import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyMethods;
import org.forester.phylogeny.PhylogenyNode;
+import org.forester.phylogeny.PhylogenyNodeI.NH_CONVERSION_SUPPORT_VALUE_STYLE;
import org.forester.phylogeny.data.BinaryCharacters;
import org.forester.phylogeny.data.Confidence;
import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
+import org.forester.protein.BasicProtein;
+import org.forester.protein.BinaryDomainCombination;
+import org.forester.protein.Domain;
+import org.forester.protein.DomainId;
+import org.forester.protein.Protein;
+import org.forester.species.Species;
import org.forester.surfacing.DomainSimilarityCalculator.Detailedness;
import org.forester.surfacing.DomainSimilarityCalculator.GoAnnotationOutput;
import org.forester.surfacing.GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder;
}
};
public final static Pattern PATTERN_SP_STYLE_TAXONOMY = Pattern.compile( "^[A-Z0-9]{3,5}$" );
+ private static final boolean USE_LAST = true;
private SurfacingUtil() {
// Hidden constructor.
final String outfilename_for_counts,
final String outfilename_for_dc,
final String outfilename_for_dc_for_go_mapping,
- final String outfilename_for_dc_for_go_mapping_unique ) {
+ final String outfilename_for_dc_for_go_mapping_unique,
+ final String outfilename_for_rank_counts,
+ final String outfilename_for_ancestor_species_counts ) {
try {
final BufferedWriter out_counts = new BufferedWriter( new FileWriter( outfilename_for_counts ) );
final BufferedWriter out_dc = new BufferedWriter( new FileWriter( outfilename_for_dc ) );
final SortedMap<Integer, PriorityQueue<String>> domain_lists_go = new TreeMap<Integer, PriorityQueue<String>>();
final SortedMap<Integer, SortedSet<String>> domain_lists_go_unique = new TreeMap<Integer, SortedSet<String>>();
final Set<String> dcs = dc_gain_counts.keySet();
+ final SortedSet<String> more_than_once = new TreeSet<String>();
for( final String dc : dcs ) {
final int count = dc_gain_counts.get( dc );
if ( histogram.containsKey( count ) ) {
set.addAll( splitDomainCombination( dc ) );
domain_lists_go_unique.put( count, set );
}
+ if ( count > 1 ) {
+ more_than_once.add( dc );
+ }
}
final Set<Integer> histogram_keys = histogram.keySet();
for( final Integer histogram_key : histogram_keys ) {
out_dc.close();
out_dc_for_go_mapping.close();
out_dc_for_go_mapping_unique.close();
+ //
+ final SortedMap<String, Integer> lca_rank_counts = new TreeMap<String, Integer>();
+ final SortedMap<String, Integer> lca_ancestor_species_counts = new TreeMap<String, Integer>();
+ for( final String dc : more_than_once ) {
+ final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
+ for( final PhylogenyNodeIterator it = local_phylogeny_l.iteratorExternalForward(); it.hasNext(); ) {
+ final PhylogenyNode n = it.next();
+ if ( n.getNodeData().getBinaryCharacters().getGainedCharacters().contains( dc ) ) {
+ nodes.add( n );
+ }
+ }
+ for( int i = 0; i < nodes.size() - 1; ++i ) {
+ for( int j = i + 1; j < nodes.size(); ++j ) {
+ final PhylogenyNode lca = PhylogenyMethods.getInstance().obtainLCA( nodes.get( i ),
+ nodes.get( j ) );
+ String rank = "unknown";
+ if ( lca.getNodeData().isHasTaxonomy()
+ && !ForesterUtil.isEmpty( lca.getNodeData().getTaxonomy().getRank() ) ) {
+ rank = lca.getNodeData().getTaxonomy().getRank();
+ }
+ addToCountMap( lca_rank_counts, rank );
+ String lca_species;
+ if ( lca.getNodeData().isHasTaxonomy()
+ && !ForesterUtil.isEmpty( lca.getNodeData().getTaxonomy().getScientificName() ) ) {
+ lca_species = lca.getNodeData().getTaxonomy().getScientificName();
+ }
+ else if ( lca.getNodeData().isHasTaxonomy()
+ && !ForesterUtil.isEmpty( lca.getNodeData().getTaxonomy().getCommonName() ) ) {
+ lca_species = lca.getNodeData().getTaxonomy().getCommonName();
+ }
+ else {
+ lca_species = lca.getName();
+ }
+ addToCountMap( lca_ancestor_species_counts, lca_species );
+ }
+ }
+ }
+ final BufferedWriter out_for_rank_counts = new BufferedWriter( new FileWriter( outfilename_for_rank_counts ) );
+ final BufferedWriter out_for_ancestor_species_counts = new BufferedWriter( new FileWriter( outfilename_for_ancestor_species_counts ) );
+ ForesterUtil.map2writer( out_for_rank_counts, lca_rank_counts, "\t", ForesterUtil.LINE_SEPARATOR );
+ ForesterUtil.map2writer( out_for_ancestor_species_counts,
+ lca_ancestor_species_counts,
+ "\t",
+ ForesterUtil.LINE_SEPARATOR );
+ out_for_rank_counts.close();
+ out_for_ancestor_species_counts.close();
}
catch ( final IOException e ) {
ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "Failure to write: " + e );
+ outfilename_for_dc_for_go_mapping_unique + "]" );
}
+ private final static void addToCountMap( final Map<String, Integer> map, final String s ) {
+ if ( map.containsKey( s ) ) {
+ map.put( s, map.get( s ) + 1 );
+ }
+ else {
+ map.put( s, 1 );
+ }
+ }
+
public static int calculateOverlap( final Domain domain, final List<Boolean> covered_positions ) {
int overlap_count = 0;
for( int i = domain.getFrom(); i <= domain.getTo(); ++i ) {
randomization = "yes, seed = " + random_number_seed_for_fitch_parsimony;
}
else {
- domain_parsimony.executeFitchParsimonyOnBinaryDomainCombintion( false );
+ domain_parsimony.executeFitchParsimonyOnBinaryDomainCombintion( USE_LAST );
}
SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossMatrix(), outfile_name
+ surfacing.PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_BINARY_COMBINATIONS, Format.FORESTER );
+ surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_OUTPUT_SUFFIX, outfile_name
+ surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_OUTPUT_SUFFIX, outfile_name
+ surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_SUFFIX, outfile_name
- + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_UNIQUE_SUFFIX );
+ + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_UNIQUE_SUFFIX, outfile_name
+ + "_indep_dc_gains_fitch_lca_ranks.txt", outfile_name + "_indep_dc_gains_fitch_lca_taxonomies.txt" );
}
}
writeToNexus( outfile_name + surfacing.NEXUS_SECONDARY_FEATURES,
secondary_features_parsimony.createMatrixOfSecondaryFeaturePresenceOrAbsence( null ),
phylogeny );
- final Phylogeny local_phylogeny_copy = phylogeny.copy();
+ Phylogeny local_phylogeny_copy = phylogeny.copy();
secondary_features_parsimony.executeDolloParsimonyOnSecondaryFeatures( mapping_results_map );
SurfacingUtil.writeMatrixToFile( secondary_features_parsimony.getGainLossMatrix(), outfile_name
+ surfacing.PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_SECONDARY_FEATURES, Format.FORESTER );
parameters_str );
SurfacingUtil.writePhylogenyToFile( local_phylogeny_copy, outfile_name
+ surfacing.SECONDARY_FEATURES_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO );
+ // FITCH DOMAIN COMBINATIONS
+ // -------------------------
+ local_phylogeny_copy = phylogeny.copy();
+ final String randomization = "no";
+ secondary_features_parsimony.executeFitchParsimonyOnBinaryDomainCombintionOnSecondaryFeatures( USE_LAST );
+ preparePhylogeny( local_phylogeny_copy,
+ secondary_features_parsimony,
+ date_time,
+ "Fitch parsimony on secondary binary domain combination presence/absence randomization: "
+ + randomization,
+ "fitch_on_binary_domain_combinations_" + outfile_name,
+ parameters_str );
+ SurfacingUtil.writePhylogenyToFile( local_phylogeny_copy, outfile_name
+ + surfacing.BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH_MAPPED );
+ calculateIndependentDomainCombinationGains( local_phylogeny_copy, outfile_name
+ + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_MAPPED_OUTPUT_SUFFIX, outfile_name
+ + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_MAPPED_OUTPUT_SUFFIX, outfile_name
+ + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_SUFFIX, outfile_name
+ + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_UNIQUE_SUFFIX, outfile_name
+ + "_MAPPED_indep_dc_gains_fitch_lca_ranks.txt", outfile_name
+ + "_MAPPED_indep_dc_gains_fitch_lca_taxonomies.txt" );
}
public static void extractProteinNames( final List<Protein> proteins,
final List<DomainId> query_domain_ids_nc_order,
final Writer out,
- final String separator ) throws IOException {
+ final String separator,
+ final String limit_to_species ) throws IOException {
for( final Protein protein : proteins ) {
- if ( protein.contains( query_domain_ids_nc_order, true ) ) {
- out.write( protein.getSpecies().getSpeciesId() );
- out.write( separator );
- out.write( protein.getProteinId().getId() );
- out.write( separator );
- out.write( "[" );
- final Set<DomainId> visited_domain_ids = new HashSet<DomainId>();
- boolean first = true;
- for( final Domain domain : protein.getProteinDomains() ) {
- if ( !visited_domain_ids.contains( domain.getDomainId() ) ) {
- visited_domain_ids.add( domain.getDomainId() );
- if ( first ) {
- first = false;
- }
- else {
- out.write( " " );
- }
- out.write( domain.getDomainId().getId() );
- out.write( " {" );
- out.write( "" + domain.getTotalCount() );
- out.write( "}" );
- }
- }
- out.write( "]" );
- out.write( separator );
- if ( !( ForesterUtil.isEmpty( protein.getDescription() ) || protein.getDescription()
- .equals( SurfacingConstants.NONE ) ) ) {
- out.write( protein.getDescription() );
- }
- out.write( separator );
- if ( !( ForesterUtil.isEmpty( protein.getAccession() ) || protein.getAccession()
- .equals( SurfacingConstants.NONE ) ) ) {
- out.write( protein.getAccession() );
- }
- out.write( SurfacingConstants.NL );
- }
- }
- out.flush();
- }
-
- public static void extractProteinNames( final SortedMap<Species, List<Protein>> protein_lists_per_species,
- final DomainId domain_id,
- final Writer out,
- final String separator ) throws IOException {
- for( final Species species : protein_lists_per_species.keySet() ) {
- for( final Protein protein : protein_lists_per_species.get( species ) ) {
- final List<Domain> domains = protein.getProteinDomains( domain_id );
- if ( domains.size() > 0 ) {
- final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
- for( final Domain domain : domains ) {
- stats.addValue( domain.getPerSequenceEvalue() );
- }
+ if ( ForesterUtil.isEmpty( limit_to_species )
+ || protein.getSpecies().getSpeciesId().equalsIgnoreCase( limit_to_species ) ) {
+ if ( protein.contains( query_domain_ids_nc_order, true ) ) {
out.write( protein.getSpecies().getSpeciesId() );
out.write( separator );
out.write( protein.getProteinId().getId() );
out.write( separator );
- out.write( "[" + FORMATTER.format( stats.median() ) + "]" );
+ out.write( "[" );
+ final Set<DomainId> visited_domain_ids = new HashSet<DomainId>();
+ boolean first = true;
+ for( final Domain domain : protein.getProteinDomains() ) {
+ if ( !visited_domain_ids.contains( domain.getDomainId() ) ) {
+ visited_domain_ids.add( domain.getDomainId() );
+ if ( first ) {
+ first = false;
+ }
+ else {
+ out.write( " " );
+ }
+ out.write( domain.getDomainId().getId() );
+ out.write( " {" );
+ out.write( "" + domain.getTotalCount() );
+ out.write( "}" );
+ }
+ }
+ out.write( "]" );
out.write( separator );
if ( !( ForesterUtil.isEmpty( protein.getDescription() ) || protein.getDescription()
.equals( SurfacingConstants.NONE ) ) ) {
out.flush();
}
+ public static void extractProteinNames( final SortedMap<Species, List<Protein>> protein_lists_per_species,
+ final DomainId domain_id,
+ final Writer out,
+ final String separator,
+ final String limit_to_species ) throws IOException {
+ for( final Species species : protein_lists_per_species.keySet() ) {
+ for( final Protein protein : protein_lists_per_species.get( species ) ) {
+ if ( ForesterUtil.isEmpty( limit_to_species )
+ || protein.getSpecies().getSpeciesId().equalsIgnoreCase( limit_to_species ) ) {
+ final List<Domain> domains = protein.getProteinDomains( domain_id );
+ if ( domains.size() > 0 ) {
+ final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
+ for( final Domain domain : domains ) {
+ stats.addValue( domain.getPerSequenceEvalue() );
+ }
+ out.write( protein.getSpecies().getSpeciesId() );
+ out.write( separator );
+ out.write( protein.getProteinId().getId() );
+ out.write( separator );
+ out.write( "[" + FORMATTER.format( stats.median() ) + "]" );
+ out.write( separator );
+ if ( !( ForesterUtil.isEmpty( protein.getDescription() ) || protein.getDescription()
+ .equals( SurfacingConstants.NONE ) ) ) {
+ out.write( protein.getDescription() );
+ }
+ out.write( separator );
+ if ( !( ForesterUtil.isEmpty( protein.getAccession() ) || protein.getAccession()
+ .equals( SurfacingConstants.NONE ) ) ) {
+ out.write( protein.getAccession() );
+ }
+ out.write( SurfacingConstants.NL );
+ }
+ }
+ }
+ }
+ out.flush();
+ }
+
public static SortedSet<DomainId> getAllDomainIds( final List<GenomeWideCombinableDomains> gwcd_list ) {
final SortedSet<DomainId> all_domains_ids = new TreeSet<DomainId>();
for( final GenomeWideCombinableDomains gwcd : gwcd_list ) {
final boolean remove_engulfed_domains,
final Protein protein ) {
final Protein pruned_protein = new BasicProtein( protein.getProteinId().getId(), protein.getSpecies()
- .getSpeciesId() );
+ .getSpeciesId(), protein.getLength() );
final List<Domain> sorted = SurfacingUtil.sortDomainsWithAscendingConfidenceValues( protein );
final List<Boolean> covered_positions = new ArrayList<Boolean>();
for( final Domain domain : sorted ) {
public static DescriptiveStatistics writeDomainSimilaritiesToFile( final StringBuilder html_desc,
final StringBuilder html_title,
- final Writer w,
+ final Writer single_writer,
+ Map<Character, Writer> split_writers,
final SortedSet<DomainSimilarity> similarities,
final boolean treat_as_binary,
final List<Species> species_order,
System.out.println( "Pearsonian skewness : n/a" );
}
}
+ if ( ( single_writer != null ) && ( ( split_writers == null ) || split_writers.isEmpty() ) ) {
+ split_writers = new HashMap<Character, Writer>();
+ split_writers.put( '_', single_writer );
+ }
switch ( print_option ) {
case SIMPLE_TAB_DELIMITED:
break;
case HTML:
- w.write( "<html>" );
- w.write( SurfacingConstants.NL );
- addHtmlHead( w, "SURFACING :: " + html_title );
- w.write( SurfacingConstants.NL );
- w.write( "<body>" );
- w.write( SurfacingConstants.NL );
- w.write( html_desc.toString() );
- w.write( SurfacingConstants.NL );
- w.write( "<hr>" );
- w.write( "<br>" );
- w.write( SurfacingConstants.NL );
- w.write( "<tt><pre>" );
- w.write( SurfacingConstants.NL );
- if ( histo != null ) {
- w.write( histo.toStringBuffer( 20, '|', 40, 5 ).toString() );
+ for( final Character key : split_writers.keySet() ) {
+ final Writer w = split_writers.get( key );
+ w.write( "<html>" );
+ w.write( SurfacingConstants.NL );
+ if ( key != '_' ) {
+ addHtmlHead( w, "DCs (" + html_title + ") " + key.toString().toUpperCase() );
+ }
+ else {
+ addHtmlHead( w, "DCs (" + html_title + ")" );
+ }
+ w.write( SurfacingConstants.NL );
+ w.write( "<body>" );
+ w.write( SurfacingConstants.NL );
+ w.write( html_desc.toString() );
+ w.write( SurfacingConstants.NL );
+ w.write( "<hr>" );
+ w.write( "<br>" );
+ w.write( SurfacingConstants.NL );
+ w.write( "<tt><pre>" );
+ w.write( SurfacingConstants.NL );
+ if ( histo != null ) {
+ w.write( histo.toStringBuffer( 20, '|', 40, 5 ).toString() );
+ w.write( SurfacingConstants.NL );
+ }
+ w.write( "</pre></tt>" );
+ w.write( SurfacingConstants.NL );
+ w.write( "<table>" );
+ w.write( SurfacingConstants.NL );
+ w.write( "<tr><td>N: </td><td>" + stats.getN() + "</td></tr>" );
+ w.write( SurfacingConstants.NL );
+ w.write( "<tr><td>Min: </td><td>" + stats.getMin() + "</td></tr>" );
+ w.write( SurfacingConstants.NL );
+ w.write( "<tr><td>Max: </td><td>" + stats.getMax() + "</td></tr>" );
+ w.write( SurfacingConstants.NL );
+ w.write( "<tr><td>Mean: </td><td>" + stats.arithmeticMean() + "</td></tr>" );
+ w.write( SurfacingConstants.NL );
+ if ( stats.getN() > 1 ) {
+ w.write( "<tr><td>SD: </td><td>" + stats.sampleStandardDeviation() + "</td></tr>" );
+ }
+ else {
+ w.write( "<tr><td>SD: </td><td>n/a</td></tr>" );
+ }
+ w.write( SurfacingConstants.NL );
+ w.write( "<tr><td>Median: </td><td>" + stats.median() + "</td></tr>" );
+ w.write( SurfacingConstants.NL );
+ if ( stats.getN() > 1 ) {
+ w.write( "<tr><td>Pearsonian skewness: </td><td>" + stats.pearsonianSkewness() + "</td></tr>" );
+ }
+ else {
+ w.write( "<tr><td>Pearsonian skewness: </td><td>n/a</td></tr>" );
+ }
+ w.write( SurfacingConstants.NL );
+ w.write( "</table>" );
+ w.write( SurfacingConstants.NL );
+ w.write( "<br>" );
+ w.write( SurfacingConstants.NL );
+ w.write( "<hr>" );
+ w.write( SurfacingConstants.NL );
+ w.write( "<br>" );
+ w.write( SurfacingConstants.NL );
+ w.write( "<table>" );
w.write( SurfacingConstants.NL );
}
- w.write( "</pre></tt>" );
- w.write( SurfacingConstants.NL );
- w.write( "<table>" );
- w.write( SurfacingConstants.NL );
- w.write( "<tr><td>N: </td><td>" + stats.getN() + "</td></tr>" );
- w.write( SurfacingConstants.NL );
- w.write( "<tr><td>Min: </td><td>" + stats.getMin() + "</td></tr>" );
- w.write( SurfacingConstants.NL );
- w.write( "<tr><td>Max: </td><td>" + stats.getMax() + "</td></tr>" );
- w.write( SurfacingConstants.NL );
- w.write( "<tr><td>Mean: </td><td>" + stats.arithmeticMean() + "</td></tr>" );
- w.write( SurfacingConstants.NL );
- if ( stats.getN() > 1 ) {
- w.write( "<tr><td>SD: </td><td>" + stats.sampleStandardDeviation() + "</td></tr>" );
- }
- else {
- w.write( "<tr><td>SD: </td><td>n/a</td></tr>" );
- }
- w.write( SurfacingConstants.NL );
- w.write( "<tr><td>Median: </td><td>" + stats.median() + "</td></tr>" );
- w.write( SurfacingConstants.NL );
- if ( stats.getN() > 1 ) {
- w.write( "<tr><td>Pearsonian skewness: </td><td>" + stats.pearsonianSkewness() + "</td></tr>" );
- }
- else {
- w.write( "<tr><td>Pearsonian skewness: </td><td>n/a</td></tr>" );
- }
- w.write( SurfacingConstants.NL );
- w.write( "</table>" );
- w.write( SurfacingConstants.NL );
- w.write( "<br>" );
- w.write( SurfacingConstants.NL );
- w.write( "<hr>" );
- w.write( SurfacingConstants.NL );
- w.write( "<br>" );
- w.write( SurfacingConstants.NL );
- w.write( "<table>" );
- w.write( SurfacingConstants.NL );
break;
}
- w.write( SurfacingConstants.NL );
+ for( final Writer w : split_writers.values() ) {
+ w.write( SurfacingConstants.NL );
+ }
for( final DomainSimilarity similarity : similarities ) {
if ( ( species_order != null ) && !species_order.isEmpty() ) {
( ( PrintableDomainSimilarity ) similarity ).setSpeciesOrder( species_order );
}
- w.write( similarity.toStringBuffer( print_option ).toString() );
- w.write( SurfacingConstants.NL );
+ if ( single_writer != null ) {
+ single_writer.write( similarity.toStringBuffer( print_option ).toString() );
+ }
+ else {
+ Writer local_writer = split_writers.get( ( similarity.getDomainId().getId().charAt( 0 ) + "" )
+ .toLowerCase().charAt( 0 ) );
+ if ( local_writer == null ) {
+ local_writer = split_writers.get( '0' );
+ }
+ local_writer.write( similarity.toStringBuffer( print_option ).toString() );
+ }
+ for( final Writer w : split_writers.values() ) {
+ w.write( SurfacingConstants.NL );
+ }
}
switch ( print_option ) {
case HTML:
- w.write( SurfacingConstants.NL );
- w.write( "</table>" );
- w.write( SurfacingConstants.NL );
- w.write( "</font>" );
- w.write( SurfacingConstants.NL );
- w.write( "</body>" );
- w.write( SurfacingConstants.NL );
- w.write( "</html>" );
- w.write( SurfacingConstants.NL );
+ for( final Writer w : split_writers.values() ) {
+ w.write( SurfacingConstants.NL );
+ w.write( "</table>" );
+ w.write( SurfacingConstants.NL );
+ w.write( "</font>" );
+ w.write( SurfacingConstants.NL );
+ w.write( "</body>" );
+ w.write( SurfacingConstants.NL );
+ w.write( "</html>" );
+ w.write( SurfacingConstants.NL );
+ }
break;
}
- w.flush();
- w.close();
+ for( final Writer w : split_writers.values() ) {
+ w.close();
+ }
return stats;
}
w.write( ForesterUtil.LINE_SEPARATOR );
my_matrix.writeNexusTaxaBlock( w );
my_matrix.writeNexusBinaryChractersBlock( w );
- PhylogenyWriter.writeNexusTreesBlock( w, phylogenies );
+ PhylogenyWriter.writeNexusTreesBlock( w, phylogenies, NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );
w.flush();
w.close();
ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote Nexus file: \"" + outfile_name + "\"" );
try {
writer.write( genome );
writer.write( "\t" );
- writer.write( stats.arithmeticMean() + "" );
- writer.write( "\t" );
- writer.write( stats.sampleStandardDeviation() + "" );
- writer.write( "\t" );
- writer.write( stats.median() + "" );
- writer.write( "\t" );
- writer.write( stats.getN() + "" );
- writer.write( "\t" );
- writer.write( stats.getMin() + "" );
- writer.write( "\t" );
- writer.write( stats.getMax() + "" );
+ if ( stats.getN() >= 1 ) {
+ writer.write( stats.arithmeticMean() + "" );
+ writer.write( "\t" );
+ if ( stats.getN() >= 2 ) {
+ writer.write( stats.sampleStandardDeviation() + "" );
+ }
+ else {
+ writer.write( "" );
+ }
+ writer.write( "\t" );
+ writer.write( stats.median() + "" );
+ writer.write( "\t" );
+ writer.write( stats.getN() + "" );
+ writer.write( "\t" );
+ writer.write( stats.getMin() + "" );
+ writer.write( "\t" );
+ writer.write( stats.getMax() + "" );
+ }
+ else {
+ writer.write( "\t" );
+ writer.write( "\t" );
+ writer.write( "\t" );
+ writer.write( "0" );
+ writer.write( "\t" );
+ writer.write( "\t" );
+ }
writer.write( "\n" );
}
catch ( final IOException e ) {
git://source.jalview.org / jalview.git / blobdiff