import java.text.DecimalFormat;
import java.util.ArrayList;
import java.util.List;
+import java.util.SortedMap;
+import java.util.regex.Pattern;
+import java.util.regex.PatternSyntaxException;
import org.forester.clade_analysis.AnalysisMulti;
-import org.forester.clade_analysis.AnalysisSingle;
import org.forester.clade_analysis.Prefix;
import org.forester.clade_analysis.ResultMulti;
-import org.forester.clade_analysis.ResultSingle;
import org.forester.io.parsers.PhylogenyParser;
import org.forester.io.parsers.util.ParserUtils;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
import org.forester.phylogeny.factories.PhylogenyFactory;
+import org.forester.util.BasicTable;
+import org.forester.util.BasicTableParser;
import org.forester.util.CommandLineArguments;
+import org.forester.util.EasyWriter;
import org.forester.util.ForesterUtil;
+import org.forester.util.UserException;
public final class cladinator {
- final static private String PRG_NAME = "cladinator";
- final static private String PRG_VERSION = "0.100";
- final static private String PRG_DATE = "170823";
- final static private String PRG_DESC = "clades within clades -- analysis of pplacer type outputs";
- final static private String E_MAIL = "phyloxml@gmail.com";
- final static private String WWW = "https://sites.google.com/site/cmzmasek/home/software/forester";
- final static private String HELP_OPTION_1 = "help";
- final static private String HELP_OPTION_2 = "h";
- final static private String SEP_OPTION = "s";
- private final static DecimalFormat df2 = new DecimalFormat( "0.0#" );
+ final static private String PRG_NAME = "cladinator";
+ final static private String PRG_VERSION = "1.04";
+ final static private String PRG_DATE = "170915";
+ final static private String PRG_DESC = "clades within clades of annotated labels -- analysis of pplacer-type outputs";
+ final static private String E_MAIL = "phyloxml@gmail.com";
+ final static private String WWW = "https://sites.google.com/site/cmzmasek/home/software/forester";
+ final static private String HELP_OPTION_1 = "help";
+ final static private String HELP_OPTION_2 = "h";
+ final static private String SEP_OPTION = "s";
+ final static private String QUERY_PATTERN_OPTION = "q";
+ final static private String SPECIFICS_CUTOFF_OPTION = "c";
+ final static private String MAPPING_FILE_OPTION = "m";
+ final static private String EXTRA_PROCESSING_OPTION1 = "x";
+ final static private String EXTRA_PROCESSING1_SEP_OPTION = "xs";
+ final static private String EXTRA_PROCESSING1_KEEP_EXTRA_OPTION = "xk";
+ final static private String QUIET_OPTION = "Q";
+ final static private String VERBOSE_OPTION = "v";
+ final static private double SPECIFICS_CUTOFF_DEFAULT = 0.8;
+ final static private String SEP_DEFAULT = ".";
+ final static private Pattern QUERY_PATTERN_DEFAULT = AnalysisMulti.DEFAULT_QUERY_PATTERN_FOR_PPLACER_TYPE;
+ final static private String EXTRA_PROCESSING1_SEP_DEFAULT = "|";
+ final static private boolean EXTRA_PROCESSING1_KEEP_EXTRA_DEFAULT = false;
+ private final static DecimalFormat df = new DecimalFormat( "0.0###" );
public static void main( final String args[] ) {
try {
print_help();
System.exit( 0 );
}
- else if ( ( args.length != 2 && args.length != 3 ) ) {
- System.out.println();
- System.out.println( "Wrong number of arguments." );
- System.out.println();
+ if ( ( cla.getNumberOfNames() != 1 ) && ( cla.getNumberOfNames() != 2 ) ) {
print_help();
System.exit( -1 );
}
- final List<String> allowed_options = new ArrayList<String>();
+ final List<String> allowed_options = new ArrayList<>();
allowed_options.add( SEP_OPTION );
+ allowed_options.add( QUERY_PATTERN_OPTION );
+ allowed_options.add( SPECIFICS_CUTOFF_OPTION );
+ allowed_options.add( MAPPING_FILE_OPTION );
+ allowed_options.add( EXTRA_PROCESSING_OPTION1 );
+ allowed_options.add( EXTRA_PROCESSING1_SEP_OPTION );
+ allowed_options.add( EXTRA_PROCESSING1_KEEP_EXTRA_OPTION );
+ allowed_options.add( VERBOSE_OPTION );
+ allowed_options.add( QUIET_OPTION );
final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options );
if ( dissallowed_options.length() > 0 ) {
ForesterUtil.fatalError( PRG_NAME, "unknown option(s): " + dissallowed_options );
}
- final String separator;
+ double cutoff_specifics = SPECIFICS_CUTOFF_DEFAULT;
+ if ( cla.isOptionSet( SPECIFICS_CUTOFF_OPTION ) ) {
+ if ( cla.isOptionValueSet( SPECIFICS_CUTOFF_OPTION ) ) {
+ cutoff_specifics = cla.getOptionValueAsDouble( SPECIFICS_CUTOFF_OPTION );
+ if ( cutoff_specifics < 0 ) {
+ ForesterUtil.fatalError( PRG_NAME, "cutoff cannot be negative" );
+ }
+ }
+ else {
+ ForesterUtil.fatalError( PRG_NAME, "no value for cutoff for specifics" );
+ }
+ }
+ String separator = SEP_DEFAULT;
if ( cla.isOptionSet( SEP_OPTION ) ) {
- separator = cla.getOptionValue( SEP_OPTION );
+ if ( cla.isOptionValueSet( SEP_OPTION ) ) {
+ separator = cla.getOptionValue( SEP_OPTION );
+ }
+ else {
+ ForesterUtil.fatalError( PRG_NAME, "no value for separator option" );
+ }
}
- else {
- separator = null;
+ Pattern compiled_query_str = null;
+ if ( cla.isOptionSet( QUERY_PATTERN_OPTION ) ) {
+ if ( cla.isOptionValueSet( QUERY_PATTERN_OPTION ) ) {
+ final String query_str = cla.getOptionValue( QUERY_PATTERN_OPTION );
+ try {
+ compiled_query_str = Pattern.compile( query_str );
+ }
+ catch ( final PatternSyntaxException e ) {
+ ForesterUtil.fatalError( PRG_NAME, "error in regular expression: " + e.getMessage() );
+ }
+ }
+ else {
+ ForesterUtil.fatalError( PRG_NAME, "no value for query pattern option" );
+ }
}
+ File mapping_file = null;
+ if ( cla.isOptionSet( MAPPING_FILE_OPTION ) ) {
+ if ( cla.isOptionValueSet( MAPPING_FILE_OPTION ) ) {
+ final String mapping_file_str = cla.getOptionValue( MAPPING_FILE_OPTION );
+ final String error = ForesterUtil.isReadableFile( mapping_file_str );
+ if ( !ForesterUtil.isEmpty( error ) ) {
+ ForesterUtil.fatalError( PRG_NAME, error );
+ }
+ mapping_file = new File( mapping_file_str );
+ }
+ else {
+ ForesterUtil.fatalError( PRG_NAME, "no value for mapping file" );
+ }
+ }
+ final Pattern pattern = ( compiled_query_str != null ) ? compiled_query_str : QUERY_PATTERN_DEFAULT;
final File intreefile = cla.getFile( 0 );
- final String query = cla.getName( 1 );
- System.out.println( "Input tree: " + intreefile );
- System.out.println( "Query : " + query );
- if ( !ForesterUtil.isEmpty( separator ) ) {
- System.out.println( "Separator : " + separator );
+ final String error_intreefile = ForesterUtil.isReadableFile( intreefile );
+ if ( !ForesterUtil.isEmpty( error_intreefile ) ) {
+ ForesterUtil.fatalError( PRG_NAME, error_intreefile );
+ }
+ final File outtablefile;
+ if ( cla.getNumberOfNames() > 1 ) {
+ outtablefile = cla.getFile( 1 );
+ final String error_outtablefile = ForesterUtil.isWritableFile( outtablefile );
+ if ( !ForesterUtil.isEmpty( error_outtablefile ) ) {
+ ForesterUtil.fatalError( PRG_NAME, error_outtablefile );
+ }
+ }
+ else {
+ outtablefile = null;
+ }
+ final BasicTable<String> t;
+ final SortedMap<String, String> map;
+ if ( mapping_file != null ) {
+ t = BasicTableParser.parse( mapping_file, '\t' );
+ if ( t.getNumberOfColumns() != 2 ) {
+ ForesterUtil.fatalError( PRG_NAME,
+ "mapping file needs to have 2 tab-separated columns, not "
+ + t.getNumberOfColumns() );
+ }
+ map = t.getColumnsAsMap( 0, 1 );
+ }
+ else {
+ t = null;
+ map = null;
+ }
+ final boolean extra_processing1;
+ if ( cla.isOptionSet( EXTRA_PROCESSING_OPTION1 ) ) {
+ extra_processing1 = true;
+ }
+ else {
+ extra_processing1 = false;
+ }
+ String extra_processing1_sep = EXTRA_PROCESSING1_SEP_DEFAULT;
+ if ( cla.isOptionSet( EXTRA_PROCESSING1_SEP_OPTION ) ) {
+ if ( !extra_processing1 ) {
+ ForesterUtil.fatalError( PRG_NAME,
+ "extra processing is not enabled, cannot set -"
+ + EXTRA_PROCESSING1_SEP_OPTION + " option" );
+ }
+ if ( cla.isOptionValueSet( EXTRA_PROCESSING1_SEP_OPTION ) ) {
+ extra_processing1_sep = cla.getOptionValue( EXTRA_PROCESSING1_SEP_OPTION );
+ }
+ else {
+ ForesterUtil.fatalError( PRG_NAME, "no value for extra processing separator" );
+ }
+ }
+ if ( ( extra_processing1_sep != null ) && extra_processing1_sep.equals( separator ) ) {
+ ForesterUtil.fatalError( PRG_NAME,
+ "extra processing separator must not be the same the annotation-separator" );
+ }
+ boolean extra_processing1_keep = EXTRA_PROCESSING1_KEEP_EXTRA_DEFAULT;
+ if ( cla.isOptionSet( EXTRA_PROCESSING1_KEEP_EXTRA_OPTION ) ) {
+ if ( !extra_processing1 ) {
+ ForesterUtil.fatalError( PRG_NAME,
+ "extra processing is not enabled, cannot set -"
+ + EXTRA_PROCESSING1_KEEP_EXTRA_OPTION + " option" );
+ }
+ extra_processing1_keep = true;
+ }
+ final boolean verbose;
+ if ( cla.isOptionSet( VERBOSE_OPTION ) ) {
+ verbose = true;
}
else {
- System.out.println( "Separator : none" );
+ verbose = false;
}
- Phylogeny p = null;
+ final boolean quit;
+ if ( cla.isOptionSet( QUIET_OPTION ) ) {
+ quit = true;
+ }
+ else {
+ quit = false;
+ }
+ System.out.println( "Input tree : " + intreefile );
+ System.out.println( "Specific-hit support cutoff: " + cutoff_specifics );
+ if ( mapping_file != null ) {
+ System.out.println( "Mapping file : " + mapping_file + " (" + t.getNumberOfRows()
+ + " rows)" );
+ }
+ System.out.println( "Annotation-separator : " + separator );
+ System.out.println( "Query pattern : " + pattern );
+ System.out.println( "Extra processing : " + extra_processing1 );
+ if ( extra_processing1 ) {
+ System.out.println( "Extra processing separator : " + extra_processing1_sep );
+ System.out.println( "Keep extra annotations : " + extra_processing1_keep );
+ }
+ if ( outtablefile != null ) {
+ System.out.println( "Output table : " + outtablefile );
+ }
+ Phylogeny phys[] = null;
try {
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
final PhylogenyParser pp = ParserUtils.createParserDependingOnFileType( intreefile, true );
- p = factory.create( intreefile, pp )[ 0 ];
+ phys = factory.create( intreefile, pp );
}
catch ( final IOException e ) {
- System.out.println( "\nCould not read \"" + intreefile + "\" [" + e.getMessage() + "]\n" );
- System.exit( -1 );
+ ForesterUtil.fatalError( PRG_NAME, "Could not read \"" + intreefile + "\" [" + e.getMessage() + "]" );
}
-
- final ResultMulti res = AnalysisMulti.execute( p, query, separator, 0.5 );
-
- System.out.println();
- System.out.println( "Result:" );
- System.out.println( "Query : " + query );
-
- ///////////////////
-
-
-
- System.out.println( "Collapsed:" );
-
- for( final Prefix prefix : res.getCollapsedMultiHitPrefixes() ) {
- System.out.println( prefix );
- }
- if ( _has_specifics ) {
-
- System.out.println( "Specifics:" );
-
- for( final Prefix prefix : _cleaned_spec ) {
- System.out.println( prefix );
-
- }
-
- System.out.println( "Collapsed With Specifics:" );
-
- for( final Prefix prefix : _collapsed ) {
- System.out.println( prefix );
-
- for( final Prefix spec : _cleaned_spec ) {
- if ( spec.getPrefix().startsWith( prefix.getPrefix() ) ) {
- System.out.println( " " + spec );
-
- }
- }
- }
- }
- if ( !ForesterUtil.isEmpty( _all_down ) ) {
-
- System.out.println( "Collapsed Down:" );
-
- for( final Prefix prefix : _collapsed_down ) {
- System.out.println( prefix );
-
- }
-
- }
- if ( !ForesterUtil.isEmpty( _all_up ) ) {
-
-
- System.out.println( "Collapsed Up:" );
-
- for( final Prefix prefix : _collapsed_up ) {
- System.out.println( prefix );
-
- }
-
- }
-
- ///////////////////
-
-
- System.out.print( "Greatest Common Prefix : " + res.getGreatestCommonPrefix() );
- if ( !ForesterUtil.isEmpty( res.getGreatestCommonPrefix() )
- && !ForesterUtil.isEmpty( res.getGreatestCommonCladeSubtreeConfidence() ) ) {
- System.out.println( "\t(" + res.getGreatestCommonCladeSubtreeConfidence() + ")" );
- }
- else {
- System.out.println();
+ if ( phys.length == 0 ) {
+ ForesterUtil.fatalError( PRG_NAME, "\"" + intreefile + "\" does not contain any trees" );
}
- System.out.print( "Greatest Common Prefix Up : " + res.getGreatestCommonPrefixUp() );
- if ( !ForesterUtil.isEmpty( res.getGreatestCommonPrefixUp() )
- && !ForesterUtil.isEmpty( res.getGreatestCommonCladeUpSubtreeConfidence() ) ) {
- System.out.println( "\t(" + res.getGreatestCommonCladeUpSubtreeConfidence() + ")" );
+ System.out.println( "Number of input trees : " + phys.length );
+ if ( phys.length == 1 ) {
+ System.out.println( "Ext. nodes in input tree : " + phys[ 0 ].getNumberOfExternalNodes() );
}
else {
- System.out.println();
+ System.out.println( "Ext. nodes in input tree 1 : " + phys[ 0 ].getNumberOfExternalNodes() );
}
- System.out.print( "Greatest Common Prefix Down : " + res.getGreatestCommonPrefixDown() );
- if ( !ForesterUtil.isEmpty( res.getGreatestCommonPrefixDown() )
- && !ForesterUtil.isEmpty( res.getGreatestCommonCladeDownSubtreeConfidence() ) ) {
- System.out.println( "\t(" + res.getGreatestCommonCladeDownSubtreeConfidence() + ")" );
+ final EasyWriter outtable_writer;
+ if ( outtablefile != null ) {
+ outtable_writer = ForesterUtil.createEasyWriter( outtablefile );
}
else {
- System.out.println();
+ outtable_writer = null;
}
- System.out.println( "Least Encompassing Clade size: " + res.getLeastEncompassingCladeSize()
- + " external nodes" );
- final double lec_ratio = ( 100.0 * res.getLeastEncompassingCladeSize() ) / res.getTreeSize();
- System.out.println( "Least Encompassing Clade size: " + df2.format( lec_ratio ) + "%" );
- System.out.println( "Total tree size : " + res.getTreeSize() + " external nodes" );
- if ( res.getWarnings().size() > 0 ) {
- System.out.println( "Warnings:" );
- for( final String s : res.getWarnings() ) {
- System.out.println( s );
+ int counter = 0;
+ for( final Phylogeny phy : phys ) {
+ if ( map != null ) {
+ AnalysisMulti.performMapping( pattern, map, phy, verbose );
+ }
+ if ( extra_processing1 ) {
+ AnalysisMulti.performExtraProcessing1( pattern,
+ phy,
+ extra_processing1_sep,
+ extra_processing1_keep,
+ separator,
+ verbose );
+ }
+ final ResultMulti res = AnalysisMulti.execute( phy, pattern, separator, cutoff_specifics );
+ if ( !quit ) {
+ if ( phys.length == 1 ) {
+ printResult( res, -1 );
+ }
+ else {
+ printResult( res, counter );
+ }
+ }
+ if ( outtable_writer != null ) {
+ writeResultToTable( res, outtable_writer );
+ outtable_writer.flush();
}
+ ++counter;
+ }
+ if ( outtable_writer != null ) {
+ outtable_writer.flush();
+ outtable_writer.close();
}
- System.out.println();
}
- catch ( final IllegalArgumentException e ) {
+ catch ( final UserException e ) {
+ ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
+ }
+ catch ( final IOException e ) {
ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
}
catch ( final Exception e ) {
}
}
+ private final static void printResult( final ResultMulti res, final int counter ) {
+ System.out.println();
+ if ( counter == -1 ) {
+ System.out.println( "Result for " + res.getQueryNamePrefix() );
+ }
+ else {
+ System.out.println( "Result for " + res.getQueryNamePrefix() + " [tree " + counter + "]" );
+ }
+ if ( ( res.getAllMultiHitPrefixes() == null ) | ( res.getAllMultiHitPrefixes().size() < 1 ) ) {
+ System.out.println( " No match to query pattern!" );
+ }
+ else {
+ System.out.println( " Matching Clade(s):" );
+ for( final Prefix prefix : res.getCollapsedMultiHitPrefixes() ) {
+ System.out.println( " " + prefix );
+ }
+ if ( res.isHasSpecificMultiHitsPrefixes() ) {
+ System.out.println();
+ System.out.println( " Specific-hit(s):" );
+ for( final Prefix prefix : res.getSpecificMultiHitPrefixes() ) {
+ System.out.println( " " + prefix );
+ }
+ System.out.println();
+ System.out.println( " Matching Clade(s) with Specific-hit(s):" );
+ for( final Prefix prefix : res.getCollapsedMultiHitPrefixes() ) {
+ System.out.println( " " + prefix );
+ for( final Prefix spec : res.getSpecificMultiHitPrefixes() ) {
+ if ( spec.getPrefix().startsWith( prefix.getPrefix() ) ) {
+ System.out.println( " " + spec );
+ }
+ }
+ }
+ }
+ if ( !ForesterUtil.isEmpty( res.getAllMultiHitPrefixesDown() ) ) {
+ System.out.println();
+ System.out.println( " Matching Down-tree Bracketing Clade(s):" );
+ for( final Prefix prefix : res.getCollapsedMultiHitPrefixesDown() ) {
+ System.out.println( " " + prefix );
+ }
+ }
+ if ( !ForesterUtil.isEmpty( res.getAllMultiHitPrefixesUp() ) ) {
+ System.out.println();
+ System.out.println( " Matching Up-tree Bracketing Clade(s):" );
+ for( final Prefix prefix : res.getCollapsedMultiHitPrefixesUp() ) {
+ System.out.println( " " + prefix );
+ }
+ }
+ System.out.println();
+ System.out.println( " Total Number of Matches: " + res.getNumberOfMatches() + "/"
+ + res.getReferenceTreeNumberOfExternalNodes() );
+ }
+ System.out.println();
+ }
+
+ private final static void writeResultToTable( final ResultMulti res, final EasyWriter w ) throws IOException {
+ if ( ( res.getAllMultiHitPrefixes() == null ) | ( res.getAllMultiHitPrefixes().size() < 1 ) ) {
+ w.print( res.getQueryNamePrefix() );
+ w.print( "\t" );
+ w.println( "No match to query pattern!" );
+ }
+ else {
+ for( final Prefix prefix : res.getCollapsedMultiHitPrefixes() ) {
+ w.print( res.getQueryNamePrefix() );
+ w.print( "\t" );
+ w.print( "Matching Clades" );
+ w.print( "\t" );
+ w.print( prefix.getPrefix() );
+ w.print( "\t" );
+ w.print( df.format( prefix.getConfidence() ) );
+ w.print( "\t" );
+ w.print( String.valueOf( res.getNumberOfMatches() ) );
+ w.print( "\t" );
+ w.print( String.valueOf( res.getReferenceTreeNumberOfExternalNodes() ) );
+ w.println();
+ }
+ if ( res.isHasSpecificMultiHitsPrefixes() ) {
+ for( final Prefix prefix : res.getSpecificMultiHitPrefixes() ) {
+ w.print( res.getQueryNamePrefix() );
+ w.print( "\t" );
+ w.print( "Specific-hits" );
+ w.print( "\t" );
+ w.print( prefix.getPrefix() );
+ w.print( "\t" );
+ w.print( df.format( prefix.getConfidence() ) );
+ w.print( "\t" );
+ w.print( String.valueOf( res.getNumberOfMatches() ) );
+ w.print( "\t" );
+ w.print( String.valueOf( res.getReferenceTreeNumberOfExternalNodes() ) );
+ w.println();
+ }
+ }
+ if ( !ForesterUtil.isEmpty( res.getAllMultiHitPrefixesDown() ) ) {
+ for( final Prefix prefix : res.getCollapsedMultiHitPrefixesDown() ) {
+ w.print( res.getQueryNamePrefix() );
+ w.print( "\t" );
+ w.print( "Matching Down-tree Bracketing Clades" );
+ w.print( "\t" );
+ w.print( prefix.getPrefix() );
+ w.print( "\t" );
+ w.print( df.format( prefix.getConfidence() ) );
+ w.print( "\t" );
+ w.print( String.valueOf( res.getNumberOfMatches() ) );
+ w.print( "\t" );
+ w.print( String.valueOf( res.getReferenceTreeNumberOfExternalNodes() ) );
+ w.println();
+ }
+ }
+ if ( !ForesterUtil.isEmpty( res.getAllMultiHitPrefixesUp() ) ) {
+ for( final Prefix prefix : res.getCollapsedMultiHitPrefixesUp() ) {
+ w.print( res.getQueryNamePrefix() );
+ w.print( "\t" );
+ w.print( "Matching Up-tree Bracketing Clades" );
+ w.print( "\t" );
+ w.print( prefix.getPrefix() );
+ w.print( "\t" );
+ w.print( df.format( prefix.getConfidence() ) );
+ w.print( "\t" );
+ w.print( String.valueOf( res.getNumberOfMatches() ) );
+ w.print( "\t" );
+ w.print( String.valueOf( res.getReferenceTreeNumberOfExternalNodes() ) );
+ w.println();
+ }
+ }
+ }
+ }
+
private final static void print_help() {
System.out.println( "Usage:" );
System.out.println();
- System.out.println( PRG_NAME + " [options] <gene tree file> <query>" );
+ System.out.println( PRG_NAME + " [options] <input tree(s) file> [output table file]" );
System.out.println();
System.out.println( " options:" );
- System.out.println( " -" + SEP_OPTION + "=<separator>: the separator to be used" );
+ System.out.println( " -" + SPECIFICS_CUTOFF_OPTION
+ + "=<double> : the cutoff for \"specific-hit\" support values (default: "
+ + SPECIFICS_CUTOFF_DEFAULT + ")" );
+ System.out.println( " -" + SEP_OPTION + "=<separator> : the annotation-separator to be used (default: "
+ + SEP_DEFAULT + ")" );
+ System.out.println( " -" + MAPPING_FILE_OPTION
+ + "=<mapping table> : to map node names to appropriate annotations (tab-separated, two columns) (default: no mapping)" );
+ System.out.println( " -" + EXTRA_PROCESSING_OPTION1
+ + " : to enable extra processing of annotations (e.g. \"Q16611|A.1.1\" becomes \"A.1.1\")" );
+ System.out.println( " -" + EXTRA_PROCESSING1_SEP_OPTION
+ + "=<separator> : the separator for extra annotations (default: \"" + EXTRA_PROCESSING1_SEP_DEFAULT
+ + "\")" );
+ System.out.println( " -" + EXTRA_PROCESSING1_KEEP_EXTRA_OPTION
+ + " : to keep extra annotations (e.g. \"Q16611|A.1.1\" becomes \"A.1.1.Q16611\")" );
+ System.out.println( " -" + VERBOSE_OPTION + " : verbose" );
+ System.out.println( " --" + QUERY_PATTERN_OPTION
+ + "=<query pattern>: the regular expression for the query (default: \"" + QUERY_PATTERN_DEFAULT
+ + "\" for pplacer output)" );
System.out.println();
- System.out.println( "Example:" );
+ System.out.println( "Examples:" );
System.out.println();
- System.out.println( " " + PRG_NAME + " -s=. my_tree.xml A.1.1.1" );
+ System.out.println( " " + PRG_NAME + " my_tree.nh result.tsv" );
+ System.out.println( " " + PRG_NAME + " -c=0.5 -s=. my_tree.nh result.tsv" );
+ System.out.println( " " + PRG_NAME + " -c=0.9 -s=_ -m=map.tsv my_tree.nh result.tsv" );
+ System.out.println( " " + PRG_NAME + " -x -xs=& -xk my_tree.nh result.tsv" );
+ System.out.println( " " + PRG_NAME + " -x -xs=\"|\" my_tree.nh result.tsv" );
+ System.out.println( " " + PRG_NAME + " -x -xk -m=map.tsv pplacer_out_trees.sing.tre result.tsv" );
System.out.println();
}
}
git://source.jalview.org / jalview.git / blobdiff