X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FMCMatrix.java;h=9eba8869655270cb914fe168f038c071d526c33d;hb=f95c61a93c12747921e69910e769b1ac308ddf4a;hp=4994573a0a83ec06bf2a7b624b434267e15c25d2;hpb=9b22c11a0e12a9320e41eca2cbcbe30f81eb1cb4;p=jalview.git

diff --git a/src/MCview/MCMatrix.java b/src/MCview/MCMatrix.java
index 4994573..9eba886 100755
--- a/src/MCview/MCMatrix.java
+++ b/src/MCview/MCMatrix.java
@@ -1,31 +1,46 @@
+/*
+ * 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[][];
-
+public class MCMatrix
+{
+  float[][] matrix;
+  float[][] tmp;
   float mycos;
   float mysin;
-  float myconst = (float)(Math.PI/180);
+  float myconst = (float) (Math.PI / 180);
 
-  public MCMatrix(int rows, int cols) {
+  public MCMatrix(int rows, int cols)
+  {
     matrix = new float[rows][cols];
-    tmp    = new float[rows][cols];
+    tmp = new float[rows][cols];
   }
 
-  public void addElement(int i, int j, float value) {
+  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));
+  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;
@@ -39,9 +54,10 @@ public class MCMatrix {
     preMultiply(tmp);
   }
 
-  public void rotatez(float degrees) {
-    mycos = (float)(Math.cos(degrees*myconst));
-    mysin = (float)(Math.sin(degrees*myconst));
+  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;
@@ -56,9 +72,10 @@ public class MCMatrix {
     preMultiply(tmp);
   }
 
-  public void rotatey(float degrees) {
-    mycos = (float)(Math.cos(degrees*myconst));
-    mysin = (float)(Math.sin(degrees*myconst));
+  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;
@@ -73,15 +90,19 @@ public class MCMatrix {
     preMultiply(tmp);
   }
 
-  public float[] vectorMultiply(float[] vect) {
-    float temp[] = new float[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++)
+    {
+      temp[i] = ( (float) matrix[i][0] * vect[0]) +
+          ( (float) matrix[i][1] * vect[1]) +
+          ( (float) matrix[i][2] * vect[2]);
     }
 
     vect[0] = temp[0];
@@ -91,43 +112,52 @@ public class MCMatrix {
     return vect;
   }
 
-  public void preMultiply(float mat[][]) {
-    float tmp[][]  = new float[3][3];
+  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++)
+      {
+        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++ ) {
+    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];
+  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++)
+      {
+        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++ ) {
+    for (int i = 0; i < 3; i++)
+    {
+      for (int j = 0; j < 3; j++)
+      {
         matrix[i][j] = tmp[i][j];
       }
     }
   }
 
-  public void setIdentity() {
+  public void setIdentity()
+  {
     matrix[0][0] = 1;
     matrix[1][1] = 1;
     matrix[2][2] = 1;
@@ -139,5 +169,3 @@ public class MCMatrix {
     matrix[2][1] = 0;
   }
 }
-
-