X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fmath%2FMatrix.java;h=036d16a6819c6416dd33f2fad3483c204f0a0622;hb=d14dc9ab689ddef65d7440facdc7b0dd512438ad;hp=b7f8705f2630c413e2f9940d22e070ad47d8e847;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git

diff --git a/src/jalview/math/Matrix.java b/src/jalview/math/Matrix.java
index b7f8705..036d16a 100755
--- a/src/jalview/math/Matrix.java
+++ b/src/jalview/math/Matrix.java
@@ -1,20 +1,22 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
  * 
- * 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 file is part of Jalview.
  * 
- * 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.
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.math;
 
@@ -48,14 +50,20 @@ public class Matrix
   public double[] e; // off diagonal
 
   /**
+   * maximum number of iterations for tqli
+   * 
+   */
+  int maxIter = 45; // fudge - add 15 iterations, just in case
+
+  /**
    * Creates a new Matrix object.
    * 
    * @param value
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param rows
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param cols
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public Matrix(double[][] value, int rows, int cols)
   {
@@ -88,7 +96,7 @@ public class Matrix
    * DOCUMENT ME!
    * 
    * @param ps
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void print(PrintStream ps)
   {
@@ -107,7 +115,7 @@ public class Matrix
    * DOCUMENT ME!
    * 
    * @param in
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    */
@@ -135,7 +143,7 @@ public class Matrix
    * DOCUMENT ME!
    * 
    * @param in
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    */
@@ -160,7 +168,7 @@ public class Matrix
    * DOCUMENT ME!
    * 
    * @param in
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    */
@@ -346,7 +354,7 @@ public class Matrix
   /**
    * DOCUMENT ME!
    */
-  public void tqli()
+  public void tqli() throws Exception
   {
     int n = rows;
 
@@ -393,10 +401,10 @@ public class Matrix
         {
           iter++;
 
-          if (iter == 30)
+          if (iter == maxIter)
           {
-            System.err.print("Too many iterations in tqli");
-            System.exit(0); // JBPNote - should this really be here ???
+            throw new Exception("Too many iterations in tqli (" + maxIter
+                    + ")");
           }
           else
           {
@@ -596,7 +604,7 @@ public class Matrix
   /**
    * DOCUMENT ME!
    */
-  public void tqli2()
+  public void tqli2() throws Exception
   {
     int n = rows;
 
@@ -643,10 +651,10 @@ public class Matrix
         {
           iter++;
 
-          if (iter == 30)
+          if (iter == maxIter)
           {
-            System.err.print("Too many iterations in tqli");
-            System.exit(0); // JBPNote - same as above - not a graceful exit!
+            throw new Exception("Too many iterations in tqli2 (max is "
+                    + maxIter + ")");
           }
           else
           {
@@ -708,9 +716,9 @@ public class Matrix
    * DOCUMENT ME!
    * 
    * @param a
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param b
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    */
@@ -730,7 +738,7 @@ public class Matrix
    * DOCUMENT ME!
    * 
    * @param n
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    */
@@ -750,7 +758,7 @@ public class Matrix
    * DOCUMENT ME!
    * 
    * @param ps
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void printD(PrintStream ps)
   {
@@ -764,7 +772,7 @@ public class Matrix
    * DOCUMENT ME!
    * 
    * @param ps
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void printE(PrintStream ps)
   {
@@ -778,9 +786,9 @@ public class Matrix
    * DOCUMENT ME!
    * 
    * @param args
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
-  public static void main(String[] args)
+  public static void main(String[] args) throws Exception
   {
     int n = Integer.parseInt(args[0]);
     double[][] in = new double[n][n];