From df165ead621c64f7c92cf3dc45060fa4983886bb Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Wed, 9 Jul 2014 20:37:08 +0000 Subject: [PATCH] in progress --- forester/java/src/org/forester/application/surfacing.java | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/forester/java/src/org/forester/application/surfacing.java b/forester/java/src/org/forester/application/surfacing.java index c5772d7..a05cac3 100644 --- a/forester/java/src/org/forester/application/surfacing.java +++ b/forester/java/src/org/forester/application/surfacing.java @@ -2192,7 +2192,10 @@ public class surfacing { System.out.println(); System.out.println(); System.out - .println( "Example: surfacing -p2g=pfam2go.txt -obo=go.obo -species_tree=tol_156.xml -last -detail=punctilious -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" ); + .println( "Example 1: surfacing -p2g=pfam2go.txt -obo=go.obo -species_tree=tol_156.xml -no_eo -ie=0.01 -dufs -genomes=genomes_all.txt -pos_filter=tf_1.txt -out_dir=_tf1 -o=tf1" ); +System.out.println(); + 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(); } } -- 1.7.10.2