From 6c436b1b2252d9d0fb42856a5285def7858399e4 Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Wed, 28 Jan 2015 03:20:29 +0000 Subject: [PATCH] compactor work --- .../org/forester/application/msa_compactor.java | 20 ++++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/forester/java/src/org/forester/application/msa_compactor.java b/forester/java/src/org/forester/application/msa_compactor.java index 15c2d4c..daa6166 100644 --- a/forester/java/src/org/forester/application/msa_compactor.java +++ b/forester/java/src/org/forester/application/msa_compactor.java @@ -418,20 +418,20 @@ public class msa_compactor { WWW, ForesterUtil.getForesterLibraryInformation() ); System.out.println( "Input MSA : " + in ); - System.out.println( " MSA length : " + msa.getLength() ); - System.out.println( " Number of sequences : " + msa.getNumberOfSequences() ); - System.out.println( " Median sequence length : " + NF_1.format( initial_msa_stats.median() ) ); - System.out.println( " Mean sequence length : " + System.out.println( "MSA length : " + msa.getLength() ); + System.out.println( "Number of sequences : " + msa.getNumberOfSequences() ); + System.out.println( "Median sequence length : " + NF_1.format( initial_msa_stats.median() ) ); + System.out.println( "Mean sequence length : " + NF_1.format( initial_msa_stats.arithmeticMean() ) ); - System.out.println( " Max sequence length : " + ( ( int ) initial_msa_stats.getMax() ) ); - System.out.println( " Min sequence length : " + ( ( int ) initial_msa_stats.getMin() ) ); - System.out.println( " Gap ratio : " + System.out.println( "Max sequence length : " + ( ( int ) initial_msa_stats.getMax() ) ); + System.out.println( "Min sequence length : " + ( ( int ) initial_msa_stats.getMin() ) ); + System.out.println( "Gap ratio : " + NF_4.format( MsaMethods.calcGapRatio( msa ) ) ); - System.out.println( " Mean gap count per 100 residues : " + System.out.println( "Mean gap count per 100 residues : " + NF_1.format( MsaMethods.calcNumberOfGapsPer100Stats( msa ).arithmeticMean() ) ); - System.out.println( " Normalized Shannon Entropy (entn7) : " + System.out.println( "Normalized Shannon Entropy (entn7) : " + NF_4.format( MsaMethods.calcNormalizedShannonsEntropy( 7, msa ) ) ); - System.out.println( " Normalized Shannon Entropy (entn21): " + System.out.println( "Normalized Shannon Entropy (entn21): " + NF_4.format( MsaMethods.calcNormalizedShannonsEntropy( 21, msa ) ) ); } -- 1.7.10.2