setVisible replaces show

[jalview.git] / src / MCview / MCMatrix.java

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