From: cmzmasek Date: Thu, 23 Mar 2017 05:13:10 +0000 (-0700) Subject: in progress X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=814c97be10a4c55b0bb642668f9ef8e1f80d5a6c;p=jalview.git in progress --- diff --git a/forester/java/src/org/forester/application/surfacing.java b/forester/java/src/org/forester/application/surfacing.java index 786c673..a3572d5 100644 --- a/forester/java/src/org/forester/application/surfacing.java +++ b/forester/java/src/org/forester/application/surfacing.java @@ -216,8 +216,8 @@ public class surfacing { final static private String INPUT_GENOMES_FILE_OPTION = "genomes"; final static private String INPUT_SPECIES_TREE_OPTION = "species_tree"; final static private String SEQ_EXTRACT_OPTION = "prot_extract"; - final static private String PRG_VERSION = "2.404"; - final static private String PRG_DATE = "170315"; + final static private String PRG_VERSION = "2.405"; + final static private String PRG_DATE = "170317"; final static private String E_MAIL = "czmasek@burnham.org"; final static private String WWW = "https://sites.google.com/site/cmzmasek/home/software/forester/surfacing"; final static private boolean IGNORE_DUFS_DEFAULT = true; @@ -271,7 +271,8 @@ public class surfacing { public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_SUFFIX = "_indep_dc_gains_fitch_lists_for_go_mapping_MAPPED.txt"; public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_UNIQUE_SUFFIX = "_indep_dc_gains_fitch_lists_for_go_mapping_unique_MAPPED.txt"; private static final boolean CALC_SIMILARITY_SCORES = false; - @SuppressWarnings("unchecked") + + @SuppressWarnings( "unchecked") public static void main( final String args[] ) { final long start_time = new Date().getTime(); // final StringBuffer log = new StringBuffer(); @@ -435,8 +436,9 @@ public class surfacing { ignore_species_specific_domains = true; } if ( !cla.isOptionValueSet( surfacing.INPUT_SPECIES_TREE_OPTION ) ) { - ForesterUtil.fatalError( surfacing.PRG_NAME, "no input species tree file given: " - + surfacing.INPUT_SPECIES_TREE_OPTION + "=" ); + ForesterUtil.fatalError( surfacing.PRG_NAME, + "no input species tree file given: " + surfacing.INPUT_SPECIES_TREE_OPTION + + "=" ); } File output_file = null; if ( cla.isOptionSet( surfacing.OUTPUT_FILE_OPTION ) ) { @@ -452,14 +454,15 @@ public class surfacing { Map individual_score_cutoffs = null; if ( cla.isOptionSet( surfacing.CUTOFF_SCORE_FILE_OPTION ) ) { if ( !cla.isOptionValueSet( surfacing.CUTOFF_SCORE_FILE_OPTION ) ) { - ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for individual domain score cutoffs file: -" - + surfacing.CUTOFF_SCORE_FILE_OPTION + "=" ); + ForesterUtil.fatalError( surfacing.PRG_NAME, + "no value for individual domain score cutoffs file: -" + + surfacing.CUTOFF_SCORE_FILE_OPTION + "=" ); } cutoff_scores_file = new File( cla.getOptionValue( surfacing.CUTOFF_SCORE_FILE_OPTION ) ); final String error = ForesterUtil.isReadableFile( cutoff_scores_file ); if ( !ForesterUtil.isEmpty( error ) ) { - ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read individual domain score cutoffs file: " - + error ); + ForesterUtil.fatalError( surfacing.PRG_NAME, + "cannot read individual domain score cutoffs file: " + error ); } try { final BasicTable scores_table = BasicTableParser.parse( cutoff_scores_file, ' ' ); @@ -479,8 +482,8 @@ public class surfacing { File out_dir = null; if ( cla.isOptionSet( surfacing.OUTPUT_DIR_OPTION ) ) { if ( !cla.isOptionValueSet( surfacing.OUTPUT_DIR_OPTION ) ) { - ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for output directory: -" - + surfacing.OUTPUT_DIR_OPTION + "=" ); + ForesterUtil.fatalError( surfacing.PRG_NAME, + "no value for output directory: -" + surfacing.OUTPUT_DIR_OPTION + "=" ); } out_dir = new File( cla.getOptionValue( surfacing.OUTPUT_DIR_OPTION ) ); if ( out_dir.exists() && ( out_dir.listFiles().length > 0 ) ) { @@ -499,50 +502,54 @@ public class surfacing { File positive_filter_file = null; File negative_filter_file = null; File negative_domains_filter_file = null; - if ( cla.isOptionSet( surfacing.FILTER_NEGATIVE_OPTION ) && cla.isOptionSet( surfacing.FILTER_POSITIVE_OPTION ) ) { + if ( cla.isOptionSet( surfacing.FILTER_NEGATIVE_OPTION ) + && cla.isOptionSet( surfacing.FILTER_POSITIVE_OPTION ) ) { ForesterUtil.fatalError( surfacing.PRG_NAME, "attempt to use both negative and positive protein filter" ); } if ( cla.isOptionSet( surfacing.FILTER_NEGATIVE_DOMAINS_OPTION ) - && ( cla.isOptionSet( surfacing.FILTER_NEGATIVE_OPTION ) || cla - .isOptionSet( surfacing.FILTER_POSITIVE_OPTION ) ) ) { + && ( cla.isOptionSet( surfacing.FILTER_NEGATIVE_OPTION ) + || cla.isOptionSet( surfacing.FILTER_POSITIVE_OPTION ) ) ) { ForesterUtil - .fatalError( surfacing.PRG_NAME, - "attempt to use both negative or positive protein filter together wirh a negative domains filter" ); + .fatalError( surfacing.PRG_NAME, + "attempt to use both negative or positive protein filter together wirh a negative domains filter" ); } if ( cla.isOptionSet( surfacing.FILTER_NEGATIVE_OPTION ) ) { if ( !cla.isOptionValueSet( surfacing.FILTER_NEGATIVE_OPTION ) ) { - ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for negative filter: -" - + surfacing.FILTER_NEGATIVE_OPTION + "=" ); + ForesterUtil + .fatalError( surfacing.PRG_NAME, + "no value for negative filter: -" + surfacing.FILTER_NEGATIVE_OPTION + "=" ); } negative_filter_file = new File( cla.getOptionValue( surfacing.FILTER_NEGATIVE_OPTION ) ); final String msg = ForesterUtil.isReadableFile( negative_filter_file ); if ( !ForesterUtil.isEmpty( msg ) ) { - ForesterUtil.fatalError( surfacing.PRG_NAME, "can not read from \"" + negative_filter_file + "\": " - + msg ); + ForesterUtil.fatalError( surfacing.PRG_NAME, + "can not read from \"" + negative_filter_file + "\": " + msg ); } } else if ( cla.isOptionSet( surfacing.FILTER_POSITIVE_OPTION ) ) { if ( !cla.isOptionValueSet( surfacing.FILTER_POSITIVE_OPTION ) ) { - ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for positive filter: -" - + surfacing.FILTER_POSITIVE_OPTION + "=" ); + ForesterUtil + .fatalError( surfacing.PRG_NAME, + "no value for positive filter: -" + surfacing.FILTER_POSITIVE_OPTION + "=" ); } positive_filter_file = new File( cla.getOptionValue( surfacing.FILTER_POSITIVE_OPTION ) ); final String msg = ForesterUtil.isReadableFile( positive_filter_file ); if ( !ForesterUtil.isEmpty( msg ) ) { - ForesterUtil.fatalError( surfacing.PRG_NAME, "can not read from \"" + positive_filter_file + "\": " - + msg ); + ForesterUtil.fatalError( surfacing.PRG_NAME, + "can not read from \"" + positive_filter_file + "\": " + msg ); } } else if ( cla.isOptionSet( surfacing.FILTER_NEGATIVE_DOMAINS_OPTION ) ) { if ( !cla.isOptionValueSet( surfacing.FILTER_NEGATIVE_DOMAINS_OPTION ) ) { - ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for negative domains filter: -" - + surfacing.FILTER_NEGATIVE_DOMAINS_OPTION + "=" ); + ForesterUtil.fatalError( surfacing.PRG_NAME, + "no value for negative domains filter: -" + + surfacing.FILTER_NEGATIVE_DOMAINS_OPTION + "=" ); } negative_domains_filter_file = new File( cla.getOptionValue( surfacing.FILTER_NEGATIVE_DOMAINS_OPTION ) ); final String msg = ForesterUtil.isReadableFile( negative_domains_filter_file ); if ( !ForesterUtil.isEmpty( msg ) ) { - ForesterUtil.fatalError( surfacing.PRG_NAME, "can not read from \"" + negative_domains_filter_file - + "\": " + msg ); + ForesterUtil.fatalError( surfacing.PRG_NAME, + "can not read from \"" + negative_domains_filter_file + "\": " + msg ); } } final List plus_minus_analysis_high_copy_base_species = new ArrayList(); @@ -557,29 +564,31 @@ public class surfacing { File input_genomes_file = null; if ( cla.isOptionSet( surfacing.INPUT_GENOMES_FILE_OPTION ) ) { if ( !cla.isOptionValueSet( surfacing.INPUT_GENOMES_FILE_OPTION ) ) { - ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for input genomes file: -" - + surfacing.INPUT_GENOMES_FILE_OPTION + "=" ); + ForesterUtil.fatalError( surfacing.PRG_NAME, + "no value for input genomes file: -" + surfacing.INPUT_GENOMES_FILE_OPTION + + "=" ); } input_genomes_file = new File( cla.getOptionValue( surfacing.INPUT_GENOMES_FILE_OPTION ) ); final String msg = ForesterUtil.isReadableFile( input_genomes_file ); if ( !ForesterUtil.isEmpty( msg ) ) { - ForesterUtil - .fatalError( surfacing.PRG_NAME, "can not read from \"" + input_genomes_file + "\": " + msg ); + ForesterUtil.fatalError( surfacing.PRG_NAME, + "can not read from \"" + input_genomes_file + "\": " + msg ); } } else { - ForesterUtil.fatalError( surfacing.PRG_NAME, "no input genomes file given: " - + surfacing.INPUT_GENOMES_FILE_OPTION + "=" ); + ForesterUtil + .fatalError( surfacing.PRG_NAME, + "no input genomes file given: " + surfacing.INPUT_GENOMES_FILE_OPTION + "=" ); } DomainSimilarity.DomainSimilarityScoring scoring = SCORING_DEFAULT; if ( cla.isOptionSet( surfacing.SCORING_OPTION ) ) { if ( !cla.isOptionValueSet( surfacing.SCORING_OPTION ) ) { - ForesterUtil.fatalError( surfacing.PRG_NAME, - "no value for scoring method for domain combinations similarity calculation: -" - + surfacing.SCORING_OPTION + "=<" - + surfacing.SCORING_DOMAIN_COUNT_BASED + "|" - + surfacing.SCORING_PROTEIN_COUNT_BASED + "|" - + surfacing.SCORING_COMBINATION_BASED + ">\"" ); + ForesterUtil + .fatalError( surfacing.PRG_NAME, + "no value for scoring method for domain combinations similarity calculation: -" + + surfacing.SCORING_OPTION + "=<" + surfacing.SCORING_DOMAIN_COUNT_BASED + + "|" + surfacing.SCORING_PROTEIN_COUNT_BASED + "|" + + surfacing.SCORING_COMBINATION_BASED + ">\"" ); } final String scoring_str = cla.getOptionValue( surfacing.SCORING_OPTION ); if ( scoring_str.equals( surfacing.SCORING_DOMAIN_COUNT_BASED ) ) { @@ -592,10 +601,13 @@ public class surfacing { scoring = DomainSimilarity.DomainSimilarityScoring.PROTEINS; } else { - ForesterUtil.fatalError( surfacing.PRG_NAME, "unknown value \"" + scoring_str - + "\" for scoring method for domain combinations similarity calculation: \"-" - + surfacing.SCORING_OPTION + "=<" + surfacing.SCORING_DOMAIN_COUNT_BASED + "|" - + surfacing.SCORING_PROTEIN_COUNT_BASED + "|" + surfacing.SCORING_COMBINATION_BASED + ">\"" ); + ForesterUtil + .fatalError( surfacing.PRG_NAME, + "unknown value \"" + scoring_str + + "\" for scoring method for domain combinations similarity calculation: \"-" + + surfacing.SCORING_OPTION + "=<" + surfacing.SCORING_DOMAIN_COUNT_BASED + + "|" + surfacing.SCORING_PROTEIN_COUNT_BASED + "|" + + surfacing.SCORING_COMBINATION_BASED + ">\"" ); } } boolean sort_by_species_count_first = false; @@ -623,9 +635,10 @@ public class surfacing { Detailedness detailedness = DETAILEDNESS_DEFAULT; if ( cla.isOptionSet( surfacing.DETAILEDNESS_OPTION ) ) { if ( !cla.isOptionValueSet( surfacing.DETAILEDNESS_OPTION ) ) { - ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for -" + surfacing.DETAILEDNESS_OPTION + "=<" - + surfacing.DETAILEDNESS_BASIC + "|" + surfacing.DETAILEDNESS_LIST_IDS + "|" - + surfacing.DETAILEDNESS_PUNCTILIOUS + ">\"" ); + ForesterUtil.fatalError( surfacing.PRG_NAME, + "no value for -" + surfacing.DETAILEDNESS_OPTION + "=<" + + surfacing.DETAILEDNESS_BASIC + "|" + surfacing.DETAILEDNESS_LIST_IDS + + "|" + surfacing.DETAILEDNESS_PUNCTILIOUS + ">\"" ); } final String detness = cla.getOptionValue( surfacing.DETAILEDNESS_OPTION ).toLowerCase(); if ( detness.equals( surfacing.DETAILEDNESS_BASIC ) ) { @@ -638,9 +651,11 @@ public class surfacing { detailedness = DomainSimilarityCalculator.Detailedness.PUNCTILIOUS; } else { - ForesterUtil.fatalError( surfacing.PRG_NAME, "unknown value \"" + detness + "\" for detailedness: \"-" - + surfacing.DETAILEDNESS_OPTION + "=<" + surfacing.DETAILEDNESS_BASIC + "|" - + surfacing.DETAILEDNESS_LIST_IDS + "|" + surfacing.DETAILEDNESS_PUNCTILIOUS + ">\"" ); + ForesterUtil.fatalError( surfacing.PRG_NAME, + "unknown value \"" + detness + "\" for detailedness: \"-" + + surfacing.DETAILEDNESS_OPTION + "=<" + surfacing.DETAILEDNESS_BASIC + + "|" + surfacing.DETAILEDNESS_LIST_IDS + "|" + + surfacing.DETAILEDNESS_PUNCTILIOUS + ">\"" ); } } String automated_pairwise_comparison_suffix = null; @@ -661,10 +676,10 @@ public class surfacing { if ( cla.isOptionSet( surfacing.SEQ_EXTRACT_OPTION ) ) { if ( !cla.isOptionValueSet( surfacing.SEQ_EXTRACT_OPTION ) ) { ForesterUtil - .fatalError( surfacing.PRG_NAME, - "no domain ids given for sequences with given domains to be extracted : -" - + surfacing.SEQ_EXTRACT_OPTION - + "=" ); + .fatalError( surfacing.PRG_NAME, + "no domain ids given for sequences with given domains to be extracted : -" + + surfacing.SEQ_EXTRACT_OPTION + + "=" ); } query_domain_ids = cla.getOptionValue( surfacing.SEQ_EXTRACT_OPTION ); } @@ -672,14 +687,18 @@ public class surfacing { DomainSimilarity.DomainSimilaritySortField domain_similarity_sort_field_for_automated_pwc = DOMAIN_SORT_FILD_DEFAULT; if ( cla.isOptionSet( surfacing.DOMAIN_SIMILARITY_SORT_OPTION ) ) { if ( !cla.isOptionValueSet( surfacing.DOMAIN_SIMILARITY_SORT_OPTION ) ) { - ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for domain combinations similarities sorting: -" - + surfacing.DOMAIN_SIMILARITY_SORT_OPTION + "=<" + surfacing.DOMAIN_SIMILARITY_SORT_ALPHA + "|" - + surfacing.DOMAIN_SIMILARITY_SORT_MAX + "|" + surfacing.DOMAIN_SIMILARITY_SORT_MIN + "|" - + surfacing.DOMAIN_SIMILARITY_SORT_MEAN + "|" + surfacing.DOMAIN_SIMILARITY_SORT_DIFF + "|" - + surfacing.DOMAIN_SIMILARITY_SORT_ABS_COUNTS_DIFF + "|" - + surfacing.DOMAIN_SIMILARITY_SORT_COUNTS_DIFF + "|" - + surfacing.DOMAIN_SIMILARITY_SORT_SPECIES_COUNT + "|" + surfacing.DOMAIN_SIMILARITY_SORT_SD - + ">\"" ); + ForesterUtil.fatalError( surfacing.PRG_NAME, + "no value for domain combinations similarities sorting: -" + + surfacing.DOMAIN_SIMILARITY_SORT_OPTION + "=<" + + surfacing.DOMAIN_SIMILARITY_SORT_ALPHA + "|" + + surfacing.DOMAIN_SIMILARITY_SORT_MAX + "|" + + surfacing.DOMAIN_SIMILARITY_SORT_MIN + "|" + + surfacing.DOMAIN_SIMILARITY_SORT_MEAN + "|" + + surfacing.DOMAIN_SIMILARITY_SORT_DIFF + "|" + + surfacing.DOMAIN_SIMILARITY_SORT_ABS_COUNTS_DIFF + "|" + + surfacing.DOMAIN_SIMILARITY_SORT_COUNTS_DIFF + "|" + + surfacing.DOMAIN_SIMILARITY_SORT_SPECIES_COUNT + "|" + + surfacing.DOMAIN_SIMILARITY_SORT_SD + ">\"" ); } final String sort_str = cla.getOptionValue( surfacing.DOMAIN_SIMILARITY_SORT_OPTION ).toLowerCase(); if ( sort_str.equals( surfacing.DOMAIN_SIMILARITY_SORT_ALPHA ) ) { @@ -719,24 +738,30 @@ public class surfacing { domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.MAX_COUNTS_DIFFERENCE; } else { - ForesterUtil.fatalError( surfacing.PRG_NAME, "unknown value \"" + sort_str - + "\" for domain combinations similarities sorting: \"-" - + surfacing.DOMAIN_SIMILARITY_SORT_OPTION + "=<" + surfacing.DOMAIN_SIMILARITY_SORT_ALPHA + "|" - + surfacing.DOMAIN_SIMILARITY_SORT_MAX + "|" + surfacing.DOMAIN_SIMILARITY_SORT_MIN + "|" - + surfacing.DOMAIN_SIMILARITY_SORT_MEAN + "|" + surfacing.DOMAIN_SIMILARITY_SORT_DIFF + "|" - + surfacing.DOMAIN_SIMILARITY_SORT_ABS_COUNTS_DIFF + "|" - + surfacing.DOMAIN_SIMILARITY_SORT_COUNTS_DIFF + "|" + "|" - + surfacing.DOMAIN_SIMILARITY_SORT_SPECIES_COUNT + "|" + surfacing.DOMAIN_SIMILARITY_SORT_SD - + ">\"" ); + ForesterUtil.fatalError( surfacing.PRG_NAME, + "unknown value \"" + sort_str + + "\" for domain combinations similarities sorting: \"-" + + surfacing.DOMAIN_SIMILARITY_SORT_OPTION + "=<" + + surfacing.DOMAIN_SIMILARITY_SORT_ALPHA + "|" + + surfacing.DOMAIN_SIMILARITY_SORT_MAX + "|" + + surfacing.DOMAIN_SIMILARITY_SORT_MIN + "|" + + surfacing.DOMAIN_SIMILARITY_SORT_MEAN + "|" + + surfacing.DOMAIN_SIMILARITY_SORT_DIFF + "|" + + surfacing.DOMAIN_SIMILARITY_SORT_ABS_COUNTS_DIFF + "|" + + surfacing.DOMAIN_SIMILARITY_SORT_COUNTS_DIFF + "|" + "|" + + surfacing.DOMAIN_SIMILARITY_SORT_SPECIES_COUNT + "|" + + surfacing.DOMAIN_SIMILARITY_SORT_SD + ">\"" ); } } DomainSimilarity.PRINT_OPTION domain_similarity_print_option = DOMAIN_SIMILARITY_PRINT_OPTION_DEFAULT; if ( cla.isOptionSet( surfacing.DOMAIN_SIMILARITY_PRINT_OPTION ) ) { if ( !cla.isOptionValueSet( surfacing.DOMAIN_SIMILARITY_PRINT_OPTION ) ) { - ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for print option: -" - + surfacing.DOMAIN_SIMILARITY_PRINT_OPTION_DETAILED_HTML + "|" - + surfacing.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_HTML + "|" - + surfacing.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_TAB_DELIMITED + ">\"" ); + ForesterUtil + .fatalError( surfacing.PRG_NAME, + "no value for print option: -" + + surfacing.DOMAIN_SIMILARITY_PRINT_OPTION_DETAILED_HTML + "|" + + surfacing.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_HTML + "|" + + surfacing.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_TAB_DELIMITED + ">\"" ); } final String sort = cla.getOptionValue( surfacing.DOMAIN_SIMILARITY_PRINT_OPTION ).toLowerCase(); if ( sort.equals( surfacing.DOMAIN_SIMILARITY_PRINT_OPTION_DETAILED_HTML ) ) { @@ -749,20 +774,23 @@ public class surfacing { domain_similarity_print_option = DomainSimilarity.PRINT_OPTION.SIMPLE_TAB_DELIMITED; } else { - ForesterUtil.fatalError( surfacing.PRG_NAME, "unknown value \"" + sort + "\" for print option: -" - + surfacing.DOMAIN_SIMILARITY_PRINT_OPTION_DETAILED_HTML + "|" - + surfacing.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_HTML + "|" - + surfacing.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_TAB_DELIMITED + ">\"" ); + ForesterUtil + .fatalError( surfacing.PRG_NAME, + "unknown value \"" + sort + "\" for print option: -" + + surfacing.DOMAIN_SIMILARITY_PRINT_OPTION_DETAILED_HTML + "|" + + surfacing.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_HTML + "|" + + surfacing.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_TAB_DELIMITED + ">\"" ); } } GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder dc_sort_order = DOMAINS_SORT_ORDER_DEFAULT; if ( cla.isOptionSet( surfacing.DOMAIN_COUNT_SORT_OPTION ) ) { if ( !cla.isOptionValueSet( surfacing.DOMAIN_COUNT_SORT_OPTION ) ) { - ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for sorting of domain counts: -" - + surfacing.DOMAIN_COUNT_SORT_OPTION + "=<" + surfacing.DOMAIN_COUNT_SORT_ALPHA + "|" - + surfacing.DOMAIN_COUNT_SORT_KEY_DOMAIN_COUNT + "|" - + surfacing.DOMAIN_COUNT_SORT_KEY_DOMAIN_PROTEINS_COUNT + "|" - + surfacing.DOMAIN_COUNT_SORT_COMBINATIONS_COUNT + ">\"" ); + ForesterUtil.fatalError( surfacing.PRG_NAME, + "no value for sorting of domain counts: -" + surfacing.DOMAIN_COUNT_SORT_OPTION + + "=<" + surfacing.DOMAIN_COUNT_SORT_ALPHA + "|" + + surfacing.DOMAIN_COUNT_SORT_KEY_DOMAIN_COUNT + "|" + + surfacing.DOMAIN_COUNT_SORT_KEY_DOMAIN_PROTEINS_COUNT + "|" + + surfacing.DOMAIN_COUNT_SORT_COMBINATIONS_COUNT + ">\"" ); } final String sort = cla.getOptionValue( surfacing.DOMAIN_COUNT_SORT_OPTION ).toLowerCase(); if ( sort.equals( surfacing.DOMAIN_COUNT_SORT_ALPHA ) ) { @@ -778,11 +806,13 @@ public class surfacing { dc_sort_order = GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder.COMBINATIONS_COUNT; } else { - ForesterUtil.fatalError( surfacing.PRG_NAME, "unknown value \"" + sort - + "\" for sorting of domain counts: \"-" + surfacing.DOMAIN_COUNT_SORT_OPTION + "=<" - + surfacing.DOMAIN_COUNT_SORT_ALPHA + "|" + surfacing.DOMAIN_COUNT_SORT_KEY_DOMAIN_COUNT + "|" - + surfacing.DOMAIN_COUNT_SORT_KEY_DOMAIN_PROTEINS_COUNT + "|" - + surfacing.DOMAIN_COUNT_SORT_COMBINATIONS_COUNT + ">\"" ); + ForesterUtil.fatalError( surfacing.PRG_NAME, + "unknown value \"" + sort + "\" for sorting of domain counts: \"-" + + surfacing.DOMAIN_COUNT_SORT_OPTION + "=<" + + surfacing.DOMAIN_COUNT_SORT_ALPHA + "|" + + surfacing.DOMAIN_COUNT_SORT_KEY_DOMAIN_COUNT + "|" + + surfacing.DOMAIN_COUNT_SORT_KEY_DOMAIN_PROTEINS_COUNT + "|" + + surfacing.DOMAIN_COUNT_SORT_COMBINATIONS_COUNT + ">\"" ); } } final String[][] input_file_properties = SurfacingUtil.processInputGenomesFile( input_genomes_file ); @@ -791,9 +821,10 @@ public class surfacing { ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot analyze less than two files" ); } if ( ( number_of_genomes < 3 ) && perform_pwc ) { - ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot use : -" - + surfacing.PAIRWISE_DOMAIN_COMPARISONS_OPTION - + "= to turn on pairwise analyses with less than three input files" ); + ForesterUtil + .fatalError( surfacing.PRG_NAME, + "cannot use : -" + surfacing.PAIRWISE_DOMAIN_COMPARISONS_OPTION + + "= to turn on pairwise analyses with less than three input files" ); } SurfacingUtil.checkWriteabilityForPairwiseComparisons( domain_similarity_print_option, input_file_properties, @@ -810,8 +841,9 @@ public class surfacing { File pfam_to_go_file = new File( "pfam2go.txt" ); if ( cla.isOptionSet( surfacing.PFAM_TO_GO_FILE_USE_OPTION ) ) { if ( !cla.isOptionValueSet( surfacing.PFAM_TO_GO_FILE_USE_OPTION ) ) { - ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for Pfam to GO mapping file: -" - + surfacing.PFAM_TO_GO_FILE_USE_OPTION + "=" ); + ForesterUtil.fatalError( surfacing.PRG_NAME, + "no value for Pfam to GO mapping file: -" + + surfacing.PFAM_TO_GO_FILE_USE_OPTION + "=" ); } pfam_to_go_file = new File( cla.getOptionValue( surfacing.PFAM_TO_GO_FILE_USE_OPTION ) ); } @@ -827,7 +859,7 @@ public class surfacing { domain_id_to_go_ids_map = SurfacingUtil.createDomainIdToGoIdMap( pfam_to_go_mappings ); if ( parser.getMappingCount() < domain_id_to_go_ids_map.size() ) { ForesterUtil.unexpectedFatalError( surfacing.PRG_NAME, - "parser.getMappingCount() < domain_id_to_go_ids_map.size()" ); + "parser.getMappingCount() < domain_id_to_go_ids_map.size()" ); } domain_id_to_go_ids_count = parser.getMappingCount(); } @@ -837,8 +869,8 @@ public class surfacing { File go_obo_file = new File( "go.obo" ); if ( cla.isOptionSet( surfacing.GO_OBO_FILE_USE_OPTION ) ) { if ( !cla.isOptionValueSet( surfacing.GO_OBO_FILE_USE_OPTION ) ) { - ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for GO OBO file: -" - + surfacing.GO_OBO_FILE_USE_OPTION + "=" ); + ForesterUtil.fatalError( surfacing.PRG_NAME, + "no value for GO OBO file: -" + surfacing.GO_OBO_FILE_USE_OPTION + "=" ); } go_obo_file = new File( cla.getOptionValue( surfacing.GO_OBO_FILE_USE_OPTION ) ); } @@ -865,17 +897,18 @@ public class surfacing { GoNameSpace go_namespace_limit = null; if ( cla.isOptionSet( surfacing.GO_NAMESPACE_LIMIT_OPTION ) ) { if ( ( go_id_to_term_map == null ) || go_id_to_term_map.isEmpty() ) { - ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot use GO namespace limit (-" - + surfacing.GO_NAMESPACE_LIMIT_OPTION + "=) without Pfam to GO mapping file (" - + surfacing.PFAM_TO_GO_FILE_USE_OPTION + "=) and GO OBO file (-" - + surfacing.GO_OBO_FILE_USE_OPTION + "=)" ); + ForesterUtil.fatalError( surfacing.PRG_NAME, + "cannot use GO namespace limit (-" + surfacing.GO_NAMESPACE_LIMIT_OPTION + + "=) without Pfam to GO mapping file (" + + surfacing.PFAM_TO_GO_FILE_USE_OPTION + "=) and GO OBO file (-" + + surfacing.GO_OBO_FILE_USE_OPTION + "=)" ); } if ( !cla.isOptionValueSet( surfacing.GO_NAMESPACE_LIMIT_OPTION ) ) { - ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for GO namespace limit: \"-" - + surfacing.GO_NAMESPACE_LIMIT_OPTION + "=<" - + surfacing.GO_NAMESPACE_LIMIT_OPTION_MOLECULAR_FUNCTION + "|" - + surfacing.GO_NAMESPACE_LIMIT_OPTION_BIOLOGICAL_PROCESS + "|" - + surfacing.GO_NAMESPACE_LIMIT_OPTION_CELLULAR_COMPONENT + ">\"" ); + ForesterUtil.fatalError( surfacing.PRG_NAME, + "no value for GO namespace limit: \"-" + surfacing.GO_NAMESPACE_LIMIT_OPTION + + "=<" + surfacing.GO_NAMESPACE_LIMIT_OPTION_MOLECULAR_FUNCTION + "|" + + surfacing.GO_NAMESPACE_LIMIT_OPTION_BIOLOGICAL_PROCESS + "|" + + surfacing.GO_NAMESPACE_LIMIT_OPTION_CELLULAR_COMPONENT + ">\"" ); } final String go_namespace_limit_str = cla.getOptionValue( surfacing.GO_NAMESPACE_LIMIT_OPTION ) .toLowerCase(); @@ -889,11 +922,12 @@ public class surfacing { go_namespace_limit = GoNameSpace.createCellularComponent(); } else { - ForesterUtil.fatalError( surfacing.PRG_NAME, "unknown value \"" + go_namespace_limit_str - + "\" for GO namespace limit: \"-" + surfacing.GO_NAMESPACE_LIMIT_OPTION + "=<" - + surfacing.GO_NAMESPACE_LIMIT_OPTION_MOLECULAR_FUNCTION + "|" - + surfacing.GO_NAMESPACE_LIMIT_OPTION_BIOLOGICAL_PROCESS + "|" - + surfacing.GO_NAMESPACE_LIMIT_OPTION_CELLULAR_COMPONENT + ">\"" ); + ForesterUtil.fatalError( surfacing.PRG_NAME, + "unknown value \"" + go_namespace_limit_str + "\" for GO namespace limit: \"-" + + surfacing.GO_NAMESPACE_LIMIT_OPTION + "=<" + + surfacing.GO_NAMESPACE_LIMIT_OPTION_MOLECULAR_FUNCTION + "|" + + surfacing.GO_NAMESPACE_LIMIT_OPTION_BIOLOGICAL_PROCESS + "|" + + surfacing.GO_NAMESPACE_LIMIT_OPTION_CELLULAR_COMPONENT + ">\"" ); } } if ( ( domain_similarity_sort_field == DomainSimilarity.DomainSimilaritySortField.MAX_COUNTS_DIFFERENCE ) @@ -904,14 +938,16 @@ public class surfacing { Phylogeny[] intrees = null; if ( cla.isOptionSet( surfacing.INPUT_SPECIES_TREE_OPTION ) ) { if ( number_of_genomes < 3 ) { - ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot infer gains and losses on input species trees (-" - + surfacing.INPUT_SPECIES_TREE_OPTION + " without pairwise analyses (" - + surfacing.PAIRWISE_DOMAIN_COMPARISONS_OPTION - + "=)" ); + ForesterUtil.fatalError( surfacing.PRG_NAME, + "cannot infer gains and losses on input species trees (-" + + surfacing.INPUT_SPECIES_TREE_OPTION + " without pairwise analyses (" + + surfacing.PAIRWISE_DOMAIN_COMPARISONS_OPTION + + "=)" ); } if ( !cla.isOptionValueSet( surfacing.INPUT_SPECIES_TREE_OPTION ) ) { - ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for input tree: -" - + surfacing.INPUT_SPECIES_TREE_OPTION + "=" ); + ForesterUtil.fatalError( surfacing.PRG_NAME, + "no value for input tree: -" + surfacing.INPUT_SPECIES_TREE_OPTION + + "=" ); } final String intrees_str = cla.getOptionValue( surfacing.INPUT_SPECIES_TREE_OPTION ); if ( intrees_str.indexOf( "#" ) > 0 ) { @@ -926,15 +962,18 @@ public class surfacing { intree_files = new File[ 1 ]; intree_files[ 0 ] = new File( intrees_str ); } - intrees = SurfacingUtil.obtainAndPreProcessIntrees( intree_files, number_of_genomes, input_file_properties ); + intrees = SurfacingUtil.obtainAndPreProcessIntrees( intree_files, + number_of_genomes, + input_file_properties ); } final Phylogeny intree_0_orig = SurfacingUtil.obtainFirstIntree( intree_files[ 0 ] ); long random_number_seed_for_fitch_parsimony = 0l; boolean radomize_fitch_parsimony = false; if ( cla.isOptionSet( surfacing.RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION ) ) { if ( !cla.isOptionValueSet( surfacing.RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION ) ) { - ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for random number seed: -" - + surfacing.RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION + "=" ); + ForesterUtil.fatalError( surfacing.PRG_NAME, + "no value for random number seed: -" + + surfacing.RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION + "=" ); } try { random_number_seed_for_fitch_parsimony = cla @@ -962,14 +1001,15 @@ public class surfacing { Map>[] domain_id_to_secondary_features_maps = null; File[] secondary_features_map_files = null; final File domain_lengths_analysis_outfile = new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file - + DOMAIN_LENGTHS_ANALYSIS_SUFFIX ); + + DOMAIN_LENGTHS_ANALYSIS_SUFFIX ); if ( domain_length_analysis ) { SurfacingUtil.checkForOutputFileWriteability( domain_lengths_analysis_outfile ); } if ( cla.isOptionSet( surfacing.SECONDARY_FEATURES_PARSIMONY_MAP_FILE ) ) { if ( !cla.isOptionValueSet( surfacing.SECONDARY_FEATURES_PARSIMONY_MAP_FILE ) ) { - ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for secondary features map file: -" - + surfacing.SECONDARY_FEATURES_PARSIMONY_MAP_FILE + "=" ); + ForesterUtil.fatalError( surfacing.PRG_NAME, + "no value for secondary features map file: -" + + surfacing.SECONDARY_FEATURES_PARSIMONY_MAP_FILE + "=" ); } final String[] secondary_features_map_files_strs = cla .getOptionValue( surfacing.SECONDARY_FEATURES_PARSIMONY_MAP_FILE ).split( "#" ); @@ -991,19 +1031,21 @@ public class surfacing { "cannot read secondary features map file: " + e.getMessage() ); } catch ( final Exception e ) { - ForesterUtil.fatalError( surfacing.PRG_NAME, "problem with contents of features map file [" - + secondary_features_map_files[ i ] + "]: " + e.getMessage() ); + ForesterUtil.fatalError( surfacing.PRG_NAME, + "problem with contents of features map file [" + + secondary_features_map_files[ i ] + "]: " + e.getMessage() ); } i++; } } if ( out_dir == null ) { - ForesterUtil.fatalError( surfacing.PRG_NAME, "no output directory indicated (-" - + surfacing.OUTPUT_DIR_OPTION + "=)" ); + ForesterUtil.fatalError( surfacing.PRG_NAME, + "no output directory indicated (-" + surfacing.OUTPUT_DIR_OPTION + "=)" ); } if ( output_file == null ) { - ForesterUtil.fatalError( surfacing.PRG_NAME, "no name for (main) output file indicated (-" - + surfacing.OUTPUT_FILE_OPTION + "=)" ); + ForesterUtil.fatalError( surfacing.PRG_NAME, + "no name for (main) output file indicated (-" + surfacing.OUTPUT_FILE_OPTION + + "=)" ); } if ( ( domain_id_to_go_ids_map == null ) || domain_id_to_go_ids_map.isEmpty() ) { ForesterUtil.fatalError( surfacing.PRG_NAME, @@ -1021,21 +1063,21 @@ public class surfacing { if ( positive_filter_file != null ) { final int filter_size = filter.size(); System.out.println( "Positive protein filter : " + positive_filter_file + " [" + filter_size - + " domain ids]" ); + + " domain ids]" ); html_desc.append( "Positive protein filter:" + positive_filter_file + " [" + filter_size - + " domain ids]" + nl ); + + " domain ids]" + nl ); } if ( negative_filter_file != null ) { final int filter_size = filter.size(); System.out.println( "Negative protein filter : " + negative_filter_file + " [" + filter_size - + " domain ids]" ); + + " domain ids]" ); html_desc.append( "Negative protein filter:" + negative_filter_file + " [" + filter_size - + " domain ids]" + nl ); + + " domain ids]" + nl ); } if ( negative_domains_filter_file != null ) { final int filter_size = filter.size(); System.out.println( "Negative domain filter : " + negative_domains_filter_file + " [" + filter_size - + " domain ids]" ); + + " domain ids]" ); html_desc.append( "Negative domain filter:" + negative_domains_filter_file + " [" + filter_size + " domain ids]" + nl ); } @@ -1054,7 +1096,7 @@ public class surfacing { } System.out.println( "Plus-minus analysis : " + plus1 + "&& " + plus0 + "&& " + minus ); html_desc.append( "Plus-minus analysis:" + plus1 + "&& " + plus0 + "&& " + minus - + "" + nl ); + + "" + nl ); } if ( cutoff_scores_file != null ) { System.out.println( "Cutoff scores file : " + cutoff_scores_file ); @@ -1076,27 +1118,28 @@ public class surfacing { System.out.println( "Ignore DUFs : " + ignore_dufs ); if ( ignore_virus_like_ids ) { System.out.println( "Ignore virus like ids : " + ignore_virus_like_ids ); - html_desc.append( "Ignore virus, phage, transposition related ids:" - + ignore_virus_like_ids + "" + nl ); + html_desc.append( "Ignore virus, phage, transposition related ids:" + ignore_virus_like_ids + + "" + nl ); } html_desc.append( "Ignore DUFs:" + ignore_dufs + "" + nl ); if ( max_allowed_overlap != surfacing.MAX_ALLOWED_OVERLAP_DEFAULT ) { System.out.println( "Max allowed domain overlap : " + max_allowed_overlap ); - html_desc.append( "Max allowed domain overlap:" + max_allowed_overlap + "" + nl ); + html_desc + .append( "Max allowed domain overlap:" + max_allowed_overlap + "" + nl ); } if ( no_engulfing_overlaps ) { System.out.println( "Ignore engulfed domains : " + no_engulfing_overlaps ); html_desc.append( "Ignore (lower confidence) engulfed domains:" + no_engulfing_overlaps - + "" + nl ); + + "" + nl ); } System.out.println( "Ignore singlet domains : " + ignore_domains_without_combs_in_all_spec ); html_desc - .append( "Ignore singlet domains for domain combination similarity analyses (not for parsimony analyses):" - + ignore_domains_without_combs_in_all_spec + "" + nl ); + .append( "Ignore singlet domains for domain combination similarity analyses (not for parsimony analyses):" + + ignore_domains_without_combs_in_all_spec + "" + nl ); System.out.println( "Ignore species specific doms: " + ignore_species_specific_domains ); html_desc - .append( "Ignore species specific domains for domain combination similarity analyses (not for parsimony analyses):" - + ignore_species_specific_domains + "" + nl ); + .append( "Ignore species specific domains for domain combination similarity analyses (not for parsimony analyses):" + + ignore_species_specific_domains + "" + nl ); System.out.println( "Ignore combination with self: " + ignore_combination_with_same ); html_desc.append( "Ignore combination with self for domain combination similarity analyses:" + ignore_combination_with_same + "" + nl ); @@ -1116,14 +1159,14 @@ public class surfacing { if ( perform_dc_fich ) { System.out.println( "Use last in Fitch parsimony : " + use_last_in_fitch_parsimony ); html_desc.append( "Use last in Fitch parsimony:" + use_last_in_fitch_parsimony - + "" + nl ); + + "" + nl ); } System.out.println( "Write to Nexus files : " + write_to_nexus ); html_desc.append( "Write to Nexus files:" + write_to_nexus + "" + nl ); if ( perform_dc_fich ) { System.out.println( "DC regain prot stats : " + perform_dc_regain_proteins_stats ); - html_desc.append( "DC regain prot stats:" + perform_dc_regain_proteins_stats - + "" + nl ); + html_desc.append( "DC regain prot stats:" + perform_dc_regain_proteins_stats + "" + + nl ); } System.out.println( "DA analysis : " + da_analysis ); html_desc.append( "DA analysis :" + da_analysis + "" + nl ); @@ -1151,7 +1194,7 @@ public class surfacing { } if ( domain_id_to_go_ids_map != null ) { System.out.println( "Pfam to GO mappings from : " + pfam_to_go_file + " [" + domain_id_to_go_ids_count - + " mappings]" ); + + " mappings]" ); html_desc.append( "Pfam to GO mappings from:" + pfam_to_go_file + " [" + domain_id_to_go_ids_count + " mappings]" + "" + nl ); } @@ -1167,7 +1210,7 @@ public class surfacing { if ( perform_pwc ) { System.out.println( "Suffix for PWC files : " + automated_pairwise_comparison_suffix ); html_desc.append( "Suffix for PWC files" + automated_pairwise_comparison_suffix - + "" + nl ); + + "" + nl ); } if ( out_dir != null ) { System.out.println( "Output directory : " + out_dir ); @@ -1303,15 +1346,15 @@ public class surfacing { html_desc.append( "counts difference" ); break; default: - ForesterUtil - .unexpectedFatalError( surfacing.PRG_NAME, "unknown value for sorting for similarities" ); + ForesterUtil.unexpectedFatalError( surfacing.PRG_NAME, + "unknown value for sorting for similarities" ); } System.out.println(); html_desc.append( "" + nl ); if ( ( intrees != null ) && ( intrees.length > 0 ) ) { for( final File intree_file : intree_files ) { html_desc.append( "Intree for gain/loss parsimony analysis:" + intree_file - + "" + nl ); + + "" + nl ); System.out.println( " Intree for gain/loss pars.: " + intree_file ); } } @@ -1320,7 +1363,8 @@ public class surfacing { + random_number_seed_for_fitch_parsimony + "" + nl ); System.out.println( " Random number seed : " + random_number_seed_for_fitch_parsimony ); } - if ( ( domain_id_to_secondary_features_maps != null ) && ( domain_id_to_secondary_features_maps.length > 0 ) ) { + if ( ( domain_id_to_secondary_features_maps != null ) + && ( domain_id_to_secondary_features_maps.length > 0 ) ) { for( int i = 0; i < secondary_features_map_files.length; i++ ) { html_desc.append( "Secondary features map file:" + secondary_features_map_files[ i ] + "" + nl ); @@ -1344,7 +1388,7 @@ public class surfacing { } // if ( perform_pwc ) { System.out.println(); html_desc.append( "Command line:" + nl + nl + cla.getCommandLineArgsAsString() + nl + nl - + "" + nl ); + + "" + nl ); System.out.println( "Command line : " + cla.getCommandLineArgsAsString() ); BufferedWriter[] query_domains_writer_ary = null; List[] query_domain_ids_array = null; @@ -1369,14 +1413,16 @@ public class surfacing { query_domains_writer_ary[ i ] = new BufferedWriter( new FileWriter( protein_names_writer_str ) ); } catch ( final IOException e ) { - ForesterUtil.fatalError( surfacing.PRG_NAME, "Could not open [" + protein_names_writer_str + "]: " - + e.getLocalizedMessage() ); + ForesterUtil.fatalError( surfacing.PRG_NAME, + "Could not open [" + protein_names_writer_str + "]: " + + e.getLocalizedMessage() ); } } } SortedMap> protein_lists_per_species = null; //This will only be created if needed. boolean need_protein_lists_per_species = false; - if ( ( plus_minus_analysis_high_copy_base_species.size() > 0 ) || output_protein_lists_for_all_domains || true ) { //TODO + if ( ( plus_minus_analysis_high_copy_base_species.size() > 0 ) || output_protein_lists_for_all_domains + || true ) { //TODO need_protein_lists_per_species = true; } if ( need_protein_lists_per_species ) { @@ -1392,7 +1438,7 @@ public class surfacing { all_bin_domain_combinations_lost_fitch = new ArrayList(); } final File per_genome_domain_promiscuity_statistics_file = new File( out_dir + ForesterUtil.FILE_SEPARATOR - + output_file + D_PROMISCUITY_FILE_SUFFIX ); + + output_file + D_PROMISCUITY_FILE_SUFFIX ); BufferedWriter per_genome_domain_promiscuity_statistics_writer = null; try { per_genome_domain_promiscuity_statistics_writer = new BufferedWriter( new FileWriter( per_genome_domain_promiscuity_statistics_file ) ); @@ -1403,8 +1449,8 @@ public class surfacing { per_genome_domain_promiscuity_statistics_writer.write( "Min:\t" ); per_genome_domain_promiscuity_statistics_writer.write( "Max:\t" ); per_genome_domain_promiscuity_statistics_writer.write( "N:\t" ); - per_genome_domain_promiscuity_statistics_writer.write( "Max Promiscuous Domains:" - + ForesterUtil.LINE_SEPARATOR ); + per_genome_domain_promiscuity_statistics_writer + .write( "Max Promiscuous Domains:" + ForesterUtil.LINE_SEPARATOR ); } catch ( final IOException e2 ) { ForesterUtil.fatalError( surfacing.PRG_NAME, e2.getMessage() ); @@ -1435,7 +1481,7 @@ public class surfacing { BufferedWriter domains_per_potein_stats_writer = null; try { domains_per_potein_stats_writer = new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR - + output_file + "_domains_per_potein_stats.txt" ) ); + + output_file + "_domains_per_potein_stats.txt" ) ); domains_per_potein_stats_writer.write( "Genome" ); domains_per_potein_stats_writer.write( "\t" ); domains_per_potein_stats_writer.write( "Mean" ); @@ -1556,8 +1602,7 @@ public class surfacing { System.out.println( "Coverage : " + ForesterUtil.roundToInt( 100.0 * coverage ) + "%" ); SurfacingUtil.log( "Coverage : " - + ForesterUtil.roundToInt( 100.0 * coverage ) + "%", - log_writer ); + + ForesterUtil.roundToInt( 100.0 * coverage ) + "%", log_writer ); System.out.println( "Domains encountered : " + parser.getDomainsEncountered() ); SurfacingUtil.log( "Domains encountered : " + parser.getDomainsEncountered(), log_writer ); @@ -1566,58 +1611,53 @@ public class surfacing { log_writer ); System.out.println( "Distinct domains stored : " + parser.getDomainsStoredSet().size() ); - SurfacingUtil.log( "Distinct domains stored : " - + parser.getDomainsStoredSet().size(), log_writer ); + SurfacingUtil + .log( "Distinct domains stored : " + parser.getDomainsStoredSet().size(), + log_writer ); System.out.println( "Domains ignored due to individual score cutoffs: " + parser.getDomainsIgnoredDueToIndividualScoreCutoff() ); SurfacingUtil.log( "Domains ignored due to individual score cutoffs: " - + parser.getDomainsIgnoredDueToIndividualScoreCutoff(), - log_writer ); + + parser.getDomainsIgnoredDueToIndividualScoreCutoff(), log_writer ); System.out.println( "Domains ignored due to FS E-value : " + parser.getDomainsIgnoredDueToFsEval() ); - SurfacingUtil.log( "Domains ignored due to FS E-value : " - + parser.getDomainsIgnoredDueToFsEval(), - log_writer ); + SurfacingUtil + .log( "Domains ignored due to FS E-value : " + parser.getDomainsIgnoredDueToFsEval(), + log_writer ); System.out.println( "Domains ignored due to iE-value : " + parser.getDomainsIgnoredDueToIEval() ); - SurfacingUtil.log( "Domains ignored due to iE-value : " - + parser.getDomainsIgnoredDueToIEval(), - log_writer ); + SurfacingUtil + .log( "Domains ignored due to iE-value : " + parser.getDomainsIgnoredDueToIEval(), + log_writer ); System.out.println( "Domains ignored due to DUF designation : " + parser.getDomainsIgnoredDueToDuf() ); - SurfacingUtil - .log( "Domains ignored due to DUF designation : " + parser.getDomainsIgnoredDueToDuf(), - log_writer ); + SurfacingUtil.log( "Domains ignored due to DUF designation : " + parser.getDomainsIgnoredDueToDuf(), + log_writer ); if ( ignore_virus_like_ids ) { System.out.println( "Domains ignored due virus like ids : " + parser.getDomainsIgnoredDueToVirusLikeIds() ); SurfacingUtil.log( "Domains ignored due virus like ids : " - + parser.getDomainsIgnoredDueToVirusLikeIds(), - log_writer ); + + parser.getDomainsIgnoredDueToVirusLikeIds(), log_writer ); } System.out.println( "Domains ignored due negative domain filter : " + parser.getDomainsIgnoredDueToNegativeDomainFilter() ); SurfacingUtil.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() ); - SurfacingUtil.log( "Domains ignored due to overlap : " - + parser.getDomainsIgnoredDueToOverlap(), - log_writer ); + SurfacingUtil + .log( "Domains ignored due to overlap : " + parser.getDomainsIgnoredDueToOverlap(), + log_writer ); if ( negative_filter_file != null ) { System.out.println( "Proteins ignored due to negative filter : " + parser.getProteinsIgnoredDueToFilter() ); SurfacingUtil.log( "Proteins ignored due to negative filter : " - + parser.getProteinsIgnoredDueToFilter(), - log_writer ); + + parser.getProteinsIgnoredDueToFilter(), log_writer ); } if ( positive_filter_file != null ) { System.out.println( "Proteins ignored due to positive filter : " + parser.getProteinsIgnoredDueToFilter() ); SurfacingUtil.log( "Proteins ignored due to positive filter : " - + parser.getProteinsIgnoredDueToFilter(), - log_writer ); + + parser.getProteinsIgnoredDueToFilter(), log_writer ); } if ( da_analysis ) { System.out.println( "Distinct domain architectures stored : " + distinct_das ); @@ -1628,8 +1668,8 @@ public class surfacing { try { int count = 0; for( final Protein protein : protein_list ) { - dc_data_writer.write( SurfacingUtil.proteinToDomainCombinations( protein, count + "", "\t" ) - .toString() ); + dc_data_writer + .write( SurfacingUtil.proteinToDomainCombinations( protein, count + "", "\t" ).toString() ); ++count; for( final Domain d : protein.getProteinDomains() ) { final String d_str = d.getDomainId().toString(); @@ -1655,23 +1695,21 @@ public class surfacing { domain_lengths_table.addLengths( protein_list ); } if ( !da_analysis ) { - gwcd_list.add( BasicGenomeWideCombinableDomains - .createInstance( protein_list, - ignore_combination_with_same, - new BasicSpecies( input_file_properties[ i ][ 1 ] ), - domain_id_to_go_ids_map, - dc_type, - protein_length_stats_by_dc, - domain_number_stats_by_dc ) ); + gwcd_list.add( BasicGenomeWideCombinableDomains.createInstance( protein_list, + ignore_combination_with_same, + new BasicSpecies( input_file_properties[ i ][ 1 ] ), + domain_id_to_go_ids_map, + dc_type, + protein_length_stats_by_dc, + domain_number_stats_by_dc ) ); if ( gwcd_list.get( i ).getSize() > 0 ) { if ( output_binary_domain_combinationsfor_counts ) { - SurfacingUtil - .writeDomainCombinationsCountsFile( input_file_properties, - out_dir, - per_genome_domain_promiscuity_statistics_writer, - gwcd_list.get( i ), - i, - dc_sort_order ); + SurfacingUtil.writeDomainCombinationsCountsFile( input_file_properties, + out_dir, + per_genome_domain_promiscuity_statistics_writer, + gwcd_list.get( i ), + i, + dc_sort_order ); } if ( output_binary_domain_combinationsfor_graph_analysis ) { SurfacingUtil.writeBinaryDomainCombinationsFileForGraphAnalysis( input_file_properties, @@ -1711,21 +1749,33 @@ public class surfacing { } System.gc(); } // for( int i = 0; i < number_of_genomes; ++i ) { - ForesterUtil.programMessage( PRG_NAME, "Wrote domain promiscuities to: " - + per_genome_domain_promiscuity_statistics_file ); + ForesterUtil + .programMessage( PRG_NAME, + "Wrote domain promiscuities to: " + per_genome_domain_promiscuity_statistics_file ); // - if (true) { //TODO - MinimalDomainomeCalculator.calc( intree_0_orig, protein_lists_per_species ); + if ( true ) { //TODO + MinimalDomainomeCalculator.calcDomainome( intree_0_orig, protein_lists_per_species, -1 ); + } + if ( true ) { //TODO + try { + MinimalDomainomeCalculator.calcDAome( intree_0_orig, + protein_lists_per_species, + "---", + 1000, + out_dir.toString() + "/" + output_file ); + } + catch ( IOException e ) { + ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() ); + } } - if ( da_analysis ) { SurfacingUtil.performDomainArchitectureAnalysis( distinct_domain_architecutures_per_genome, distinct_domain_architecuture_counts, 10, new File( out_dir.toString() + "/" + output_file - + "_DA_counts.txt" ), - new File( out_dir.toString() + "/" + output_file - + "_unique_DAs.txt" ) ); + + "_DA_counts.txt" ), + new File( out_dir.toString() + "/" + output_file + + "_unique_DAs.txt" ) ); distinct_domain_architecutures_per_genome.clear(); distinct_domain_architecuture_counts.clear(); System.gc(); @@ -1735,7 +1785,8 @@ public class surfacing { domains_per_potein_stats_writer.write( "\t" ); domains_per_potein_stats_writer.write( all_genomes_domains_per_potein_stats.arithmeticMean() + "" ); domains_per_potein_stats_writer.write( "\t" ); - domains_per_potein_stats_writer.write( all_genomes_domains_per_potein_stats.sampleStandardDeviation() + "" ); + domains_per_potein_stats_writer + .write( all_genomes_domains_per_potein_stats.sampleStandardDeviation() + "" ); domains_per_potein_stats_writer.write( "\t" ); if ( all_genomes_domains_per_potein_stats.getN() <= 300 ) { domains_per_potein_stats_writer.write( all_genomes_domains_per_potein_stats.median() + "" ); @@ -1750,29 +1801,43 @@ public class surfacing { domains_per_potein_stats_writer.close(); all_genomes_domains_per_potein_stats = null; SurfacingUtil.printOutPercentageOfMultidomainProteins( all_genomes_domains_per_potein_histo, log_writer ); - ForesterUtil.map2file( new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file - + "_all_genomes_domains_per_potein_histo.txt" ), all_genomes_domains_per_potein_histo, "\t", "\n" ); - ForesterUtil.collection2file( new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file - + "_domains_always_single_.txt" ), domains_which_are_always_single, "\n" ); - ForesterUtil.collection2file( new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file - + "_domains_single_or_combined.txt" ), domains_which_are_sometimes_single_sometimes_not, "\n" ); - ForesterUtil.collection2file( new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file - + "_domains_always_combined.txt" ), domains_which_never_single, "\n" ); + ForesterUtil.map2file( + new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file + + "_all_genomes_domains_per_potein_histo.txt" ), + all_genomes_domains_per_potein_histo, + "\t", + "\n" ); + ForesterUtil.collection2file( + new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file + + "_domains_always_single_.txt" ), + domains_which_are_always_single, + "\n" ); + ForesterUtil.collection2file( + new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file + + "_domains_single_or_combined.txt" ), + domains_which_are_sometimes_single_sometimes_not, + "\n" ); + ForesterUtil.collection2file( + new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file + + "_domains_always_combined.txt" ), + domains_which_never_single, + "\n" ); ForesterUtil.programMessage( PRG_NAME, "Average of proteins with a least one domain assigned: " + ( 100 * protein_coverage_stats.arithmeticMean() ) + "% (+/-" + ( 100 * protein_coverage_stats.sampleStandardDeviation() ) + "%)" ); - ForesterUtil.programMessage( PRG_NAME, "Range of proteins with a least one domain assigned: " - + ( 100 * protein_coverage_stats.getMin() ) + "%-" + ( 100 * protein_coverage_stats.getMax() ) - + "%" ); - SurfacingUtil.log( "Average of prot with a least one dom assigned : " - + ( 100 * protein_coverage_stats.arithmeticMean() ) + "% (+/-" - + ( 100 * protein_coverage_stats.sampleStandardDeviation() ) + "%)", - log_writer ); + ForesterUtil.programMessage( PRG_NAME, + "Range of proteins with a least one domain assigned: " + + ( 100 * protein_coverage_stats.getMin() ) + "%-" + + ( 100 * protein_coverage_stats.getMax() ) + "%" ); + SurfacingUtil.log( + "Average of prot with a least one dom assigned : " + + ( 100 * protein_coverage_stats.arithmeticMean() ) + "% (+/-" + + ( 100 * protein_coverage_stats.sampleStandardDeviation() ) + "%)", + log_writer ); SurfacingUtil.log( "Range of prot with a least one dom assigned : " - + ( 100 * protein_coverage_stats.getMin() ) + "%-" - + ( 100 * protein_coverage_stats.getMax() ) + "%", - log_writer ); + + ( 100 * protein_coverage_stats.getMin() ) + "%-" + ( 100 * protein_coverage_stats.getMax() ) + + "%", log_writer ); protein_coverage_stats = null; } catch ( final IOException e2 ) { @@ -1835,11 +1900,10 @@ public class surfacing { if ( domain_id_to_go_ids_map != null ) { go_annotation_output = DomainSimilarityCalculator.GoAnnotationOutput.ALL; } - final SortedSet similarities = calc - .calculateSimilarities( pw_calc, - gwcd_list, - ignore_domains_without_combs_in_all_spec, - ignore_species_specific_domains ); + final SortedSet similarities = calc.calculateSimilarities( pw_calc, + gwcd_list, + ignore_domains_without_combs_in_all_spec, + ignore_species_specific_domains ); SurfacingUtil.decoratePrintableDomainSimilarities( similarities, detailedness ); final Map tax_code_to_id_map = SurfacingUtil.createTaxCodeToIdMap( intrees[ 0 ] ); try { @@ -1867,13 +1931,13 @@ public class surfacing { html_desc.append( "Sum of all distinct binary combinations:" + all_bin_domain_combinations_encountered.size() + "" + nl ); html_desc.append( "Sum of all distinct domains:" + all_domains_encountered.size() - + "" + nl ); + + "" + nl ); html_desc.append( "Analysis date/time:" + new java.text.SimpleDateFormat( "yyyy.MM.dd HH:mm:ss" ).format( new java.util.Date() ) + "" + nl ); html_desc.append( "" + nl ); final Writer simple_tab_writer = new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR - + my_outfile + ".tsv" ) ); + + my_outfile.replaceFirst( ".html", ".tsv" ) ) ); SurfacingUtil.writeDomainSimilaritiesToFile( html_desc, new StringBuilder( number_of_genomes + " genomes" ), simple_tab_writer, @@ -1889,12 +1953,16 @@ public class surfacing { intree_0_orig, positive_filter_file != null ? filter : null ); simple_tab_writer.close(); - ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote main output (includes domain similarities) to: \"" - + ( out_dir == null ? my_outfile : out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile ) + "\"" ); + ForesterUtil.programMessage( surfacing.PRG_NAME, + "Wrote main output (includes domain similarities) to: \"" + + ( out_dir == null ? my_outfile + : out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile ) + + "\"" ); } catch ( final IOException e ) { - ForesterUtil.fatalError( surfacing.PRG_NAME, "Failed to write similarites to: \"" + output_file + "\" [" - + e.getMessage() + "]" ); + ForesterUtil + .fatalError( surfacing.PRG_NAME, + "Failed to write similarites to: \"" + output_file + "\" [" + e.getMessage() + "]" ); } System.out.println(); final Species[] species = new Species[ number_of_genomes ]; @@ -1936,24 +2004,32 @@ public class surfacing { matrix_output_file = out_dir + ForesterUtil.FILE_SEPARATOR + matrix_output_file; output_file = new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file ); } - 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_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX ), - pwgc.getSharedDomainsBasedDistances() ); + 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_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 ) ); - final Phylogeny nj_bc = SurfacingUtil.createNjTreeBasedOnMatrixToFile( new File( matrix_output_file - + surfacing.NJ_TREE_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX ), pwgc - .getSharedBinaryCombinationsBasedDistances().get( 0 ) ); - final Phylogeny nj_d = SurfacingUtil.createNjTreeBasedOnMatrixToFile( new File( matrix_output_file - + surfacing.NJ_TREE_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX ), pwgc - .getSharedDomainsBasedDistances().get( 0 ) ); + + surfacing.NJ_TREE_MEAN_SCORE_BASED_GENOME_DISTANCE_SUFFIX ), + pwgc.getDomainDistanceScoresMeans() + .get( 0 ) ); + final Phylogeny nj_bc = SurfacingUtil.createNjTreeBasedOnMatrixToFile( + new File( matrix_output_file + + surfacing.NJ_TREE_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX ), + pwgc.getSharedBinaryCombinationsBasedDistances() + .get( 0 ) ); + final Phylogeny nj_d = SurfacingUtil.createNjTreeBasedOnMatrixToFile( + new File( matrix_output_file + + surfacing.NJ_TREE_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX ), + pwgc.getSharedDomainsBasedDistances() + .get( 0 ) ); inferred_trees = new ArrayList(); inferred_trees.add( nj_gd ); inferred_trees.add( nj_bc ); @@ -1981,8 +2057,8 @@ public class surfacing { for( final Phylogeny intree : intrees ) { final String outfile_name = ForesterUtil.removeSuffix( output_file.toString() ) + s + ForesterUtil.removeSuffix( intree_files[ i ].toString() ); - final DomainParsimonyCalculator domain_parsimony = DomainParsimonyCalculator.createInstance( intree, - gwcd_list ); + final DomainParsimonyCalculator domain_parsimony = DomainParsimonyCalculator + .createInstance( intree, gwcd_list ); SurfacingUtil.executeParsimonyAnalysis( random_number_seed_for_fitch_parsimony, radomize_fitch_parsimony, outfile_name, @@ -1994,17 +2070,17 @@ public class surfacing { parameters_sb.toString(), domain_id_to_secondary_features_maps, positive_filter_file == null ? null : filter, - output_binary_domain_combinationsfor_graph_analysis, - all_bin_domain_combinations_gained_fitch, - all_bin_domain_combinations_lost_fitch, - dc_type, - protein_length_stats_by_dc, - domain_number_stats_by_dc, - domain_length_stats_by_domain, - tax_code_to_id_map, - write_to_nexus, - use_last_in_fitch_parsimony, - perform_dc_fich ); + output_binary_domain_combinationsfor_graph_analysis, + all_bin_domain_combinations_gained_fitch, + all_bin_domain_combinations_lost_fitch, + dc_type, + protein_length_stats_by_dc, + domain_number_stats_by_dc, + domain_length_stats_by_domain, + tax_code_to_id_map, + write_to_nexus, + use_last_in_fitch_parsimony, + perform_dc_fich ); // Listing of all domain combinations gained is only done if only one input tree is used. if ( ( domain_id_to_secondary_features_maps != null ) && ( domain_id_to_secondary_features_maps.length > 0 ) ) { @@ -2013,15 +2089,13 @@ public class surfacing { final Map mapping_results_map = new TreeMap(); final DomainParsimonyCalculator secondary_features_parsimony = DomainParsimonyCalculator .createInstance( intree, gwcd_list, domain_id_to_secondary_features_map ); - SurfacingUtil - .executeParsimonyAnalysisForSecondaryFeatures( outfile_name - + "_" - + secondary_features_map_files[ j++ ], - secondary_features_parsimony, - intree, - parameters_sb.toString(), - mapping_results_map, - use_last_in_fitch_parsimony ); + SurfacingUtil.executeParsimonyAnalysisForSecondaryFeatures( outfile_name + "_" + + secondary_features_map_files[ j++ ], + secondary_features_parsimony, + intree, + parameters_sb.toString(), + mapping_results_map, + use_last_in_fitch_parsimony ); if ( i == 0 ) { System.out.println(); System.out.println( "Mapping to secondary features:" ); @@ -2067,13 +2141,13 @@ public class surfacing { gwcd_list = null; if ( all_bin_domain_combinations_gained_fitch != null ) { try { - SurfacingUtil - .executeFitchGainsAnalysis( new File( output_file - + surfacing.OUTPUT_DOMAIN_COMBINATIONS_GAINED_MORE_THAN_ONCE_ANALYSIS_SUFFIX ), - all_bin_domain_combinations_gained_fitch, - all_domains_encountered.size(), - all_bin_domain_combinations_encountered, - true ); + SurfacingUtil.executeFitchGainsAnalysis( + new File( output_file + + surfacing.OUTPUT_DOMAIN_COMBINATIONS_GAINED_MORE_THAN_ONCE_ANALYSIS_SUFFIX ), + all_bin_domain_combinations_gained_fitch, + all_domains_encountered.size(), + all_bin_domain_combinations_encountered, + true ); } catch ( final IOException e ) { ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() ); @@ -2081,13 +2155,13 @@ public class surfacing { } if ( all_bin_domain_combinations_lost_fitch != null ) { try { - SurfacingUtil - .executeFitchGainsAnalysis( new File( output_file - + surfacing.OUTPUT_DOMAIN_COMBINATIONS_LOST_MORE_THAN_ONCE_ANALYSIS_SUFFIX ), - all_bin_domain_combinations_lost_fitch, - all_domains_encountered.size(), - all_bin_domain_combinations_encountered, - false ); + SurfacingUtil.executeFitchGainsAnalysis( + new File( output_file + + surfacing.OUTPUT_DOMAIN_COMBINATIONS_LOST_MORE_THAN_ONCE_ANALYSIS_SUFFIX ), + all_bin_domain_combinations_lost_fitch, + all_domains_encountered.size(), + all_bin_domain_combinations_encountered, + false ); } catch ( final IOException e ) { ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() ); @@ -2096,11 +2170,12 @@ public class surfacing { final Runtime rt = java.lang.Runtime.getRuntime(); final long free_memory = rt.freeMemory() / 1000000; final long total_memory = rt.totalMemory() / 1000000; - ForesterUtil.programMessage( PRG_NAME, "Time for analysis : " + ( new Date().getTime() - analysis_start_time ) - + "ms" ); + ForesterUtil.programMessage( PRG_NAME, + "Time for analysis : " + ( new Date().getTime() - analysis_start_time ) + "ms" ); ForesterUtil.programMessage( PRG_NAME, "Total running time: " + ( new Date().getTime() - start_time ) + "ms " ); - ForesterUtil.programMessage( PRG_NAME, "Free memory : " + free_memory + "MB, total memory: " - + total_memory + "MB" ); + ForesterUtil + .programMessage( PRG_NAME, + "Free memory : " + free_memory + "MB, total memory: " + total_memory + "MB" ); ForesterUtil.programMessage( PRG_NAME, "If this application is useful to you, please cite:" ); ForesterUtil.programMessage( PRG_NAME, surfacing.WWW ); ForesterUtil.programMessage( PRG_NAME, "OK" ); @@ -2112,28 +2187,25 @@ public class surfacing { System.out.println( "Usage:" ); System.out.println(); System.out.println( "% java -Xms256m -Xmx512m -cp forester.jar org.forester.applications." + surfacing.PRG_NAME - + " [options] [external node name 1] [name 2] ... [name n]" ); + + " [options] [external node name 1] [name 2] ... [name n]" ); System.out.println(); System.out.println( " Note: This software might need a significant amount of memory (heap space);" ); System.out - .println( " hence use \"-Xms128m -Xmx512m\" (or more) to prevent a \"java.lang.OutOfMemoryError\"." ); + .println( " hence use \"-Xms128m -Xmx512m\" (or more) to prevent a \"java.lang.OutOfMemoryError\"." ); System.out.println(); System.out.println( " Options: " ); System.out.println( surfacing.DETAILEDNESS_OPTION + ": level of detail for similarities output file (default:" + DETAILEDNESS_DEFAULT + ")" ); System.out.println( surfacing.IGNORE_COMBINATION_WITH_SAME_OPTION - + ": to ignore combinations with self (default: not to ignore)" ); - System.out - .println( surfacing.IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_OPTION - + ": to ignore domains without combinations in any species (for similarity calc purposes, not for parsimony analyses) (default: not to ignore)" ); - System.out - .println( surfacing.IGNORE_DOMAINS_SPECIFIC_TO_ONE_SPECIES_OPTION - + ": to ignore domains specific to one species (for similarity calc purposes, not for parsimony analyses) (default: not to ignore)" ); + + ": to ignore combinations with self (default: not to ignore)" ); + System.out.println( surfacing.IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_OPTION + + ": to ignore domains without combinations in any species (for similarity calc purposes, not for parsimony analyses) (default: not to ignore)" ); + System.out.println( surfacing.IGNORE_DOMAINS_SPECIFIC_TO_ONE_SPECIES_OPTION + + ": to ignore domains specific to one species (for similarity calc purposes, not for parsimony analyses) (default: not to ignore)" ); System.out.println( surfacing.NOT_IGNORE_DUFS_OPTION - + ": to _not_ ignore DUFs (domains with unknown function) (default: ignore DUFs)" ); - System.out - .println( surfacing.IGNORE_VIRAL_IDS - + ": to ignore domains with ids containing 'vir', 'retro', 'transpos', 'phage', or starting with 'rv' or 'gag_'" ); + + ": to _not_ ignore DUFs (domains with unknown function) (default: ignore DUFs)" ); + System.out.println( surfacing.IGNORE_VIRAL_IDS + + ": to ignore domains with ids containing 'vir', 'retro', 'transpos', 'phage', or starting with 'rv' or 'gag_'" ); System.out.println( surfacing.DOMAIN_SIMILARITY_SORT_OPTION + ": sorting for similarities (default: " + DOMAIN_SORT_FILD_DEFAULT + ")" ); System.out.println( surfacing.OUTPUT_FILE_OPTION + ": name for (main) output file (mandatory)" ); @@ -2149,45 +2221,42 @@ public class surfacing { + DOMAIN_SIMILARITY_PRINT_OPTION_DEFAULT + ")" ); System.out.println( surfacing.CUTOFF_SCORE_FILE_OPTION + ": cutoff score file" ); System.out.println( surfacing.DOMAIN_SIMILARITY_SORT_BY_SPECIES_COUNT_FIRST_OPTION - + ": sort by species count first" ); + + ": sort by species count first" ); System.out.println( surfacing.OUTPUT_DIR_OPTION + ": output directory" ); System.out.println( surfacing.PFAM_TO_GO_FILE_USE_OPTION + ": Pfam to GO mapping file" ); System.out.println( surfacing.GO_OBO_FILE_USE_OPTION + ": GO terms file (OBO format)" ); System.out.println( surfacing.GO_NAMESPACE_LIMIT_OPTION + ": limit GO term to one GO namespace" ); System.out.println( surfacing.PAIRWISE_DOMAIN_COMPARISONS_OPTION - + "[=]: to perform pairwise comparison based analyses" ); + + "[=]: to perform pairwise comparison based analyses" ); System.out.println( surfacing.INPUT_SPECIES_TREE_OPTION - + ": species tree, to perform (Dollo, Fitch) parismony analyses" ); - System.out - .println( surfacing.INPUT_SPECIES_TREE_OPTION - + "=: to infer domain/binary domain combination gains/losses on given species trees" ); + + ": species tree, to perform (Dollo, Fitch) parismony analyses" ); + System.out.println( surfacing.INPUT_SPECIES_TREE_OPTION + + "=: to infer domain/binary domain combination gains/losses on given species trees" ); System.out.println( surfacing.FILTER_POSITIVE_OPTION - + "=: to filter out proteins not containing at least one domain listed in " ); + + "=: to filter out proteins not containing at least one domain listed in " ); System.out.println( surfacing.FILTER_NEGATIVE_OPTION - + "=: to filter out proteins containing at least one domain listed in " ); + + "=: to filter out proteins containing at least one domain listed in " ); System.out.println( surfacing.FILTER_NEGATIVE_DOMAINS_OPTION - + "=: to filter out (ignore) domains listed in " ); + + "=: to filter out (ignore) domains listed in " ); System.out.println( surfacing.INPUT_GENOMES_FILE_OPTION + "=: to read input files from " ); - System.out - .println( surfacing.RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION - + "=: seed for random number generator for Fitch Parsimony analysis (type: long, default: no randomization - given a choice, prefer absence" ); + System.out.println( surfacing.RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION + + "=: seed for random number generator for Fitch Parsimony analysis (type: long, default: no randomization - given a choice, prefer absence" ); System.out.println( surfacing.CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS - + ": to consider directedness in binary combinations: e.g. A-B != B-A" ); + + ": to consider directedness in binary combinations: e.g. A-B != B-A" ); System.out.println( surfacing.CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS_AND_ADJACENCY - + ": to consider directedness and adjacency in binary combinations" ); - System.out - .println( surfacing.SEQ_EXTRACT_OPTION - + "=: to extract sequence names of sequences containing matching domains and/or domain-sequences (order N to C) (domain separator: '~', domain sequences speparator: '#', e.g. 'NACHT#BIR~CARD')" ); + + ": to consider directedness and adjacency in binary combinations" ); + System.out.println( surfacing.SEQ_EXTRACT_OPTION + + "=: to extract sequence names of sequences containing matching domains and/or domain-sequences (order N to C) (domain separator: '~', domain sequences speparator: '#', e.g. 'NACHT#BIR~CARD')" ); System.out.println( surfacing.SECONDARY_FEATURES_PARSIMONY_MAP_FILE - + "=: to perfom parsimony analysis on secondary features" ); + + "=: to perfom parsimony analysis on secondary features" ); System.out.println( surfacing.PLUS_MINUS_ANALYSIS_OPTION + "=: to presence/absence genome analysis" ); System.out.println( surfacing.DOMAIN_COMBINITONS_COUNTS_OUTPUT_OPTION - + ": to output binary domain counts (as individual files)" ); + + ": to output binary domain counts (as individual files)" ); System.out.println( surfacing.DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS - + ": to output binary domain combinations for (downstream) graph analysis" ); + + ": to output binary domain combinations for (downstream) graph analysis" ); System.out.println( surfacing.OUTPUT_LIST_OF_ALL_PROTEINS_OPTIONS + ": to output all proteins per domain" ); System.out.println( surfacing.OUTPUT_LIST_OF_ALL_PROTEINS_PER_DOMAIN_E_VALUE_OPTION - + ": e value max per domain for output of all proteins per domain" ); + + ": e value max per domain for output of all proteins per domain" ); System.out.println( surfacing.USE_LAST_IN_FITCH_OPTION + ": to use last in Fitch parsimony" ); System.out.println( surfacing.WRITE_TO_NEXUS_OPTION + ": to output in Nexus format" ); System.out.println( PERFORM_DC_FITCH + ": to perform DC Fitch parsimony" ); @@ -2197,10 +2266,10 @@ public class surfacing { System.out.println(); System.out.println(); System.out - .println( "Example 1: surfacing -p2g=pfam2go.txt -obo=go.obo -species_tree=tol_156.xml -no_eo -ie=0.01 -dufs -genomes=genomes_all.txt -pos_filter=tf_1.txt -out_dir=_tf1 -o=tf1" ); + .println( "Example 1: surfacing -p2g=pfam2go.txt -obo=go.obo -species_tree=tol_156.xml -no_eo -ie=0.01 -dufs -genomes=genomes_all.txt -pos_filter=tf_1.txt -out_dir=_tf1 -o=tf1" ); System.out.println(); System.out - .println( "Example 2: surfacing -p2g=pfam2go.txt -obo=go.obo -species_tree=tol_156.xml -last -ignore_viral_ids -no_eo -ie=0.1 -dufs -genomes=genomes_all.txt -pos_filter=tf_1.txt -all_prot -all_prot_e=0.1 -out_dir=_tf1_e01_ape01 -o=tf1_e01_ape01" ); + .println( "Example 2: surfacing -p2g=pfam2go.txt -obo=go.obo -species_tree=tol_156.xml -last -ignore_viral_ids -no_eo -ie=0.1 -dufs -genomes=genomes_all.txt -pos_filter=tf_1.txt -all_prot -all_prot_e=0.1 -out_dir=_tf1_e01_ape01 -o=tf1_e01_ape01" ); System.out.println(); } } diff --git a/forester/java/src/org/forester/archaeopteryx/AptxConstants.java b/forester/java/src/org/forester/archaeopteryx/AptxConstants.java index 262bb1e..d5db636 100644 --- a/forester/java/src/org/forester/archaeopteryx/AptxConstants.java +++ b/forester/java/src/org/forester/archaeopteryx/AptxConstants.java @@ -39,7 +39,7 @@ public final class AptxConstants { final static boolean __ALLOW_PHYLOGENETIC_INFERENCE = true; public final static String PRG_NAME = "Archaeopteryx"; final static String VERSION = "0.9921 beta"; - final static String PRG_DATE = "170301"; + final static String PRG_DATE = "170322"; final static String DEFAULT_CONFIGURATION_FILE_NAME = "_aptx_configuration_file"; final static String[] DEFAULT_FONT_CHOICES = { "Arial Unicode MS", "Dialog", "SansSerif", "Sans", "Arial", "Helvetica" }; diff --git a/forester/java/src/org/forester/archaeopteryx/Configuration.java b/forester/java/src/org/forester/archaeopteryx/Configuration.java index f764e7f..3696136 100644 --- a/forester/java/src/org/forester/archaeopteryx/Configuration.java +++ b/forester/java/src/org/forester/archaeopteryx/Configuration.java @@ -135,7 +135,7 @@ public final class Configuration { { "Vector Data", "nodisplay", "no" }, { "Taxonomy Images", "display", "no" }, { "Properties", "display", "no" }, { "Gene Name", "display", "yes" }, { "Multiple Seq Alignment", "display", "no" }, { "Branch Length Values", "display", "no" } - , { "Taxonomy Rank", "display", "no" }}; + , { "Taxonomy Rank", "display", "no" }, { "Show External Data", "display", "yes" }}; final static int display_as_phylogram = 0; final static int show_node_names = 1; final static int show_tax_code = 2; @@ -166,6 +166,7 @@ public final class Configuration { final static int show_mol_seqs = 27; final static int write_branch_length_values = 28; final static int show_tax_rank = 29; + final static int display_external_data = 30; static final String VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA = "validate_against_phyloxml_xsd_schema"; private static Hashtable _sequence_colors; @@ -526,6 +527,10 @@ public final class Configuration { public void setDisplayInternalData( final boolean b ) { display_options[ display_internal_data ][ 2 ] = b ? "yes" : "no"; } + + public void setDisplayExternalData( final boolean b ) { + display_options[ display_external_data ][ 2 ] = b ? "yes" : "no"; + } public void setDisplayMultipleSequenceAlignment( final boolean b ) { display_options[ show_mol_seqs ][ 2 ] = b ? "yes" : "no"; @@ -1434,6 +1439,9 @@ public final class Configuration { else if ( key.equals( "display_internal_data" ) ) { key_index = Configuration.display_internal_data; } + else if ( key.equals( "display_external_data" ) ) { + key_index = Configuration.display_external_data; + } else if ( key.equals( "dynamically_hide_data" ) ) { key_index = Configuration.dynamically_hide_data; } diff --git a/forester/java/src/org/forester/archaeopteryx/ControlPanel.java b/forester/java/src/org/forester/archaeopteryx/ControlPanel.java index 05d3ca0..a8bd500 100644 --- a/forester/java/src/org/forester/archaeopteryx/ControlPanel.java +++ b/forester/java/src/org/forester/archaeopteryx/ControlPanel.java @@ -73,7 +73,6 @@ import org.forester.phylogeny.data.SequenceRelation.SEQUENCE_RELATION_TYPE; import org.forester.phylogeny.iterators.PhylogenyNodeIterator; import org.forester.util.ForesterUtil; - final class ControlPanel extends JPanel implements ActionListener { enum NodeClickAction { @@ -101,120 +100,121 @@ final class ControlPanel extends JPanel implements ActionListener { UNCOLLAPSE_ALL, ORDER_SUBTREE; } - final static Font jcb_bold_font = new Font( Configuration + final static Font jcb_bold_font = new Font( Configuration .getDefaultFontFamilyName(), Font.BOLD, Configuration.getGuiFontSize() ); - final static Font jcb_font = new Font( Configuration - .getDefaultFontFamilyName(), Font.PLAIN, Configuration.getGuiFontSize()); - final static Font js_font = new Font( Configuration + final static Font jcb_font = new Font( Configuration + .getDefaultFontFamilyName(), Font.PLAIN, Configuration.getGuiFontSize() ); + final static Font js_font = new Font( Configuration .getDefaultFontFamilyName(), Font.PLAIN, Configuration.getGuiFontSize() ); - private static final String RETURN_TO_SUPER_TREE_TEXT = "R"; - private static final String SEARCH_TIP_TEXT = "Enter text to search for. Use ',' for logical OR and '+' for logical AND (not used in this manner for regular expression searches)."; - private static final long serialVersionUID = -8463483932821545633L; - private NodeClickAction _action_when_node_clicked; - private int _add_new_node_item; - private Map _all_click_to_names; - private Map _annotation_colors; - private int _blast_item; - private JComboBox _click_to_combobox; - private JLabel _click_to_label; - private List _click_to_names; - private int _collapse_cb_item; - private int _uncollapse_all_cb_item; - private int _order_subtree_cb_item; - private JCheckBox _color_acc_species; - private JCheckBox _color_acc_sequence; - private JCheckBox _color_according_to_annotation; - private boolean _color_branches; - private JCheckBox _use_visual_styles_cb; - private int _color_subtree_cb_item; - private int _change_node_font_item; + private static final String RETURN_TO_SUPER_TREE_TEXT = "R"; + private static final String SEARCH_TIP_TEXT = "Enter text to search for. Use ',' for logical OR and '+' for logical AND (not used in this manner for regular expression searches)."; + private static final long serialVersionUID = -8463483932821545633L; + private NodeClickAction _action_when_node_clicked; + private int _add_new_node_item; + private Map _all_click_to_names; + private Map _annotation_colors; + private int _blast_item; + private JComboBox _click_to_combobox; + private JLabel _click_to_label; + private List _click_to_names; + private int _collapse_cb_item; + private int _uncollapse_all_cb_item; + private int _order_subtree_cb_item; + private JCheckBox _color_acc_species; + private JCheckBox _color_acc_sequence; + private JCheckBox _color_according_to_annotation; + private boolean _color_branches; + private JCheckBox _use_visual_styles_cb; + private int _color_subtree_cb_item; + private int _change_node_font_item; // The settings from the conf file - private final Configuration _configuration; - private int _copy_subtree_item; - private int _cut_subtree_item; - private JButton _decr_domain_structure_evalue_thr; - private int _delete_node_or_subtree_item; - private JRadioButton _display_as_unaligned_phylogram_rb; - private JRadioButton _display_as_aligned_phylogram_rb; - private JRadioButton _display_as_cladogram_rb; - private ButtonGroup _display_as_buttongroup; + private final Configuration _configuration; + private int _copy_subtree_item; + private int _cut_subtree_item; + private JButton _decr_domain_structure_evalue_thr; + private int _delete_node_or_subtree_item; + private JRadioButton _display_as_unaligned_phylogram_rb; + private JRadioButton _display_as_aligned_phylogram_rb; + private JRadioButton _display_as_cladogram_rb; + private ButtonGroup _display_as_buttongroup; // Tree checkboxes - private JCheckBox _display_internal_data; - private JLabel _domain_display_label; - private JTextField _domain_structure_evalue_thr_tf; - private JTextField _depth_collapse_depth_tf; - private JTextField _rank_collapse_depth_tf; - private List _tree_display_types; - private JCheckBox _dynamically_hide_data; - private int _edit_node_data_item; - private int _get_ext_desc_data; - private JButton _incr_domain_structure_evalue_thr; - private final MainPanel _mainpanel; - private JCheckBox _node_desc_popup_cb; - private int _open_pdb_item; - private int _open_seq_web_item; - private int _open_tax_web_item; - private int _color_node_font_item; - private JButton _order; - private int _paste_subtree_item; - private int _reroot_cb_item; - private JButton _return_to_super_tree; + private JCheckBox _display_internal_data; + private JCheckBox _display_external_data; + private JLabel _domain_display_label; + private JTextField _domain_structure_evalue_thr_tf; + private JTextField _depth_collapse_depth_tf; + private JTextField _rank_collapse_depth_tf; + private List _tree_display_types; + private JCheckBox _dynamically_hide_data; + private int _edit_node_data_item; + private int _get_ext_desc_data; + private JButton _incr_domain_structure_evalue_thr; + private final MainPanel _mainpanel; + private JCheckBox _node_desc_popup_cb; + private int _open_pdb_item; + private int _open_seq_web_item; + private int _open_tax_web_item; + private int _color_node_font_item; + private JButton _order; + private int _paste_subtree_item; + private int _reroot_cb_item; + private JButton _return_to_super_tree; // Search - private JLabel _search_found_label_0; - private JLabel _search_found_label_1; - private JButton _search_reset_button_0; - private JButton _search_reset_button_1; - private JTextField _search_tf_0; - private JTextField _search_tf_1; - private int _select_nodes_item; - private Sequence _selected_query_seq; - private JCheckBox _seq_relation_confidence_switch; - private JComboBox _sequence_relation_type_box; - private JCheckBox _show_annotation; - private JCheckBox _show_binary_character_counts; - private JCheckBox _show_binary_characters; + private JLabel _search_found_label_0; + private JLabel _search_found_label_1; + private JButton _search_reset_button_0; + private JButton _search_reset_button_1; + private JTextField _search_tf_0; + private JTextField _search_tf_1; + private int _select_nodes_item; + private Sequence _selected_query_seq; + private JCheckBox _seq_relation_confidence_switch; + private JComboBox _sequence_relation_type_box; + private JCheckBox _show_annotation; + private JCheckBox _show_binary_character_counts; + private JCheckBox _show_binary_characters; // Indices for the click-to options in the combo box - private int _show_data_item; - private JCheckBox _show_domain_architectures; - private JCheckBox _show_mol_seqs; - private JCheckBox _write_branch_length_values; - private JCheckBox _show_events; - private JCheckBox _show_gene_names; - private JCheckBox _show_node_names; - private JCheckBox _show_properties_cb; - private JCheckBox _show_seq_names; - private JCheckBox _show_seq_symbols; - private JCheckBox _show_sequence_acc; - private JComboBox _show_sequence_relations; - private JCheckBox _show_taxo_code; - private JCheckBox _show_taxo_rank; - private JCheckBox _show_taxo_common_names; - private JCheckBox _show_taxo_images_cb; - private JCheckBox _show_taxo_scientific_names; - private JCheckBox _show_vector_data_cb; - private JButton _show_whole; - private int _sort_descendents_item; - private Map _species_colors; - private Map _sequence_colors; - private int _subtree_cb_item; - private int _swap_cb_item; - private JButton _uncollapse_all; - private JCheckBox _width_branches; - private JCheckBox _write_confidence; - private JButton _zoom_in_domain_structure; - private JButton _zoom_in_x; - private JButton _zoom_in_y; - private JLabel _zoom_label; - private JButton _zoom_out_domain_structure; - private JButton _zoom_out_x; - private JButton _zoom_out_y; - private JButton _decr_depth_collapse_level; - private JButton _incr_depth_collapse_level; - private JLabel _depth_collapse_label; - private JButton _decr_rank_collapse_level; - private JButton _incr_rank_collapse_level; - private JLabel _rank_collapse_label; - + private int _show_data_item; + private JCheckBox _show_domain_architectures; + private JCheckBox _show_mol_seqs; + private JCheckBox _write_branch_length_values; + private JCheckBox _show_events; + private JCheckBox _show_gene_names; + private JCheckBox _show_node_names; + private JCheckBox _show_properties_cb; + private JCheckBox _show_seq_names; + private JCheckBox _show_seq_symbols; + private JCheckBox _show_sequence_acc; + private JComboBox _show_sequence_relations; + private JCheckBox _show_taxo_code; + private JCheckBox _show_taxo_rank; + private JCheckBox _show_taxo_common_names; + private JCheckBox _show_taxo_images_cb; + private JCheckBox _show_taxo_scientific_names; + private JCheckBox _show_vector_data_cb; + private JButton _show_whole; + private int _sort_descendents_item; + private Map _species_colors; + private Map _sequence_colors; + private int _subtree_cb_item; + private int _swap_cb_item; + private JButton _uncollapse_all; + private JCheckBox _width_branches; + private JCheckBox _write_confidence; + private JButton _zoom_in_domain_structure; + private JButton _zoom_in_x; + private JButton _zoom_in_y; + private JLabel _zoom_label; + private JButton _zoom_out_domain_structure; + private JButton _zoom_out_x; + private JButton _zoom_out_y; + private JButton _decr_depth_collapse_level; + private JButton _incr_depth_collapse_level; + private JLabel _depth_collapse_label; + private JButton _decr_rank_collapse_level; + private JButton _incr_rank_collapse_level; + private JLabel _rank_collapse_label; + ControlPanel( final MainPanel ap, final Configuration configuration ) { init(); _mainpanel = ap; @@ -637,7 +637,7 @@ final class ControlPanel extends JPanel implements ActionListener { return _tree_display_types; } - final private MainFrame getMainFrame() { + final private MainFrame getMainFrame() { return getMainPanel().getMainFrame(); } @@ -1013,7 +1013,6 @@ final class ControlPanel extends JPanel implements ActionListener { } private void setupDisplayCheckboxes() { - if ( _configuration.doDisplayOption( Configuration.dynamically_hide_data ) ) { addCheckbox( Configuration.dynamically_hide_data, _configuration.getDisplayTitle( Configuration.dynamically_hide_data ) ); @@ -1031,6 +1030,12 @@ final class ControlPanel extends JPanel implements ActionListener { setCheckbox( Configuration.display_internal_data, _configuration.doCheckOption( Configuration.display_internal_data ) ); } + if ( _configuration.doDisplayOption( Configuration.display_external_data ) ) { + addCheckbox( Configuration.display_external_data, + _configuration.getDisplayTitle( Configuration.display_external_data ) ); + setCheckbox( Configuration.display_external_data, + _configuration.doCheckOption( Configuration.display_external_data ) ); + } if ( _configuration.doDisplayOption( Configuration.color_according_to_sequence ) ) { addCheckbox( Configuration.color_according_to_sequence, _configuration.getDisplayTitle( Configuration.color_according_to_sequence ) ); @@ -1314,6 +1319,12 @@ final class ControlPanel extends JPanel implements ActionListener { addJCheckBox( _display_internal_data, ch_panel ); add( ch_panel ); break; + case Configuration.display_external_data: + _display_external_data = new JCheckBox( title ); + _display_external_data.setToolTipText( "To allow or disallow display of external labels" ); + addJCheckBox( _display_external_data, ch_panel ); + add( ch_panel ); + break; case Configuration.color_according_to_species: _color_acc_species = new JCheckBox( title ); _color_acc_species.setToolTipText( "To colorize node labels as a function of taxonomy" ); @@ -1637,7 +1648,8 @@ final class ControlPanel extends JPanel implements ActionListener { boolean isDrawPhylogram() { final Options.PHYLOGENY_DISPLAY_TYPE t = getTreeDisplayType( getMainPanel().getCurrentTabIndex() ); - return ((t == Options.PHYLOGENY_DISPLAY_TYPE.ALIGNED_PHYLOGRAM) ||( t == Options.PHYLOGENY_DISPLAY_TYPE.UNALIGNED_PHYLOGRAM)); + return ( ( t == Options.PHYLOGENY_DISPLAY_TYPE.ALIGNED_PHYLOGRAM ) + || ( t == Options.PHYLOGENY_DISPLAY_TYPE.UNALIGNED_PHYLOGRAM ) ); } boolean isDynamicallyHideData() { @@ -1680,6 +1692,10 @@ final class ControlPanel extends JPanel implements ActionListener { return ( ( _display_internal_data == null ) || _display_internal_data.isSelected() ); } + boolean isShowExternalData() { + return ( ( _display_external_data == null ) || _display_external_data.isSelected() ); + } + boolean isShowNodeNames() { return ( ( _show_node_names != null ) && _show_node_names.isSelected() ); } @@ -1734,11 +1750,11 @@ final class ControlPanel extends JPanel implements ActionListener { } void phylogenyAdded( final Configuration configuration ) { - if (configuration.isDrawAsPhylogram()) { - getTreeDisplayTypes().add( Options.PHYLOGENY_DISPLAY_TYPE.UNALIGNED_PHYLOGRAM); + if ( configuration.isDrawAsPhylogram() ) { + getTreeDisplayTypes().add( Options.PHYLOGENY_DISPLAY_TYPE.UNALIGNED_PHYLOGRAM ); } else { - getTreeDisplayTypes().add( Options.PHYLOGENY_DISPLAY_TYPE.CLADOGRAM); + getTreeDisplayTypes().add( Options.PHYLOGENY_DISPLAY_TYPE.CLADOGRAM ); } } @@ -1822,6 +1838,11 @@ final class ControlPanel extends JPanel implements ActionListener { _display_internal_data.setSelected( state ); } break; + case Configuration.display_external_data: + if ( _display_external_data != null ) { + _display_external_data.setSelected( state ); + } + break; case Configuration.color_according_to_species: if ( _color_acc_species != null ) { _color_acc_species.setSelected( state ); @@ -2063,30 +2084,27 @@ final class ControlPanel extends JPanel implements ActionListener { } void setTreeDisplayType( final Options.PHYLOGENY_DISPLAY_TYPE t ) { - switch (t) { + switch ( t ) { case UNALIGNED_PHYLOGRAM: getDisplayAsUnalignedPhylogramRb().setSelected( true ); break; case ALIGNED_PHYLOGRAM: getDisplayAsAlignedPhylogramRb().setSelected( true ); break; - case CLADOGRAM: + case CLADOGRAM: getDisplayAsCladogramRb().setSelected( true ); break; } - setTreeDisplayType( getMainPanel().getCurrentTabIndex(), t ); + setTreeDisplayType( getMainPanel().getCurrentTabIndex(), t ); } void setDrawPhylogramEnabled( final boolean b ) { - if ( getDisplayAsAlignedPhylogramRb() != null && - getDisplayAsUnalignedPhylogramRb() != null && - getDisplayAsCladogramRb() != null - ) { - - getDisplayAsAlignedPhylogramRb().setEnabled( b ); - getDisplayAsUnalignedPhylogramRb().setEnabled( b ); - getDisplayAsCladogramRb().setEnabled( b ); - } + if ( getDisplayAsAlignedPhylogramRb() != null && getDisplayAsUnalignedPhylogramRb() != null + && getDisplayAsCladogramRb() != null ) { + getDisplayAsAlignedPhylogramRb().setEnabled( b ); + getDisplayAsUnalignedPhylogramRb().setEnabled( b ); + getDisplayAsCladogramRb().setEnabled( b ); + } } void setDynamicHidingIsOn( final boolean is_on ) { @@ -2127,7 +2145,6 @@ final class ControlPanel extends JPanel implements ActionListener { } void setupControls() { - setupTreeDisplayTypeOptions(); setupDisplayCheckboxes(); /* GUILHEM_BEG */ @@ -2160,19 +2177,18 @@ final class ControlPanel extends JPanel implements ActionListener { setupJRadioButton( getDisplayAsUnalignedPhylogramRb() ); setupJRadioButton( getDisplayAsAlignedPhylogramRb() ); setupJRadioButton( getDisplayAsCladogramRb() ); - final JPanel p = new JPanel(new GridLayout( 1, 3, 0, 0 )); + final JPanel p = new JPanel( new GridLayout( 1, 3, 0, 0 ) ); p.setFont( ControlPanel.jcb_font ); if ( !_configuration.isUseNativeUI() ) { p.setBackground( getConfiguration().getGuiBackgroundColor() ); p.setForeground( getConfiguration().getGuiCheckboxTextColor() ); } - p.add( _display_as_unaligned_phylogram_rb ); + p.add( _display_as_unaligned_phylogram_rb ); p.add( _display_as_aligned_phylogram_rb ); p.add( _display_as_cladogram_rb ); add( p ); } - - + void setUpControlsForDomainStrucures() { _domain_display_label = new JLabel( "Domain Architectures:" ); add( customizeLabel( _domain_display_label, getConfiguration() ) ); @@ -2586,17 +2602,14 @@ final class ControlPanel extends JPanel implements ActionListener { if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( getCurrentTreePanel().getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) { setDrawPhylogramEnabled( true ); - - setTreeDisplayType( getTreeDisplayType( getMainPanel().getCurrentTabIndex() ) ); + setTreeDisplayType( getTreeDisplayType( getMainPanel().getCurrentTabIndex() ) ); } else { setDrawPhylogramEnabled( false ); setTreeDisplayType( Options.PHYLOGENY_DISPLAY_TYPE.CLADOGRAM ); } - - getMainPanel().getMainFrame() - .setSelectedTypeInTypeMenu( getMainPanel().getCurrentTreePanel().getPhylogenyGraphicsType() ); - + getMainPanel().getMainFrame() + .setSelectedTypeInTypeMenu( getMainPanel().getCurrentTreePanel().getPhylogenyGraphicsType() ); getMainPanel().getCurrentTreePanel().updateSubSuperTreeButton(); getMainPanel().getCurrentTreePanel().updateButtonToUncollapseAll(); getMainPanel().getControlPanel().search0(); @@ -2797,8 +2810,8 @@ final class ControlPanel extends JPanel implements ActionListener { private final boolean isDrawPhylogram( int currentTabIndex ) { Options.PHYLOGENY_DISPLAY_TYPE t = getTreeDisplayType( currentTabIndex ); - return ((t==Options.PHYLOGENY_DISPLAY_TYPE.ALIGNED_PHYLOGRAM)|(t==Options.PHYLOGENY_DISPLAY_TYPE.UNALIGNED_PHYLOGRAM)); - + return ( ( t == Options.PHYLOGENY_DISPLAY_TYPE.ALIGNED_PHYLOGRAM ) + | ( t == Options.PHYLOGENY_DISPLAY_TYPE.UNALIGNED_PHYLOGRAM ) ); } final void zoomOutY( final float factor ) { @@ -2833,10 +2846,10 @@ final class ControlPanel extends JPanel implements ActionListener { } public Options.PHYLOGENY_DISPLAY_TYPE getTreeDisplayType() { - if (_display_as_unaligned_phylogram_rb.isSelected() ) { + if ( _display_as_unaligned_phylogram_rb.isSelected() ) { return Options.PHYLOGENY_DISPLAY_TYPE.UNALIGNED_PHYLOGRAM; } - else if (_display_as_aligned_phylogram_rb.isSelected() ) { + else if ( _display_as_aligned_phylogram_rb.isSelected() ) { return Options.PHYLOGENY_DISPLAY_TYPE.ALIGNED_PHYLOGRAM; } return Options.PHYLOGENY_DISPLAY_TYPE.CLADOGRAM; diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanel.java b/forester/java/src/org/forester/archaeopteryx/TreePanel.java index e0706da..9bc89cc 100644 --- a/forester/java/src/org/forester/archaeopteryx/TreePanel.java +++ b/forester/java/src/org/forester/archaeopteryx/TreePanel.java @@ -379,7 +379,6 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee init(); // if ( !_phylogeny.isEmpty() ) { _phylogeny.recalculateNumberOfExternalDescendants( true ); - // } setBackground( getTreeColorSet().getBackgroundColor() ); final MouseListener mouse_listener = new MouseListener( this ); @@ -736,8 +735,6 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee type = 'n'; } } - - try { Blast.openNcbiBlastWeb( query, type == 'n', this ); } @@ -1737,8 +1734,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee decreaseOvSize(); } } - if ( e.getKeyCode() == KeyEvent.VK_HOME - || e.getKeyCode() == KeyEvent.VK_ESCAPE ) { + if ( e.getKeyCode() == KeyEvent.VK_HOME || e.getKeyCode() == KeyEvent.VK_ESCAPE ) { getControlPanel().showWhole(); } else if ( e.getKeyCode() == KeyEvent.VK_PAGE_UP ) { @@ -1998,8 +1994,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee if ( !ForesterUtil.isEmpty( uri_strs ) ) { for( final String uri_str : uri_strs ) { try { - AptxUtil.launchWebBrowser( new URI( uri_str ), - "_aptx_seq" ); + AptxUtil.launchWebBrowser( new URI( uri_str ), "_aptx_seq" ); } catch ( final IOException e ) { AptxUtil.showErrorMessage( this, e.toString() ); @@ -2024,9 +2019,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee final String uri_str = TreePanelUtil.createUriForSeqWeb( node, getConfiguration(), this ); if ( !ForesterUtil.isEmpty( uri_str ) ) { try { - AptxUtil.launchWebBrowser( new URI( uri_str ), - - "_aptx_seq" ); + AptxUtil.launchWebBrowser( new URI( uri_str ), "_aptx_seq" ); } catch ( final IOException e ) { AptxUtil.showErrorMessage( this, e.toString() ); @@ -2105,8 +2098,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } if ( !ForesterUtil.isEmpty( uri_str ) ) { try { - AptxUtil.launchWebBrowser( new URI( uri_str ), - "_aptx_tax" ); + AptxUtil.launchWebBrowser( new URI( uri_str ), "_aptx_tax" ); } catch ( final IOException e ) { AptxUtil.showErrorMessage( this, e.toString() ); @@ -2584,11 +2576,12 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee ( node.getYcoord() - getFontMetricsForLargeDefaultFont().getMaxDescent() ), g ); g.setColor( getTreeColorSet().getLostCharactersColor() ); - TreePanel.drawString( lost, - parent_x + ( ( x - parent_x - - getFontMetricsForLargeDefaultFont().stringWidth( lost ) ) / 2 ), - ( node.getYcoord() + getFontMetricsForLargeDefaultFont().getMaxAscent() ), - g ); + TreePanel + .drawString( lost, + parent_x + ( ( x - parent_x - getFontMetricsForLargeDefaultFont().stringWidth( lost ) ) + / 2 ), + ( node.getYcoord() + getFontMetricsForLargeDefaultFont().getMaxAscent() ), + g ); } } @@ -2649,14 +2642,11 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee || ( getOptions().isShowDefaultNodeShapesForMarkedNodes() && ( node.getNodeData().getNodeVisualData() != null ) && ( !node.getNodeData().getNodeVisualData().isEmpty() ) ) - || ( getControlPanel().isUseVisualStyles() - && ( ( node.getNodeData().getNodeVisualData() != null ) - && ( ( node.getNodeData().getNodeVisualData().getNodeColor() != null ) - || ( node.getNodeData().getNodeVisualData() - .getSize() != NodeVisualData.DEFAULT_SIZE ) - || ( node.getNodeData().getNodeVisualData().getFillType() != NodeFill.DEFAULT ) - || ( node.getNodeData().getNodeVisualData() - .getShape() != NodeShape.DEFAULT ) ) ) ) + || ( getControlPanel().isUseVisualStyles() && ( ( node.getNodeData().getNodeVisualData() != null ) + && ( ( node.getNodeData().getNodeVisualData().getNodeColor() != null ) + || ( node.getNodeData().getNodeVisualData().getSize() != NodeVisualData.DEFAULT_SIZE ) + || ( node.getNodeData().getNodeVisualData().getFillType() != NodeFill.DEFAULT ) + || ( node.getNodeData().getNodeVisualData().getShape() != NodeShape.DEFAULT ) ) ) ) || ( getControlPanel().isEvents() && node.isHasAssignedEvent() && ( node.getNodeData().getEvent().isDuplication() || node.getNodeData().getEvent().isSpeciation() @@ -2840,6 +2830,9 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee if ( !getControlPanel().isShowInternalData() && !node.isExternal() && !node.isCollapse() ) { return 0; } + if ( !getControlPanel().isShowExternalData() && ( node.isExternal() || node.isCollapse() ) ) { + return 0; + } _sb.setLength( 0 ); int x = 0; if ( add > 0 ) { @@ -2901,9 +2894,9 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } else if ( ( _sb.length() > 0 ) || saw_species ) { // _sb.setLength( 0 ); - _sb.append( " (" ); + _sb.append( " [" ); _sb.append( node.getAllExternalDescendants().size() ); - _sb.append( ")" ); + _sb.append( "]" ); } } else { @@ -3416,8 +3409,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee && ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) ) { paintMolecularSequences( g, node, to_pdf ); } - if ( dynamically_hide && ( ( node.isExternal() - && ( ( _external_node_index % dynamic_hiding_factor ) != 1 ) ) + if ( dynamically_hide && ( ( node.isExternal() && ( ( _external_node_index % dynamic_hiding_factor ) != 1 ) ) || ( !node.isExternal() && ( ( new_x_min < 20 ) || ( ( _y_distance * node.getNumberOfExternalNodes() ) < getFontMetricsForLargeDefaultFont() .getHeight() ) ) ) ) ) { @@ -3438,6 +3430,9 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee if ( ( !getControlPanel().isShowInternalData() && !node.isExternal() ) ) { return; } + if ( ( !getControlPanel().isShowExternalData() && node.isExternal() ) ) { + return; + } if ( getControlPanel().isShowDomainArchitectures() && node.getNodeData().isHasSequence() && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) && ( node.getNodeData() .getSequence().getDomainArchitecture() instanceof RenderableDomainArchitecture ) ) { @@ -3639,7 +3634,8 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee final boolean using_visual_font = setFont( g, node, is_in_found_nodes ); setColor( g, node, to_graphics_file, to_pdf, is_in_found_nodes, getTreeColorSet().getTaxonomyColor() ); float start_x = node.getXcoord() + 3 + ( getOptions().getDefaultNodeShapeSize() / 2 ) + x_shift; - if ( getControlPanel().getTreeDisplayType() == Options.PHYLOGENY_DISPLAY_TYPE.ALIGNED_PHYLOGRAM && node.isExternal() ) { + if ( getControlPanel().getTreeDisplayType() == Options.PHYLOGENY_DISPLAY_TYPE.ALIGNED_PHYLOGRAM + && node.isExternal() ) { start_x = ( float ) ( ( getMaxDistanceToRoot() * getXcorrectionFactor() ) + ( getOptions().getDefaultNodeShapeSize() / 2 ) + x_shift + ( 2 * TreePanel.MOVE ) + getXdistance() + 3 ); @@ -3879,7 +3875,6 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } private final StringBuffer propertiesToString( final PhylogenyNode node ) { - return node.getNodeData().getProperties().asText(); } @@ -4240,9 +4235,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee + ", unique entries: " + size; } final String s = sb.toString().trim(); - - getMainPanel().getMainFrame().showTextFrame( s, title ); - + getMainPanel().getMainFrame().showTextFrame( s, title ); } } } @@ -4436,8 +4429,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee if ( _popup_buffer.length() > 0 ) { _popup_buffer.append( "\n" ); } - _popup_buffer.append(node.getNodeData().getProperties().asText()); - + _popup_buffer.append( node.getNodeData().getProperties().asText() ); } if ( _popup_buffer.length() > 0 ) { if ( !getConfiguration().isUseNativeUI() ) { @@ -4548,9 +4540,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee else { getControlPanel().setDrawPhylogramEnabled( false ); } - - getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( getPhylogenyGraphicsType() ); - + getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( getPhylogenyGraphicsType() ); } final void calcMaxDepth() { @@ -4833,8 +4823,6 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } } - - void clearCurrentExternalNodesDataBuffer() { setCurrentExternalNodesDataBuffer( new StringBuilder() ); } @@ -5198,8 +5186,6 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee && ( e.getY() <= ( getOvRectangle().getY() + getOvRectangle().getHeight() + 1 ) ) ); } - - final boolean isCanCollapse() { return ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ); } @@ -5501,8 +5487,6 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee _urt_factor *= f; } - - final void paintBranchCircular( final PhylogenyNode p, final PhylogenyNode c, final Graphics2D g, @@ -5709,7 +5693,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } } final boolean disallow_shortcutting = ( dynamic_hiding_factor < 40 ) - /* || getControlPanel().isUseVisualStyles() || getOptions().isShowDefaultNodeShapesForMarkedNodes()*/ //TODO check if this is really not needed. + /* || getControlPanel().isUseVisualStyles() || getOptions().isShowDefaultNodeShapesForMarkedNodes()*/ //TODO check if this is really not needed. || to_graphics_file || to_pdf; for( final PhylogenyNode element : _nodes_in_preorder ) { paintNodeRectangular( g, diff --git a/forester/java/src/org/forester/phylogeny/PhylogenyNode.java b/forester/java/src/org/forester/phylogeny/PhylogenyNode.java index 2ced361..25b33d7 100644 --- a/forester/java/src/org/forester/phylogeny/PhylogenyNode.java +++ b/forester/java/src/org/forester/phylogeny/PhylogenyNode.java @@ -248,10 +248,7 @@ public final class PhylogenyNode implements Comparable { } } - final public List getAllDescendants() { - return _descendants; - } - + /** * Returns a List containing references to all external children of this * PhylogenyNode. @@ -641,10 +638,7 @@ public final class PhylogenyNode implements Comparable { * @return true if this PhylogenyNode is external, false otherwise */ final public boolean isExternal() { - if ( _descendants == null ) { - return true; - } - return ( getNumberOfDescendants() < 1 ); + return ( _descendants == null ) || ( _descendants.size() == 0 ); } final public boolean isFirstChildNode() { diff --git a/forester/java/src/org/forester/protein/BasicProtein.java b/forester/java/src/org/forester/protein/BasicProtein.java index 03bf129..975e48d 100644 --- a/forester/java/src/org/forester/protein/BasicProtein.java +++ b/forester/java/src/org/forester/protein/BasicProtein.java @@ -50,16 +50,18 @@ public class BasicProtein implements Protein { private final List _protein_domains; public static Comparator DomainMidPositionComparator = new Comparator() { - @Override - public int compare( final Domain d1, - final Domain d2 ) { - final int m1 = ( d1.getTo() + d1.getFrom() ); - final int m2 = ( d2.getTo() + d2.getFrom() ); - return m1 < m2 ? -1 : m1 > m2 ? 1 : d1 - .getDomainId() - .compareTo( d2.getDomainId() ); - } - }; + @Override + public int compare( final Domain d1, + final Domain d2 ) { + final int m1 = ( d1.getTo() + d1.getFrom() ); + final int m2 = ( d2.getTo() + d2.getFrom() ); + return m1 < m2 ? -1 + : m1 > m2 ? 1 + : d1.getDomainId() + .compareTo( d2 + .getDomainId() ); + } + }; public BasicProtein( final String id_str, final String species_str, final int length ) { if ( length < 0 ) { @@ -213,20 +215,27 @@ public class BasicProtein implements Protein { _name = name; } - public String toDomainArchitectureString( final String separator ) { + @Override + public final String toDomainArchitectureString( final String separator, final double ie_cutoff ) { final StringBuilder sb = new StringBuilder(); boolean first = true; for( final Domain d : getDomainsSortedByPosition() ) { - if ( first ) { - first = false; - } - else { - sb.append( separator ); + if ( ( ie_cutoff <= -1 ) || ( d.getPerDomainEvalue() <= ie_cutoff ) ) { + if ( first ) { + first = false; + } + else { + sb.append( separator ); + } + sb.append( d.getDomainId() ); } - sb.append( d.getDomainId() ); } return sb.toString(); } + + public final String toDomainArchitectureString( final String separator ) { + return toDomainArchitectureString( separator, -1 ); + } public String toDomainArchitectureString( final String separator, final int repeats_limit, @@ -269,7 +278,7 @@ public class BasicProtein implements Protein { @Override public String toString() { - return toDomainArchitectureString( "~" ); + return toDomainArchitectureString( "--", 1 ); } private List getProteinDomainIds() { diff --git a/forester/java/src/org/forester/protein/Protein.java b/forester/java/src/org/forester/protein/Protein.java index eccc7d7..8e8b655 100644 --- a/forester/java/src/org/forester/protein/Protein.java +++ b/forester/java/src/org/forester/protein/Protein.java @@ -71,4 +71,7 @@ public interface Protein { public Species getSpecies(); public List getDomainsSortedByPosition(); + + public String toDomainArchitectureString( final String separator, final double ie_cutoff ); + } \ No newline at end of file diff --git a/forester/java/src/org/forester/surfacing/DomainSimilarity.java b/forester/java/src/org/forester/surfacing/DomainSimilarity.java index db25dd5..1c65f1c 100644 --- a/forester/java/src/org/forester/surfacing/DomainSimilarity.java +++ b/forester/java/src/org/forester/surfacing/DomainSimilarity.java @@ -405,11 +405,15 @@ public class DomainSimilarity implements Comparable { final Map tax_code_to_id_map, final Phylogeny phy ) { final StringBuffer sb = new StringBuffer(); - sb.append( "" ); + if (html) { + sb.append( "
" ); + } for( final Species species : getSpeciesData().keySet() ) { addSpeciesSpecificDomainData( sb, species, html, tax_code_to_id_map, phy ); } - sb.append( "
" ); + if (html) { + sb.append( "" ); + } return sb; } diff --git a/forester/java/src/org/forester/surfacing/MinimalDomainomeCalculator.java b/forester/java/src/org/forester/surfacing/MinimalDomainomeCalculator.java index a98e036..f252202 100644 --- a/forester/java/src/org/forester/surfacing/MinimalDomainomeCalculator.java +++ b/forester/java/src/org/forester/surfacing/MinimalDomainomeCalculator.java @@ -1,23 +1,199 @@ package org.forester.surfacing; +import java.io.BufferedWriter; +import java.io.File; +import java.io.FileWriter; +import java.io.IOException; import java.util.ArrayList; +import java.util.HashMap; import java.util.HashSet; import java.util.List; +import java.util.Map; +import java.util.Map.Entry; import java.util.Set; import java.util.SortedMap; +import java.util.SortedSet; +import java.util.TreeMap; +import java.util.TreeSet; +import org.forester.application.surfacing; import org.forester.phylogeny.Phylogeny; -import org.forester.phylogeny.PhylogenyMethods; import org.forester.phylogeny.PhylogenyNode; import org.forester.phylogeny.iterators.PhylogenyNodeIterator; import org.forester.protein.Domain; import org.forester.protein.Protein; import org.forester.species.BasicSpecies; import org.forester.species.Species; +import org.forester.util.ForesterUtil; public final class MinimalDomainomeCalculator { + static final public void calcDomainome( final Phylogeny tre, + final SortedMap> protein_lists_per_species, + final double ie_cutoff ) { + if ( protein_lists_per_species == null || tre == null ) { + throw new IllegalArgumentException( "argument is null" ); + } + if ( protein_lists_per_species.size() < 2 ) { + throw new IllegalArgumentException( "not enough genomes" ); + } + for( final PhylogenyNodeIterator iter = tre.iteratorPostorder(); iter.hasNext(); ) { + final PhylogenyNode node = iter.next(); + if ( node.isInternal() ) { + System.out.println(); + if ( node.getNodeData().isHasTaxonomy() ) { + System.out.println( node.getNodeData().getTaxonomy().getScientificName() + ":" ); + } + else { + System.out.println( node.getName() + ":" ); + } + final List external_descs = node.getAllExternalDescendants(); + final List> domains_per_genome_list = new ArrayList>(); + for( final PhylogenyNode external_desc : external_descs ) { + final String code = external_desc.getNodeData().getTaxonomy().getTaxonomyCode(); + System.out.print( code + " " ); + final List proteins_per_species = protein_lists_per_species + .get( new BasicSpecies( code ) ); + if ( proteins_per_species != null ) { + final SortedSet domains_per_genome = new TreeSet(); + for( final Protein protein : proteins_per_species ) { + List domains = protein.getProteinDomains(); + for( final Domain domain : domains ) { + if ( ( domain.getPerDomainEvalue() <= ie_cutoff ) || ( ie_cutoff <= -1 ) ) { + domains_per_genome.add( domain.getDomainId() ); + } + } + } + if ( domains_per_genome.size() > 0 ) { + domains_per_genome_list.add( domains_per_genome ); + } + } + } + System.out.println(); + if ( domains_per_genome_list.size() > 0 ) { + Set intersection = calcIntersection( domains_per_genome_list ); + System.out.println( intersection ); + } + } + } + } + + static final public void calcDAome( final Phylogeny tre, + final SortedMap> protein_lists_per_species, + final String separator, + final double ie_cutoff, + final String outfile_base ) + throws IOException { + final SortedMap> species_to_das_map = new TreeMap>(); + if ( protein_lists_per_species == null || tre == null ) { + throw new IllegalArgumentException( "argument is null" ); + } + if ( protein_lists_per_species.size() < 2 ) { + throw new IllegalArgumentException( "not enough genomes" ); + } + final File outfile = new File( outfile_base + "_minimal_daome.txt" ); + final File outfile_table = new File( outfile_base + "_minimal_daome.tsv" ); + SurfacingUtil.checkForOutputFileWriteability( outfile ); + SurfacingUtil.checkForOutputFileWriteability( outfile_table ); + final BufferedWriter out = new BufferedWriter( new FileWriter( outfile ) ); + final BufferedWriter out_table = new BufferedWriter( new FileWriter( outfile_table ) ); + for( final PhylogenyNodeIterator iter = tre.iteratorPostorder(); iter.hasNext(); ) { + final PhylogenyNode node = iter.next(); + final String species_name = node.getNodeData().isHasTaxonomy() + ? node.getNodeData().getTaxonomy().getScientificName() : node.getName(); + out.write( species_name ); + final List external_descs = node.getAllExternalDescendants(); + out.write( "\t[" + external_descs.size() + "]:" ); + final List> das_per_genome_list = new ArrayList>(); + for( final PhylogenyNode external_desc : external_descs ) { + final String code = external_desc.getNodeData().getTaxonomy().getTaxonomyCode(); + out.write( '\t' + code ); + final List proteins_per_species = protein_lists_per_species.get( new BasicSpecies( code ) ); + if ( proteins_per_species != null ) { + final SortedSet das_per_genome = new TreeSet(); + for( final Protein protein : proteins_per_species ) { + final String da = protein.toDomainArchitectureString( separator, ie_cutoff ); + das_per_genome.add( da ); + } + if ( das_per_genome.size() > 0 ) { + das_per_genome_list.add( das_per_genome ); + } + } + } + if ( das_per_genome_list.size() > 0 ) { + SortedSet intersection = calcIntersection( das_per_genome_list ); + out.write( "\t[" + intersection.size() + "]:" ); + for( final String s : intersection ) { + out.write( '\t' + s ); + } + out.write( ForesterUtil.LINE_SEPARATOR ); + out.write( ForesterUtil.LINE_SEPARATOR ); + species_to_das_map.put( species_name, intersection ); + } + } + final SortedSet all_species_names = new TreeSet(); + final SortedSet all_das = new TreeSet(); + for( final Entry> e : species_to_das_map.entrySet() ) { + all_species_names.add( e.getKey() ); + for( final String das : e.getValue() ) { + all_das.add( das ); + } + } + out_table.write( '\t' ); + boolean first = true; + for( final String species_name : all_species_names ) { + if ( first ) { + first = false; + } + else { + out_table.write( '\t' ); + } + out_table.write( species_name ); + } + out_table.write( ForesterUtil.LINE_SEPARATOR ); + for( final String das : all_das ) { + out_table.write( das ); + out_table.write( '\t' ); + first = true; + for( final String species_name : all_species_names ) { + if ( first ) { + first = false; + } + else { + out_table.write( '\t' ); + } + if ( species_to_das_map.get( species_name ).contains( das ) ) { + out_table.write( '1' ); + } + else { + out_table.write( '0' ); + } + } + out_table.write( ForesterUtil.LINE_SEPARATOR ); + } + out.flush(); + out.close(); + out_table.flush(); + out_table.close(); + ForesterUtil.programMessage( surfacing.PRG_NAME, + "Wrote minimal DAome data to : " + outfile ); + ForesterUtil.programMessage( surfacing.PRG_NAME, + "Wrote minimal DAome data to (as table): " + outfile_table ); + } + + private final static SortedSet calcIntersection( final List> features_per_genome_list ) { + final Set first = features_per_genome_list.get( 0 ); + final SortedSet my_first = new TreeSet(); + for( final String s : first ) { + my_first.add( s ); + } + for( int i = 1; i < features_per_genome_list.size(); ++i ) { + my_first.retainAll( features_per_genome_list.get( i ) ); + } + return my_first; + } + public static void main( final String[] args ) { Set a = new HashSet(); Set b = new HashSet(); @@ -37,56 +213,12 @@ public final class MinimalDomainomeCalculator { d.add( "a" ); d.add( "c" ); d.add( "d" ); - List> domains_per_genome_list = new ArrayList(); + List> domains_per_genome_list = new ArrayList>(); domains_per_genome_list.add( a ); domains_per_genome_list.add( b ); domains_per_genome_list.add( c ); domains_per_genome_list.add( d ); - Set x = x( domains_per_genome_list ); + Set x = calcIntersection( domains_per_genome_list ); System.out.println( x ); } - - static final public void calc( Phylogeny tre, SortedMap> protein_lists_per_species ) { - for( final PhylogenyNodeIterator iter = tre.iteratorPostorder(); iter.hasNext(); ) { - final PhylogenyNode node = iter.next(); - if ( node.isInternal() ) { - System.out.println(); - if ( node.getNodeData().isHasTaxonomy() ) { - System.out.println( node.getNodeData().getTaxonomy().getScientificName() + ":" ); - } - else { - System.out.println( node.getName() + ":" ); - } - final List e = node.getAllExternalDescendants(); - final List> domains_per_genome_list = new ArrayList(); - for( PhylogenyNode en : e ) { - final String code = en.getNodeData().getTaxonomy().getTaxonomyCode(); - System.out.print( code + " " ); - //System.out.println( protein_lists_per_species ); - final List x = protein_lists_per_species.get( new BasicSpecies( code ) ); - if ( x != null ) { - final Set d = new HashSet(); - for( Protein protein : x ) { - List domains = protein.getProteinDomains(); - for( Domain domain : domains ) { - d.add( domain.getDomainId() ); - } - } - domains_per_genome_list.add( d ); - } - } - System.out.println(); - Set x = x( domains_per_genome_list ); - System.out.println( x ); - } - } - } - - static final Set x( List> domains_per_genome_list ) { - Set first = domains_per_genome_list.get( 0 ); - for( int i = 1; i < domains_per_genome_list.size(); ++i ) { - first.retainAll( domains_per_genome_list.get( i ) ); - } - return first; - } } diff --git a/forester/java/src/org/forester/surfacing/SurfacingUtil.java b/forester/java/src/org/forester/surfacing/SurfacingUtil.java index 660cbfd..3b52234 100644 --- a/forester/java/src/org/forester/surfacing/SurfacingUtil.java +++ b/forester/java/src/org/forester/surfacing/SurfacingUtil.java @@ -1354,13 +1354,6 @@ public final class SurfacingUtil { 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 ) { @@ -1600,7 +1593,6 @@ public final class SurfacingUtil { } } } - // final List igns = PhylogenyMethods.deleteExternalNodesPositiveSelection( genomes, intree ); if ( igns.size() > 0 ) { System.out.println( "Not using the following " + igns.size() + " nodes:" ); @@ -1609,16 +1601,29 @@ public final class SurfacingUtil { } System.out.println( "--" ); } + //Test for node names: + final SortedSet not_found = new TreeSet(); + final SortedSet not_unique = new TreeSet(); 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 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 all_genomes_domains_per_potein_histo, diff --git a/forester/java/src/org/forester/test/Test.java b/forester/java/src/org/forester/test/Test.java index cc50fa7..de674db 100644 --- a/forester/java/src/org/forester/test/Test.java +++ b/forester/java/src/org/forester/test/Test.java @@ -13210,7 +13210,8 @@ public final class Test { return false; } final PhylogenyNode n6 = PhylogenyNode - .createInstanceFromNhxString( "BLAGG-12345-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); + .createInstanceFromNhxString( "BLAGG-12345-blag", + NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); if ( n6.getNodeData().isHasTaxonomy() ) { System.out.println( n6.toString() ); return false; @@ -13222,31 +13223,36 @@ public final class Test { return false; } final PhylogenyNode n8 = PhylogenyNode - .createInstanceFromNhxString( "BLAGG_12345-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); + .createInstanceFromNhxString( "BLAGG_12345-blag", + NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); if ( !n8.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) { System.out.println( n8.toString() ); return false; } final PhylogenyNode n9 = PhylogenyNode - .createInstanceFromNhxString( "BLAGG_12345/blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); + .createInstanceFromNhxString( "BLAGG_12345/blag", + NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); if ( !n9.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) { System.out.println( n9.toString() ); return false; } final PhylogenyNode n10x = PhylogenyNode - .createInstanceFromNhxString( "BLAG!_12X45-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); + .createInstanceFromNhxString( "BLAG!_12X45-blag", + NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); if ( n10x.getNodeData().isHasTaxonomy() ) { System.out.println( n10x.toString() ); return false; } final PhylogenyNode n10xx = PhylogenyNode - .createInstanceFromNhxString( "BLAG!_1YX45-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); + .createInstanceFromNhxString( "BLAG!_1YX45-blag", + NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); if ( n10xx.getNodeData().isHasTaxonomy() ) { System.out.println( n10xx.toString() ); return false; } final PhylogenyNode n10 = PhylogenyNode - .createInstanceFromNhxString( "BLAGG_9YX45-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); + .createInstanceFromNhxString( "BLAGG_9YX45-blag", + NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); if ( !n10.getNodeData().getTaxonomy().getTaxonomyCode().equals( "9YX45" ) ) { System.out.println( n10.toString() ); return false;