in progress...

diff --git a/forester/java/src/org/forester/application/fasta_split.java b/forester/java/src/org/forester/application/fasta_split.java
index 16999c7..f71d0a1 100644 (file)
--- a/forester/java/src/org/forester/application/fasta_split.java
+++ b/forester/java/src/org/forester/application/fasta_split.java
@@ -51,7 +51,7 @@ public final class fasta_split {
 
     final static private String PRG_NAME    = "fasta_split";
     final static private String PRG_VERSION = "1.00";
-    final static private String PRG_DATE    = "150331";
+    final static private String PRG_DATE    = "170516";
 
     public static void main( final String args[] ) {
         ForesterUtil.printProgramInformation( fasta_split.PRG_NAME, fasta_split.PRG_VERSION, fasta_split.PRG_DATE );
@@ -98,9 +98,8 @@ public final class fasta_split {
         }
         System.out.println( "Read " + seqs.size() + " sequences" );
         final Map<String, List<MolecularSequence>> output = new HashMap<String, List<MolecularSequence>>();
-        int cc = 0;
+    
         for( final MolecularSequence seq : seqs ) {
-            ++cc;
             final Matcher m = pa.matcher( seq.getIdentifier() );
             if ( m.find() ) {
                 final String key = m.group( 1 );
@@ -139,7 +138,10 @@ public final class fasta_split {
 
     private static void argumentsError() {
         System.out.println( PRG_NAME + " <pattern> <infile> <outdir>" );
-        System.out.println( "Example: " + PRG_NAME + " \"v-germ=(\\S+)\" tt.fasta outdir" );
+        System.out.println();
+        System.out.println( "Examples: " );
+        System.out.println( "  " + PRG_NAME + " \"v-germ=(\\S+)\" tt.fasta outdir" );
+        System.out.println( "  " + PRG_NAME + " \"(\\S+?)\\|\" seqs.fasta outdir" );
         System.out.println();
         System.exit( -1 );
     }

diff --git a/forester/java/src/org/forester/application/surfacing.java b/forester/java/src/org/forester/application/surfacing.java
index 9326929..fc87a96 100644 (file)
--- a/forester/java/src/org/forester/application/surfacing.java
+++ b/forester/java/src/org/forester/application/surfacing.java
@@ -217,8 +217,8 @@ public class surfacing {
     final static private String                                     INPUT_GENOMES_FILE_OPTION                                                     = "genomes";
     final static private String                                     INPUT_SPECIES_TREE_OPTION                                                     = "species_tree";
     final static private String                                     SEQ_EXTRACT_OPTION                                                            = "prot_extract";
-    final static private String                                     PRG_VERSION                                                                   = "2.502";
-    final static private String                                     PRG_DATE                                                                      = "170511";
+    final static private String                                     PRG_VERSION                                                                   = "2.503";
+    final static private String                                     PRG_DATE                                                                      = "170518";
     final static private String                                     E_MAIL                                                                        = "phyloxml@gmail.com";
     final static private String                                     WWW                                                                           = "https://sites.google.com/site/cmzmasek/home/software/forester/surfacing";
     final static private boolean                                    IGNORE_DUFS_DEFAULT                                                           = true;
@@ -1776,7 +1776,7 @@ public class surfacing {
         ForesterUtil
                 .programMessage( PRG_NAME,
                                  "Wrote domain promiscuities to: " + per_genome_domain_promiscuity_statistics_file );
-        final int LEVEL = 2;
+        final int LEVEL = 0;
         try {
             MinimalDomainomeCalculator.calc( false,
                                              intrees[ 0 ],
@@ -2315,7 +2315,7 @@ public class surfacing {
                 .println( "Example 3: surfacing -species_tree=master_tree.xml -no_eo -ie=1e-6 -mrel=0.5 -mo=10 -dufs -genomes=genomes.txt -out_dir=a605 -o=a605" );
         System.out.println();
         System.out
-        .println("[next step for phylogenomic analysis pipeline (example, in \"DAS\" dir): % mse.rb .prot . FL_seqs DA_seqs path/to/genome_locations.txt]" );
+                .println( "[next step for phylogenomic analysis pipeline (example, in \"DAS\" dir): % mse.rb .prot . FL_seqs DA_seqs path/to/genome_locations.txt]" );
         System.out.println();
     }
 }

diff --git a/forester/java/src/org/forester/surfacing/MinimalDomainomeCalculator.java b/forester/java/src/org/forester/surfacing/MinimalDomainomeCalculator.java
index d48cc2b..0c9ca73 100644 (file)
--- a/forester/java/src/org/forester/surfacing/MinimalDomainomeCalculator.java
+++ b/forester/java/src/org/forester/surfacing/MinimalDomainomeCalculator.java
@@ -85,7 +85,7 @@ public final class MinimalDomainomeCalculator {
             final String rank = node.getNodeData().isHasTaxonomy() ? node.getNodeData().getTaxonomy().getRank() : "";
             final List<PhylogenyNode> external_descs = node.getAllExternalDescendants();
             if ( ( target_level < 1 ) || ( node_level >= target_level ) ) {
-                out.write( species_name + " " + node_level);
+                out.write( species_name );
                 if ( !ForesterUtil.isEmpty( common ) ) {
                     out.write( "\t" + common );
                 }