X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fmath%2FMatrix.java;h=b9c514a5e5eabf26b082dc423773b5d93640aeac;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=958fabe0087427619ed3c667006ecdf81fca5016;hpb=59d682209891099d46b960509907c79e3fb276fe;p=jalview.git

diff --git a/src/jalview/math/Matrix.java b/src/jalview/math/Matrix.java
index 958fabe..b9c514a 100755
--- a/src/jalview/math/Matrix.java
+++ b/src/jalview/math/Matrix.java
@@ -1,25 +1,29 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * 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.
+ * 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/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.math;
 
-import java.io.*;
+import jalview.util.Format;
+import jalview.util.MessageManager;
 
-import jalview.util.*;
+import java.io.PrintStream;
 
 /**
  * DOCUMENT ME!
@@ -47,6 +51,12 @@ 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
@@ -345,7 +355,7 @@ public class Matrix
   /**
    * DOCUMENT ME!
    */
-  public void tqli()
+  public void tqli() throws Exception
   {
     int n = rows;
 
@@ -392,10 +402,11 @@ 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(MessageManager.formatMessage(
+                    "exception.matrix_too_many_iteration", new String[] {
+                        "tqli", Integer.valueOf(maxIter).toString() }));
           }
           else
           {
@@ -595,7 +606,7 @@ public class Matrix
   /**
    * DOCUMENT ME!
    */
-  public void tqli2()
+  public void tqli2() throws Exception
   {
     int n = rows;
 
@@ -642,10 +653,11 @@ 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(MessageManager.formatMessage(
+                    "exception.matrix_too_many_iteration", new String[] {
+                        "tqli2", Integer.valueOf(maxIter).toString() }));
           }
           else
           {
@@ -779,7 +791,7 @@ public class Matrix
    * @param args
    *          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];