X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fapplication%2Fconfadd.java;h=b48cde9f84b19b4eba9eda218a3c8306f2a9aae0;hb=c2f18ef75d93bcf32df987ba5a817150b73ad93e;hp=dbc4d507e46ae80d0b5da8d5c272bff050531e8c;hpb=eee996a6476a1e3d84c07f8f690dcde3ff4b2ef5;p=jalview.git

diff --git a/forester/java/src/org/forester/application/confadd.java b/forester/java/src/org/forester/application/confadd.java
index dbc4d50..b48cde9 100644
--- a/forester/java/src/org/forester/application/confadd.java
+++ b/forester/java/src/org/forester/application/confadd.java
@@ -22,7 +22,7 @@
 // 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;
 
@@ -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 );
@@ -145,7 +152,7 @@ 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,
@@ -170,7 +177,7 @@ public class confadd {
         }
         try {
             evaluators = factory.create( evaluators_file,
-                                         ForesterUtil.createParserDependingOnFileType( evaluators_file, true ) );
+                                         ParserUtils.createParserDependingOnFileType( evaluators_file, true ) );
         }
         catch ( final IOException e ) {
             ForesterUtil.fatalError( PRG_NAME, "failed to read evaluator topologies from [" + evaluators_file + "]: "
@@ -197,7 +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 = "";
@@ -205,7 +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 ) + ")" );
         }