From e779d10d20ff0b7b7e3e95b39297e4d69fe5268b Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Tue, 11 Mar 2014 22:37:37 +0000 Subject: [PATCH] inprogress --- forester/java/src/org/forester/application/surfacing.java | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/forester/java/src/org/forester/application/surfacing.java b/forester/java/src/org/forester/application/surfacing.java index 847a8db..35346b1 100644 --- a/forester/java/src/org/forester/application/surfacing.java +++ b/forester/java/src/org/forester/application/surfacing.java @@ -2196,16 +2196,17 @@ 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: java -Xms128m -Xmx512m -cp path/to/forester.jar" - + " org.forester.application.surfacing p2g=pfam2go_2012_02_07.txt -dufs -cos=Pfam_260_NC1" + 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: java -Xms128m -Xmx512m -cp path/to/forester.jar" - + " org.forester.application.surfacing -detail=punctilious -o=TEST.html -pwc=TEST" + 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" ); + System.out.println(); } } -- 1.7.10.2