X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fapplication%2Fcount_support.java;h=e094f69ed4313b6948f5cd4fdfb8e8968a7243c5;hb=e47fb4d682262076a44ebb802276ae237ed4cf96;hp=67dfc1b83bcd3ace363da5e16b282ee242097d1b;hpb=493e40b0c936b65da342134da37e8b856b9b80af;p=jalview.git

diff --git a/forester/java/src/org/forester/application/count_support.java b/forester/java/src/org/forester/application/count_support.java
index 67dfc1b..e094f69 100644
--- a/forester/java/src/org/forester/application/count_support.java
+++ b/forester/java/src/org/forester/application/count_support.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
@@ -15,7 +15,7 @@
 // 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
@@ -108,8 +108,8 @@ public class count_support {
             p = factory.create( phylogeny_infile, pp )[ 0 ];
         }
         catch ( final Exception e ) {
-            ForesterUtil.fatalError( count_support.PRG_NAME, "Could not read \"" + phylogeny_infile + "\" ["
-                    + e.getMessage() + "]" );
+            ForesterUtil.fatalError( count_support.PRG_NAME,
+                                     "Could not read \"" + phylogeny_infile + "\" [" + e.getMessage() + "]" );
         }
         try {
             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
@@ -117,8 +117,8 @@ public class count_support {
             ev = factory.create( evaluators_infile, pp );
         }
         catch ( final Exception e ) {
-            ForesterUtil.fatalError( count_support.PRG_NAME, "Could not read \"" + evaluators_infile + "\" ["
-                    + e.getMessage() + "]" );
+            ForesterUtil.fatalError( count_support.PRG_NAME,
+                                     "Could not read \"" + evaluators_infile + "\" [" + e.getMessage() + "]" );
         }
         boolean strip = false;
         if ( cla.isOptionSet( "s" ) ) {
@@ -187,8 +187,9 @@ public class count_support {
                 else {
                     System.out.println( "Writing " + ev.length + " evaluator phylogenies to :" + evaluators_outfile );
                     if ( count_support.WRITE_EVALUATORS_AS_NHX ) {
-                        w.toNewHampshireX( Arrays.asList( ev ), evaluators_outfile, ";"
-                                + ForesterUtil.getLineSeparator() );
+                        w.toNewHampshireX( Arrays.asList( ev ),
+                                           evaluators_outfile,
+                                           ";" + ForesterUtil.getLineSeparator() );
                     }
                     else {
                         w.toNewHampshire( Arrays.asList( ev ), true, branch_lengths_in_ev_out, evaluators_outfile, ";"