X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fdevelopment%2FDevelopmentTools.java;h=9c26d2cf8c4ba9ec0c68ab15eaf43b7c15121063;hb=b5fe992f707cdad84255eb85040effbee97d61b3;hp=d41194a7fe3e67526a188d0023f5219ca0494893;hpb=eccc2fdb674f76be1815fd7984295661bff8a2be;p=jalview.git

diff --git a/forester/java/src/org/forester/development/DevelopmentTools.java b/forester/java/src/org/forester/development/DevelopmentTools.java
index d41194a..9c26d2c 100644
--- a/forester/java/src/org/forester/development/DevelopmentTools.java
+++ b/forester/java/src/org/forester/development/DevelopmentTools.java
@@ -5,7 +5,7 @@
 // Copyright (C) 2008-2009 Christian M. Zmasek
 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
 // All rights reserved
-// 
+//
 // This library is free software; you can redistribute it and/or
 // modify it under the terms of the GNU Lesser General Public
 // License as published by the Free Software Foundation; either
@@ -15,18 +15,19 @@
 // but WITHOUT ANY WARRANTY; without even the implied warranty of
 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
 // Lesser General Public License for more details.
-// 
+//
 // You should have received a copy of the GNU Lesser General Public
 // License along with this library; if not, write to the Free Software
 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
 //
 // Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
 
 package org.forester.development;
 
 import java.util.Random;
 
+import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
 import org.forester.phylogeny.Phylogeny;
 import org.forester.phylogeny.PhylogenyMethods;
 import org.forester.phylogeny.PhylogenyNode;
@@ -35,7 +36,7 @@ public final class DevelopmentTools {
 
     /**
      * Creates a completely unbalanced Phylogeny with i external nodes.
-     * 
+     *
      * @return a newly created unbalanced Phylogeny
      */
     // public static Phylogeny createUnbalancedTree( int i ) {
@@ -45,7 +46,7 @@ public final class DevelopmentTools {
     // try {
     // PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
     // t1 = factory.create( ":S=", new SimpleNHXParser() );
-    //            
+    //
     // t1.setRooted( true );
     //
     // for ( int j = 1; j < i; ++j ) {
@@ -70,7 +71,7 @@ public final class DevelopmentTools {
     /**
      * Creates a completely balanced rooted phylogeny with a given number of levels and
      * children per node.
-     * 
+     *
      * @param levels
      * @param children_per_node
      * @return a completely balanced rooted phylogeny
@@ -133,7 +134,12 @@ public final class DevelopmentTools {
         PhylogenyNode n = t.getFirstExternalNode();
         int j = t.getRoot().getNumberOfExternalNodes();
         while ( n != null ) {
-            PhylogenyMethods.setTaxonomyCode( n, j + "" );
+            try {
+                PhylogenyMethods.setTaxonomyCode( n, j + "" );
+            }
+            catch ( final PhyloXmlDataFormatException e ) {
+                e.printStackTrace();
+            }
             j--;
             n = n.getNextExternalNode();
         }
@@ -159,7 +165,7 @@ public final class DevelopmentTools {
     /**
      * Sets the species names of the external Nodes of Phylogeny t to a random
      * positive integer number between (and including) min and max.
-     * 
+     *
      * @param t
      *            whose external species names are to be randomized
      * @param min
@@ -176,8 +182,13 @@ public final class DevelopmentTools {
         final Random r = new Random();
         PhylogenyNode n = t.getFirstExternalNode();
         while ( n != null ) {
-            final String code = ( ( Math.abs( r.nextInt() ) % ( ma - mi + 1 ) ) + mi ) + "";
-            PhylogenyMethods.setTaxonomyCode( n, code );
+            final String code = ( ( Math.abs( r.nextInt() ) % ( ( ma - mi ) + 1 ) ) + mi ) + "";
+            try {
+                PhylogenyMethods.setTaxonomyCode( n, code );
+            }
+            catch ( final PhyloXmlDataFormatException e ) {
+                e.printStackTrace();
+            }
             n = n.getNextExternalNode();
         }
     }