msa_props = mc.chart( step, realign, norm );
}
Chart.display( msa_props, initial_number_of_seqs, report_entropy, in.getName() );
+ System.out.println();
+ System.out.println( "Final MSA properties" );
+ printMsaInfo( msa, MsaMethods.calculateEffectiveLengthStatistics( msa ));
}
}
catch ( final IllegalArgumentException iae ) {
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 : "
+ printMsaInfo( msa, initial_msa_stats );
+ }
+
+ private static void printMsaInfo( DeleteableMsa msa, final DescriptiveStatistics msa_stats ) {
+ System.out.println( "MSA length : " + msa.getLength() );
+ System.out.println( "Number of sequences : " + msa.getNumberOfSequences() );
+ System.out.println( "Median sequence length : " + NF_1.format( msa_stats.median() ) );
+ System.out.println( "Mean sequence length : "
+ + NF_1.format( msa_stats.arithmeticMean() ) );
+ System.out.println( "Max sequence length : " + ( ( int ) msa_stats.getMax() ) );
+ System.out.println( "Min sequence length : " + ( ( int ) 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) : "
+ System.out.println( "Mean gap count per sequence : "
+ + NF_1.format( MsaMethods.calcNumberOfGapsStats( msa ).arithmeticMean() ) );
+ 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 ) ) );
}