import java.text.DecimalFormat;
import java.text.NumberFormat;
import java.util.ArrayList;
+import java.util.Arrays;
import java.util.Collections;
import java.util.Comparator;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
+import java.util.PriorityQueue;
import java.util.Set;
import java.util.SortedMap;
import java.util.SortedSet;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
-import org.forester.application.surfacing_old;
+import org.forester.application.surfacing;
import org.forester.evoinference.distance.NeighborJoining;
import org.forester.evoinference.matrix.character.BasicCharacterStateMatrix;
import org.forester.evoinference.matrix.character.CharacterStateMatrix;
import org.forester.go.GoId;
import org.forester.go.GoNameSpace;
import org.forester.go.GoTerm;
-import org.forester.go.GoUtils;
import org.forester.go.PfamToGoMapping;
import org.forester.io.parsers.nexus.NexusConstants;
import org.forester.io.writers.PhylogenyWriter;
return stats;
}
+ private static void calculateIndependentDomainCombinationGains( final Phylogeny local_phylogeny_l,
+ final String outfilename_for_counts,
+ final String outfilename_for_dc,
+ final String outfilename_for_dc_for_go_mapping,
+ final String outfilename_for_dc_for_go_mapping_unique,
+ final String outfilename_for_rank_counts,
+ final String outfilename_for_ancestor_species_counts ) {
+ try {
+ final BufferedWriter out_counts = new BufferedWriter( new FileWriter( outfilename_for_counts ) );
+ final BufferedWriter out_dc = new BufferedWriter( new FileWriter( outfilename_for_dc ) );
+ final BufferedWriter out_dc_for_go_mapping = new BufferedWriter( new FileWriter( outfilename_for_dc_for_go_mapping ) );
+ final BufferedWriter out_dc_for_go_mapping_unique = new BufferedWriter( new FileWriter( outfilename_for_dc_for_go_mapping_unique ) );
+ final SortedMap<String, Integer> dc_gain_counts = new TreeMap<String, Integer>();
+ for( final PhylogenyNodeIterator it = local_phylogeny_l.iteratorPostorder(); it.hasNext(); ) {
+ final PhylogenyNode n = it.next();
+ final Set<String> gained_dc = n.getNodeData().getBinaryCharacters().getGainedCharacters();
+ for( final String dc : gained_dc ) {
+ if ( dc_gain_counts.containsKey( dc ) ) {
+ dc_gain_counts.put( dc, dc_gain_counts.get( dc ) + 1 );
+ }
+ else {
+ dc_gain_counts.put( dc, 1 );
+ }
+ }
+ }
+ final SortedMap<Integer, Integer> histogram = new TreeMap<Integer, Integer>();
+ final SortedMap<Integer, StringBuilder> domain_lists = new TreeMap<Integer, StringBuilder>();
+ final SortedMap<Integer, PriorityQueue<String>> domain_lists_go = new TreeMap<Integer, PriorityQueue<String>>();
+ final SortedMap<Integer, SortedSet<String>> domain_lists_go_unique = new TreeMap<Integer, SortedSet<String>>();
+ final Set<String> dcs = dc_gain_counts.keySet();
+ final SortedSet<String> more_than_once = new TreeSet<String>();
+ for( final String dc : dcs ) {
+ final int count = dc_gain_counts.get( dc );
+ if ( histogram.containsKey( count ) ) {
+ histogram.put( count, histogram.get( count ) + 1 );
+ domain_lists.get( count ).append( ", " + dc );
+ domain_lists_go.get( count ).addAll( splitDomainCombination( dc ) );
+ domain_lists_go_unique.get( count ).addAll( splitDomainCombination( dc ) );
+ }
+ else {
+ histogram.put( count, 1 );
+ domain_lists.put( count, new StringBuilder( dc ) );
+ final PriorityQueue<String> q = new PriorityQueue<String>();
+ q.addAll( splitDomainCombination( dc ) );
+ domain_lists_go.put( count, q );
+ final SortedSet<String> set = new TreeSet<String>();
+ set.addAll( splitDomainCombination( dc ) );
+ domain_lists_go_unique.put( count, set );
+ }
+ if ( count > 1 ) {
+ more_than_once.add( dc );
+ }
+ }
+ final Set<Integer> histogram_keys = histogram.keySet();
+ for( final Integer histogram_key : histogram_keys ) {
+ final int count = histogram.get( histogram_key );
+ final StringBuilder dc = domain_lists.get( histogram_key );
+ out_counts.write( histogram_key + "\t" + count + ForesterUtil.LINE_SEPARATOR );
+ out_dc.write( histogram_key + "\t" + dc + ForesterUtil.LINE_SEPARATOR );
+ out_dc_for_go_mapping.write( "#" + histogram_key + ForesterUtil.LINE_SEPARATOR );
+ final Object[] sorted = domain_lists_go.get( histogram_key ).toArray();
+ Arrays.sort( sorted );
+ for( final Object domain : sorted ) {
+ out_dc_for_go_mapping.write( domain + ForesterUtil.LINE_SEPARATOR );
+ }
+ out_dc_for_go_mapping_unique.write( "#" + histogram_key + ForesterUtil.LINE_SEPARATOR );
+ for( final String domain : domain_lists_go_unique.get( histogram_key ) ) {
+ out_dc_for_go_mapping_unique.write( domain + ForesterUtil.LINE_SEPARATOR );
+ }
+ }
+ out_counts.close();
+ out_dc.close();
+ out_dc_for_go_mapping.close();
+ out_dc_for_go_mapping_unique.close();
+ //
+ final SortedMap<String, Integer> lca_rank_counts = new TreeMap<String, Integer>();
+ final SortedMap<String, Integer> lca_ancestor_species_counts = new TreeMap<String, Integer>();
+ for( final String dc : more_than_once ) {
+ final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
+ for( final PhylogenyNodeIterator it = local_phylogeny_l.iteratorExternalForward(); it.hasNext(); ) {
+ final PhylogenyNode n = it.next();
+ if ( n.getNodeData().getBinaryCharacters().getGainedCharacters().contains( dc ) ) {
+ nodes.add( n );
+ }
+ }
+ for( int i = 0; i < nodes.size() - 1; ++i ) {
+ for( int j = i + 1; j < nodes.size(); ++j ) {
+ final PhylogenyNode lca = PhylogenyMethods.getInstance().obtainLCA( nodes.get( i ),
+ nodes.get( j ) );
+ String rank = "unknown";
+ if ( lca.getNodeData().isHasTaxonomy()
+ && !ForesterUtil.isEmpty( lca.getNodeData().getTaxonomy().getRank() ) ) {
+ rank = lca.getNodeData().getTaxonomy().getRank();
+ }
+ addToCountMap( lca_rank_counts, rank );
+ String lca_species;
+ if ( lca.getNodeData().isHasTaxonomy()
+ && !ForesterUtil.isEmpty( lca.getNodeData().getTaxonomy().getScientificName() ) ) {
+ lca_species = lca.getNodeData().getTaxonomy().getScientificName();
+ }
+ else if ( lca.getNodeData().isHasTaxonomy()
+ && !ForesterUtil.isEmpty( lca.getNodeData().getTaxonomy().getCommonName() ) ) {
+ lca_species = lca.getNodeData().getTaxonomy().getCommonName();
+ }
+ else {
+ lca_species = lca.getName();
+ }
+ addToCountMap( lca_ancestor_species_counts, lca_species );
+ }
+ }
+ }
+ final BufferedWriter out_for_rank_counts = new BufferedWriter( new FileWriter( outfilename_for_rank_counts ) );
+ final BufferedWriter out_for_ancestor_species_counts = new BufferedWriter( new FileWriter( outfilename_for_ancestor_species_counts ) );
+ ForesterUtil.map2writer( out_for_rank_counts, lca_rank_counts, "\t", ForesterUtil.LINE_SEPARATOR );
+ ForesterUtil.map2writer( out_for_ancestor_species_counts,
+ lca_ancestor_species_counts,
+ "\t",
+ ForesterUtil.LINE_SEPARATOR );
+ out_for_rank_counts.close();
+ out_for_ancestor_species_counts.close();
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "Failure to write: " + e );
+ }
+ 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 + "]" );
+ ForesterUtil.programMessage( surfacing.PRG_NAME,
+ "Wrote independent domain combination gains fitch lists to (for GO mapping, unique) ["
+ + outfilename_for_dc_for_go_mapping_unique + "]" );
+ }
+
+ private final static void addToCountMap( final Map<String, Integer> map, final String s ) {
+ if ( map.containsKey( s ) ) {
+ map.put( s, map.get( s ) + 1 );
+ }
+ else {
+ map.put( s, 1 );
+ }
+ }
+
public static int calculateOverlap( final Domain domain, final List<Boolean> covered_positions ) {
int overlap_count = 0;
for( int i = domain.getFrom(); i <= domain.getTo(); ++i ) {
public static void checkForOutputFileWriteability( final File outfile ) {
final String error = ForesterUtil.isWritableFile( outfile );
if ( !ForesterUtil.isEmpty( error ) ) {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME, error );
+ ForesterUtil.fatalError( surfacing.PRG_NAME, error );
}
}
domain_parsimony.executeDolloParsimonyOnDomainPresence();
}
SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossMatrix(), outfile_name
- + surfacing_old.PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_DOMAINS, Format.FORESTER );
+ + surfacing.PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_DOMAINS, Format.FORESTER );
SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossCountsMatrix(), outfile_name
- + surfacing_old.PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_DOMAINS, Format.FORESTER );
+ + surfacing.PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_DOMAINS, Format.FORESTER );
SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
CharacterStateMatrix.GainLossStates.GAIN,
- outfile_name + surfacing_old.PARSIMONY_OUTPUT_DOLLO_GAINS_D,
+ outfile_name + surfacing.PARSIMONY_OUTPUT_DOLLO_GAINS_D,
+ sep,
+ ForesterUtil.LINE_SEPARATOR,
+ null );
+ SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
+ CharacterStateMatrix.GainLossStates.LOSS,
+ outfile_name + surfacing.PARSIMONY_OUTPUT_DOLLO_LOSSES_D,
sep,
ForesterUtil.LINE_SEPARATOR,
null );
- SurfacingUtil
- .writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
- CharacterStateMatrix.GainLossStates.LOSS,
- outfile_name + surfacing_old.PARSIMONY_OUTPUT_DOLLO_LOSSES_D,
- sep,
- ForesterUtil.LINE_SEPARATOR,
- null );
SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(), null, outfile_name
- + surfacing_old.PARSIMONY_OUTPUT_DOLLO_PRESENT_D, sep, ForesterUtil.LINE_SEPARATOR, null );
+ + surfacing.PARSIMONY_OUTPUT_DOLLO_PRESENT_D, sep, ForesterUtil.LINE_SEPARATOR, null );
//HTML:
writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
go_id_to_term_map,
false,
domain_parsimony.getGainLossMatrix(),
CharacterStateMatrix.GainLossStates.GAIN,
- outfile_name + surfacing_old.PARSIMONY_OUTPUT_DOLLO_GAINS_HTML_D,
+ outfile_name + surfacing.PARSIMONY_OUTPUT_DOLLO_GAINS_HTML_D,
sep,
ForesterUtil.LINE_SEPARATOR,
"Dollo Parsimony | Gains | Domains",
false,
domain_parsimony.getGainLossMatrix(),
CharacterStateMatrix.GainLossStates.LOSS,
- outfile_name + surfacing_old.PARSIMONY_OUTPUT_DOLLO_LOSSES_HTML_D,
+ outfile_name + surfacing.PARSIMONY_OUTPUT_DOLLO_LOSSES_HTML_D,
sep,
ForesterUtil.LINE_SEPARATOR,
"Dollo Parsimony | Losses | Domains",
false,
domain_parsimony.getGainLossMatrix(),
null,
- outfile_name + surfacing_old.PARSIMONY_OUTPUT_DOLLO_PRESENT_HTML_D,
+ outfile_name + surfacing.PARSIMONY_OUTPUT_DOLLO_PRESENT_HTML_D,
sep,
ForesterUtil.LINE_SEPARATOR,
"Dollo Parsimony | Present | Domains",
"dollo_on_domains_" + outfile_name,
parameters_str );
SurfacingUtil.writePhylogenyToFile( local_phylogeny_l, outfile_name
- + surfacing_old.DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO );
+ + 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" );
}
catch ( final IOException e ) {
e.printStackTrace();
- ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getLocalizedMessage() );
+ ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
}
if ( domain_parsimony.calculateNumberOfBinaryDomainCombination() > 0 ) {
// FITCH DOMAIN COMBINATIONS
domain_parsimony.executeFitchParsimonyOnBinaryDomainCombintion( false );
}
SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossMatrix(), outfile_name
- + surfacing_old.PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_BINARY_COMBINATIONS, Format.FORESTER );
+ + surfacing.PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_BINARY_COMBINATIONS, Format.FORESTER );
SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossCountsMatrix(), outfile_name
- + surfacing_old.PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_BINARY_COMBINATIONS, Format.FORESTER );
- SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
- CharacterStateMatrix.GainLossStates.GAIN,
- outfile_name
- + surfacing_old.PARSIMONY_OUTPUT_FITCH_GAINS_BC,
- sep,
- ForesterUtil.LINE_SEPARATOR,
- null );
+ + surfacing.PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_BINARY_COMBINATIONS, Format.FORESTER );
SurfacingUtil
.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
- CharacterStateMatrix.GainLossStates.LOSS,
- outfile_name + surfacing_old.PARSIMONY_OUTPUT_FITCH_LOSSES_BC,
+ 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
+ + surfacing.PARSIMONY_OUTPUT_FITCH_LOSSES_BC,
+ sep,
+ ForesterUtil.LINE_SEPARATOR,
+ null );
SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(), null, outfile_name
- + surfacing_old.PARSIMONY_OUTPUT_FITCH_PRESENT_BC, sep, ForesterUtil.LINE_SEPARATOR, null );
+ + 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,
.getGainLossMatrix(),
null,
outfile_name
- + surfacing_old.PARSIMONY_OUTPUT_FITCH_PRESENT_BC_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS,
+ + surfacing.PARSIMONY_OUTPUT_FITCH_PRESENT_BC_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS,
sep,
ForesterUtil.LINE_SEPARATOR,
BinaryDomainCombination.OutputFormat.DOT );
true,
domain_parsimony.getGainLossMatrix(),
CharacterStateMatrix.GainLossStates.GAIN,
- outfile_name + surfacing_old.PARSIMONY_OUTPUT_FITCH_GAINS_HTML_BC,
+ outfile_name + surfacing.PARSIMONY_OUTPUT_FITCH_GAINS_HTML_BC,
sep,
ForesterUtil.LINE_SEPARATOR,
"Fitch Parsimony | Gains | Domain Combinations",
true,
domain_parsimony.getGainLossMatrix(),
CharacterStateMatrix.GainLossStates.LOSS,
- outfile_name + surfacing_old.PARSIMONY_OUTPUT_FITCH_LOSSES_HTML_BC,
+ outfile_name + surfacing.PARSIMONY_OUTPUT_FITCH_LOSSES_HTML_BC,
sep,
ForesterUtil.LINE_SEPARATOR,
"Fitch Parsimony | Losses | Domain Combinations",
true,
domain_parsimony.getGainLossMatrix(),
null,
- outfile_name + surfacing_old.PARSIMONY_OUTPUT_FITCH_PRESENT_HTML_BC,
+ outfile_name + surfacing.PARSIMONY_OUTPUT_FITCH_PRESENT_HTML_BC,
sep,
ForesterUtil.LINE_SEPARATOR,
"Fitch Parsimony | Present | Domain Combinations",
go_id_to_term_map,
outfile_name,
all_pfams_encountered );
- writePfamsToFile( outfile_name + surfacing_old.ALL_PFAMS_GAINED_AS_DOMAINS_SUFFIX,
- all_pfams_gained_as_domains );
- writePfamsToFile( outfile_name + surfacing_old.ALL_PFAMS_LOST_AS_DOMAINS_SUFFIX, all_pfams_lost_as_domains );
- writePfamsToFile( outfile_name + surfacing_old.ALL_PFAMS_GAINED_AS_DC_SUFFIX,
+ 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_old.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,
"fitch_on_binary_domain_combinations_" + outfile_name,
parameters_str );
SurfacingUtil.writePhylogenyToFile( local_phylogeny_l, outfile_name
- + surfacing_old.BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH );
+ + surfacing.BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH );
+ calculateIndependentDomainCombinationGains( local_phylogeny_l, outfile_name
+ + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_OUTPUT_SUFFIX, outfile_name
+ + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_OUTPUT_SUFFIX, outfile_name
+ + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_SUFFIX, outfile_name
+ + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_UNIQUE_SUFFIX, outfile_name
+ + "_indep_dc_gains_fitch_lca_ranks.txt", outfile_name + "_indep_dc_gains_fitch_lca_taxonomies.txt" );
}
}
final String sep = ForesterUtil.LINE_SEPARATOR + "###################" + ForesterUtil.LINE_SEPARATOR;
final String date_time = ForesterUtil.getCurrentDateTime();
System.out.println();
- writeToNexus( outfile_name + surfacing_old.NEXUS_SECONDARY_FEATURES,
+ writeToNexus( outfile_name + surfacing.NEXUS_SECONDARY_FEATURES,
secondary_features_parsimony.createMatrixOfSecondaryFeaturePresenceOrAbsence( null ),
phylogeny );
final Phylogeny local_phylogeny_copy = phylogeny.copy();
secondary_features_parsimony.executeDolloParsimonyOnSecondaryFeatures( mapping_results_map );
SurfacingUtil.writeMatrixToFile( secondary_features_parsimony.getGainLossMatrix(), outfile_name
- + surfacing_old.PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_SECONDARY_FEATURES, Format.FORESTER );
+ + surfacing.PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_SECONDARY_FEATURES, Format.FORESTER );
SurfacingUtil.writeMatrixToFile( secondary_features_parsimony.getGainLossCountsMatrix(), outfile_name
- + surfacing_old.PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_SECONDARY_FEATURES, Format.FORESTER );
+ + surfacing.PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_SECONDARY_FEATURES, Format.FORESTER );
SurfacingUtil
.writeBinaryStatesMatrixAsListToFile( secondary_features_parsimony.getGainLossMatrix(),
CharacterStateMatrix.GainLossStates.GAIN,
outfile_name
- + surfacing_old.PARSIMONY_OUTPUT_DOLLO_GAINS_SECONDARY_FEATURES,
+ + surfacing.PARSIMONY_OUTPUT_DOLLO_GAINS_SECONDARY_FEATURES,
sep,
ForesterUtil.LINE_SEPARATOR,
null );
.writeBinaryStatesMatrixAsListToFile( secondary_features_parsimony.getGainLossMatrix(),
CharacterStateMatrix.GainLossStates.LOSS,
outfile_name
- + surfacing_old.PARSIMONY_OUTPUT_DOLLO_LOSSES_SECONDARY_FEATURES,
+ + surfacing.PARSIMONY_OUTPUT_DOLLO_LOSSES_SECONDARY_FEATURES,
sep,
ForesterUtil.LINE_SEPARATOR,
null );
.writeBinaryStatesMatrixAsListToFile( secondary_features_parsimony.getGainLossMatrix(),
null,
outfile_name
- + surfacing_old.PARSIMONY_OUTPUT_DOLLO_PRESENT_SECONDARY_FEATURES,
+ + surfacing.PARSIMONY_OUTPUT_DOLLO_PRESENT_SECONDARY_FEATURES,
sep,
ForesterUtil.LINE_SEPARATOR,
null );
"dollo_on_secondary_features_" + outfile_name,
parameters_str );
SurfacingUtil.writePhylogenyToFile( local_phylogeny_copy, outfile_name
- + surfacing_old.SECONDARY_FEATURES_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO );
+ + surfacing.SECONDARY_FEATURES_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO );
}
public static void extractProteinNames( final List<Protein> proteins,
final PhylogenyNode n = it.next();
if ( ForesterUtil.isEmpty( n.getName() )
&& ( !n.getNodeData().isHasTaxonomy() || ForesterUtil.isEmpty( n.getNodeData().getTaxonomy()
- .getScientificName() ) ) ) {
+ .getScientificName() ) )
+ && ( !n.getNodeData().isHasTaxonomy() || ForesterUtil.isEmpty( n.getNodeData().getTaxonomy()
+ .getCommonName() ) ) ) {
if ( n.getParent() != null ) {
names.append( " " );
names.append( n.getParent().getName() );
}
+ final List l = n.getAllExternalDescendants();
+ for( final Object object : l ) {
+ System.out.println( l.toString() );
+ }
++c;
}
}
p.setRooted( true );
}
+ /*
+ * 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,
+ final String separator ) {
+ final StringBuffer sb = new StringBuffer();
+ if ( protein.getSpecies() == null ) {
+ throw new IllegalArgumentException( "species must not be null" );
+ }
+ if ( ForesterUtil.isEmpty( protein.getSpecies().getSpeciesId() ) ) {
+ throw new IllegalArgumentException( "species id must not be empty" );
+ }
+ final List<Domain> domains = protein.getProteinDomains();
+ if ( domains.size() > 1 ) {
+ final Map<String, Integer> counts = new HashMap<String, Integer>();
+ for( final Domain domain : domains ) {
+ final String id = domain.getDomainId().getId();
+ if ( counts.containsKey( id ) ) {
+ counts.put( id, counts.get( id ) + 1 );
+ }
+ else {
+ counts.put( id, 1 );
+ }
+ }
+ final Set<String> dcs = new HashSet<String>();
+ for( int i = 1; i < domains.size(); ++i ) {
+ for( int j = 0; j < i; ++j ) {
+ Domain domain_n = domains.get( i );
+ Domain domain_c = domains.get( j );
+ if ( domain_n.getFrom() > domain_c.getFrom() ) {
+ domain_n = domains.get( j );
+ domain_c = domains.get( i );
+ }
+ final String dc = domain_n.getDomainId().getId() + domain_c.getDomainId().getId();
+ if ( !dcs.contains( dc ) ) {
+ dcs.add( dc );
+ sb.append( protein.getSpecies() );
+ sb.append( separator );
+ sb.append( protein_id );
+ sb.append( separator );
+ sb.append( domain_n.getDomainId().getId() );
+ sb.append( separator );
+ sb.append( domain_c.getDomainId().getId() );
+ sb.append( separator );
+ sb.append( domain_n.getPerDomainEvalue() );
+ sb.append( separator );
+ sb.append( domain_c.getPerDomainEvalue() );
+ sb.append( separator );
+ sb.append( counts.get( domain_n.getDomainId().getId() ) );
+ sb.append( separator );
+ sb.append( counts.get( domain_c.getDomainId().getId() ) );
+ sb.append( ForesterUtil.LINE_SEPARATOR );
+ }
+ }
+ }
+ }
+ else if ( domains.size() == 1 ) {
+ sb.append( protein.getSpecies() );
+ sb.append( separator );
+ sb.append( protein_id );
+ sb.append( separator );
+ sb.append( domains.get( 0 ).getDomainId().getId() );
+ sb.append( separator );
+ sb.append( separator );
+ sb.append( domains.get( 0 ).getPerDomainEvalue() );
+ sb.append( separator );
+ sb.append( separator );
+ sb.append( 1 );
+ sb.append( separator );
+ sb.append( ForesterUtil.LINE_SEPARATOR );
+ }
+ else {
+ sb.append( protein.getSpecies() );
+ sb.append( separator );
+ sb.append( protein_id );
+ sb.append( separator );
+ sb.append( separator );
+ sb.append( separator );
+ sb.append( separator );
+ sb.append( separator );
+ sb.append( separator );
+ sb.append( ForesterUtil.LINE_SEPARATOR );
+ }
+ return sb;
+ }
+
/**
*
* Example regarding engulfment: ------------0.1 ----------0.2 --0.3 =>
return pruned_protein;
}
- static List<Domain> sortDomainsWithAscendingConfidenceValues( final Protein protein ) {
+ public static List<Domain> sortDomainsWithAscendingConfidenceValues( final Protein protein ) {
final List<Domain> domains = new ArrayList<Domain>();
for( final Domain d : protein.getProteinDomains() ) {
domains.add( d );
return domains;
}
+ 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 );
+ System.exit( -1 );
+ }
+ final List<String> l = new ArrayList<String>( 2 );
+ l.add( s[ 0 ] );
+ l.add( s[ 1 ] );
+ return l;
+ }
+
public static void writeAllDomainsChangedOnAllSubtrees( final Phylogeny p,
final boolean get_gains,
final String outdir,
if ( !get_gains ) {
state = CharacterStateMatrix.GainLossStates.LOSS;
}
- final File base_dir = createBaseDirForPerNodeDomainFiles( surfacing_old.BASE_DIRECTORY_PER_SUBTREE_DOMAIN_GAIN_LOSS_FILES,
+ final File base_dir = createBaseDirForPerNodeDomainFiles( surfacing.BASE_DIRECTORY_PER_SUBTREE_DOMAIN_GAIN_LOSS_FILES,
false,
state,
outdir );
final Map<GoId, GoTerm> go_id_to_term_map,
final String outfile_name,
final SortedSet<String> all_pfams_encountered ) {
- final File all_pfams_encountered_file = new File( outfile_name + surfacing_old.ALL_PFAMS_ENCOUNTERED_SUFFIX );
+ 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_old.ALL_PFAMS_ENCOUNTERED_WITH_GO_ANNOTATION_SUFFIX );
- final File encountered_pfams_summary_file = new File( outfile_name
- + surfacing_old.ENCOUNTERED_PFAMS_SUMMARY_SUFFIX );
+ + surfacing.ALL_PFAMS_ENCOUNTERED_WITH_GO_ANNOTATION_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_old.PRG_NAME, "Wrote all [" + 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_old.PRG_NAME, "Wrote all [" + pfams_with_mappings_counter
+ 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_old.PRG_NAME, "Wrote summary (including all ["
+ 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_old.PRG_NAME, "Sum of Pfams encountered : "
+ ForesterUtil.programMessage( surfacing.PRG_NAME, "Sum of Pfams encountered : "
+ all_pfams_encountered.size() );
- ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Pfams without a mapping : "
+ 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_old.PRG_NAME, "Pfams without mapping to proc. or func. : "
+ 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_old.PRG_NAME,
+ 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_old.PRG_NAME, "Pfams with a mapping to proc. or func. : "
+ 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_old.PRG_NAME,
+ 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_old.PRG_NAME,
+ 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_old.PRG_NAME,
+ ForesterUtil.programMessage( surfacing.PRG_NAME,
"Pfams with mapping to cellular component: " + cellular_component_counter
+ " ["
+ ( 100 * cellular_component_counter / all_pfams_encountered.size() )
summary_writer.close();
}
catch ( final IOException e ) {
- ForesterUtil.printWarningMessage( surfacing_old.PRG_NAME, "Failure to write: " + e );
+ ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "Failure to write: " + e );
}
}
final int i,
final GenomeWideCombinableDomainsSortOrder dc_sort_order ) {
File dc_outfile_dot = new File( input_file_properties[ i ][ 0 ]
- + surfacing_old.DOMAIN_COMBINITONS_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS );
+ + surfacing.DOMAIN_COMBINITONS_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS );
if ( output_dir != null ) {
dc_outfile_dot = new File( output_dir + ForesterUtil.FILE_SEPARATOR + dc_outfile_dot );
}
out_dot.close();
}
catch ( final IOException e ) {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getMessage() );
+ ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
}
- ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote binary domain combination for \""
+ 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 + "\"" );
}
- /*
- * 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,
- final String separator ) {
- final StringBuffer sb = new StringBuffer();
- if ( protein.getSpecies() == null ) {
- throw new IllegalArgumentException( "species must not be null" );
- }
- if ( ForesterUtil.isEmpty( protein.getSpecies().getSpeciesId() ) ) {
- throw new IllegalArgumentException( "species id must not be empty" );
- }
- final List<Domain> domains = protein.getProteinDomains();
- if ( domains.size() > 1 ) {
- final Map<String, Integer> counts = new HashMap<String, Integer>();
- for( final Domain domain : domains ) {
- final String id = domain.getDomainId().getId();
- if ( counts.containsKey( id ) ) {
- counts.put( id, counts.get( id ) + 1 );
- }
- else {
- counts.put( id, 1 );
- }
- }
- final Set<String> dcs = new HashSet<String>();
- for( int i = 1; i < domains.size(); ++i ) {
- for( int j = 0; j < i; ++j ) {
- Domain domain_n = domains.get( i );
- Domain domain_c = domains.get( j );
- if ( domain_n.getFrom() > domain_c.getFrom() ) {
- domain_n = domains.get( j );
- domain_c = domains.get( i );
- }
- final String dc = domain_n.getDomainId().getId() + domain_c.getDomainId().getId();
- if ( !dcs.contains( dc ) ) {
- dcs.add( dc );
- sb.append( protein.getSpecies() );
- sb.append( separator );
- sb.append( protein_id );
- sb.append( separator );
- sb.append( domain_n.getDomainId().getId() );
- sb.append( separator );
- sb.append( domain_c.getDomainId().getId() );
- sb.append( separator );
- sb.append( domain_n.getPerDomainEvalue() );
- sb.append( separator );
- sb.append( domain_c.getPerDomainEvalue() );
- sb.append( separator );
- sb.append( counts.get( domain_n.getDomainId().getId() ) );
- sb.append( separator );
- sb.append( counts.get( domain_c.getDomainId().getId() ) );
- sb.append( ForesterUtil.LINE_SEPARATOR );
- }
- }
- }
- }
- else if ( domains.size() == 1 ) {
- sb.append( protein.getSpecies() );
- sb.append( separator );
- sb.append( protein_id );
- sb.append( separator );
- sb.append( domains.get( 0 ).getDomainId().getId() );
- sb.append( separator );
- sb.append( separator );
- sb.append( domains.get( 0 ).getPerDomainEvalue() );
- sb.append( separator );
- sb.append( separator );
- sb.append( 1 );
- sb.append( separator );
- sb.append( ForesterUtil.LINE_SEPARATOR );
- }
- else {
- sb.append( protein.getSpecies() );
- sb.append( separator );
- sb.append( protein_id );
- sb.append( separator );
- sb.append( separator );
- sb.append( separator );
- sb.append( separator );
- sb.append( separator );
- sb.append( separator );
- sb.append( ForesterUtil.LINE_SEPARATOR );
- }
- return sb;
- }
-
public static void writeBinaryStatesMatrixAsListToFile( final CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
final CharacterStateMatrix.GainLossStates state,
final String filename,
out.close();
}
catch ( final IOException e ) {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getMessage() );
+ ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
}
- ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote characters list: \"" + filename + "\"" );
+ ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote characters list: \"" + filename + "\"" );
}
public static void writeBinaryStatesMatrixAsListToFileForBinaryCombinationsForGraphAnalysis( final CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
bdc = BasicBinaryDomainCombination.createInstance( matrix.getCharacter( c ) );
}
catch ( final Exception e ) {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getLocalizedMessage() );
+ ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
}
out.write( bdc.toGraphDescribingLanguage( bc_output_format, null, null ).toString() );
out.write( character_separator );
out.close();
}
catch ( final IOException e ) {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getMessage() );
+ ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
}
- ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote characters list: \"" + filename + "\"" );
+ ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote characters list: \"" + filename + "\"" );
}
public static void writeBinaryStatesMatrixToList( final Map<DomainId, List<GoId>> domain_id_to_go_ids_map,
}
try {
final Writer out = new BufferedWriter( new FileWriter( outfile ) );
- final File per_node_go_mapped_domain_gain_loss_files_base_dir = createBaseDirForPerNodeDomainFiles( surfacing_old.BASE_DIRECTORY_PER_NODE_DOMAIN_GAIN_LOSS_FILES,
+ final File per_node_go_mapped_domain_gain_loss_files_base_dir = createBaseDirForPerNodeDomainFiles( surfacing.BASE_DIRECTORY_PER_NODE_DOMAIN_GAIN_LOSS_FILES,
domain_combinations,
state,
filename );
out.close();
}
catch ( final IOException e ) {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getMessage() );
+ ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
}
- ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote characters detailed HTML list: \"" + filename
- + "\"" );
+ ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote characters detailed HTML list: \"" + filename + "\"" );
}
public static void writeBinaryStatesMatrixToListORIGIG( final Map<DomainId, List<GoId>> domain_id_to_go_ids_map,
}
try {
final Writer out = new BufferedWriter( new FileWriter( outfile ) );
- final File per_node_go_mapped_domain_gain_loss_files_base_dir = createBaseDirForPerNodeDomainFiles( surfacing_old.BASE_DIRECTORY_PER_NODE_DOMAIN_GAIN_LOSS_FILES,
+ final File per_node_go_mapped_domain_gain_loss_files_base_dir = createBaseDirForPerNodeDomainFiles( surfacing.BASE_DIRECTORY_PER_NODE_DOMAIN_GAIN_LOSS_FILES,
domain_combinations,
state,
filename );
out.close();
}
catch ( final IOException e ) {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getMessage() );
+ ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
}
- ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote characters detailed HTML list: \"" + filename
- + "\"" );
+ ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote characters detailed HTML list: \"" + filename + "\"" );
}
public static void writeDomainCombinationsCountsFile( final String[][] input_file_properties,
final int i,
final GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder dc_sort_order ) {
File dc_outfile = new File( input_file_properties[ i ][ 0 ]
- + surfacing_old.DOMAIN_COMBINITON_COUNTS_OUTPUTFILE_SUFFIX );
+ + surfacing.DOMAIN_COMBINITON_COUNTS_OUTPUTFILE_SUFFIX );
if ( output_dir != null ) {
dc_outfile = new File( output_dir + ForesterUtil.FILE_SEPARATOR + dc_outfile );
}
out.close();
}
catch ( final IOException e ) {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getMessage() );
+ ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
}
final DescriptiveStatistics stats = gwcd.getPerGenomeDomainPromiscuityStatistics();
try {
per_genome_domain_promiscuity_statistics_writer.write( ForesterUtil.LINE_SEPARATOR );
}
catch ( final IOException e ) {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getMessage() );
+ ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
}
if ( input_file_properties[ i ].length == 3 ) {
- ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote domain combination counts for \""
+ 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_old.PRG_NAME, "Wrote domain combination counts for \""
+ ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote domain combination counts for \""
+ input_file_properties[ i ][ 0 ] + "\" (" + input_file_properties[ i ][ 1 ] + ") to: \""
+ dc_outfile + "\"" );
}
}
}
- private static void writeDomainDataORIG( final Map<DomainId, List<GoId>> domain_id_to_go_ids_map,
- final Map<GoId, GoTerm> go_id_to_term_map,
- final GoNameSpace go_namespace_limit,
- final Writer out,
- final String domain_0,
- final String domain_1,
- final String prefix_for_html,
- final String character_separator_for_non_html_output,
- final Map<DomainId, Set<String>>[] domain_id_to_secondary_features_maps,
- 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.
- for( int d = 0; d < domain_count; ++d ) {
- List<GoId> go_ids = null;
- boolean go_annotation_present = false;
- if ( d == 0 ) {
- final DomainId domain_id = new DomainId( domain_0 );
- if ( domain_id_to_go_ids_map.containsKey( domain_id ) ) {
- go_annotation_present = true;
- any_go_annotation_present = true;
- go_ids = domain_id_to_go_ids_map.get( domain_id );
- }
- else {
- first_has_no_go = true;
- }
- }
- else {
- final DomainId domain_id = new DomainId( domain_1 );
- if ( domain_id_to_go_ids_map.containsKey( domain_id ) ) {
- go_annotation_present = true;
- any_go_annotation_present = true;
- go_ids = domain_id_to_go_ids_map.get( domain_id );
- }
- }
- if ( go_annotation_present ) {
- boolean first = ( ( d == 0 ) || ( ( d == 1 ) && first_has_no_go ) );
- for( final GoId go_id : go_ids ) {
- out.write( "<tr>" );
- if ( first ) {
- first = false;
- writeDomainIdsToHtml( out,
- domain_0,
- domain_1,
- prefix_for_html,
- domain_id_to_secondary_features_maps );
- }
- else {
- out.write( "<td></td>" );
- }
- if ( !go_id_to_term_map.containsKey( go_id ) ) {
- throw new IllegalArgumentException( "GO-id [" + go_id + "] not found in GO-id to GO-term map" );
- }
- final GoTerm go_term = go_id_to_term_map.get( go_id );
- if ( ( go_namespace_limit == null ) || go_namespace_limit.equals( go_term.getGoNameSpace() ) ) {
- final String top = GoUtils.getPenultimateGoTerm( go_term, go_id_to_term_map ).getName();
- final String go_id_str = go_id.getId();
- out.write( "<td>" );
- out.write( "<a href=\"" + SurfacingConstants.AMIGO_LINK + go_id_str
- + "\" target=\"amigo_window\">" + go_id_str + "</a>" );
- out.write( "</td><td>" );
- out.write( go_term.getName() );
- if ( domain_count == 2 ) {
- out.write( " (" + d + ")" );
- }
- out.write( "</td><td>" );
- out.write( top );
- out.write( "</td><td>" );
- out.write( "[" );
- out.write( go_term.getGoNameSpace().toShortString() );
- out.write( "]" );
- out.write( "</td>" );
- if ( all_go_ids != null ) {
- all_go_ids.add( go_id );
- }
- }
- else {
- out.write( "<td>" );
- out.write( "</td><td>" );
- out.write( "</td><td>" );
- out.write( "</td><td>" );
- out.write( "</td>" );
- }
- out.write( "</tr>" );
- out.write( SurfacingConstants.NL );
- }
- }
- } // 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 );
- out.write( "<td>" );
- out.write( "</td><td>" );
- out.write( "</td><td>" );
- out.write( "</td><td>" );
- out.write( "</td>" );
- out.write( "</tr>" );
- out.write( SurfacingConstants.NL );
- }
- }
-
private static void writeDomainIdsToHtml( final Writer out,
final String domain_0,
final String domain_1,
out.write( " " );
}
out.write( "<a href=\"" + SurfacingConstants.PFAM_FAMILY_ID_LINK + domain_0 + "\">" + domain_0 + "</a>" );
- //if ( ForesterUtil.isEmpty( domain_1 ) ) {
- // out.write( " <a href=\"" + SurfacingConstants.GOOGLE_SCHOLAR_LINK + domain_0
- // + SurfacingConstants.GOOGLE_SCHOLAR_LIMITS + "\">[gs]</a>" );
- //}
- // if ( !ForesterUtil.isEmpty( domain_1 ) ) {
- // out.write( "=" );
- // out.write( "<a href=\"" + SurfacingConstants.PFAM_FAMILY_ID_LINK + domain_1 + "\">" + domain_1 + "</a>" );
- //}
- // else if ( ( domain_id_to_secondary_features_maps != null )
- // && ( domain_id_to_secondary_features_maps.length > 0 ) ) {
- // out.write( " [" );
- // boolean first = true;
- // for( final Map<DomainId, Set<String>> domain_id_to_secondary_features_map : domain_id_to_secondary_features_maps ) {
- // final Set<String> sec_features = domain_id_to_secondary_features_map.get( new DomainId( domain_0 ) );
- // if ( ( sec_features != null ) && ( sec_features.size() > 0 ) ) {
- // for( final String sec_feature : sec_features ) {
- // if ( first ) {
- // first = false;
- // }
- // else {
- // out.write( ", " );
- // }
- // if ( SurfacingConstants.SECONDARY_FEATURES_ARE_SCOP
- // && ( SurfacingConstants.SECONDARY_FEATURES_SCOP_LINK != null ) ) {
- // out.write( "<a href=\"" + SurfacingConstants.SECONDARY_FEATURES_SCOP_LINK + sec_feature
- // + "\" target=\"scop_window\">" + sec_feature + "</a>" );
- // }
- // else {
- // out.write( sec_feature );
- // }
- // }
- // }
- // }
- // out.write( "]" );
- // }
- out.write( "</td>" );
- }
-
- private static void writeDomainIdsToHtmlORIG( final Writer out,
- final String domain_0,
- final String domain_1,
- final String prefix_for_detailed_html,
- final Map<DomainId, Set<String>>[] domain_id_to_secondary_features_maps )
- throws IOException {
- out.write( "<td>" );
- if ( !ForesterUtil.isEmpty( prefix_for_detailed_html ) ) {
- out.write( prefix_for_detailed_html );
- out.write( " " );
- }
- out.write( "<a href=\"" + SurfacingConstants.PFAM_FAMILY_ID_LINK + domain_0 + "\">" + domain_0 + "</a>" );
- if ( ForesterUtil.isEmpty( domain_1 ) ) {
- out.write( " <a href=\"" + SurfacingConstants.GOOGLE_SCHOLAR_LINK + domain_0
- + SurfacingConstants.GOOGLE_SCHOLAR_LIMITS + "\">[gs]</a>" );
- }
- if ( !ForesterUtil.isEmpty( domain_1 ) ) {
- out.write( "=" );
- out.write( "<a href=\"" + SurfacingConstants.PFAM_FAMILY_ID_LINK + domain_1 + "\">" + domain_1 + "</a>" );
- }
- else if ( ( domain_id_to_secondary_features_maps != null )
- && ( domain_id_to_secondary_features_maps.length > 0 ) ) {
- out.write( " [" );
- boolean first = true;
- for( final Map<DomainId, Set<String>> domain_id_to_secondary_features_map : domain_id_to_secondary_features_maps ) {
- final Set<String> sec_features = domain_id_to_secondary_features_map.get( new DomainId( domain_0 ) );
- if ( ( sec_features != null ) && ( sec_features.size() > 0 ) ) {
- for( final String sec_feature : sec_features ) {
- if ( first ) {
- first = false;
- }
- else {
- out.write( ", " );
- }
- if ( SurfacingConstants.SECONDARY_FEATURES_ARE_SCOP
- && ( SurfacingConstants.SECONDARY_FEATURES_SCOP_LINK != null ) ) {
- out.write( "<a href=\"" + SurfacingConstants.SECONDARY_FEATURES_SCOP_LINK + sec_feature
- + "\" target=\"scop_window\">" + sec_feature + "</a>" );
- }
- else {
- out.write( sec_feature );
- }
- }
- }
- }
- out.write( "]" );
- }
out.write( "</td>" );
}
out.close();
}
catch ( final IOException e ) {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getMessage() );
+ ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
}
- ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote matrix: \"" + filename + "\"" );
+ ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote matrix: \"" + filename + "\"" );
}
public static void writeMatrixToFile( final File matrix_outfile, final List<DistanceMatrix> matrices ) {
out.close();
}
catch ( final IOException e ) {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getMessage() );
+ ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
}
- ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote distance matrices to \"" + matrix_outfile + "\"" );
+ ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote distance matrices to \"" + matrix_outfile + "\"" );
}
private static void writePfamsToFile( final String outfile_name, final SortedSet<String> pfams ) {
writer.write( ForesterUtil.LINE_SEPARATOR );
}
writer.close();
- ForesterUtil.programMessage( surfacing_old.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_old.PRG_NAME, "Failure to write: " + e );
+ ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "Failure to write: " + e );
}
}
writer.toPhyloXML( new File( filename ), phylogeny, 1 );
}
catch ( final IOException e ) {
- ForesterUtil.printWarningMessage( surfacing_old.PRG_NAME, "failed to write phylogeny to \"" + filename
- + "\": " + e );
+ ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "failed to write phylogeny to \"" + filename + "\": "
+ + e );
}
- ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote phylogeny to \"" + filename + "\"" );
+ ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote phylogeny to \"" + filename + "\"" );
}
public static void writeTaxonomyLinks( final Writer writer, final String species ) throws IOException {
}
}
- public static void writeTaxonomyLinksORIG( final Writer writer, final String species ) throws IOException {
- if ( ( species.length() > 1 ) && ( species.indexOf( '_' ) < 1 ) ) {
- final Matcher matcher = PATTERN_SP_STYLE_TAXONOMY.matcher( species );
- writer.write( " [" );
- if ( matcher.matches() ) {
- writer.write( "<a href=\"" + SurfacingConstants.UNIPROT_LINK + species
- + "\" target=\"taxonomy_window\">uniprot</a>" );
- }
- else {
- writer.write( "<a href=\"" + SurfacingConstants.EOL_LINK + species
- + "\" target=\"taxonomy_window\">eol</a>" );
- writer.write( "|" );
- writer.write( "<a href=\"" + SurfacingConstants.TOL_LINK + species
- + "\" target=\"taxonomy_window\">tol</a>" );
- writer.write( "|" );
- writer.write( "<a href=\"" + SurfacingConstants.WIKIPEDIA_LINK + species
- + "\" target=\"taxonomy_window\">wikipedia</a>" );
- writer.write( "|" );
- writer.write( "<a href=\"" + SurfacingConstants.GOOGLE_SCHOLAR_LINK + species
- + "\" target=\"taxonomy_window\">gs</a>" );
- }
- writer.write( "]" );
- }
- }
-
- private static void writeToNexus( final String outfile_name, final CharacterStateMatrix<BinaryStates> matrix ) {
- if ( !( matrix instanceof BasicCharacterStateMatrix ) ) {
- throw new IllegalArgumentException( "can only write matrices of type [" + BasicCharacterStateMatrix.class
- + "] to nexus" );
- }
- final BasicCharacterStateMatrix<BinaryStates> my_matrix = ( org.forester.evoinference.matrix.character.BasicCharacterStateMatrix<BinaryStates> ) matrix;
- try {
- final BufferedWriter w = new BufferedWriter( new FileWriter( outfile_name ) );
- w.write( NexusConstants.NEXUS );
- w.write( ForesterUtil.LINE_SEPARATOR );
- my_matrix.writeNexusTaxaBlock( w );
- my_matrix.writeNexusBinaryChractersBlock( w );
- w.flush();
- w.close();
- ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote Nexus file: \"" + outfile_name + "\"" );
- }
- catch ( final IOException e ) {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getMessage() );
- }
- }
-
private static void writeToNexus( final String outfile_name,
final CharacterStateMatrix<BinaryStates> matrix,
final Phylogeny phylogeny ) {
PhylogenyWriter.writeNexusTreesBlock( w, phylogenies );
w.flush();
w.close();
- ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote Nexus file: \"" + outfile_name + "\"" );
+ ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote Nexus file: \"" + outfile_name + "\"" );
}
catch ( final IOException e ) {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getMessage() );
+ ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
}
}
- private static void writeToNexus( final String outfile_name, final DomainParsimonyCalculator domain_parsimony ) {
- writeToNexus( outfile_name + surfacing_old.NEXUS_EXTERNAL_DOMAINS,
- domain_parsimony.createMatrixOfDomainPresenceOrAbsence() );
- writeToNexus( outfile_name + surfacing_old.NEXUS_EXTERNAL_DOMAIN_COMBINATIONS,
- domain_parsimony.createMatrixOfBinaryDomainCombinationPresenceOrAbsence() );
- }
-
private static void writeToNexus( final String outfile_name,
final DomainParsimonyCalculator domain_parsimony,
final Phylogeny phylogeny ) {
- writeToNexus( outfile_name + surfacing_old.NEXUS_EXTERNAL_DOMAINS,
+ writeToNexus( outfile_name + surfacing.NEXUS_EXTERNAL_DOMAINS,
domain_parsimony.createMatrixOfDomainPresenceOrAbsence(),
phylogeny );
- writeToNexus( outfile_name + surfacing_old.NEXUS_EXTERNAL_DOMAIN_COMBINATIONS,
+ writeToNexus( outfile_name + surfacing.NEXUS_EXTERNAL_DOMAIN_COMBINATIONS,
domain_parsimony.createMatrixOfBinaryDomainCombinationPresenceOrAbsence(),
phylogeny );
}
+
+ public static void domainsPerProteinsStatistics( final String genome,
+ final List<Protein> protein_list,
+ final DescriptiveStatistics all_genomes_domains_per_potein_stats,
+ final SortedMap<Integer, Integer> all_genomes_domains_per_potein_histo,
+ final SortedSet<String> domains_which_are_always_single,
+ final SortedSet<String> domains_which_are_sometimes_single_sometimes_not,
+ final SortedSet<String> domains_which_never_single,
+ final Writer writer ) {
+ final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
+ for( final Protein protein : protein_list ) {
+ final int domains = protein.getNumberOfProteinDomains();
+ //System.out.println( domains );
+ stats.addValue( domains );
+ all_genomes_domains_per_potein_stats.addValue( domains );
+ if ( !all_genomes_domains_per_potein_histo.containsKey( domains ) ) {
+ all_genomes_domains_per_potein_histo.put( domains, 1 );
+ }
+ else {
+ all_genomes_domains_per_potein_histo.put( domains,
+ 1 + all_genomes_domains_per_potein_histo.get( domains ) );
+ }
+ if ( domains == 1 ) {
+ final String domain = protein.getProteinDomain( 0 ).getDomainId().getId();
+ if ( !domains_which_are_sometimes_single_sometimes_not.contains( domain ) ) {
+ if ( domains_which_never_single.contains( domain ) ) {
+ domains_which_never_single.remove( domain );
+ domains_which_are_sometimes_single_sometimes_not.add( domain );
+ }
+ else {
+ domains_which_are_always_single.add( domain );
+ }
+ }
+ }
+ else if ( domains > 1 ) {
+ for( final Domain d : protein.getProteinDomains() ) {
+ final String domain = d.getDomainId().getId();
+ // System.out.println( domain );
+ if ( !domains_which_are_sometimes_single_sometimes_not.contains( domain ) ) {
+ if ( domains_which_are_always_single.contains( domain ) ) {
+ domains_which_are_always_single.remove( domain );
+ domains_which_are_sometimes_single_sometimes_not.add( domain );
+ }
+ else {
+ domains_which_never_single.add( domain );
+ }
+ }
+ }
+ }
+ }
+ try {
+ writer.write( genome );
+ writer.write( "\t" );
+ writer.write( stats.arithmeticMean() + "" );
+ writer.write( "\t" );
+ writer.write( stats.sampleStandardDeviation() + "" );
+ writer.write( "\t" );
+ writer.write( stats.median() + "" );
+ writer.write( "\t" );
+ writer.write( stats.getN() + "" );
+ writer.write( "\t" );
+ writer.write( stats.getMin() + "" );
+ writer.write( "\t" );
+ writer.write( stats.getMax() + "" );
+ writer.write( "\n" );
+ }
+ catch ( final IOException e ) {
+ e.printStackTrace();
+ }
+ }
}
git://source.jalview.org / jalview.git / blobdiff