in progress...

[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 dbc4d50..7684899 100644 (file)
--- 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 );
@@ -135,8 +142,8 @@ public class confadd {
         }
         if ( ( first < 0 ) || ( last < 0 ) ) {
             ForesterUtil
-                    .fatalError( PRG_NAME,
-                                 "attempt to set first or last evaluator topology to use to a number less than zero" );
+            .fatalError( PRG_NAME,
+                         "attempt to set first or last evaluator topology to use to a number less than zero" );
         }
         if ( norm < 0 ) {
             ForesterUtil.fatalError( PRG_NAME, "illegal value for normalizer [" + norm + "]" );
@@ -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 + "]: "
@@ -193,11 +200,11 @@ public class confadd {
         }
         if ( ( last >= evaluators.length ) || ( last <= first ) ) {
             ForesterUtil.fatalError( PRG_NAME, "illegal value for first or last evaluator topology to use [" + first
-                    + ", " + last + "]" );
+                                     + ", " + last + "]" );
         }
         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 ) + ")" );
         }
@@ -237,17 +244,17 @@ public class confadd {
         System.out.println( "Usage:" );
         System.out.println();
         System.out.println( PRG_NAME
-                + " [options] <confidence type> <target tree file> <evaluators tree file> <outfile>" );
+                            + " [options] <confidence type> <target tree file> <evaluators tree file> <outfile>" );
         System.out.println();
         System.out.println( "options:" );
         System.out.println();
         System.out.println( " -" + STRICT_OPTION
-                + "    : strict [default: non-strict]: all nodes between 'target' and 'evaluators' must match" );
+                            + "    : strict [default: non-strict]: all nodes between 'target' and 'evaluators' must match" );
         System.out.println( " -" + NORMALIZE_OPTION
-                + "=<d>: normalize to this value (e.g. 100 for most bootstrap analyses) [default: no normalization]" );
+                            + "=<d>: normalize to this value (e.g. 100 for most bootstrap analyses) [default: no normalization]" );
         System.out.println( " -" + FIRST_OPTION + "=<i>: first evaluator topology to use (0-based) [default: 0]" );
         System.out.println( " -" + LAST_OPTION
-                + "=<i>: last evaluator topology to use (0-based) [default: use all until final topology]" );
+                            + "=<i>: last evaluator topology to use (0-based) [default: use all until final topology]" );
         System.out.println();
     }
 
@@ -258,7 +265,7 @@ public class confadd {
             final PhylogenyNode node = it.next();
             if ( ext_nodes.contains( node ) ) {
                 throw new IllegalArgumentException( "external node [" + node.toString() + "] of " + msg
-                        + " is not unique" );
+                                                    + " is not unique" );
             }
             ext_nodes.add( node );
         }