From 47608e88e2f88eb5729d4eceb47af7e402495b27 Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Fri, 21 Jun 2013 22:21:51 +0000 Subject: [PATCH] inprogress --- .../java/src/org/forester/application/surfacing.java | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/forester/java/src/org/forester/application/surfacing.java b/forester/java/src/org/forester/application/surfacing.java index ce716fe..f15ea36 100644 --- a/forester/java/src/org/forester/application/surfacing.java +++ b/forester/java/src/org/forester/application/surfacing.java @@ -1020,8 +1020,8 @@ public class surfacing { } final String[][] input_file_properties = processInputGenomesFile( input_genomes_file ); for( final String[] input_file_propertie : input_file_properties ) { - for( int j = 0; j < input_file_propertie.length; j++ ) { - System.out.print( input_file_propertie[ j ] + " " ); + for( final String element : input_file_propertie ) { + System.out.print( element + " " ); } System.out.println(); } @@ -1710,7 +1710,7 @@ public class surfacing { BufferedWriter domains_per_potein_stats_writer = null; try { domains_per_potein_stats_writer = new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR - + output_file + "__domains_per_potein_stats.txt" ) ); + + output_file + "_domains_per_potein_stats.txt" ) ); domains_per_potein_stats_writer.write( "Genome" ); domains_per_potein_stats_writer.write( "\t" ); domains_per_potein_stats_writer.write( "Mean" ); @@ -2006,13 +2006,13 @@ public class surfacing { domains_per_potein_stats_writer.close(); printOutPercentageOfMultidomainProteins( all_genomes_domains_per_potein_histo, log_writer ); ForesterUtil.map2file( new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file - + "__all_genomes_domains_per_potein_histo.txt" ), all_genomes_domains_per_potein_histo, "\t", "\n" ); + + "_all_genomes_domains_per_potein_histo.txt" ), all_genomes_domains_per_potein_histo, "\t", "\n" ); ForesterUtil.collection2file( new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file - + "__domains_always_single_.txt" ), domains_which_are_always_single, "\n" ); + + "_domains_always_single_.txt" ), domains_which_are_always_single, "\n" ); ForesterUtil.collection2file( new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file - + "__domains_single_or_combined.txt" ), domains_which_are_sometimes_single_sometimes_not, "\n" ); + + "_domains_single_or_combined.txt" ), domains_which_are_sometimes_single_sometimes_not, "\n" ); ForesterUtil.collection2file( new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file - + "__domains_always_combined.txt" ), domains_which_never_single, "\n" ); + + "_domains_always_combined.txt" ), domains_which_never_single, "\n" ); ForesterUtil.programMessage( PRG_NAME, "Average of proteins with a least one domain assigned: " + ( 100 * protein_coverage_stats.arithmeticMean() ) + "% (+/-" -- 1.7.10.2