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.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.surfacing.PrintableDomainSimilarity.PRINT_OPTION;
import org.forester.util.AsciiHistogram;
import org.forester.util.BasicDescriptiveStatistics;
import org.forester.util.BasicTable;
import org.forester.util.DescriptiveStatistics;
import org.forester.util.ForesterUtil;
import org.forester.util.TaxonomyColors;
+import org.forester.util.TaxonomyGroups;
public final class SurfacingUtil {
@Override
public int compare( final Domain d1,
final Domain d2 ) {
- if ( d1.getPerSequenceEvalue() < d2
- .getPerSequenceEvalue() ) {
+ if ( d1.getPerDomainEvalue() < d2
+ .getPerDomainEvalue() ) {
return -1;
}
else if ( d1
- .getPerSequenceEvalue() > d2
- .getPerSequenceEvalue() ) {
+ .getPerDomainEvalue() > d2
+ .getPerDomainEvalue() ) {
return 1;
}
else {
}
}
- public static DescriptiveStatistics calculateDescriptiveStatisticsForMeanValues( final Set<PrintableDomainSimilarity> similarities ) {
+ public static DescriptiveStatistics calculateDescriptiveStatisticsForMeanValues( final Set<DomainSimilarity> similarities ) {
final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
- for( final PrintableDomainSimilarity similarity : similarities ) {
+ for( final DomainSimilarity similarity : similarities ) {
stats.addValue( similarity.getMeanSimilarityScore() );
}
return stats;
}
}
- public static void checkWriteabilityForPairwiseComparisons( final PrintableDomainSimilarity.PRINT_OPTION domain_similarity_print_option,
+ 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 ) {
break;
}
final String error = ForesterUtil
- .isWritableFile( new File( outdir == null ? pairwise_similarities_output_file_str : outdir
- + ForesterUtil.FILE_SEPARATOR + pairwise_similarities_output_file_str ) );
+ .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 );
}
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 e_value_max,
+ 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( "E-value: " + e_value_max );
+ 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 );
}
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" ) ) );
+ 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 ) {
return m;
}
- public static void decoratePrintableDomainSimilarities( final SortedSet<PrintableDomainSimilarity> domain_similarities,
+ public static void decoratePrintableDomainSimilarities( final SortedSet<DomainSimilarity> domain_similarities,
final Detailedness detailedness ) {
- for( final PrintableDomainSimilarity domain_similarity : domain_similarities ) {
- if ( domain_similarity instanceof PrintableDomainSimilarity ) {
- final PrintableDomainSimilarity printable_domain_similarity = domain_similarity;
+ for( final DomainSimilarity domain_similarity : domain_similarities ) {
+ 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 ) );
/**
* 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
+ * @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 {
+ 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
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
- + "\"" );
+ 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 consider_directedness_and_adjacency_for_bin_combinations
+ *
+ * @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,
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 + "\"" );
+ 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 {
+ 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 + ":" );
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() );
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 );
+ 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" );
+ 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" );
+ 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 );
+ 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" );
}
- if ( intree.getNumberOfExternalNodes() < number_of_genomes ) {
- ForesterUtil.fatalError( surfacing.PRG_NAME,
- "number of external nodes [" + intree.getNumberOfExternalNodes()
- + "] of input tree [" + intree_file
- + "] is smaller than the number of genomes the be analyzed ["
- + number_of_genomes + "]" );
- }
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 + "]" );
+ 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" );
+ ForesterUtil.printWarningMessage( surfacing.PRG_NAME,
+ "input tree [" + intree_file + "] is not completely binary" );
}
intrees[ i++ ] = intree;
}
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 );
+ 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" );
+ 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" );
+ 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 );
+ 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" );
while ( n != null ) {
if ( n.getNodeData().isHasTaxonomy()
&& !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) {
- group = ForesterUtil.obtainNormalizedTaxonomyGroup( n.getNodeData().getTaxonomy()
- .getScientificName() );
+ group = ForesterUtil
+ .obtainNormalizedTaxonomyGroup( n.getNodeData().getTaxonomy().getScientificName() );
}
if ( ForesterUtil.isEmpty( group ) && !ForesterUtil.isEmpty( n.getName() ) ) {
group = ForesterUtil.obtainNormalizedTaxonomyGroup( n.getName() );
n = n.getParent();
}
if ( ForesterUtil.isEmpty( group ) ) {
- throw new IllegalArgumentException( "no group found for taxonomy code \"" + tax_code + "\"" );
+ group = TaxonomyGroups.OTHER;
}
_TAXCODE_TAXGROUP_MAP.put( tax_code, group );
}
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() );
+ 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 List<String> igns = PhylogenyMethods.deleteExternalNodesPositiveSelection( genomes, intree );
if ( igns.size() > 0 ) {
System.out.println( "Not using the following " + igns.size() + " nodes:" );
}
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 ) {
- try {
- intree.getNode( input_file_propertie[ 1 ] );
+ final String name = input_file_propertie[ 1 ];
+ final List<PhylogenyNode> nodes = intree.getNodes( name );
+ if ( ( nodes == null ) || ( nodes.size() < 1 ) ) {
+ not_found.add( name );
}
- catch ( final IllegalArgumentException e ) {
- ForesterUtil.fatalError( surfacing.PRG_NAME, "node named [" + input_file_propertie[ 1 ]
- + "] not present/not unique in input tree" );
+ 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 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 ] );
+ 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" );
+ 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" );
+ 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 ] ) );
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>" );
+ 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 );
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 ) + "\"" );
+ 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 + "\"" );
+ 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 + "" ) );
/*
* 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,
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() );
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
+ + "\"" );
}
}
final Writer simple_tab_writer,
final Writer single_writer,
Map<Character, Writer> split_writers,
- final SortedSet<PrintableDomainSimilarity> similarities,
+ final SortedSet<DomainSimilarity> similarities,
final boolean treat_as_binary,
final List<Species> species_order,
- final PrintableDomainSimilarity.PRINT_OPTION print_option,
- final PrintableDomainSimilarity.DomainSimilarityScoring scoring,
+ final DomainSimilarity.PRINT_OPTION print_option,
+ final DomainSimilarity.DomainSimilarityScoring scoring,
final boolean verbose,
final Map<String, Integer> tax_code_to_id_map,
final Phylogeny phy,
- final Set<String> pos_filter_doms ) throws IOException {
+ final Set<String> pos_filter_doms )
+ throws IOException {
if ( ( single_writer != null ) && ( ( split_writers == null ) || split_writers.isEmpty() ) ) {
split_writers = new HashMap<Character, Writer>();
split_writers.put( '_', single_writer );
break;
}
//
- for( final PrintableDomainSimilarity similarity : similarities ) {
+ for( final DomainSimilarity similarity : similarities ) {
if ( ( species_order != null ) && !species_order.isEmpty() ) {
( similarity ).setSpeciesOrder( species_order );
}
if ( single_writer != null ) {
- if ( !ForesterUtil.isEmpty( pos_filter_doms ) && pos_filter_doms.contains( similarity.getDomainId() ) ) {
+ 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>" );
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' );
}
- if ( !ForesterUtil.isEmpty( pos_filter_doms ) && pos_filter_doms.contains( similarity.getDomainId() ) ) {
+ 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>" );
w.write( SurfacingConstants.NL );
}
//
- for( final PrintableDomainSimilarity similarity : similarities ) {
+ for( final DomainSimilarity similarity : similarities ) {
if ( ( species_order != null ) && !species_order.isEmpty() ) {
( 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() );
+ 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, 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' );
}
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 + "\"" );
}
final SortedSet<String> filter,
final List<GenomeWideCombinableDomains> gwcd_list ) {
try {
- writeMatrixToFile( DomainParsimonyCalculator.createMatrixOfDomainPresenceOrAbsence( gwcd_list,
- positive_filter_file == null ? null
- : filter ),
+ 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 ),
+ writeMatrixToFile( DomainParsimonyCalculator
+ .createMatrixOfBinaryDomainCombinationPresenceOrAbsence( gwcd_list ),
output_file + surfacing.BDC_PRESENT_NEXUS,
Format.NEXUS_BINARY );
}
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 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 ) {
- final File out = new File( output_dir + ForesterUtil.FILE_SEPARATOR + domain + surfacing.SEQ_EXTRACT_SUFFIX );
+ 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 ) );
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 + "]" );
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 + " ["
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 );
git://source.jalview.org / jalview.git / blobdiff