inprogress

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

diff --git a/forester/java/src/org/forester/application/confadd.java b/forester/java/src/org/forester/application/confadd.java
index efccace..b48cde9 100644 (file)
--- a/forester/java/src/org/forester/application/confadd.java
+++ b/forester/java/src/org/forester/application/confadd.java
@@ -6,7 +6,7 @@
 // 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
@@ -16,13 +16,13 @@
 // 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.application;
 
@@ -33,6 +33,7 @@ import java.util.HashSet;
 import java.util.List;
 import java.util.Set;
 
+import org.forester.io.parsers.util.ParserUtils;
 import org.forester.io.writers.PhylogenyWriter;
 import org.forester.phylogeny.Phylogeny;
 import org.forester.phylogeny.PhylogenyNode;
@@ -54,11 +55,17 @@ public class confadd {
     final static private String PRG_NAME         = "confadd";
     final static private String PRG_VERSION      = "1.01";
     final static private String PRG_DATE         = "2010.10.26";
-    final static private String E_MAIL           = "czmasek@burnham.org";
+    final static private String E_MAIL           = "phylosoft@gmail.com";
     final static private String WWW              = "www.phylosoft.org/forester/";
 
     public static void main( final String args[] ) {
-        ForesterUtil.printProgramInformation( PRG_NAME, PRG_VERSION, PRG_DATE, E_MAIL, WWW );
+        ForesterUtil.printProgramInformation( PRG_NAME,
+                                              null,
+                                              PRG_VERSION,
+                                              PRG_DATE,
+                                              E_MAIL,
+                                              WWW,
+                                              ForesterUtil.getForesterLibraryInformation() );
         CommandLineArguments cla = null;
         try {
             cla = new CommandLineArguments( args );
@@ -145,11 +152,12 @@ public class confadd {
         Phylogeny[] evaluators = null;
         final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
         try {
-            targets = factory.create( target_file, ForesterUtil.createParserDependingOnFileType( target_file, true ) );
+            targets = factory.create( target_file, ParserUtils.createParserDependingOnFileType( target_file, true ) );
         }
         catch ( final IOException e ) {
-            ForesterUtil.fatalError( PRG_NAME, "failed to read target phylogenies from [" + target_file + "]: "
-                    + e.getLocalizedMessage() );
+            ForesterUtil.fatalError( PRG_NAME,
+                                     "failed to read target phylogenies from [" + target_file + "]: "
+                                             + e.getLocalizedMessage() );
         }
         int counter = 0;
         for( final Phylogeny target : targets ) {
@@ -168,8 +176,8 @@ public class confadd {
             ForesterUtil.programMessage( PRG_NAME, "read in a total of " + targets.length + " targets" );
         }
         try {
-            evaluators = factory.create( evaluators_file, ForesterUtil
-                    .createParserDependingOnFileType( evaluators_file, true ) );
+            evaluators = factory.create( evaluators_file,
+                                         ParserUtils.createParserDependingOnFileType( evaluators_file, true ) );
         }
         catch ( final IOException e ) {
             ForesterUtil.fatalError( PRG_NAME, "failed to read evaluator topologies from [" + evaluators_file + "]: "
@@ -196,7 +204,7 @@ public class confadd {
         }
         double value = 1;
         if ( norm > 0 ) {
-            value = norm / ( 1 + last - first );
+            value = norm / ( ( 1 + last ) - first );
         }
         ForesterUtil.programMessage( PRG_NAME, "first topology to use: " + first );
         String is_last = "";
@@ -204,7 +212,7 @@ public class confadd {
             is_last = " (corresponds to last topology in file)";
         }
         ForesterUtil.programMessage( PRG_NAME, "last topology to use : " + last + is_last );
-        ForesterUtil.programMessage( PRG_NAME, "sum of topologies used as evaluators: " + ( last - first + 1 ) );
+        ForesterUtil.programMessage( PRG_NAME, "sum of topologies used as evaluators: " + ( ( last - first ) + 1 ) );
         if ( norm > 0 ) {
             ForesterUtil.programMessage( PRG_NAME, "normalizer: " + norm + " (" + ForesterUtil.round( value, 6 ) + ")" );
         }