320e41eca2cbcbe30f81eb1cb4;p=jalview.git

diff --git a/src/MCview/MCMatrix.java b/src/MCview/MCMatrix.java
index 4994573..298fcc4 100755
--- a/src/MCview/MCMatrix.java
+++ b/src/MCview/MCMatrix.java
@@ -1,143 +1,174 @@
-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];
-    }
-
-    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 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 
+ * 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/>.
+ */
+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;
+  }
+}