From 2adeeb19652f83aa4f9deef48e420106d914fe56 Mon Sep 17 00:00:00 2001 From: cmzmasek Date: Tue, 28 Mar 2017 21:08:51 -0700 Subject: [PATCH] in progress --- forester/java/src/org/forester/application/surfacing.java | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/forester/java/src/org/forester/application/surfacing.java b/forester/java/src/org/forester/application/surfacing.java index c7319e0..c8ea6d3 100644 --- a/forester/java/src/org/forester/application/surfacing.java +++ b/forester/java/src/org/forester/application/surfacing.java @@ -2212,7 +2212,7 @@ public class surfacing { ForesterUtil.programMessage( PRG_NAME, surfacing.WWW ); ForesterUtil .programMessage( PRG_NAME, - "[next step for phylogenomic analysis pipeline (example, in \"DAS\" dir): % mse.rb .prot . FL_seqs DA_seqs ../../genome_locations.txt]" ); + "[next step for phylogenomic analysis pipeline (example, in \"DAS\" dir): % mse.rb .prot . FL_seqs DA_seqs path/to/genome_locations.txt]" ); ForesterUtil.programMessage( PRG_NAME, "OK" ); System.out.println(); } @@ -2308,5 +2308,11 @@ public class surfacing { System.out .println( "Example 2: surfacing -p2g=pfam2go.txt -obo=go.obo -species_tree=tol_156.xml -last -ignore_viral_ids -no_eo -ie=0.1 -dufs -genomes=genomes_all.txt -pos_filter=tf_1.txt -all_prot -all_prot_e=0.1 -out_dir=_tf1_e01_ape01 -o=tf1_e01_ape01" ); System.out.println(); + System.out + .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]" ); + System.out.println(); } } -- 1.7.10.2