// Copyright (C) 2008-2009 Christian M. Zmasek
// Copyright (C) 2008-2009 Burnham Institute for Medical Research
// All rights reserved
-//
+//
// This library is free software; you can redistribute it and/or
// modify it under the terms of the GNU Lesser General Public
// License as published by the Free Software Foundation; either
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
// Lesser General Public License for more details.
-//
+//
// You should have received a copy of the GNU Lesser General Public
// License along with this library; if not, write to the Free Software
// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
import org.forester.surfacing.DomainLengthsTable;
import org.forester.surfacing.DomainParsimonyCalculator;
import org.forester.surfacing.DomainSimilarity;
+import org.forester.surfacing.DomainSimilarity.DomainSimilarityScoring;
+import org.forester.surfacing.DomainSimilarity.DomainSimilaritySortField;
import org.forester.surfacing.DomainSimilarityCalculator;
+import org.forester.surfacing.DomainSimilarityCalculator.Detailedness;
import org.forester.surfacing.GenomeWideCombinableDomains;
+import org.forester.surfacing.GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder;
import org.forester.surfacing.MappingResults;
import org.forester.surfacing.PairwiseDomainSimilarityCalculator;
import org.forester.surfacing.PairwiseGenomeComparator;
import org.forester.surfacing.PrintableDomainSimilarity;
+import org.forester.surfacing.PrintableDomainSimilarity.PRINT_OPTION;
import org.forester.surfacing.Protein;
import org.forester.surfacing.ProteinCountsBasedPairwiseDomainSimilarityCalculator;
import org.forester.surfacing.Species;
import org.forester.surfacing.SurfacingUtil;
-import org.forester.surfacing.DomainSimilarity.DomainSimilarityScoring;
-import org.forester.surfacing.DomainSimilarity.DomainSimilaritySortField;
-import org.forester.surfacing.DomainSimilarityCalculator.Detailedness;
-import org.forester.surfacing.GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder;
-import org.forester.surfacing.PrintableDomainSimilarity.PRINT_OPTION;
import org.forester.util.BasicTable;
import org.forester.util.BasicTableParser;
import org.forester.util.CommandLineArguments;
public final static String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_DOMAINS = "_fitch_glc_d";
public final static String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_BINARY_COMBINATIONS = "_fitch_glc_dc";
// tables:
- // public final static String PARSIMONY_OUTPUT_FITCH_GAINS_BC = "_fitch_gains_dc";
- // public final static String PARSIMONY_OUTPUT_FITCH_GAINS_HTML_BC = "_fitch_gains_dc.html";
- // public final static String PARSIMONY_OUTPUT_FITCH_LOSSES_BC = "_fitch_losses_dc";
- // public final static String PARSIMONY_OUTPUT_FITCH_LOSSES_HTML_BC = "_fitch_losses_dc.html";
- // public final static String PARSIMONY_OUTPUT_FITCH_PRESENT_BC = "_fitch_present_dc";
- // public final static String PARSIMONY_OUTPUT_FITCH_PRESENT_HTML_BC = "_fitch_present_dc.html";
- // public final static String PARSIMONY_OUTPUT_DOLLO_GAINS_D = "_dollo_gains_d";
- // public final static String PARSIMONY_OUTPUT_DOLLO_GAINS_GOID_D = "_dollo_gains_goid_d";
- // public final static String PARSIMONY_OUTPUT_DOLLO_GAINS_HTML_D = "_dollo_gains_d.html";
- // public final static String PARSIMONY_OUTPUT_DOLLO_LOSSES_D = "_dollo_losses_d";
- //public final static String PARSIMONY_OUTPUT_DOLLO_LOSSES_HTML_D = "_dollo_losses_d.html";
- // public final static String PARSIMONY_OUTPUT_DOLLO_PRESENT_D = "_dollo_present_d";
- public final static String PARSIMONY_OUTPUT_DOLLO_PRESENT_GOID_D = "_dollo_present_goid_d";
- //public final static String PARSIMONY_OUTPUT_DOLLO_PRESENT_HTML_D = "_dollo_present_d.html";
+ public final static String PARSIMONY_OUTPUT_FITCH_GAINS_BC = "_fitch_gains_dc";
+ public final static String PARSIMONY_OUTPUT_FITCH_GAINS_HTML_BC = "_fitch_gains_dc.html";
+ public final static String PARSIMONY_OUTPUT_FITCH_LOSSES_BC = "_fitch_losses_dc";
+ public final static String PARSIMONY_OUTPUT_FITCH_LOSSES_HTML_BC = "_fitch_losses_dc.html";
+ public final static String PARSIMONY_OUTPUT_FITCH_PRESENT_BC = "_fitch_present_dc";
+ public final static String PARSIMONY_OUTPUT_FITCH_PRESENT_HTML_BC = "_fitch_present_dc.html";
+ public final static String PARSIMONY_OUTPUT_DOLLO_GAINS_D = "_dollo_gains_d";
+ public final static String PARSIMONY_OUTPUT_DOLLO_GAINS_HTML_D = "_dollo_gains_d.html";
+ public final static String PARSIMONY_OUTPUT_DOLLO_LOSSES_D = "_dollo_losses_d";
+ public final static String PARSIMONY_OUTPUT_DOLLO_LOSSES_HTML_D = "_dollo_losses_d.html";
+ public final static String PARSIMONY_OUTPUT_DOLLO_PRESENT_D = "_dollo_present_d";
+ public final static String PARSIMONY_OUTPUT_DOLLO_PRESENT_HTML_D = "_dollo_present_d.html";
public final static String DOMAINS_PRESENT_NEXUS = "_dom.nex";
public final static String BDC_PRESENT_NEXUS = "_dc.nex";
// ---
public static final String PARSIMONY_OUTPUT_DOLLO_PRESENT_SECONDARY_FEATURES = "_dollo_present_secondary_features";
public static final String SECONDARY_FEATURES_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO = "_secondary_features_dollo"
+ ForesterConstants.PHYLO_XML_SUFFIX;
- public static final String PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_BIOLOGICAL_PROCESS = "_dollo_biol_proc_goid_d";
- public static final String PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_CELLULAR_COMPONENT = "_dollo_cell_comp_goid_d";
- public static final String PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_MOLECULAR_FUNCTION = "_dollo_mol_funct_goid_d";
public static final String PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_ALL_NAMESPACES = "_dollo_goid_d";
- public static final String PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_BIOLOGICAL_PROCESS = "_fitch_biol_proc_goid_dc";
- public static final String PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_CELLULAR_COMPONENT = "_fitch_cell_comp_goid_dc";
- public static final String PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_MOLECULAR_FUNCTION = "_fitch_mol_funct_goid_dc";
public static final String PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_ALL_NAMESPACES = "_fitch_goid_dc";
final static private String HELP_OPTION_1 = "help";
final static private String HELP_OPTION_2 = "h";
+ ForesterConstants.PHYLO_XML_SUFFIX;
final static private String NJ_TREE_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX = "_bin_combinations_NJ"
+ ForesterConstants.PHYLO_XML_SUFFIX;
- final static private String DISPLAY_M_HISTOGRAMS_OPTION = "mhisto";
- // final static private boolean DISPLAY_M_HISTOGRAMS_OPTION_DEFAULT = false;
final static private String JACKNIFE_OPTION = "jack";
final static private String JACKNIFE_RANDOM_SEED_OPTION = "seed";
final static private String JACKNIFE_RATIO_OPTION = "jack_ratio";
final static private String INPUT_SPECIES_TREE_OPTION = "species_tree";
final static private String SEQ_EXTRACT_OPTION = "prot_extract";
final static private char SEPARATOR_FOR_INPUT_VALUES = '#';
- final static private String PRG_VERSION = "2.003";
- final static private String PRG_DATE = "2010.12.03";
+ final static private String PRG_VERSION = "2.100";
+ final static private String PRG_DATE = "2011.06.17";
final static private String E_MAIL = "czmasek@burnham.org";
final static private String WWW = "www.phylosoft.org/forester/applications/surfacing";
final static private boolean IGNORE_DUFS_DEFAULT = true;
final static private boolean IGNORE_COMBINATION_WITH_SAME_DEFAULLT = false;
final static private double MAX_E_VALUE_DEFAULT = -1;
final static private int MAX_ALLOWED_OVERLAP_DEFAULT = -1;
- final static private String DEFAULT_SEARCH_PARAMETER = "ls";
- final private static boolean VERBOSE_DEFAULT = true;
private static final String RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION = "random_seed";
private static final String CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS = "consider_bdc_direction";
private static final String CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS_AND_ADJACENCY = "consider_bdc_adj";
private static final String DATA_FILE_SUFFIX = "_domain_combination_data.txt";
private static final String DATA_FILE_DESC = "#SPECIES\tPRTEIN_ID\tN_TERM_DOMAIN\tC_TERM_DOMAIN\tN_TERM_DOMAIN_PER_DOMAIN_E_VALUE\tC_TERM_DOMAIN_PER_DOMAIN_E_VALUE\tN_TERM_DOMAIN_COUNTS_PER_PROTEIN\tC_TERM_DOMAIN_COUNTS_PER_PROTEIN";
private static final INDIVIDUAL_SCORE_CUTOFF INDIVIDUAL_SCORE_CUTOFF_DEFAULT = INDIVIDUAL_SCORE_CUTOFF.FULL_SEQUENCE;
+ public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_OUTPUT_SUFFIX = "_indep_dc_gains_fitch_counts.txt";
+ public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_DC_OUTPUT_SUFFIX = "_indep_dc_gains_fitch_lists.txt";
+ public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_SUFFIX = "_indep_dc_gains_fitch_lists_for_go_mapping.txt";
+ public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_UNIQUE_SUFFIX = "_indep_dc_gains_fitch_lists_for_go_mapping_unique.txt";
- // final String error = ForesterUtil.isReadableFile( new File(
- // input_file_properties[ i ][ 0 ] ) );
- // if ( !ForesterUtil.isEmpty( error ) ) {
- // ForesterUtil.fatalError( surfacing.PRG_NAME, error );
- // }
private static void checkWriteabilityForPairwiseComparisons( final PrintableDomainSimilarity.PRINT_OPTION domain_similarity_print_option,
final String[][] input_file_properties,
final String automated_pairwise_comparison_suffix,
}
/**
- * Warning: This sideeffects 'all_bin_domain_combinations_encountered'!
+ * Warning: This side-effects 'all_bin_domain_combinations_encountered'!
*
*
* @param output_file
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 + "]" );
+ 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 = SurfacingUtil.getNumberOfNodesLackingName( intree, parent_names );
allowed_options.add( surfacing.GO_NAMESPACE_LIMIT_OPTION );
allowed_options.add( surfacing.PAIRWISE_DOMAIN_COMPARISONS_OPTION );
allowed_options.add( surfacing.IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_OPTION );
- allowed_options.add( surfacing.DISPLAY_M_HISTOGRAMS_OPTION );
allowed_options.add( surfacing.CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS );
allowed_options.add( JACKNIFE_OPTION );
allowed_options.add( JACKNIFE_RANDOM_SEED_OPTION );
.createDomainIdToSecondaryFeaturesMap( secondary_features_map_files[ i ] );
}
catch ( final IOException e ) {
- ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read secondary features map file: "
- + e.getMessage() );
+ ForesterUtil.fatalError( surfacing.PRG_NAME,
+ "cannot read secondary features map file: " + e.getMessage() );
}
catch ( final Exception e ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, "problem with contents of features map file ["
"no (acceptable) go id to term mapping file provided ('GO OBO file') (-"
+ surfacing.GO_OBO_FILE_USE_OPTION + "=<file>)" );
}
- boolean display_histograms = false;
- if ( cla.isOptionSet( surfacing.DISPLAY_M_HISTOGRAMS_OPTION ) ) {
- display_histograms = true;
- }
System.out.println( "Output directory : " + out_dir );
if ( input_file_names_from_file != null ) {
System.out.println( "Input files names from : " + input_files_file + " ["
if ( max_allowed_overlap != surfacing.MAX_ALLOWED_OVERLAP_DEFAULT ) {
parser.setMaxAllowedOverlap( max_allowed_overlap );
}
- parser
- .setReturnType( HmmscanPerDomainTableParser.ReturnType.UNORDERED_PROTEIN_DOMAIN_COLLECTION_PER_PROTEIN );
+ parser.setReturnType( HmmscanPerDomainTableParser.ReturnType.UNORDERED_PROTEIN_DOMAIN_COLLECTION_PER_PROTEIN );
if ( individual_score_cutoffs != null ) {
parser.setIndividualScoreCutoffs( individual_score_cutoffs );
}
System.out.println( "Domains ignored due to individual score cutoffs: "
+ parser.getDomainsIgnoredDueToIndividualScoreCutoff() );
log( "Domains ignored due to individual score cutoffs: "
- + parser.getDomainsIgnoredDueToIndividualScoreCutoff(), log_writer );
+ + parser.getDomainsIgnoredDueToIndividualScoreCutoff(),
+ log_writer );
System.out.println( "Domains ignored due to E-value : "
+ parser.getDomainsIgnoredDueToEval() );
log( "Domains ignored due to E-value : " + parser.getDomainsIgnoredDueToEval(), log_writer );
System.out.println( "Domains ignored due negative domain filter : "
+ parser.getDomainsIgnoredDueToNegativeDomainFilter() );
log( "Domains ignored due negative domain filter : "
- + parser.getDomainsIgnoredDueToNegativeDomainFilter(), log_writer );
+ + parser.getDomainsIgnoredDueToNegativeDomainFilter(),
+ log_writer );
System.out.println( "Domains ignored due to overlap : "
+ parser.getDomainsIgnoredDueToOverlap() );
log( "Domains ignored due to overlap : " + parser.getDomainsIgnoredDueToOverlap(),
true,
surfacing.PAIRWISE_DOMAIN_COMPARISONS_PREFIX,
surfacing.PRG_NAME,
- display_histograms,
out_dir,
write_pwc_files );
String matrix_output_file = new String( output_file.toString() );
}
SurfacingUtil.writeMatrixToFile( new File( matrix_output_file
+ surfacing.MATRIX_MEAN_SCORE_BASED_GENOME_DISTANCE_SUFFIX ), pwgc.getDomainDistanceScoresMeans() );
+ SurfacingUtil
+ .writeMatrixToFile( new File( matrix_output_file
+ + surfacing.MATRIX_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX ),
+ pwgc.getSharedBinaryCombinationsBasedDistances() );
SurfacingUtil.writeMatrixToFile( new File( matrix_output_file
- + surfacing.MATRIX_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX ), pwgc
- .getSharedBinaryCombinationsBasedDistances() );
- SurfacingUtil.writeMatrixToFile( new File( matrix_output_file
- + surfacing.MATRIX_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX ), pwgc
- .getSharedDomainsBasedDistances() );
+ + surfacing.MATRIX_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX ),
+ pwgc.getSharedDomainsBasedDistances() );
final Phylogeny nj_gd = SurfacingUtil.createNjTreeBasedOnMatrixToFile( new File( matrix_output_file
+ surfacing.NJ_TREE_MEAN_SCORE_BASED_GENOME_DISTANCE_SUFFIX ), pwgc.getDomainDistanceScoresMeans()
.get( 0 ) );
inferred_trees.add( nj_gd );
inferred_trees.add( nj_bc );
inferred_trees.add( nj_d );
- // final List<HistogramData> histogram_datas = pwgc.getHistogramDatas();
- // if ( infer_species_trees ) {
- // inferred_trees = new ArrayList<Phylogeny>();
- // final List<Phylogeny> inferred_trees_bc = inferSpeciesTrees( new File( output_file + INFERRED_SBC_BASED_NJ_SPECIES_TREE_SUFFIX ), pwgc
- // .getSharedBinaryCombinationsBasedDistances() );
- // final List<Phylogeny> inferred_trees_d = inferSpeciesTrees( new File( output_file + INFERRED_SD_BASED_NJ_SPECIES_TREE_SUFFIX ), pwgc
- // .getSharedDomainsBasedDistances() );
- // inferred_trees.addAll( inferred_trees_bc );
- // inferred_trees.addAll( inferred_trees_d );
- // }
if ( jacknifed_distances ) {
pwgc.performPairwiseComparisonsJacknifed( species,
number_of_genomes,
jacknife_resamplings,
jacknife_ratio,
random_seed );
- SurfacingUtil.writeMatrixToFile( new File( matrix_output_file + "_"
- + ForesterUtil.round( jacknife_ratio, 2 ) + "_" + jacknife_resamplings
- + surfacing.MATRIX_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX ), pwgc
- .getSharedBinaryCombinationsBasedDistances() );
- SurfacingUtil.writeMatrixToFile( new File( matrix_output_file + "_"
- + ForesterUtil.round( jacknife_ratio, 2 ) + "_" + jacknife_resamplings
- + surfacing.MATRIX_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX ), pwgc
- .getSharedDomainsBasedDistances() );
+ SurfacingUtil
+ .writeMatrixToFile( new File( matrix_output_file
+ + "_"
+ + ForesterUtil.round( jacknife_ratio, 2 )
+ + "_"
+ + jacknife_resamplings
+ + surfacing.MATRIX_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX ),
+ pwgc.getSharedBinaryCombinationsBasedDistances() );
+ SurfacingUtil
+ .writeMatrixToFile( new File( matrix_output_file + "_" + ForesterUtil.round( jacknife_ratio, 2 )
+ + "_" + jacknife_resamplings
+ + surfacing.MATRIX_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX ),
+ pwgc.getSharedDomainsBasedDistances() );
// if ( infer_species_trees ) {
// inferSpeciesTrees( new File( output_file + "_" + jacknife_resamplings
// + INFERRED_SBC_BASED_NJ_SPECIES_TREE_SUFFIX ), pwgc
// + INFERRED_SD_BASED_NJ_SPECIES_TREE_SUFFIX ), pwgc.getSharedDomainsBasedDistances() );
// }
}
- if ( display_histograms ) {
- // final List<HistogramData> histogram_datas_all = new ArrayList<HistogramData>();
- // histogram_datas_all.add( new HistogramData( "all",
- // values_for_all_scores_histogram,
- // null,
- // 20 ) );
- // final HistogramsFrame hf_all = new HistogramsFrame( histogram_datas_all );
- // final HistogramsFrame hf = new HistogramsFrame( histogram_datas );
- // hf_all.setVisible( true );
- // hf.setVisible( true );
- }
} // if ( ( output_file != null ) && ( number_of_genomes > 2 ) && !isEmpty( automated_pairwise_comparison_suffix ) )
if ( ( out_dir != null ) && ( !perform_pwc ) ) {
output_file = new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file );
System.out.println( surfacing.INPUT_SPECIES_TREE_OPTION
+ ": species tree, to perform (Dollo, Fitch) parismony analyses" );
System.out
- .println( surfacing.DISPLAY_M_HISTOGRAMS_OPTION + ": to display multiple histograms (using fluorite)" );
- System.out
.println( JACKNIFE_OPTION
+ ": perform jacknife resampling for domain and binary domain combination based distance matrices [default resamplings: "
+ JACKNIFE_NUMBER_OF_RESAMPLINGS_DEFAULT + "]" );
System.out.println();
System.out.println();
System.out.println( "Example: java -Xms128m -Xmx512m -cp path/to/forester.jar"
- + "org.forester.application.surfacing -detail=punctilious -o=TEST.html -pwc=TEST"
+ + " org.forester.application.surfacing -detail=punctilious -o=TEST.html -pwc=TEST"
+ " -cos=Pfam_ls_22_TC2 -p2g=pfam2go -obo=gene_ontology_edit.obo "
+ "-dc_sort=dom -ignore_with_self -no_singles -e=0.001 -mo=1 -no_eo "
+ "-ds_output=detailed_html -scoring=domains -sort=alpha -" + JACKNIFE_OPTION
git://source.jalview.org / jalview.git / blobdiff