in progress...

[jalview.git] / forester / java / src / org / forester / application / gene_tree_preprocess.java

diff --git a/forester/java/src/org/forester/application/gene_tree_preprocess.java b/forester/java/src/org/forester/application/gene_tree_preprocess.java
index bcb93f4..581381c 100644 (file)
--- a/forester/java/src/org/forester/application/gene_tree_preprocess.java
+++ b/forester/java/src/org/forester/application/gene_tree_preprocess.java
@@ -21,7 +21,7 @@
 // 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.application;
 
@@ -73,7 +73,7 @@ public class gene_tree_preprocess {
                                          "failed to read phylogeny from [" + in + "]: " + e.getLocalizedMessage() );
             }
             final File outtree = new File( ForesterUtil.removeSuffix( in.toString() )
-                    + "_preprocessed_gene_tree.phylo.xml" );
+                                           + "_preprocessed_gene_tree.phylo.xml" );
             final File removed_nodes = new File( ForesterUtil.removeSuffix( in.toString() ) + "_removed_nodes.txt" );
             final File present_species = new File( ForesterUtil.removeSuffix( in.toString() ) + "_species_present.txt" );
             checkForOutputFileWriteability( outtree );
@@ -81,7 +81,7 @@ public class gene_tree_preprocess {
             checkForOutputFileWriteability( present_species );
             if ( phy.getNumberOfExternalNodes() < 2 ) {
                 ForesterUtil.fatalError( PRG_NAME, "phylogeny has " + phy.getNumberOfExternalNodes()
-                        + " external node(s), aborting" );
+                                         + " external node(s), aborting" );
             }
             final SortedSet<String> not_found = SequenceDbWsTools.obtainSeqInformation( phy,
                                                                                         true,