From fd847171bd527f7e119f04145ce3abd8caa88803 Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Tue, 11 Mar 2014 23:04:39 +0000 Subject: [PATCH] inprogress --- forester/java/src/org/forester/application/surfacing.java | 10 +--------- 1 file changed, 1 insertion(+), 9 deletions(-) diff --git a/forester/java/src/org/forester/application/surfacing.java b/forester/java/src/org/forester/application/surfacing.java index 35346b1..7f66eca 100644 --- a/forester/java/src/org/forester/application/surfacing.java +++ b/forester/java/src/org/forester/application/surfacing.java @@ -2196,17 +2196,9 @@ public class surfacing { System.out.println( DA_ANALYSIS_OPTION + ": to perform DA analysis" ); System.out.println( PERFORM_DOMAIN_LENGTH_ANALYSIS_OPTION + ": to perform domain length analysis" ); System.out.println(); - System.out.println( "Example 1: surfacing -p2g=pfam2go_2012_02_07.txt -dufs -cos=Pfam_260_NC1" - + " -no_eo -mo=0 -genomes=eukaryotes.txt -out_dir=out -o=o " - + " -species_tree=tol.xml -obo=gene_ontology_2012_02_07.obo -pos_filter=f.txt -all_prot" ); - System.out.println(); - System.out.println( "Example 2: surfacing -detail=punctilious -o=TEST.html -pwc=TEST" - + " -cos=Pfam_ls_22_TC2 -p2g=pfam2go -obo=gene_ontology_edit.obo " - + "-dc_sort=dom -ignore_with_self -no_singles -ie=0.001 -mo=1 -no_eo -genomes=eukaryotes.txt " - + "-ds_output=detailed_html -scoring=domains -sort=alpha " ); System.out.println(); System.out - .println( "Example 3: surfacing -p2g=pfam2go_130621.txt -obo=gene_onotology_130621.obo -species_tree=tol_155.xml -last -detail=punctilious -ignore_viral_ids -no_eo -ie=1 -dufs -genomes=genomes_all.txt -pos_filter=tf_1.txt -all_prot -all_prot_e=1 -out_dir=_tf1_e1_ape1 -o=tf1_e1_ape1" ); + .println( "Example: surfacing -p2g=pfam2go_130621.txt -obo=gene_onotology_130621.obo -species_tree=tol_155.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" ); System.out.println(); } } -- 1.7.10.2