+ private static void printInfo( final File in, DeleteableMsa msa, final DescriptiveStatistics initial_msa_stats ) {
+ ForesterUtil.printProgramInformation( PRG_NAME,
+ PRG_DESC,
+ PRG_VERSION,
+ PRG_DATE,
+ E_MAIL,
+ 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 : "
+ + 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 : "
+ + NF_4.format( MsaMethods.calcGapRatio( msa ) ) );
+ System.out.println( " Mean gap count per 100 residues : "
+ + NF_1.format( MsaMethods.calcNumberOfGapsPer100Stats( msa ).arithmeticMean() ) );
+ System.out.println( " Normalized Shannon Entropy (entn7) : "
+ + NF_4.format( MsaMethods.calcNormalizedShannonsEntropy( 7, msa ) ) );
+ System.out.println( " Normalized Shannon Entropy (entn21): "
+ + NF_4.format( MsaMethods.calcNormalizedShannonsEntropy( 21, msa ) ) );
+ }
+