/*
- * 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;
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)
{
* DOCUMENT ME!
*
* @param ps
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void print(PrintStream ps)
{
* DOCUMENT ME!
*
* @param in
- * DOCUMENT ME!
+ * DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
* DOCUMENT ME!
*
* @param in
- * DOCUMENT ME!
+ * DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
* DOCUMENT ME!
*
* @param in
- * DOCUMENT ME!
+ * DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
/**
* DOCUMENT ME!
*/
- public void tqli()
+ public void tqli() throws Exception
{
int n = rows;
{
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
{
/**
* DOCUMENT ME!
*/
- public void tqli2()
+ public void tqli2() throws Exception
{
int n = rows;
{
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
{
* DOCUMENT ME!
*
* @param a
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param b
- * DOCUMENT ME!
+ * DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
* DOCUMENT ME!
*
* @param n
- * DOCUMENT ME!
+ * DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
* DOCUMENT ME!
*
* @param ps
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void printD(PrintStream ps)
{
* DOCUMENT ME!
*
* @param ps
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void printE(PrintStream ps)
{
* 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];