X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fapplication%2Fmsa_compactor.java;h=15c2d4c7e164cd1284fb9c41309bfd89d64a06bb;hb=02bf2b081aed88622e3279e816f0aeb45cba546e;hp=d48df0547d9ce0d29c32f393f9d3a0a0fe87acf5;hpb=10297bd8b8a4b4ab198a17a42fc6ff24ae2ed49b;p=jalview.git diff --git a/forester/java/src/org/forester/application/msa_compactor.java b/forester/java/src/org/forester/application/msa_compactor.java index d48df05..15c2d4c 100644 --- a/forester/java/src/org/forester/application/msa_compactor.java +++ b/forester/java/src/org/forester/application/msa_compactor.java @@ -46,6 +46,12 @@ import org.forester.util.CommandLineArguments; import org.forester.util.DescriptiveStatistics; import org.forester.util.ForesterUtil; + +/* +java -cp C:\Users\czmasek\SOFTWARE_DEV\ECLIPSE\forester\java\fo +rester.jar org.forester.application.msa_compactor Bcl-2_e1_20_mafft -t +*/ + public class msa_compactor { final private static NumberFormat NF_1 = new DecimalFormat( "0.#" ); @@ -61,6 +67,7 @@ public class msa_compactor { final static private String STEP_OPTION = "s"; final static private String LENGTH_OPTION = "l"; final static private String REALIGN_OPTION = "a"; + final static private String INFO_ONLY_OPTION = "i"; // final static private String STEP_FOR_DIAGNOSTICS_OPTION = "sd"; final static private String MIN_LENGTH_OPTION = "ml"; @@ -124,6 +131,7 @@ public class msa_compactor { allowed_options.add( OUTPUT_REMOVED_SEQS_OPTION ); allowed_options.add( MAFFT_OPTIONS ); allowed_options.add( PERFORM_PHYLOGENETIC_INFERENCE ); + allowed_options.add( INFO_ONLY_OPTION ); final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options ); if ( dissallowed_options.length() > 0 ) { ForesterUtil.fatalError( PRG_NAME, "unknown option(s): " + dissallowed_options ); @@ -137,6 +145,11 @@ public class msa_compactor { msa = DeleteableMsa.createInstance( GeneralMsaParser.parse( is ) ); } final DescriptiveStatistics initial_msa_stats = MsaMethods.calculateEffectiveLengthStatistics( msa ); + if (cla.isOptionSet( INFO_ONLY_OPTION ) ) { + printInfo( in, msa, initial_msa_stats ); + System.exit( 0 ); + } + final boolean chart_only = ( !cla.isOptionSet( LENGTH_OPTION ) ) && ( !cla.isOptionSet( REMOVE_WORST_OFFENDERS_OPTION ) ) && ( !cla.isOptionSet( AV_GAPINESS_OPTION ) && ( !cla.isOptionSet( MIN_LENGTH_OPTION ) ) ); @@ -284,31 +297,11 @@ public class msa_compactor { "step for diagnostics reports needs to be set to 1 for tree calculation" ); } } - 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( " Normalized Shannon Entropy (entn21): " - + NF_4.format( MsaMethods.calcNormalizedShannonsEntropy( 21, msa ) ) ); + printInfo( in, msa, initial_msa_stats ); if ( !chart_only ) { System.out.println( "Output : " + out ); } - else { - System.out.println( "Output : n/a" ); - } + if ( removed_seqs_out_base != null ) { System.out.println( "Write removed sequences to : " + removed_seqs_out_base ); } @@ -416,6 +409,32 @@ public class msa_compactor { } } + 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 ) ) ); + } + private static void checkPathToMafft( final String path_to_mafft ) { if ( !ForesterUtil.isEmpty( path_to_mafft ) && MsaInferrer.isInstalled( path_to_mafft ) ) { } @@ -448,10 +467,12 @@ public class msa_compactor { } System.out.println( "Usage:" ); System.out.println(); - System.out.println( PRG_NAME + " " ); + System.out.println( PRG_NAME + " [options] [output file base]" ); System.out.println(); System.out.println( " options: " ); System.out.println(); + System.out.println( " -" + INFO_ONLY_OPTION + + " to only display same basic information about the MSA" ); System.out.println( " -" + REMOVE_WORST_OFFENDERS_OPTION + "= number of worst offender sequences to remove" ); System.out.println( " -" + LENGTH_OPTION + "= target MSA length" );