package org.forester.surfacing;
+import java.awt.Color;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileWriter;
import org.forester.evoinference.matrix.character.CharacterStateMatrix.BinaryStates;
import org.forester.evoinference.matrix.character.CharacterStateMatrix.Format;
import org.forester.evoinference.matrix.character.CharacterStateMatrix.GainLossStates;
-import org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix;
import org.forester.evoinference.matrix.distance.DistanceMatrix;
import org.forester.go.GoId;
import org.forester.go.GoNameSpace;
import org.forester.go.GoTerm;
import org.forester.go.PfamToGoMapping;
import org.forester.io.parsers.nexus.NexusConstants;
+import org.forester.io.parsers.phyloxml.PhyloXmlUtil;
+import org.forester.io.parsers.util.ParserUtils;
import org.forester.io.writers.PhylogenyWriter;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyMethods;
import org.forester.phylogeny.data.BinaryCharacters;
import org.forester.phylogeny.data.Confidence;
import org.forester.phylogeny.data.Taxonomy;
+import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
import org.forester.protein.BasicDomain;
import org.forester.protein.BasicProtein;
import org.forester.protein.Domain;
import org.forester.protein.Protein;
import org.forester.species.Species;
+import org.forester.surfacing.DomainSimilarity.PRINT_OPTION;
import org.forester.surfacing.DomainSimilarityCalculator.Detailedness;
import org.forester.surfacing.GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder;
import org.forester.util.AsciiHistogram;
import org.forester.util.BasicDescriptiveStatistics;
import org.forester.util.BasicTable;
import org.forester.util.BasicTableParser;
+import org.forester.util.CommandLineArguments;
import org.forester.util.DescriptiveStatistics;
import org.forester.util.ForesterUtil;
+import org.forester.util.TaxonomyColors;
+import org.forester.util.TaxonomyGroups;
public final class SurfacingUtil {
- private final static NumberFormat FORMATTER_3 = new DecimalFormat( "0.000" );
- private static final Comparator<Domain> ASCENDING_CONFIDENCE_VALUE_ORDER = new Comparator<Domain>() {
-
- @Override
- public int compare( final Domain d1,
- final Domain d2 ) {
- if ( d1.getPerSequenceEvalue() < d2
- .getPerSequenceEvalue() ) {
- return -1;
- }
- else if ( d1
- .getPerSequenceEvalue() > d2
- .getPerSequenceEvalue() ) {
- return 1;
- }
- else {
- return d1.compareTo( d2 );
- }
- }
- };
- public final static Pattern PATTERN_SP_STYLE_TAXONOMY = Pattern.compile( "^[A-Z0-9]{3,5}$" );
+ public final static Pattern PATTERN_SP_STYLE_TAXONOMY = Pattern.compile( "^[A-Z0-9]{3,5}$" );
+ private final static Map<String, String> _TAXCODE_HEXCOLORSTRING_MAP = new HashMap<String, String>();
+ private final static Map<String, String> _TAXCODE_TAXGROUP_MAP = new HashMap<String, String>();
+ private static final Comparator<Domain> ASCENDING_CONFIDENCE_VALUE_ORDER = new Comparator<Domain>() {
+
+ @Override
+ public int compare( final Domain d1,
+ final Domain d2 ) {
+ if ( d1.getPerDomainEvalue() < d2
+ .getPerDomainEvalue() ) {
+ return -1;
+ }
+ else if ( d1
+ .getPerDomainEvalue() > d2
+ .getPerDomainEvalue() ) {
+ return 1;
+ }
+ else {
+ return d1.compareTo( d2 );
+ }
+ }
+ };
+ private final static NumberFormat FORMATTER_3 = new DecimalFormat( "0.000" );
private SurfacingUtil() {
// Hidden constructor.
}
}
- public static void addHtmlHead( final Writer w, final String title ) throws IOException {
- w.write( SurfacingConstants.NL );
- w.write( "<head>" );
- w.write( "<title>" );
- w.write( title );
- w.write( "</title>" );
- w.write( SurfacingConstants.NL );
- w.write( "<style>" );
- w.write( SurfacingConstants.NL );
- w.write( "a:visited { color : #6633FF; text-decoration : none; }" );
- w.write( SurfacingConstants.NL );
- w.write( "a:link { color : #6633FF; text-decoration : none; }" );
- w.write( SurfacingConstants.NL );
- w.write( "a:active { color : #99FF00; text-decoration : none; }" );
- w.write( SurfacingConstants.NL );
- w.write( "a:hover { color : #FFFFFF; background-color : #99FF00; text-decoration : none; }" );
- w.write( SurfacingConstants.NL );
- //
- w.write( "a.pl:visited { color : #505050; text-decoration : none; font-size: 7pt;}" );
- w.write( SurfacingConstants.NL );
- w.write( "a.pl:link { color : #505050; text-decoration : none; font-size: 7pt;}" );
- w.write( SurfacingConstants.NL );
- w.write( "a.pl:active { color : #505050; text-decoration : none; font-size: 7pt;}" );
- w.write( SurfacingConstants.NL );
- w.write( "a.pl:hover { color : #FFFFFF; background-color : #99FF00; text-decoration : none; font-size: 7pt;}" );
- w.write( SurfacingConstants.NL );
- //
- w.write( "a.ps:visited { color : #707070; text-decoration : none; font-size: 7pt;}" );
- w.write( SurfacingConstants.NL );
- w.write( "a.ps:link { color : #707070; text-decoration : none; font-size: 7pt;}" );
- w.write( SurfacingConstants.NL );
- w.write( "a.ps:active { color : #707070; text-decoration : none; font-size: 7pt;}" );
- w.write( SurfacingConstants.NL );
- w.write( "a.ps:hover { color : #FFFFFF; background-color : #99FF00; text-decoration : none; font-size: 7pt;}" );
- w.write( SurfacingConstants.NL );
- //
- w.write( "td { text-align: left; vertical-align: top; font-family: Verdana, Arial, Helvetica; font-size: 8pt}" );
- w.write( SurfacingConstants.NL );
- w.write( "h1 { color : #0000FF; font-family: Verdana, Arial, Helvetica; font-size: 18pt; font-weight: bold }" );
- w.write( SurfacingConstants.NL );
- w.write( "h2 { color : #0000FF; font-family: Verdana, Arial, Helvetica; font-size: 16pt; font-weight: bold }" );
- w.write( SurfacingConstants.NL );
- w.write( "</style>" );
- w.write( SurfacingConstants.NL );
- w.write( "</head>" );
- w.write( SurfacingConstants.NL );
- }
-
public static DescriptiveStatistics calculateDescriptiveStatisticsForMeanValues( final Set<DomainSimilarity> similarities ) {
final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
for( final DomainSimilarity similarity : similarities ) {
return stats;
}
- 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 ) {
- if ( ( i < covered_positions.size() ) && ( covered_positions.get( i ) == true ) ) {
- ++overlap_count;
- }
- }
- return overlap_count;
- }
-
public static void checkForOutputFileWriteability( final File outfile ) {
final String error = ForesterUtil.isWritableFile( outfile );
if ( !ForesterUtil.isEmpty( error ) ) {
}
}
+ public static void checkWriteabilityForPairwiseComparisons( final DomainSimilarity.PRINT_OPTION domain_similarity_print_option,
+ final String[][] input_file_properties,
+ final String automated_pairwise_comparison_suffix,
+ final File outdir ) {
+ for( int i = 0; i < input_file_properties.length; ++i ) {
+ for( int j = 0; j < i; ++j ) {
+ final String species_i = input_file_properties[ i ][ 1 ];
+ final String species_j = input_file_properties[ j ][ 1 ];
+ String pairwise_similarities_output_file_str = surfacing.PAIRWISE_DOMAIN_COMPARISONS_PREFIX + species_i
+ + "_" + species_j + automated_pairwise_comparison_suffix;
+ switch ( domain_similarity_print_option ) {
+ case HTML:
+ if ( !pairwise_similarities_output_file_str.endsWith( ".html" ) ) {
+ pairwise_similarities_output_file_str += ".html";
+ }
+ break;
+ }
+ final String error = ForesterUtil
+ .isWritableFile( new File( outdir == null ? pairwise_similarities_output_file_str
+ : outdir + ForesterUtil.FILE_SEPARATOR + pairwise_similarities_output_file_str ) );
+ if ( !ForesterUtil.isEmpty( error ) ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, error );
+ }
+ }
+ }
+ }
+
public static void collectChangedDomainCombinationsFromBinaryStatesMatrixAsListToFile( final CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
final BinaryDomainCombination.DomainCombinationType dc_type,
final List<BinaryDomainCombination> all_binary_domains_combination_gained,
for( final String id : sorted_ids ) {
for( int c = 0; c < matrix.getNumberOfCharacters(); ++c ) {
if ( ( get_gains && ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.GAIN ) )
- || ( !get_gains && ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.LOSS ) ) ) {
+ || ( !get_gains
+ && ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.LOSS ) ) ) {
if ( dc_type == BinaryDomainCombination.DomainCombinationType.DIRECTED_ADJACTANT ) {
all_binary_domains_combination_gained.add( AdjactantDirectedBinaryDomainCombination
- .createInstance( matrix.getCharacter( c ) ) );
+ .obtainInstance( matrix.getCharacter( c ) ) );
}
else if ( dc_type == BinaryDomainCombination.DomainCombinationType.DIRECTED ) {
- all_binary_domains_combination_gained.add( DirectedBinaryDomainCombination
- .createInstance( matrix.getCharacter( c ) ) );
+ all_binary_domains_combination_gained
+ .add( DirectedBinaryDomainCombination.obtainInstance( matrix.getCharacter( c ) ) );
}
else {
- all_binary_domains_combination_gained.add( BasicBinaryDomainCombination.createInstance( matrix
- .getCharacter( c ) ) );
+ all_binary_domains_combination_gained
+ .add( BasicBinaryDomainCombination.obtainInstance( matrix.getCharacter( c ) ) );
}
}
}
}
public static Map<String, List<GoId>> createDomainIdToGoIdMap( final List<PfamToGoMapping> pfam_to_go_mappings ) {
- final Map<String, List<GoId>> domain_id_to_go_ids_map = new HashMap<String, List<GoId>>( pfam_to_go_mappings.size() );
+ final Map<String, List<GoId>> domain_id_to_go_ids_map = new HashMap<String, List<GoId>>( pfam_to_go_mappings
+ .size() );
for( final PfamToGoMapping pfam_to_go : pfam_to_go_mappings ) {
if ( !domain_id_to_go_ids_map.containsKey( pfam_to_go.getKey() ) ) {
domain_id_to_go_ids_map.put( pfam_to_go.getKey(), new ArrayList<GoId>() );
return map;
}
- public static Phylogeny createNjTreeBasedOnMatrixToFile( final File nj_tree_outfile, final DistanceMatrix distance ) {
+ public static Phylogeny createNjTreeBasedOnMatrixToFile( final File nj_tree_outfile,
+ final DistanceMatrix distance ) {
checkForOutputFileWriteability( nj_tree_outfile );
final NeighborJoining nj = NeighborJoining.createInstance();
- final Phylogeny phylogeny = nj.execute( ( BasicSymmetricalDistanceMatrix ) distance );
+ final Phylogeny phylogeny = nj.execute( ( DistanceMatrix ) distance );
phylogeny.setName( nj_tree_outfile.getName() );
writePhylogenyToFile( phylogeny, nj_tree_outfile.toString() );
return phylogeny;
}
+ public static StringBuilder createParametersAsString( final boolean ignore_dufs,
+ final double ie_value_max,
+ final double fs_e_value_max,
+ final int max_allowed_overlap,
+ final boolean no_engulfing_overlaps,
+ final File cutoff_scores_file,
+ final BinaryDomainCombination.DomainCombinationType dc_type ) {
+ final StringBuilder parameters_sb = new StringBuilder();
+ parameters_sb.append( "iE-value: " + ie_value_max );
+ parameters_sb.append( ", FS E-value: " + fs_e_value_max );
+ if ( cutoff_scores_file != null ) {
+ parameters_sb.append( ", Cutoff-scores-file: " + cutoff_scores_file );
+ }
+ else {
+ parameters_sb.append( ", Cutoff-scores-file: not-set" );
+ }
+ if ( max_allowed_overlap != surfacing.MAX_ALLOWED_OVERLAP_DEFAULT ) {
+ parameters_sb.append( ", Max-overlap: " + max_allowed_overlap );
+ }
+ else {
+ parameters_sb.append( ", Max-overlap: not-set" );
+ }
+ if ( no_engulfing_overlaps ) {
+ parameters_sb.append( ", Engulfing-overlaps: not-allowed" );
+ }
+ else {
+ parameters_sb.append( ", Engulfing-overlaps: allowed" );
+ }
+ if ( ignore_dufs ) {
+ parameters_sb.append( ", Ignore-dufs: true" );
+ }
+ else {
+ parameters_sb.append( ", Ignore-dufs: false" );
+ }
+ parameters_sb.append( ", DC type (if applicable): " + dc_type );
+ return parameters_sb;
+ }
+
+ public static void createSplitWriters( final File out_dir,
+ final String my_outfile,
+ final Map<Character, Writer> split_writers )
+ throws IOException {
+ split_writers.put( 'a',
+ new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
+ + "_domains_A.html" ) ) );
+ split_writers.put( 'b',
+ new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
+ + "_domains_B.html" ) ) );
+ split_writers.put( 'c',
+ new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
+ + "_domains_C.html" ) ) );
+ split_writers.put( 'd',
+ new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
+ + "_domains_D.html" ) ) );
+ split_writers.put( 'e',
+ new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
+ + "_domains_E.html" ) ) );
+ split_writers.put( 'f',
+ new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
+ + "_domains_F.html" ) ) );
+ split_writers.put( 'g',
+ new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
+ + "_domains_G.html" ) ) );
+ split_writers.put( 'h',
+ new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
+ + "_domains_H.html" ) ) );
+ split_writers.put( 'i',
+ new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
+ + "_domains_I.html" ) ) );
+ split_writers.put( 'j',
+ new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
+ + "_domains_J.html" ) ) );
+ split_writers.put( 'k',
+ new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
+ + "_domains_K.html" ) ) );
+ split_writers.put( 'l',
+ new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
+ + "_domains_L.html" ) ) );
+ split_writers.put( 'm',
+ new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
+ + "_domains_M.html" ) ) );
+ split_writers.put( 'n',
+ new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
+ + "_domains_N.html" ) ) );
+ split_writers.put( 'o',
+ new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
+ + "_domains_O.html" ) ) );
+ split_writers.put( 'p',
+ new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
+ + "_domains_P.html" ) ) );
+ split_writers.put( 'q',
+ new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
+ + "_domains_Q.html" ) ) );
+ split_writers.put( 'r',
+ new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
+ + "_domains_R.html" ) ) );
+ split_writers.put( 's',
+ new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
+ + "_domains_S.html" ) ) );
+ split_writers.put( 't',
+ new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
+ + "_domains_T.html" ) ) );
+ split_writers.put( 'u',
+ new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
+ + "_domains_U.html" ) ) );
+ split_writers.put( 'v',
+ new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
+ + "_domains_V.html" ) ) );
+ split_writers.put( 'w',
+ new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
+ + "_domains_W.html" ) ) );
+ split_writers.put( 'x',
+ new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
+ + "_domains_X.html" ) ) );
+ split_writers.put( 'y',
+ new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
+ + "_domains_Y.html" ) ) );
+ split_writers.put( 'z',
+ new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
+ + "_domains_Z.html" ) ) );
+ split_writers.put( '0',
+ new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
+ + "_domains_0.html" ) ) );
+ }
+
public static Map<String, Integer> createTaxCodeToIdMap( final Phylogeny phy ) {
final Map<String, Integer> m = new HashMap<String, Integer>();
for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {
public static void decoratePrintableDomainSimilarities( final SortedSet<DomainSimilarity> domain_similarities,
final Detailedness detailedness ) {
for( final DomainSimilarity domain_similarity : domain_similarities ) {
- if ( domain_similarity instanceof PrintableDomainSimilarity ) {
- final PrintableDomainSimilarity printable_domain_similarity = ( PrintableDomainSimilarity ) domain_similarity;
+ if ( domain_similarity instanceof DomainSimilarity ) {
+ final DomainSimilarity printable_domain_similarity = domain_similarity;
printable_domain_similarity.setDetailedness( detailedness );
}
}
final Writer out,
final String separator,
final String limit_to_species,
- final Map<String, List<Integer>> average_protein_lengths_by_dc ) throws IOException {
+ final Map<String, List<Integer>> average_protein_lengths_by_dc )
+ throws IOException {
for( final Protein protein : proteins ) {
if ( ForesterUtil.isEmpty( limit_to_species )
|| protein.getSpecies().getSpeciesId().equalsIgnoreCase( limit_to_species ) ) {
}
out.write( "]" );
out.write( separator );
- if ( !( ForesterUtil.isEmpty( protein.getDescription() ) || protein.getDescription()
- .equals( SurfacingConstants.NONE ) ) ) {
+ 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 ) ) ) {
+ if ( !( ForesterUtil.isEmpty( protein.getAccession() )
+ || protein.getAccession().equals( SurfacingConstants.NONE ) ) ) {
out.write( protein.getAccession() );
}
out.write( SurfacingConstants.NL );
public static void executeDomainLengthAnalysis( final String[][] input_file_properties,
final int number_of_genomes,
final DomainLengthsTable domain_lengths_table,
- final File outfile ) throws IOException {
+ final File outfile )
+ throws IOException {
final DecimalFormat df = new DecimalFormat( "#.00" );
checkForOutputFileWriteability( outfile );
final BufferedWriter out = new BufferedWriter( new FileWriter( outfile ) );
}
/**
- *
- * @param all_binary_domains_combination_lost_fitch
- * @param use_last_in_fitch_parsimony
- * @param consider_directedness_and_adjacency_for_bin_combinations
+ * Warning: This side-effects 'all_bin_domain_combinations_encountered'!
+ *
+ *
+ * @param output_file
+ * @param all_bin_domain_combinations_changed
+ * @param sum_of_all_domains_encountered
+ * @param all_bin_domain_combinations_encountered
+ * @param is_gains_analysis
+ * @param protein_length_stats_by_dc
+ * @throws IOException
+ */
+ public static void executeFitchGainsAnalysis( final File output_file,
+ final List<BinaryDomainCombination> all_bin_domain_combinations_changed,
+ final int sum_of_all_domains_encountered,
+ final SortedSet<BinaryDomainCombination> all_bin_domain_combinations_encountered,
+ final boolean is_gains_analysis )
+ throws IOException {
+ checkForOutputFileWriteability( output_file );
+ final Writer out = ForesterUtil.createBufferedWriter( output_file );
+ final SortedMap<Object, Integer> bdc_to_counts = ForesterUtil
+ .listToSortedCountsMap( all_bin_domain_combinations_changed );
+ final SortedSet<String> all_domains_in_combination_changed_more_than_once = new TreeSet<String>();
+ final SortedSet<String> all_domains_in_combination_changed_only_once = new TreeSet<String>();
+ int above_one = 0;
+ int one = 0;
+ for( final Object bdc_object : bdc_to_counts.keySet() ) {
+ final BinaryDomainCombination bdc = ( BinaryDomainCombination ) bdc_object;
+ final int count = bdc_to_counts.get( bdc_object );
+ if ( count < 1 ) {
+ ForesterUtil.unexpectedFatalError( surfacing.PRG_NAME, "count < 1 " );
+ }
+ out.write( bdc + "\t" + count + ForesterUtil.LINE_SEPARATOR );
+ if ( count > 1 ) {
+ all_domains_in_combination_changed_more_than_once.add( bdc.getId0() );
+ all_domains_in_combination_changed_more_than_once.add( bdc.getId1() );
+ above_one++;
+ }
+ else if ( count == 1 ) {
+ all_domains_in_combination_changed_only_once.add( bdc.getId0() );
+ all_domains_in_combination_changed_only_once.add( bdc.getId1() );
+ one++;
+ }
+ }
+ final int all = all_bin_domain_combinations_encountered.size();
+ int never_lost = -1;
+ if ( !is_gains_analysis ) {
+ all_bin_domain_combinations_encountered.removeAll( all_bin_domain_combinations_changed );
+ never_lost = all_bin_domain_combinations_encountered.size();
+ for( final BinaryDomainCombination bdc : all_bin_domain_combinations_encountered ) {
+ out.write( bdc + "\t" + "0" + ForesterUtil.LINE_SEPARATOR );
+ }
+ }
+ if ( is_gains_analysis ) {
+ out.write( "Sum of all distinct domain combinations appearing once : " + one
+ + ForesterUtil.LINE_SEPARATOR );
+ out.write( "Sum of all distinct domain combinations appearing more than once : " + above_one
+ + ForesterUtil.LINE_SEPARATOR );
+ out.write( "Sum of all distinct domains in combinations apppearing only once : "
+ + all_domains_in_combination_changed_only_once.size() + ForesterUtil.LINE_SEPARATOR );
+ out.write( "Sum of all distinct domains in combinations apppearing more than once: "
+ + all_domains_in_combination_changed_more_than_once.size() + ForesterUtil.LINE_SEPARATOR );
+ }
+ else {
+ out.write( "Sum of all distinct domain combinations never lost : " + never_lost
+ + ForesterUtil.LINE_SEPARATOR );
+ out.write( "Sum of all distinct domain combinations lost once : " + one
+ + ForesterUtil.LINE_SEPARATOR );
+ out.write( "Sum of all distinct domain combinations lost more than once : " + above_one
+ + ForesterUtil.LINE_SEPARATOR );
+ out.write( "Sum of all distinct domains in combinations lost only once : "
+ + all_domains_in_combination_changed_only_once.size() + ForesterUtil.LINE_SEPARATOR );
+ out.write( "Sum of all distinct domains in combinations lost more than once: "
+ + all_domains_in_combination_changed_more_than_once.size() + ForesterUtil.LINE_SEPARATOR );
+ }
+ out.write( "All binary combinations : " + all
+ + ForesterUtil.LINE_SEPARATOR );
+ out.write( "All domains : "
+ + sum_of_all_domains_encountered );
+ out.close();
+ ForesterUtil
+ .programMessage( surfacing.PRG_NAME,
+ "Wrote fitch domain combination dynamics counts analysis to \"" + output_file + "\"" );
+ }
+
+ /**
+ *
+ * @param all_binary_domains_combination_lost_fitch
+ * @param use_last_in_fitch_parsimony
+ * @param perform_dc_fich
+ * @param consider_directedness_and_adjacency_for_bin_combinations
* @param all_binary_domains_combination_gained if null ignored, otherwise this is to list all binary domain combinations
* which were gained under unweighted (Fitch) parsimony.
*/
final Map<String, DescriptiveStatistics> domain_length_stats_by_domain,
final Map<String, Integer> tax_code_to_id_map,
final boolean write_to_nexus,
- final boolean use_last_in_fitch_parsimony ) {
+ final boolean use_last_in_fitch_parsimony,
+ final boolean perform_dc_fich ) {
final String sep = ForesterUtil.LINE_SEPARATOR + "###################" + ForesterUtil.LINE_SEPARATOR;
final String date_time = ForesterUtil.getCurrentDateTime();
final SortedSet<String> all_pfams_encountered = new TreeSet<String>();
else {
domain_parsimony.executeDolloParsimonyOnDomainPresence();
}
- SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossMatrix(), outfile_name
- + surfacing.PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_DOMAINS, Format.FORESTER );
- SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossCountsMatrix(), outfile_name
- + surfacing.PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_DOMAINS, Format.FORESTER );
+ SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossMatrix(),
+ outfile_name + surfacing.PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_DOMAINS,
+ Format.FORESTER );
+ SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossCountsMatrix(),
+ outfile_name + surfacing.PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_DOMAINS,
+ Format.FORESTER );
SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
CharacterStateMatrix.GainLossStates.GAIN,
outfile_name + surfacing.PARSIMONY_OUTPUT_DOLLO_GAINS_D,
sep,
ForesterUtil.LINE_SEPARATOR,
null );
- SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(), null, outfile_name
- + surfacing.PARSIMONY_OUTPUT_DOLLO_PRESENT_D, sep, ForesterUtil.LINE_SEPARATOR, null );
+ SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
+ null,
+ outfile_name + surfacing.PARSIMONY_OUTPUT_DOLLO_PRESENT_D,
+ sep,
+ ForesterUtil.LINE_SEPARATOR,
+ null );
//HTML:
writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
go_id_to_term_map,
all_pfams_lost_as_domains,
"_dollo_losses_d",
tax_code_to_id_map );
- // writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
- // go_id_to_term_map,
- // go_namespace_limit,
- // false,
- // domain_parsimony.getGainLossMatrix(),
- // null,
- // outfile_name + surfacing.PARSIMONY_OUTPUT_DOLLO_PRESENT_HTML_D,
- // sep,
- // ForesterUtil.LINE_SEPARATOR,
- // "Dollo Parsimony | Present | Domains",
- // "",
- // domain_id_to_secondary_features_maps,
- // all_pfams_encountered,
- // null,
- // "_dollo_present_d",
- // tax_code_to_id_map );
+ writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
+ go_id_to_term_map,
+ go_namespace_limit,
+ false,
+ domain_parsimony.getGainLossMatrix(),
+ null,
+ outfile_name + surfacing.PARSIMONY_OUTPUT_DOLLO_PRESENT_HTML_D,
+ sep,
+ ForesterUtil.LINE_SEPARATOR,
+ "Dollo Parsimony | Present | Domains",
+ "",
+ domain_id_to_secondary_features_maps,
+ all_pfams_encountered,
+ null,
+ "_dollo_present_d",
+ tax_code_to_id_map );
preparePhylogeny( local_phylogeny_l,
domain_parsimony,
date_time,
"Dollo parsimony on domain presence/absence",
"dollo_on_domains_" + outfile_name,
parameters_str );
- SurfacingUtil.writePhylogenyToFile( local_phylogeny_l, outfile_name
- + surfacing.DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO );
+ SurfacingUtil.writePhylogenyToFile( local_phylogeny_l,
+ outfile_name + surfacing.DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO );
try {
writeAllDomainsChangedOnAllSubtrees( local_phylogeny_l, true, outfile_name, "_dollo_all_gains_d" );
writeAllDomainsChangedOnAllSubtrees( local_phylogeny_l, false, outfile_name, "_dollo_all_losses_d" );
e.printStackTrace();
ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
}
- if ( domain_parsimony.calculateNumberOfBinaryDomainCombination() > 0 ) {
+ if ( perform_dc_fich && ( domain_parsimony.calculateNumberOfBinaryDomainCombination() > 0 ) ) {
// FITCH DOMAIN COMBINATIONS
// -------------------------
local_phylogeny_l = phylogeny.copy();
String randomization = "no";
if ( radomize_fitch_parsimony ) {
- domain_parsimony.executeFitchParsimonyOnBinaryDomainCombintion( random_number_seed_for_fitch_parsimony );
+ domain_parsimony
+ .executeFitchParsimonyOnBinaryDomainCombintion( random_number_seed_for_fitch_parsimony );
randomization = "yes, seed = " + random_number_seed_for_fitch_parsimony;
}
else {
domain_parsimony.executeFitchParsimonyOnBinaryDomainCombintion( use_last_in_fitch_parsimony );
}
- SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossMatrix(), outfile_name
- + surfacing.PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_BINARY_COMBINATIONS, Format.FORESTER );
- SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossCountsMatrix(), outfile_name
- + surfacing.PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_BINARY_COMBINATIONS, Format.FORESTER );
- SurfacingUtil
- .writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
- CharacterStateMatrix.GainLossStates.GAIN,
- outfile_name + surfacing.PARSIMONY_OUTPUT_FITCH_GAINS_BC,
- sep,
- ForesterUtil.LINE_SEPARATOR,
- null );
+ SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossMatrix(),
+ outfile_name
+ + surfacing.PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_BINARY_COMBINATIONS,
+ Format.FORESTER );
+ SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossCountsMatrix(),
+ outfile_name
+ + surfacing.PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_BINARY_COMBINATIONS,
+ Format.FORESTER );
+ SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
+ CharacterStateMatrix.GainLossStates.GAIN,
+ outfile_name + surfacing.PARSIMONY_OUTPUT_FITCH_GAINS_BC,
+ sep,
+ ForesterUtil.LINE_SEPARATOR,
+ null );
SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
CharacterStateMatrix.GainLossStates.LOSS,
outfile_name
sep,
ForesterUtil.LINE_SEPARATOR,
null );
- SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(), null, outfile_name
- + surfacing.PARSIMONY_OUTPUT_FITCH_PRESENT_BC, sep, ForesterUtil.LINE_SEPARATOR, null );
+ SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
+ null,
+ outfile_name
+ + surfacing.PARSIMONY_OUTPUT_FITCH_PRESENT_BC,
+ sep,
+ ForesterUtil.LINE_SEPARATOR,
+ null );
if ( all_binary_domains_combination_gained_fitch != null ) {
- collectChangedDomainCombinationsFromBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
- dc_type,
- all_binary_domains_combination_gained_fitch,
- true );
+ collectChangedDomainCombinationsFromBinaryStatesMatrixAsListToFile( domain_parsimony
+ .getGainLossMatrix(), dc_type, all_binary_domains_combination_gained_fitch, true );
}
if ( all_binary_domains_combination_lost_fitch != null ) {
- collectChangedDomainCombinationsFromBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
- dc_type,
- all_binary_domains_combination_lost_fitch,
- false );
+ collectChangedDomainCombinationsFromBinaryStatesMatrixAsListToFile( domain_parsimony
+ .getGainLossMatrix(), dc_type, all_binary_domains_combination_lost_fitch, false );
}
if ( output_binary_domain_combinations_for_graphs ) {
- SurfacingUtil
- .writeBinaryStatesMatrixAsListToFileForBinaryCombinationsForGraphAnalysis( domain_parsimony
- .getGainLossMatrix(),
- null,
- outfile_name
- + surfacing.PARSIMONY_OUTPUT_FITCH_PRESENT_BC_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS,
- sep,
- ForesterUtil.LINE_SEPARATOR,
- BinaryDomainCombination.OutputFormat.DOT );
+ SurfacingUtil.writeBinaryStatesMatrixAsListToFileForBinaryCombinationsForGraphAnalysis( domain_parsimony
+ .getGainLossMatrix(),
+ null,
+ outfile_name
+ + surfacing.PARSIMONY_OUTPUT_FITCH_PRESENT_BC_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS,
+ sep,
+ ForesterUtil.LINE_SEPARATOR,
+ BinaryDomainCombination.OutputFormat.DOT );
}
// HTML:
writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
go_id_to_term_map,
outfile_name,
all_pfams_encountered );
- writePfamsToFile( outfile_name + surfacing.ALL_PFAMS_GAINED_AS_DOMAINS_SUFFIX, all_pfams_gained_as_domains );
+ writePfamsToFile( outfile_name + surfacing.ALL_PFAMS_GAINED_AS_DOMAINS_SUFFIX,
+ all_pfams_gained_as_domains );
writePfamsToFile( outfile_name + surfacing.ALL_PFAMS_LOST_AS_DOMAINS_SUFFIX, all_pfams_lost_as_domains );
writePfamsToFile( outfile_name + surfacing.ALL_PFAMS_GAINED_AS_DC_SUFFIX,
all_pfams_gained_as_dom_combinations );
- writePfamsToFile( outfile_name + surfacing.ALL_PFAMS_LOST_AS_DC_SUFFIX, all_pfams_lost_as_dom_combinations );
+ writePfamsToFile( outfile_name + surfacing.ALL_PFAMS_LOST_AS_DC_SUFFIX,
+ all_pfams_lost_as_dom_combinations );
preparePhylogeny( local_phylogeny_l,
domain_parsimony,
date_time,
+ randomization,
"fitch_on_binary_domain_combinations_" + outfile_name,
parameters_str );
- SurfacingUtil.writePhylogenyToFile( local_phylogeny_l, outfile_name
- + surfacing.BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH );
+ SurfacingUtil
+ .writePhylogenyToFile( local_phylogeny_l,
+ outfile_name
+ + surfacing.BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH );
calculateIndependentDomainCombinationGains( local_phylogeny_l,
outfile_name
+ surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_OUTPUT_SUFFIX,
phylogeny );
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 );
- SurfacingUtil.writeMatrixToFile( secondary_features_parsimony.getGainLossCountsMatrix(), outfile_name
- + surfacing.PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_SECONDARY_FEATURES, Format.FORESTER );
- SurfacingUtil
- .writeBinaryStatesMatrixAsListToFile( secondary_features_parsimony.getGainLossMatrix(),
- CharacterStateMatrix.GainLossStates.GAIN,
- outfile_name
- + surfacing.PARSIMONY_OUTPUT_DOLLO_GAINS_SECONDARY_FEATURES,
- sep,
- ForesterUtil.LINE_SEPARATOR,
- null );
- SurfacingUtil
- .writeBinaryStatesMatrixAsListToFile( secondary_features_parsimony.getGainLossMatrix(),
- CharacterStateMatrix.GainLossStates.LOSS,
- outfile_name
- + surfacing.PARSIMONY_OUTPUT_DOLLO_LOSSES_SECONDARY_FEATURES,
- sep,
- ForesterUtil.LINE_SEPARATOR,
- null );
- SurfacingUtil
- .writeBinaryStatesMatrixAsListToFile( secondary_features_parsimony.getGainLossMatrix(),
- null,
- outfile_name
- + surfacing.PARSIMONY_OUTPUT_DOLLO_PRESENT_SECONDARY_FEATURES,
- sep,
- ForesterUtil.LINE_SEPARATOR,
- null );
+ SurfacingUtil.writeMatrixToFile( secondary_features_parsimony.getGainLossMatrix(),
+ outfile_name + surfacing.PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_SECONDARY_FEATURES,
+ Format.FORESTER );
+ SurfacingUtil.writeMatrixToFile( secondary_features_parsimony.getGainLossCountsMatrix(),
+ outfile_name
+ + surfacing.PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_SECONDARY_FEATURES,
+ Format.FORESTER );
+ SurfacingUtil.writeBinaryStatesMatrixAsListToFile( secondary_features_parsimony.getGainLossMatrix(),
+ CharacterStateMatrix.GainLossStates.GAIN,
+ outfile_name
+ + surfacing.PARSIMONY_OUTPUT_DOLLO_GAINS_SECONDARY_FEATURES,
+ sep,
+ ForesterUtil.LINE_SEPARATOR,
+ null );
+ SurfacingUtil.writeBinaryStatesMatrixAsListToFile( secondary_features_parsimony.getGainLossMatrix(),
+ CharacterStateMatrix.GainLossStates.LOSS,
+ outfile_name
+ + surfacing.PARSIMONY_OUTPUT_DOLLO_LOSSES_SECONDARY_FEATURES,
+ sep,
+ ForesterUtil.LINE_SEPARATOR,
+ null );
+ SurfacingUtil.writeBinaryStatesMatrixAsListToFile( secondary_features_parsimony.getGainLossMatrix(),
+ null,
+ outfile_name
+ + surfacing.PARSIMONY_OUTPUT_DOLLO_PRESENT_SECONDARY_FEATURES,
+ sep,
+ ForesterUtil.LINE_SEPARATOR,
+ null );
preparePhylogeny( local_phylogeny_copy,
secondary_features_parsimony,
date_time,
"Dollo parsimony on secondary feature presence/absence",
"dollo_on_secondary_features_" + outfile_name,
parameters_str );
- SurfacingUtil.writePhylogenyToFile( local_phylogeny_copy, outfile_name
- + surfacing.SECONDARY_FEATURES_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO );
+ SurfacingUtil
+ .writePhylogenyToFile( local_phylogeny_copy,
+ outfile_name + surfacing.SECONDARY_FEATURES_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO );
// FITCH DOMAIN COMBINATIONS
// -------------------------
local_phylogeny_copy = phylogeny.copy();
+ 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", null, null, null, null );
+ 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",
+ null,
+ null,
+ null,
+ null );
+ }
+
+ public static void executePlusMinusAnalysis( final File output_file,
+ final List<String> plus_minus_analysis_high_copy_base,
+ final List<String> plus_minus_analysis_high_copy_target,
+ final List<String> plus_minus_analysis_low_copy,
+ final List<GenomeWideCombinableDomains> gwcd_list,
+ final SortedMap<Species, List<Protein>> protein_lists_per_species,
+ final Map<String, List<GoId>> domain_id_to_go_ids_map,
+ final Map<GoId, GoTerm> go_id_to_term_map,
+ final List<Object> plus_minus_analysis_numbers ) {
+ final Set<String> all_spec = new HashSet<String>();
+ for( final GenomeWideCombinableDomains gwcd : gwcd_list ) {
+ all_spec.add( gwcd.getSpecies().getSpeciesId() );
+ }
+ final File html_out_dom = new File( output_file + surfacing.PLUS_MINUS_DOM_SUFFIX_HTML );
+ final File plain_out_dom = new File( output_file + surfacing.PLUS_MINUS_DOM_SUFFIX );
+ final File html_out_dc = new File( output_file + surfacing.PLUS_MINUS_DC_SUFFIX_HTML );
+ final File all_domains_go_ids_out_dom = new File( output_file + surfacing.PLUS_MINUS_ALL_GO_IDS_DOM_SUFFIX );
+ final File passing_domains_go_ids_out_dom = new File( output_file
+ + surfacing.PLUS_MINUS_PASSING_GO_IDS_DOM_SUFFIX );
+ final File proteins_file_base = new File( output_file + "" );
+ final int min_diff = ( ( Integer ) plus_minus_analysis_numbers.get( 0 ) ).intValue();
+ final double factor = ( ( Double ) plus_minus_analysis_numbers.get( 1 ) ).doubleValue();
+ try {
+ DomainCountsDifferenceUtil.calculateCopyNumberDifferences( gwcd_list,
+ protein_lists_per_species,
+ plus_minus_analysis_high_copy_base,
+ plus_minus_analysis_high_copy_target,
+ plus_minus_analysis_low_copy,
+ min_diff,
+ factor,
+ plain_out_dom,
+ html_out_dom,
+ html_out_dc,
+ domain_id_to_go_ids_map,
+ go_id_to_term_map,
+ all_domains_go_ids_out_dom,
+ passing_domains_go_ids_out_dom,
+ proteins_file_base );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
+ }
+ ForesterUtil.programMessage( surfacing.PRG_NAME,
+ "Wrote plus minus domain analysis results to \"" + html_out_dom + "\"" );
+ ForesterUtil.programMessage( surfacing.PRG_NAME,
+ "Wrote plus minus domain analysis results to \"" + plain_out_dom + "\"" );
+ ForesterUtil.programMessage( surfacing.PRG_NAME,
+ "Wrote plus minus domain analysis results to \"" + html_out_dc + "\"" );
+ ForesterUtil.programMessage( surfacing.PRG_NAME,
+ "Wrote plus minus domain analysis based passing GO ids to \""
+ + passing_domains_go_ids_out_dom + "\"" );
+ ForesterUtil.programMessage( surfacing.PRG_NAME,
+ "Wrote plus minus domain analysis based all GO ids to \""
+ + all_domains_go_ids_out_dom + "\"" );
}
public static void extractProteinNames( final List<Protein> proteins,
final List<String> query_domain_ids_nc_order,
final Writer out,
final String separator,
- final String limit_to_species ) throws IOException {
+ final String limit_to_species )
+ throws IOException {
for( final Protein protein : proteins ) {
if ( ForesterUtil.isEmpty( limit_to_species )
|| protein.getSpecies().getSpeciesId().equalsIgnoreCase( limit_to_species ) ) {
}
out.write( "]" );
out.write( separator );
- if ( !( ForesterUtil.isEmpty( protein.getDescription() ) || protein.getDescription()
- .equals( SurfacingConstants.NONE ) ) ) {
+ 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 ) ) ) {
+ if ( !( ForesterUtil.isEmpty( protein.getAccession() )
+ || protein.getAccession().equals( SurfacingConstants.NONE ) ) ) {
out.write( protein.getAccession() );
}
out.write( SurfacingConstants.NL );
final Writer out,
final String separator,
final String limit_to_species,
- final double domain_e_cutoff ) throws IOException {
- System.out.println( "Per domain E-value: " + domain_e_cutoff );
+ final double domain_e_cutoff )
+ throws IOException {
+ //System.out.println( "Per domain E-value: " + domain_e_cutoff );
for( final Species species : protein_lists_per_species.keySet() ) {
- System.out.println( species + ":" );
+ //System.out.println( species + ":" );
for( final Protein protein : protein_lists_per_species.get( species ) ) {
if ( ForesterUtil.isEmpty( limit_to_species )
|| protein.getSpecies().getSpeciesId().equalsIgnoreCase( limit_to_species ) ) {
out.write( domain.getFrom() + "-" + domain.getTo() );
if ( prev_to >= 0 ) {
final int l = domain.getFrom() - prev_to;
- System.out.println( l );
+ // System.out.println( l );
}
prev_to = domain.getTo();
}
out.write( ":" + domain.getPerDomainEvalue() );
}
out.write( "}" );
- if ( !( ForesterUtil.isEmpty( protein.getDescription() ) || protein.getDescription()
- .equals( SurfacingConstants.NONE ) ) ) {
+ 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 ) ) ) {
+ if ( !( ForesterUtil.isEmpty( protein.getAccession() )
+ || protein.getAccession().equals( SurfacingConstants.NONE ) ) ) {
out.write( protein.getAccession() );
}
out.write( SurfacingConstants.NL );
while ( it.hasNext() ) {
final PhylogenyNode n = it.next();
if ( ForesterUtil.isEmpty( n.getName() )
- && ( !n.getNodeData().isHasTaxonomy() || ForesterUtil.isEmpty( n.getNodeData().getTaxonomy()
- .getScientificName() ) )
- && ( !n.getNodeData().isHasTaxonomy() || ForesterUtil.isEmpty( n.getNodeData().getTaxonomy()
- .getCommonName() ) ) ) {
+ && ( !n.getNodeData().isHasTaxonomy()
+ || ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) )
+ && ( !n.getNodeData().isHasTaxonomy()
+ || ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getCommonName() ) ) ) {
if ( n.getParent() != null ) {
names.append( " " );
names.append( n.getParent().getName() );
return c;
}
- /**
- * Returns true is Domain domain falls in an uninterrupted stretch of
- * covered positions.
- *
- * @param domain
- * @param covered_positions
- * @return
- */
- public static boolean isEngulfed( final Domain domain, final List<Boolean> covered_positions ) {
- for( int i = domain.getFrom(); i <= domain.getTo(); ++i ) {
- if ( ( i >= covered_positions.size() ) || ( covered_positions.get( i ) != true ) ) {
- return false;
+ public static void log( final String msg, final Writer w ) {
+ try {
+ w.write( msg );
+ w.write( ForesterUtil.LINE_SEPARATOR );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
+ }
+ }
+
+ public static Phylogeny[] obtainAndPreProcessIntrees( final File[] intree_files,
+ final int number_of_genomes,
+ final String[][] input_file_properties ) {
+ final Phylogeny[] intrees = new Phylogeny[ intree_files.length ];
+ int i = 0;
+ for( final File intree_file : intree_files ) {
+ Phylogeny intree = null;
+ final String error = ForesterUtil.isReadableFile( intree_file );
+ if ( !ForesterUtil.isEmpty( error ) ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME,
+ "cannot read input tree file [" + intree_file + "]: " + error );
+ }
+ try {
+ final Phylogeny[] p_array = ParserBasedPhylogenyFactory.getInstance()
+ .create( intree_file, ParserUtils.createParserDependingOnFileType( intree_file, true ) );
+ if ( p_array.length < 1 ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME,
+ "file [" + intree_file
+ + "] does not contain any phylogeny in phyloXML format" );
+ }
+ else if ( p_array.length > 1 ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME,
+ "file [" + intree_file
+ + "] contains more than one phylogeny in phyloXML format" );
+ }
+ intree = p_array[ 0 ];
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME,
+ "failed to read input tree from file [" + intree_file + "]: " + error );
+ }
+ if ( ( intree == null ) || intree.isEmpty() ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "input tree [" + intree_file + "] is empty" );
+ }
+ if ( !intree.isRooted() ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "input tree [" + intree_file + "] is not rooted" );
+ }
+ final StringBuilder parent_names = new StringBuilder();
+ final int nodes_lacking_name = getNumberOfNodesLackingName( intree, parent_names );
+ if ( nodes_lacking_name > 0 ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME,
+ "input tree [" + intree_file + "] has " + nodes_lacking_name
+ + " node(s) lacking a name [parent names:" + parent_names + "]" );
+ }
+ preparePhylogenyForParsimonyAnalyses( intree, input_file_properties );
+ if ( !intree.isCompletelyBinary() ) {
+ ForesterUtil.printWarningMessage( surfacing.PRG_NAME,
+ "input tree [" + intree_file + "] is not completely binary" );
+ }
+ intrees[ i++ ] = intree;
+ }
+ return intrees;
+ }
+
+ public static Phylogeny obtainFirstIntree( final File intree_file ) {
+ Phylogeny intree = null;
+ final String error = ForesterUtil.isReadableFile( intree_file );
+ if ( !ForesterUtil.isEmpty( error ) ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME,
+ "cannot read input tree file [" + intree_file + "]: " + error );
+ }
+ try {
+ final Phylogeny[] phys = ParserBasedPhylogenyFactory.getInstance()
+ .create( intree_file, ParserUtils.createParserDependingOnFileType( intree_file, true ) );
+ if ( phys.length < 1 ) {
+ ForesterUtil
+ .fatalError( surfacing.PRG_NAME,
+ "file [" + intree_file + "] does not contain any phylogeny in phyloXML format" );
+ }
+ else if ( phys.length > 1 ) {
+ ForesterUtil
+ .fatalError( surfacing.PRG_NAME,
+ "file [" + intree_file + "] contains more than one phylogeny in phyloXML format" );
+ }
+ intree = phys[ 0 ];
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME,
+ "failed to read input tree from file [" + intree_file + "]: " + error );
+ }
+ if ( ( intree == null ) || intree.isEmpty() ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "input tree [" + intree_file + "] is empty" );
+ }
+ if ( !intree.isRooted() ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "input tree [" + intree_file + "] is not rooted" );
+ }
+ return intree;
+ }
+
+ public static String obtainHexColorStringDependingOnTaxonomyGroup( final String tax_code, final Phylogeny phy )
+ throws IllegalArgumentException {
+ if ( !_TAXCODE_HEXCOLORSTRING_MAP.containsKey( tax_code ) ) {
+ if ( ( phy != null ) && !phy.isEmpty() ) {
+ // final List<PhylogenyNode> nodes = phy.getNodesViaTaxonomyCode( tax_code );
+ // Color c = null;
+ // if ( ( nodes == null ) || nodes.isEmpty() ) {
+ // throw new IllegalArgumentException( "code " + tax_code + " is not found" );
+ // }
+ // if ( nodes.size() != 1 ) {
+ // throw new IllegalArgumentException( "code " + tax_code + " is not unique" );
+ // }
+ // PhylogenyNode n = nodes.get( 0 );
+ // while ( n != null ) {
+ // if ( n.getNodeData().isHasTaxonomy()
+ // && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) {
+ // c = ForesterUtil.obtainColorDependingOnTaxonomyGroup( n.getNodeData().getTaxonomy()
+ // .getScientificName(), tax_code );
+ // }
+ // if ( ( c == null ) && !ForesterUtil.isEmpty( n.getName() ) ) {
+ // c = ForesterUtil.obtainColorDependingOnTaxonomyGroup( n.getName(), tax_code );
+ // }
+ // if ( c != null ) {
+ // break;
+ // }
+ // n = n.getParent();
+ // }
+ final String group = obtainTaxonomyGroup( tax_code, phy );
+ final Color c = ForesterUtil.obtainColorDependingOnTaxonomyGroup( group );
+ if ( c == null ) {
+ throw new IllegalArgumentException( "no color found for taxonomy group \"" + group
+ + "\" for code \"" + tax_code + "\"" );
+ }
+ final String hex = String.format( "#%02x%02x%02x", c.getRed(), c.getGreen(), c.getBlue() );
+ _TAXCODE_HEXCOLORSTRING_MAP.put( tax_code, hex );
+ }
+ else {
+ throw new IllegalArgumentException( "unable to obtain color for code " + tax_code
+ + " (tree is null or empty and code is not in map)" );
+ }
+ }
+ return _TAXCODE_HEXCOLORSTRING_MAP.get( tax_code );
+ }
+
+ public static String obtainTaxonomyGroup( final String tax_code, final Phylogeny species_tree )
+ throws IllegalArgumentException {
+ if ( !_TAXCODE_TAXGROUP_MAP.containsKey( tax_code ) ) {
+ if ( ( species_tree != null ) && !species_tree.isEmpty() ) {
+ final List<PhylogenyNode> nodes = species_tree.getNodesViaTaxonomyCode( tax_code );
+ if ( ( nodes == null ) || nodes.isEmpty() ) {
+ throw new IllegalArgumentException( "code " + tax_code + " is not found" );
+ }
+ if ( nodes.size() != 1 ) {
+ throw new IllegalArgumentException( "code " + tax_code + " is not unique" );
+ }
+ PhylogenyNode n = nodes.get( 0 );
+ String group = null;
+ while ( n != null ) {
+ if ( n.getNodeData().isHasTaxonomy()
+ && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) {
+ group = ForesterUtil
+ .obtainNormalizedTaxonomyGroup( n.getNodeData().getTaxonomy().getScientificName() );
+ }
+ if ( ForesterUtil.isEmpty( group ) && !ForesterUtil.isEmpty( n.getName() ) ) {
+ group = ForesterUtil.obtainNormalizedTaxonomyGroup( n.getName() );
+ }
+ if ( !ForesterUtil.isEmpty( group ) ) {
+ break;
+ }
+ n = n.getParent();
+ }
+ if ( ForesterUtil.isEmpty( group ) ) {
+ group = TaxonomyGroups.OTHER;
+ }
+ _TAXCODE_TAXGROUP_MAP.put( tax_code, group );
+ }
+ else {
+ throw new IllegalArgumentException( "unable to obtain group for code " + tax_code
+ + " (tree is null or empty and code is not in map)" );
}
}
- return true;
+ return _TAXCODE_TAXGROUP_MAP.get( tax_code );
}
public static void performDomainArchitectureAnalysis( final SortedMap<String, Set<String>> domain_architecutures,
p.setRooted( true );
}
+ public static void preparePhylogenyForParsimonyAnalyses( final Phylogeny intree,
+ final String[][] input_file_properties ) {
+ final String[] genomes = new String[ input_file_properties.length ];
+ for( int i = 0; i < input_file_properties.length; ++i ) {
+ if ( intree.getNodes( input_file_properties[ i ][ 1 ] ).size() > 1 ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME,
+ "node named [" + input_file_properties[ i ][ 1 ]
+ + "] is not unique in input tree " + intree.getName() );
+ }
+ genomes[ i ] = input_file_properties[ i ][ 1 ];
+ }
+ //
+ final PhylogenyNodeIterator it = intree.iteratorPostorder();
+ while ( it.hasNext() ) {
+ final PhylogenyNode n = it.next();
+ if ( ForesterUtil.isEmpty( n.getName() ) ) {
+ if ( n.getNodeData().isHasTaxonomy()
+ && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) {
+ n.setName( n.getNodeData().getTaxonomy().getTaxonomyCode() );
+ }
+ else if ( n.getNodeData().isHasTaxonomy()
+ && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) {
+ n.setName( n.getNodeData().getTaxonomy().getScientificName() );
+ }
+ else if ( n.getNodeData().isHasTaxonomy()
+ && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getCommonName() ) ) {
+ n.setName( n.getNodeData().getTaxonomy().getCommonName() );
+ }
+ else {
+ ForesterUtil
+ .fatalError( surfacing.PRG_NAME,
+ "node with no name, scientific name, common name, or taxonomy code present" );
+ }
+ }
+ }
+ final List<String> igns = PhylogenyMethods.deleteExternalNodesPositiveSelection( genomes, intree );
+ if ( igns.size() > 0 ) {
+ System.out.println( "Not using the following " + igns.size() + " nodes:" );
+ for( int i = 0; i < igns.size(); ++i ) {
+ System.out.println( " " + i + ": " + igns.get( i ) );
+ }
+ System.out.println( "--" );
+ }
+ //Test for node names:
+ final SortedSet<String> not_found = new TreeSet<String>();
+ final SortedSet<String> not_unique = new TreeSet<String>();
+ for( final String[] input_file_propertie : input_file_properties ) {
+ final String name = input_file_propertie[ 1 ];
+ final List<PhylogenyNode> nodes = intree.getNodes( name );
+ if ( ( nodes == null ) || ( nodes.size() < 1 ) ) {
+ not_found.add( name );
+ }
+ if ( nodes.size() > 1 ) {
+ not_unique.add( name );
+ }
+ }
+ if ( not_found.size() > 0 ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME,
+ "the following " + not_found.size()
+ + " node(s) are not present in the input tree: " + not_found );
+ }
+ if ( not_unique.size() > 0 ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME,
+ "the following " + not_unique.size()
+ + " node(s) are not unique in the input tree: " + not_unique );
+ }
+ }
+
+ public static void printOutPercentageOfMultidomainProteins( final SortedMap<Integer, Integer> all_genomes_domains_per_potein_histo,
+ final Writer log_writer ) {
+ int sum = 0;
+ for( final Entry<Integer, Integer> entry : all_genomes_domains_per_potein_histo.entrySet() ) {
+ sum += entry.getValue();
+ }
+ final double percentage = ( 100.0 * ( sum - all_genomes_domains_per_potein_histo.get( 1 ) ) ) / sum;
+ ForesterUtil.programMessage( surfacing.PRG_NAME, "Percentage of multidomain proteins: " + percentage + "%" );
+ log( "Percentage of multidomain proteins: : " + percentage + "%", log_writer );
+ }
+
+ public static void processFilter( final File filter_file, final SortedSet<String> filter ) {
+ SortedSet<String> filter_str = null;
+ try {
+ filter_str = ForesterUtil.file2set( filter_file );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
+ }
+ if ( filter_str != null ) {
+ for( final String string : filter_str ) {
+ filter.add( string );
+ }
+ }
+ if ( surfacing.VERBOSE ) {
+ System.out.println( "Filter:" );
+ for( final String domainId : filter ) {
+ System.out.println( domainId );
+ }
+ }
+ }
+
+ public static String[][] processInputGenomesFile( final File input_genomes ) {
+ String[][] input_file_properties = null;
+ try {
+ input_file_properties = ForesterUtil.file22dArray( input_genomes );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME,
+ "genomes files is to be in the following format \"<hmmpfam output file> <species>\": "
+ + e.getLocalizedMessage() );
+ }
+ final Set<String> specs = new HashSet<String>();
+ final Set<String> paths = new HashSet<String>();
+ for( int i = 0; i < input_file_properties.length; ++i ) {
+ if ( !PhyloXmlUtil.TAXOMONY_CODE_PATTERN.matcher( input_file_properties[ i ][ 1 ] ).matches() ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME,
+ "illegal format for species code: " + input_file_properties[ i ][ 1 ] );
+ }
+ if ( specs.contains( input_file_properties[ i ][ 1 ] ) ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME,
+ "species code " + input_file_properties[ i ][ 1 ] + " is not unique" );
+ }
+ specs.add( input_file_properties[ i ][ 1 ] );
+ if ( paths.contains( input_file_properties[ i ][ 0 ] ) ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME,
+ "path " + input_file_properties[ i ][ 0 ] + " is not unique" );
+ }
+ paths.add( input_file_properties[ i ][ 0 ] );
+ final String error = ForesterUtil.isReadableFile( new File( input_file_properties[ i ][ 0 ] ) );
+ if ( !ForesterUtil.isEmpty( error ) ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, error );
+ }
+ }
+ return input_file_properties;
+ }
+
+ public static void processPlusMinusAnalysisOption( final CommandLineArguments cla,
+ final List<String> high_copy_base,
+ final List<String> high_copy_target,
+ final List<String> low_copy,
+ final List<Object> numbers ) {
+ if ( cla.isOptionSet( surfacing.PLUS_MINUS_ANALYSIS_OPTION ) ) {
+ if ( !cla.isOptionValueSet( surfacing.PLUS_MINUS_ANALYSIS_OPTION ) ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME,
+ "no value for 'plus-minus' file: -" + surfacing.PLUS_MINUS_ANALYSIS_OPTION
+ + "=<file>" );
+ }
+ final File plus_minus_file = new File( cla.getOptionValue( surfacing.PLUS_MINUS_ANALYSIS_OPTION ) );
+ final String msg = ForesterUtil.isReadableFile( plus_minus_file );
+ if ( !ForesterUtil.isEmpty( msg ) ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "can not read from \"" + plus_minus_file + "\": " + msg );
+ }
+ processPlusMinusFile( plus_minus_file, high_copy_base, high_copy_target, low_copy, numbers );
+ }
+ }
+
+ // First numbers is minimal difference, second is factor.
+ public static void processPlusMinusFile( final File plus_minus_file,
+ final List<String> high_copy_base,
+ final List<String> high_copy_target,
+ final List<String> low_copy,
+ final List<Object> numbers ) {
+ Set<String> species_set = null;
+ int min_diff = surfacing.PLUS_MINUS_ANALYSIS_MIN_DIFF_DEFAULT;
+ double factor = surfacing.PLUS_MINUS_ANALYSIS_FACTOR_DEFAULT;
+ try {
+ species_set = ForesterUtil.file2set( plus_minus_file );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
+ }
+ if ( species_set != null ) {
+ for( final String species : species_set ) {
+ final String species_trimmed = species.substring( 1 );
+ if ( species.startsWith( "+" ) ) {
+ if ( low_copy.contains( species_trimmed ) ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME,
+ "species/genome names can not appear with both '+' and '-' suffix, as appears the case for: \""
+ + species_trimmed + "\"" );
+ }
+ high_copy_base.add( species_trimmed );
+ }
+ else if ( species.startsWith( "*" ) ) {
+ if ( low_copy.contains( species_trimmed ) ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME,
+ "species/genome names can not appear with both '*' and '-' suffix, as appears the case for: \""
+ + species_trimmed + "\"" );
+ }
+ high_copy_target.add( species_trimmed );
+ }
+ else if ( species.startsWith( "-" ) ) {
+ if ( high_copy_base.contains( species_trimmed ) || high_copy_target.contains( species_trimmed ) ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME,
+ "species/genome names can not appear with both '+' or '*' and '-' suffix, as appears the case for: \""
+ + species_trimmed + "\"" );
+ }
+ low_copy.add( species_trimmed );
+ }
+ else if ( species.startsWith( "$D" ) ) {
+ try {
+ min_diff = Integer.parseInt( species.substring( 3 ) );
+ }
+ catch ( final NumberFormatException e ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME,
+ "could not parse integer value for minimal difference from: \""
+ + species.substring( 3 ) + "\"" );
+ }
+ }
+ else if ( species.startsWith( "$F" ) ) {
+ try {
+ factor = Double.parseDouble( species.substring( 3 ) );
+ }
+ catch ( final NumberFormatException e ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME,
+ "could not parse double value for factor from: \""
+ + species.substring( 3 ) + "\"" );
+ }
+ }
+ else if ( species.startsWith( "#" ) ) {
+ // Comment, ignore.
+ }
+ else {
+ ForesterUtil.fatalError( surfacing.PRG_NAME,
+ "species/genome names in 'plus minus' file must begin with '*' (high copy target genome), '+' (high copy base genomes), '-' (low copy genomes), '$D=<integer>' minimal Difference (default is 1), '$F=<double>' factor (default is 1.0), double), or '#' (ignore) suffix, encountered: \""
+ + species + "\"" );
+ }
+ numbers.add( new Integer( min_diff + "" ) );
+ numbers.add( new Double( factor + "" ) );
+ }
+ }
+ else {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "'plus minus' file [" + plus_minus_file + "] appears empty" );
+ }
+ }
+
/*
* species | protein id | n-terminal domain | c-terminal domain | n-terminal domain per domain E-value | c-terminal domain per domain E-value
- *
- *
+ *
+ *
*/
static public StringBuffer proteinToDomainCombinations( final Protein protein,
final String protein_id,
return sb;
}
- /**
- *
- * Example regarding engulfment: ------------0.1 ----------0.2 --0.3 =>
- * domain with 0.3 is ignored
- *
- * -----------0.1 ----------0.2 --0.3 => domain with 0.3 is ignored
- *
- *
- * ------------0.1 ----------0.3 --0.2 => domains with 0.3 and 0.2 are _not_
- * ignored
- *
- * @param max_allowed_overlap
- * maximal allowed overlap (inclusive) to be still considered not
- * overlapping (zero or negative value to allow any overlap)
- * @param remove_engulfed_domains
- * to remove domains which are completely engulfed by coverage of
- * domains with better support
- * @param protein
- * @return
- */
- public static Protein removeOverlappingDomains( final int max_allowed_overlap,
- final boolean remove_engulfed_domains,
- final Protein protein ) {
- final Protein pruned_protein = new BasicProtein( protein.getProteinId().getId(), protein.getSpecies()
- .getSpeciesId(), protein.getLength() );
- final List<Domain> sorted = SurfacingUtil.sortDomainsWithAscendingConfidenceValues( protein );
- final List<Boolean> covered_positions = new ArrayList<Boolean>();
- for( final Domain domain : sorted ) {
- if ( ( ( max_allowed_overlap < 0 ) || ( SurfacingUtil.calculateOverlap( domain, covered_positions ) <= max_allowed_overlap ) )
- && ( !remove_engulfed_domains || !isEngulfed( domain, covered_positions ) ) ) {
- final int covered_positions_size = covered_positions.size();
- for( int i = covered_positions_size; i < domain.getFrom(); ++i ) {
- covered_positions.add( false );
- }
- final int new_covered_positions_size = covered_positions.size();
- for( int i = domain.getFrom(); i <= domain.getTo(); ++i ) {
- if ( i < new_covered_positions_size ) {
- covered_positions.set( i, true );
- }
- else {
- covered_positions.add( true );
- }
- }
- pruned_protein.addProteinDomain( domain );
- }
- }
- return pruned_protein;
- }
-
public static List<Domain> sortDomainsWithAscendingConfidenceValues( final Protein protein ) {
final List<Domain> domains = new ArrayList<Domain>();
for( final Domain d : protein.getProteinDomains() ) {
public static void writeAllDomainsChangedOnAllSubtrees( final Phylogeny p,
final boolean get_gains,
final String outdir,
- final String suffix_for_filename ) throws IOException {
+ final String suffix_for_filename )
+ throws IOException {
CharacterStateMatrix.GainLossStates state = CharacterStateMatrix.GainLossStates.GAIN;
if ( !get_gains ) {
state = CharacterStateMatrix.GainLossStates.LOSS;
catch ( final IOException e ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
}
- ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote binary domain combination for \""
- + input_file_properties[ i ][ 0 ] + "\" (" + input_file_properties[ i ][ 1 ] + ", "
- + input_file_properties[ i ][ 2 ] + ") to: \"" + dc_outfile_dot + "\"" );
+ if ( input_file_properties[ i ].length == 3 ) {
+ ForesterUtil
+ .programMessage( surfacing.PRG_NAME,
+ "Wrote binary domain combination for \"" + input_file_properties[ i ][ 0 ] + "\" ("
+ + input_file_properties[ i ][ 1 ] + ", " + input_file_properties[ i ][ 2 ]
+ + ") to: \"" + dc_outfile_dot + "\"" );
+ }
+ else {
+ ForesterUtil.programMessage( surfacing.PRG_NAME,
+ "Wrote binary domain combination for \"" + input_file_properties[ i ][ 0 ]
+ + "\" (" + input_file_properties[ i ][ 1 ] + ") to: \""
+ + dc_outfile_dot + "\"" );
+ }
}
public static void writeBinaryStatesMatrixAsListToFile( final CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
for( int c = 0; c < matrix.getNumberOfCharacters(); ++c ) {
// Not nice:
// using null to indicate either UNCHANGED_PRESENT or GAIN.
- if ( ( matrix.getState( id, c ) == state )
- || ( ( state == null ) && ( ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.GAIN ) || ( matrix
- .getState( id, c ) == CharacterStateMatrix.GainLossStates.UNCHANGED_PRESENT ) ) ) ) {
+ if ( ( matrix.getState( id, c ) == state ) || ( ( state == null )
+ && ( ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.GAIN ) || ( matrix
+ .getState( id,
+ c ) == CharacterStateMatrix.GainLossStates.UNCHANGED_PRESENT ) ) ) ) {
out.write( matrix.getCharacter( c ) );
if ( ( descriptions != null ) && !descriptions.isEmpty()
&& descriptions.containsKey( matrix.getCharacter( c ) ) ) {
for( int c = 0; c < matrix.getNumberOfCharacters(); ++c ) {
// Not nice:
// using null to indicate either UNCHANGED_PRESENT or GAIN.
- if ( ( matrix.getState( id, c ) == state )
- || ( ( state == null ) && ( ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.GAIN ) || ( matrix
- .getState( id, c ) == CharacterStateMatrix.GainLossStates.UNCHANGED_PRESENT ) ) ) ) {
+ if ( ( matrix.getState( id, c ) == state ) || ( ( state == null )
+ && ( ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.GAIN ) || ( matrix
+ .getState( id,
+ c ) == CharacterStateMatrix.GainLossStates.UNCHANGED_PRESENT ) ) ) ) {
BinaryDomainCombination bdc = null;
try {
- bdc = BasicBinaryDomainCombination.createInstance( matrix.getCharacter( c ) );
+ bdc = BasicBinaryDomainCombination.obtainInstance( matrix.getCharacter( c ) );
}
catch ( final Exception e ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
int per_node_counter = 0;
out.write( "<html>" );
out.write( SurfacingConstants.NL );
- addHtmlHead( out, title_for_html );
+ writeHtmlHead( out, title_for_html );
out.write( SurfacingConstants.NL );
out.write( "<body>" );
out.write( SurfacingConstants.NL );
for( int c = 0; c < matrix.getNumberOfCharacters(); ++c ) {
// Not nice:
// using null to indicate either UNCHANGED_PRESENT or GAIN.
- if ( ( matrix.getState( id, c ) == state )
- || ( ( state == null ) && ( ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.UNCHANGED_PRESENT ) || ( matrix
- .getState( id, c ) == CharacterStateMatrix.GainLossStates.GAIN ) ) ) ) {
+ if ( ( matrix.getState( id, c ) == state ) || ( ( state == null )
+ && ( ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.UNCHANGED_PRESENT )
+ || ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.GAIN ) ) ) ) {
final String character = matrix.getCharacter( c );
String domain_0 = "";
String domain_1 = "";
out.write( SurfacingConstants.NL );
out.write( "<hr>" );
out.write( SurfacingConstants.NL );
- } // for( final String id : sorted_ids ) {
+ } // for( final String id : sorted_ids ) {
out.write( "</body>" );
out.write( SurfacingConstants.NL );
out.write( "</html>" );
final DescriptiveStatistics stats = gwcd.getPerGenomeDomainPromiscuityStatistics();
try {
per_genome_domain_promiscuity_statistics_writer.write( input_file_properties[ i ][ 1 ] + "\t" );
- per_genome_domain_promiscuity_statistics_writer.write( FORMATTER_3.format( stats.arithmeticMean() ) + "\t" );
+ per_genome_domain_promiscuity_statistics_writer
+ .write( FORMATTER_3.format( stats.arithmeticMean() ) + "\t" );
if ( stats.getN() < 2 ) {
per_genome_domain_promiscuity_statistics_writer.write( "n/a" + "\t" );
}
else {
- per_genome_domain_promiscuity_statistics_writer.write( FORMATTER_3.format( stats
- .sampleStandardDeviation() ) + "\t" );
+ per_genome_domain_promiscuity_statistics_writer
+ .write( FORMATTER_3.format( stats.sampleStandardDeviation() ) + "\t" );
}
per_genome_domain_promiscuity_statistics_writer.write( FORMATTER_3.format( stats.median() ) + "\t" );
per_genome_domain_promiscuity_statistics_writer.write( ( int ) stats.getMin() + "\t" );
ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
}
if ( input_file_properties[ i ].length == 3 ) {
- ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote domain combination counts for \""
- + input_file_properties[ i ][ 0 ] + "\" (" + input_file_properties[ i ][ 1 ] + ", "
- + input_file_properties[ i ][ 2 ] + ") to: \"" + dc_outfile + "\"" );
+ ForesterUtil.programMessage( surfacing.PRG_NAME,
+ "Wrote domain combination counts for \"" + input_file_properties[ i ][ 0 ]
+ + "\" (" + input_file_properties[ i ][ 1 ] + ", "
+ + input_file_properties[ i ][ 2 ] + ") to: \"" + dc_outfile + "\"" );
}
else {
- ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote domain combination counts for \""
- + input_file_properties[ i ][ 0 ] + "\" (" + input_file_properties[ i ][ 1 ] + ") to: \""
- + dc_outfile + "\"" );
+ ForesterUtil.programMessage( surfacing.PRG_NAME,
+ "Wrote domain combination counts for \"" + input_file_properties[ i ][ 0 ]
+ + "\" (" + input_file_properties[ i ][ 1 ] + ") to: \"" + dc_outfile
+ + "\"" );
}
}
public static void writeDomainSimilaritiesToFile( final StringBuilder html_desc,
final StringBuilder html_title,
+ final Writer simple_tab_writer,
final Writer single_writer,
Map<Character, Writer> split_writers,
final SortedSet<DomainSimilarity> similarities,
final boolean treat_as_binary,
final List<Species> species_order,
- final PrintableDomainSimilarity.PRINT_OPTION print_option,
+ final DomainSimilarity.PRINT_OPTION print_option,
final DomainSimilarity.DomainSimilarityScoring scoring,
final boolean verbose,
- final Map<String, Integer> tax_code_to_id_map )
+ final Map<String, Integer> tax_code_to_id_map,
+ final Phylogeny phy,
+ final Set<String> pos_filter_doms )
throws IOException {
if ( ( single_writer != null ) && ( ( split_writers == null ) || split_writers.isEmpty() ) ) {
split_writers = new HashMap<Character, Writer>();
w.write( "<html>" );
w.write( SurfacingConstants.NL );
if ( key != '_' ) {
- addHtmlHead( w, "DC analysis (" + html_title + ") " + key.toString().toUpperCase() );
+ writeHtmlHead( w, "DC analysis (" + html_title + ") " + key.toString().toUpperCase() );
}
else {
- addHtmlHead( w, "DC analysis (" + html_title + ")" );
+ writeHtmlHead( w, "DC analysis (" + html_title + ")" );
}
w.write( SurfacingConstants.NL );
w.write( "<body>" );
//
for( final DomainSimilarity similarity : similarities ) {
if ( ( species_order != null ) && !species_order.isEmpty() ) {
- ( ( PrintableDomainSimilarity ) similarity ).setSpeciesOrder( species_order );
+ ( similarity ).setSpeciesOrder( species_order );
}
if ( single_writer != null ) {
- single_writer.write( "<tr><td><b><a href=\"#" + similarity.getDomainId() + "\">"
- + similarity.getDomainId() + "</a></b></td></tr>" );
+ if ( !ForesterUtil.isEmpty( pos_filter_doms )
+ && pos_filter_doms.contains( similarity.getDomainId() ) ) {
+ single_writer.write( "<tr><td><b><a href=\"#" + similarity.getDomainId()
+ + "\"><span style=\"color:#00ff00\">" + similarity.getDomainId()
+ + "</span></a></b></td></tr>" );
+ }
+ else {
+ single_writer.write( "<tr><td><b><a href=\"#" + similarity.getDomainId() + "\">"
+ + similarity.getDomainId() + "</a></b></td></tr>" );
+ }
single_writer.write( SurfacingConstants.NL );
}
else {
- Writer local_writer = split_writers.get( ( similarity.getDomainId().charAt( 0 ) + "" ).toLowerCase()
- .charAt( 0 ) );
+ Writer local_writer = split_writers
+ .get( ( similarity.getDomainId().charAt( 0 ) + "" ).toLowerCase().charAt( 0 ) );
if ( local_writer == null ) {
local_writer = split_writers.get( '0' );
}
- local_writer.write( "<tr><td><b><a href=\"#" + similarity.getDomainId() + "\">"
- + similarity.getDomainId() + "</a></b></td></tr>" );
+ if ( !ForesterUtil.isEmpty( pos_filter_doms )
+ && pos_filter_doms.contains( similarity.getDomainId() ) ) {
+ local_writer.write( "<tr><td><b><a href=\"#" + similarity.getDomainId()
+ + "\"><span style=\"color:#00ff00\">" + similarity.getDomainId()
+ + "</span></a></b></td></tr>" );
+ }
+ else {
+ local_writer.write( "<tr><td><b><a href=\"#" + similarity.getDomainId() + "\">"
+ + similarity.getDomainId() + "</a></b></td></tr>" );
+ }
local_writer.write( SurfacingConstants.NL );
}
}
w.write( SurfacingConstants.NL );
w.write( "<hr>" );
w.write( SurfacingConstants.NL );
+ //
+ w.write( "<table>" );
+ w.write( SurfacingConstants.NL );
+ w.write( "<tr><td><b>" );
+ w.write( "Species group colors:" );
+ w.write( "</b></td></tr>" );
+ w.write( SurfacingConstants.NL );
+ writeColorLabels( "Deuterostomia", TaxonomyColors.DEUTEROSTOMIA_COLOR, w );
+ writeColorLabels( "Protostomia", TaxonomyColors.PROTOSTOMIA_COLOR, w );
+ writeColorLabels( "Cnidaria", TaxonomyColors.CNIDARIA_COLOR, w );
+ writeColorLabels( "Placozoa", TaxonomyColors.PLACOZOA_COLOR, w );
+ writeColorLabels( "Ctenophora (comb jellies)", TaxonomyColors.CTENOPHORA_COLOR, w );
+ writeColorLabels( "Porifera (sponges)", TaxonomyColors.PORIFERA_COLOR, w );
+ writeColorLabels( "Choanoflagellida", TaxonomyColors.CHOANOFLAGELLIDA, w );
+ writeColorLabels( "Ichthyosporea & Filasterea", TaxonomyColors.ICHTHYOSPOREA_AND_FILASTEREA, w );
+ writeColorLabels( "Dikarya (Ascomycota & Basidiomycota, so-called \"higher fungi\")",
+ TaxonomyColors.DIKARYA_COLOR,
+ w );
+ writeColorLabels( "other Fungi", TaxonomyColors.OTHER_FUNGI_COLOR, w );
+ writeColorLabels( "Nucleariidae and Fonticula group",
+ TaxonomyColors.NUCLEARIIDAE_AND_FONTICULA_GROUP_COLOR,
+ w );
+ writeColorLabels( "Amoebozoa", TaxonomyColors.AMOEBOZOA_COLOR, w );
+ writeColorLabels( "Embryophyta (plants)", TaxonomyColors.EMBRYOPHYTA_COLOR, w );
+ writeColorLabels( "Chlorophyta (green algae)", TaxonomyColors.CHLOROPHYTA_COLOR, w );
+ writeColorLabels( "Rhodophyta (red algae)", TaxonomyColors.RHODOPHYTA_COLOR, w );
+ writeColorLabels( "Glaucocystophyce (Glaucophyta)", TaxonomyColors.GLAUCOPHYTA_COLOR, w );
+ writeColorLabels( "Hacrobia (Cryptophyta & Haptophyceae & Centroheliozoa)",
+ TaxonomyColors.HACROBIA_COLOR,
+ w );
+ writeColorLabels( "Stramenopiles (Chromophyta, heterokonts)", TaxonomyColors.STRAMENOPILES_COLOR, w );
+ writeColorLabels( "Alveolata", TaxonomyColors.ALVEOLATA_COLOR, w );
+ writeColorLabels( "Rhizaria", TaxonomyColors.RHIZARIA_COLOR, w );
+ writeColorLabels( "Excavata", TaxonomyColors.EXCAVATA_COLOR, w );
+ writeColorLabels( "Apusozoa", TaxonomyColors.APUSOZOA_COLOR, w );
+ writeColorLabels( "Archaea", TaxonomyColors.ARCHAEA_COLOR, w );
+ writeColorLabels( "Bacteria", TaxonomyColors.BACTERIA_COLOR, w );
+ w.write( "</table>" );
+ w.write( SurfacingConstants.NL );
+ //
+ w.write( "<hr>" );
+ w.write( SurfacingConstants.NL );
w.write( "<table>" );
w.write( SurfacingConstants.NL );
}
//
for( final DomainSimilarity similarity : similarities ) {
if ( ( species_order != null ) && !species_order.isEmpty() ) {
- ( ( PrintableDomainSimilarity ) similarity ).setSpeciesOrder( species_order );
+ ( similarity ).setSpeciesOrder( species_order );
+ }
+ if ( simple_tab_writer != null ) {
+ simple_tab_writer.write( similarity
+ .toStringBuffer( PRINT_OPTION.SIMPLE_TAB_DELIMITED, tax_code_to_id_map, null ).toString() );
}
if ( single_writer != null ) {
- single_writer.write( similarity.toStringBuffer( print_option, tax_code_to_id_map ).toString() );
+ single_writer.write( similarity.toStringBuffer( print_option, tax_code_to_id_map, phy ).toString() );
single_writer.write( SurfacingConstants.NL );
}
else {
- Writer local_writer = split_writers.get( ( similarity.getDomainId().charAt( 0 ) + "" ).toLowerCase()
- .charAt( 0 ) );
+ Writer local_writer = split_writers
+ .get( ( similarity.getDomainId().charAt( 0 ) + "" ).toLowerCase().charAt( 0 ) );
if ( local_writer == null ) {
local_writer = split_writers.get( '0' );
}
- local_writer.write( similarity.toStringBuffer( print_option, tax_code_to_id_map ).toString() );
+ local_writer.write( similarity.toStringBuffer( print_option, tax_code_to_id_map, phy ).toString() );
local_writer.write( SurfacingConstants.NL );
}
}
w.write( SurfacingConstants.NL );
}
break;
+ default:
+ break;
}
for( final Writer w : split_writers.values() ) {
w.close();
}
}
- private static void printSomeStats( final DescriptiveStatistics stats, final AsciiHistogram histo, final Writer w )
- throws IOException {
- w.write( "<hr>" );
- w.write( "<br>" );
+ public static void writeHtmlHead( final Writer w, final String title ) throws IOException {
w.write( SurfacingConstants.NL );
- w.write( "<tt><pre>" );
+ w.write( "<head>" );
+ w.write( "<title>" );
+ w.write( title );
+ w.write( "</title>" );
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( "<style>" );
w.write( SurfacingConstants.NL );
- w.write( "<table>" );
+ w.write( "a:visited { color : #000066; text-decoration : none; }" );
w.write( SurfacingConstants.NL );
- w.write( "<tr><td>N: </td><td>" + stats.getN() + "</td></tr>" );
+ w.write( "a:link { color : #000066; text-decoration : none; }" );
w.write( SurfacingConstants.NL );
- w.write( "<tr><td>Min: </td><td>" + stats.getMin() + "</td></tr>" );
+ w.write( "a:active { color : ##000066; text-decoration : none; }" );
w.write( SurfacingConstants.NL );
- w.write( "<tr><td>Max: </td><td>" + stats.getMax() + "</td></tr>" );
+ w.write( "a:hover { color : #FFFFFF; background-color : #000000; text-decoration : none; }" );
w.write( SurfacingConstants.NL );
- w.write( "<tr><td>Mean: </td><td>" + stats.arithmeticMean() + "</td></tr>" );
+ //
+ w.write( "a.pl:visited { color : #505050; text-decoration : none; font-size: 7px;}" );
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( "a.pl:link { color : #505050; text-decoration : none; font-size: 7px;}" );
w.write( SurfacingConstants.NL );
- w.write( "</table>" );
+ w.write( "a.pl:active { color : #505050; text-decoration : none; font-size: 7px;}" );
w.write( SurfacingConstants.NL );
- w.write( "<br>" );
+ w.write( "a.pl:hover { color : #FFFFFF; background-color : #000000; text-decoration : none; font-size: 7px;}" );
+ w.write( SurfacingConstants.NL );
+ //
+ w.write( "a.ps:visited { color : #707070; text-decoration : none; font-size: 7px;}" );
+ w.write( SurfacingConstants.NL );
+ w.write( "a.ps:link { color : #707070; text-decoration : none; font-size: 7px;}" );
+ w.write( SurfacingConstants.NL );
+ w.write( "a.ps:active { color : #707070; text-decoration : none; font-size: 7px;}" );
+ w.write( SurfacingConstants.NL );
+ w.write( "a.ps:hover { color : #FFFFFF; background-color : #000000; text-decoration : none; font-size: 7px;}" );
+ w.write( SurfacingConstants.NL );
+ //
+ w.write( "td { text-align: left; vertical-align: top; font-family: Verdana, Arial, Helvetica; font-size: 8pt}" );
+ w.write( SurfacingConstants.NL );
+ w.write( "h1 { color : #0000FF; font-family: Verdana, Arial, Helvetica; font-size: 18pt; font-weight: bold }" );
+ w.write( SurfacingConstants.NL );
+ w.write( "h2 { color : #0000FF; font-family: Verdana, Arial, Helvetica; font-size: 16pt; font-weight: bold }" );
+ w.write( SurfacingConstants.NL );
+ w.write( "</style>" );
+ w.write( SurfacingConstants.NL );
+ w.write( "</head>" );
w.write( SurfacingConstants.NL );
}
writer.toPhyloXML( new File( filename ), phylogeny, 1 );
}
catch ( final IOException e ) {
- ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "failed to write phylogeny to \"" + filename + "\": "
- + e );
+ ForesterUtil.printWarningMessage( surfacing.PRG_NAME,
+ "failed to write phylogeny to \"" + filename + "\": " + e );
}
ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote phylogeny to \"" + filename + "\"" );
}
+ public static void writePresentToNexus( final File output_file,
+ final File positive_filter_file,
+ final SortedSet<String> filter,
+ final List<GenomeWideCombinableDomains> gwcd_list ) {
+ try {
+ writeMatrixToFile( DomainParsimonyCalculator
+ .createMatrixOfDomainPresenceOrAbsence( gwcd_list, positive_filter_file == null ? null : filter ),
+ output_file + surfacing.DOMAINS_PRESENT_NEXUS,
+ Format.NEXUS_BINARY );
+ writeMatrixToFile( DomainParsimonyCalculator
+ .createMatrixOfBinaryDomainCombinationPresenceOrAbsence( gwcd_list ),
+ output_file + surfacing.BDC_PRESENT_NEXUS,
+ Format.NEXUS_BINARY );
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
+ }
+ }
+
+ public static void writeProteinListsForAllSpecies( final File output_dir,
+ final SortedMap<Species, List<Protein>> protein_lists_per_species,
+ final List<GenomeWideCombinableDomains> gwcd_list,
+ final double domain_e_cutoff,
+ final Set<String> pos_filter_doms ) {
+ final SortedSet<String> all_domains = new TreeSet<String>();
+ for( final GenomeWideCombinableDomains gwcd : gwcd_list ) {
+ all_domains.addAll( gwcd.getAllDomainIds() );
+ }
+ for( final String domain : all_domains ) {
+ if ( !ForesterUtil.isEmpty( pos_filter_doms ) && !pos_filter_doms.contains( domain ) ) {
+ continue;
+ }
+ final File out = new File( output_dir + ForesterUtil.FILE_SEPARATOR + domain
+ + surfacing.SEQ_EXTRACT_SUFFIX );
+ checkForOutputFileWriteability( out );
+ try {
+ final Writer proteins_file_writer = new BufferedWriter( new FileWriter( out ) );
+ extractProteinNames( protein_lists_per_species,
+ domain,
+ proteins_file_writer,
+ "\t",
+ surfacing.LIMIT_SPEC_FOR_PROT_EX,
+ domain_e_cutoff );
+ proteins_file_writer.close();
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
+ }
+ ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote proteins list to \"" + out + "\"" );
+ }
+ }
+
public static void writeTaxonomyLinks( final Writer writer,
final String species,
- final Map<String, Integer> tax_code_to_id_map ) throws IOException {
+ final Map<String, Integer> tax_code_to_id_map )
+ throws IOException {
if ( ( species.length() > 1 ) && ( species.indexOf( '_' ) < 1 ) ) {
writer.write( " [" );
if ( ( tax_code_to_id_map != null ) && tax_code_to_id_map.containsKey( species ) ) {
if ( !dc_reapp_counts_to_protein_length_stats.containsKey( count ) ) {
dc_reapp_counts_to_protein_length_stats.put( count, new BasicDescriptiveStatistics() );
}
- dc_reapp_counts_to_protein_length_stats.get( count ).addValue( protein_length_stats_by_dc.get( dc )
- .arithmeticMean() );
+ dc_reapp_counts_to_protein_length_stats.get( count )
+ .addValue( protein_length_stats_by_dc.get( dc ).arithmeticMean() );
}
if ( domain_number_stats_by_dc != null ) {
if ( !dc_reapp_counts_to_domain_number_stats.containsKey( count ) ) {
dc_reapp_counts_to_domain_number_stats.put( count, new BasicDescriptiveStatistics() );
}
- dc_reapp_counts_to_domain_number_stats.get( count ).addValue( domain_number_stats_by_dc.get( dc )
- .arithmeticMean() );
+ dc_reapp_counts_to_domain_number_stats.get( count )
+ .addValue( domain_number_stats_by_dc.get( dc ).arithmeticMean() );
}
if ( domain_length_stats_by_domain != null ) {
if ( !dc_reapp_counts_to_domain_lengths_stats.containsKey( count ) ) {
dc_reapp_counts_to_domain_lengths_stats.put( count, new BasicDescriptiveStatistics() );
}
final String[] ds = dc.split( "=" );
- dc_reapp_counts_to_domain_lengths_stats.get( count ).addValue( domain_length_stats_by_domain
- .get( ds[ 0 ] ).arithmeticMean() );
- dc_reapp_counts_to_domain_lengths_stats.get( count ).addValue( domain_length_stats_by_domain
- .get( ds[ 1 ] ).arithmeticMean() );
+ dc_reapp_counts_to_domain_lengths_stats.get( count )
+ .addValue( domain_length_stats_by_domain.get( ds[ 0 ] ).arithmeticMean() );
+ dc_reapp_counts_to_domain_lengths_stats.get( count )
+ .addValue( domain_length_stats_by_domain.get( ds[ 1 ] ).arithmeticMean() );
}
if ( count > 1 ) {
more_than_once.add( dc );
ForesterUtil.LINE_SEPARATOR );
out_for_rank_counts.close();
out_for_ancestor_species_counts.close();
- if ( !ForesterUtil.isEmpty( outfilename_for_protein_stats )
- && ( ( domain_length_stats_by_domain != null ) || ( protein_length_stats_by_dc != null ) || ( domain_number_stats_by_dc != null ) ) ) {
+ if ( !ForesterUtil.isEmpty( outfilename_for_protein_stats ) && ( ( domain_length_stats_by_domain != null )
+ || ( protein_length_stats_by_dc != null ) || ( domain_number_stats_by_dc != null ) ) ) {
final BufferedWriter w = new BufferedWriter( new FileWriter( outfilename_for_protein_stats ) );
w.write( "Domain Lengths: " );
w.write( "\n" );
w.write( "\n" );
w.write( "N: " + gained_multiple_times_domain_length_count );
w.write( "\n" );
- w.write( "Avg: "
- + ( ( double ) gained_multiple_times_domain_length_sum / gained_multiple_times_domain_length_count ) );
+ w.write( "Avg: " + ( ( double ) gained_multiple_times_domain_length_sum
+ / gained_multiple_times_domain_length_count ) );
w.write( "\n" );
w.write( "\n" );
w.write( "\n" );
catch ( final IOException e ) {
ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "Failure to write: " + e );
}
- ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote independent domain combination gains fitch counts to ["
- + outfilename_for_counts + "]" );
- ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote independent domain combination gains fitch lists to ["
- + outfilename_for_dc + "]" );
+ ForesterUtil.programMessage( surfacing.PRG_NAME,
+ "Wrote independent domain combination gains fitch counts to ["
+ + outfilename_for_counts + "]" );
+ ForesterUtil.programMessage( surfacing.PRG_NAME,
+ "Wrote independent domain combination gains fitch lists to [" + outfilename_for_dc
+ + "]" );
ForesterUtil.programMessage( surfacing.PRG_NAME,
"Wrote independent domain combination gains fitch lists to (for GO mapping) ["
+ outfilename_for_dc_for_go_mapping + "]" );
return binary_combinations;
}
+ private static void printSomeStats( final DescriptiveStatistics stats, final AsciiHistogram histo, final Writer w )
+ throws IOException {
+ 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( "</table>" );
+ w.write( SurfacingConstants.NL );
+ w.write( "<br>" );
+ w.write( SurfacingConstants.NL );
+ }
+
private static List<String> splitDomainCombination( final String dc ) {
final String[] s = dc.split( "=" );
if ( s.length != 2 ) {
- ForesterUtil.printErrorMessage( surfacing.PRG_NAME, "Stringyfied domain combination has illegal format: "
- + dc );
+ ForesterUtil.printErrorMessage( surfacing.PRG_NAME,
+ "Stringyfied domain combination has illegal format: " + dc );
System.exit( -1 );
}
final List<String> l = new ArrayList<String>( 2 );
final File all_pfams_encountered_file = new File( outfile_name + surfacing.ALL_PFAMS_ENCOUNTERED_SUFFIX );
final File all_pfams_encountered_with_go_annotation_file = new File( outfile_name
+ surfacing.ALL_PFAMS_ENCOUNTERED_WITH_GO_ANNOTATION_SUFFIX );
- final File encountered_pfams_summary_file = new File( outfile_name + surfacing.ENCOUNTERED_PFAMS_SUMMARY_SUFFIX );
+ final File encountered_pfams_summary_file = new File( outfile_name
+ + surfacing.ENCOUNTERED_PFAMS_SUMMARY_SUFFIX );
int biological_process_counter = 0;
int cellular_component_counter = 0;
int molecular_function_counter = 0;
}
all_pfams_encountered_writer.close();
all_pfams_encountered_with_go_annotation_writer.close();
- ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote all [" + all_pfams_encountered.size()
- + "] encountered Pfams to: \"" + all_pfams_encountered_file + "\"" );
- ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote all [" + pfams_with_mappings_counter
- + "] encountered Pfams with GO mappings to: \"" + all_pfams_encountered_with_go_annotation_file
- + "\"" );
- ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote summary (including all ["
- + pfams_without_mappings_counter + "] encountered Pfams without GO mappings) to: \""
- + encountered_pfams_summary_file + "\"" );
- ForesterUtil.programMessage( surfacing.PRG_NAME, "Sum of Pfams encountered : "
- + all_pfams_encountered.size() );
- ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams without a mapping : "
- + pfams_without_mappings_counter + " ["
- + ( ( 100 * pfams_without_mappings_counter ) / all_pfams_encountered.size() ) + "%]" );
- ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams without mapping to proc. or func. : "
- + pfams_without_mappings_to_bp_or_mf_counter + " ["
- + ( ( 100 * pfams_without_mappings_to_bp_or_mf_counter ) / all_pfams_encountered.size() ) + "%]" );
- ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with a mapping : "
- + pfams_with_mappings_counter + " ["
- + ( ( 100 * pfams_with_mappings_counter ) / all_pfams_encountered.size() ) + "%]" );
- ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with a mapping to proc. or func. : "
- + pfams_with_mappings_to_bp_or_mf_counter + " ["
- + ( ( 100 * pfams_with_mappings_to_bp_or_mf_counter ) / all_pfams_encountered.size() ) + "%]" );
- ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with mapping to biological process: "
- + biological_process_counter + " ["
- + ( ( 100 * biological_process_counter ) / all_pfams_encountered.size() ) + "%]" );
- ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with mapping to molecular function: "
- + molecular_function_counter + " ["
- + ( ( 100 * molecular_function_counter ) / all_pfams_encountered.size() ) + "%]" );
- ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with mapping to cellular component: "
- + cellular_component_counter + " ["
- + ( ( 100 * cellular_component_counter ) / all_pfams_encountered.size() ) + "%]" );
+ ForesterUtil.programMessage( surfacing.PRG_NAME,
+ "Wrote all [" + all_pfams_encountered.size() + "] encountered Pfams to: \""
+ + all_pfams_encountered_file + "\"" );
+ ForesterUtil.programMessage( surfacing.PRG_NAME,
+ "Wrote all [" + pfams_with_mappings_counter
+ + "] encountered Pfams with GO mappings to: \""
+ + all_pfams_encountered_with_go_annotation_file + "\"" );
+ ForesterUtil.programMessage( surfacing.PRG_NAME,
+ "Wrote summary (including all [" + pfams_without_mappings_counter
+ + "] encountered Pfams without GO mappings) to: \""
+ + encountered_pfams_summary_file + "\"" );
+ ForesterUtil.programMessage( surfacing.PRG_NAME,
+ "Sum of Pfams encountered : " + all_pfams_encountered.size() );
+ ForesterUtil.programMessage( surfacing.PRG_NAME,
+ "Pfams without a mapping : " + pfams_without_mappings_counter
+ + " [" + ( ( 100 * pfams_without_mappings_counter )
+ / all_pfams_encountered.size() )
+ + "%]" );
+ ForesterUtil.programMessage( surfacing.PRG_NAME,
+ "Pfams without mapping to proc. or func. : "
+ + pfams_without_mappings_to_bp_or_mf_counter + " ["
+ + ( ( 100 * pfams_without_mappings_to_bp_or_mf_counter )
+ / all_pfams_encountered.size() )
+ + "%]" );
+ ForesterUtil
+ .programMessage( surfacing.PRG_NAME,
+ "Pfams with a mapping : " + pfams_with_mappings_counter + " ["
+ + ( ( 100 * pfams_with_mappings_counter ) / all_pfams_encountered.size() )
+ + "%]" );
+ ForesterUtil.programMessage( surfacing.PRG_NAME,
+ "Pfams with a mapping to proc. or func. : "
+ + pfams_with_mappings_to_bp_or_mf_counter + " ["
+ + ( ( 100 * pfams_with_mappings_to_bp_or_mf_counter )
+ / all_pfams_encountered.size() )
+ + "%]" );
+ ForesterUtil
+ .programMessage( surfacing.PRG_NAME,
+ "Pfams with mapping to biological process: " + biological_process_counter + " ["
+ + ( ( 100 * biological_process_counter ) / all_pfams_encountered.size() )
+ + "%]" );
+ ForesterUtil
+ .programMessage( surfacing.PRG_NAME,
+ "Pfams with mapping to molecular function: " + molecular_function_counter + " ["
+ + ( ( 100 * molecular_function_counter ) / all_pfams_encountered.size() )
+ + "%]" );
+ ForesterUtil
+ .programMessage( surfacing.PRG_NAME,
+ "Pfams with mapping to cellular component: " + cellular_component_counter + " ["
+ + ( ( 100 * cellular_component_counter ) / all_pfams_encountered.size() )
+ + "%]" );
summary_writer.write( ForesterUtil.LINE_SEPARATOR );
summary_writer.write( "# Sum of Pfams encountered : " + all_pfams_encountered.size() );
summary_writer.write( ForesterUtil.LINE_SEPARATOR );
- summary_writer.write( "# Pfams without a mapping : " + pfams_without_mappings_counter
- + " [" + ( ( 100 * pfams_without_mappings_counter ) / all_pfams_encountered.size() ) + "%]" );
+ summary_writer.write( "# Pfams without a mapping : " + pfams_without_mappings_counter + " ["
+ + ( ( 100 * pfams_without_mappings_counter ) / all_pfams_encountered.size() ) + "%]" );
summary_writer.write( ForesterUtil.LINE_SEPARATOR );
summary_writer.write( "# Pfams without mapping to proc. or func. : "
+ pfams_without_mappings_to_bp_or_mf_counter + " ["
}
}
+ private final static void writeColorLabels( final String l, final Color c, final Writer w ) throws IOException {
+ w.write( "<tr><td><b><span style=\"color:" );
+ w.write( String.format( "#%02x%02x%02x", c.getRed(), c.getGreen(), c.getBlue() ) );
+ w.write( "\">" );
+ w.write( l );
+ w.write( "</span></b></td></tr>" );
+ w.write( SurfacingConstants.NL );
+ }
+
private static void writeDomainData( final Map<String, List<GoId>> domain_id_to_go_ids_map,
final Map<GoId, GoTerm> go_id_to_term_map,
final GoNameSpace go_namespace_limit,
final String prefix_for_html,
final String character_separator_for_non_html_output,
final Map<String, Set<String>>[] domain_id_to_secondary_features_maps,
- final Set<GoId> all_go_ids ) throws IOException {
+ final Set<GoId> all_go_ids )
+ throws IOException {
boolean any_go_annotation_present = false;
boolean first_has_no_go = false;
int domain_count = 2; // To distinguish between domains and binary domain combinations.
if ( ForesterUtil.isEmpty( domain_1 ) ) {
domain_count = 1;
}
- // The following has a difficult to understand logic.
+ // The following has a difficult to understand logic.
for( int d = 0; d < domain_count; ++d ) {
List<GoId> go_ids = null;
boolean go_annotation_present = false;
out.write( SurfacingConstants.NL );
}
}
- } // for( int d = 0; d < domain_count; ++d )
+ } // for( int d = 0; d < domain_count; ++d )
if ( !any_go_annotation_present ) {
out.write( "<tr>" );
writeDomainIdsToHtml( out, domain_0, domain_1, prefix_for_html, domain_id_to_secondary_features_maps );
private static void writeDomainsToIndividualFilePerTreeNode( final Writer individual_files_writer,
final String domain_0,
- final String domain_1 ) throws IOException {
+ final String domain_1 )
+ throws IOException {
individual_files_writer.write( domain_0 );
individual_files_writer.write( ForesterUtil.LINE_SEPARATOR );
if ( !ForesterUtil.isEmpty( domain_1 ) ) {
writer.write( ForesterUtil.LINE_SEPARATOR );
}
writer.close();
- ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote " + pfams.size() + " pfams to [" + outfile_name
- + "]" );
+ ForesterUtil.programMessage( surfacing.PRG_NAME,
+ "Wrote " + pfams.size() + " pfams to [" + outfile_name + "]" );
}
catch ( final IOException e ) {
ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "Failure to write: " + e );