X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fapplication%2Fsurfacing.java;h=99e946cfab2541c9f18ae453abdf5bb938658ec3;hb=4acc1443d8c6c6f47c26a7c57357bdcdad27ecf8;hp=328fd6c3aa632d09cd0f0d7343971a88c849aab8;hpb=cec76926e7d634373e238e61b805c723ef4c0ca7;p=jalview.git diff --git a/forester/java/src/org/forester/application/surfacing.java b/forester/java/src/org/forester/application/surfacing.java index 328fd6c..99e946c 100644 --- a/forester/java/src/org/forester/application/surfacing.java +++ b/forester/java/src/org/forester/application/surfacing.java @@ -44,7 +44,6 @@ import java.util.SortedSet; import java.util.TreeMap; import java.util.TreeSet; - import org.forester.evoinference.matrix.character.CharacterStateMatrix.Format; import org.forester.go.GoId; import org.forester.go.GoNameSpace; @@ -224,7 +223,7 @@ public class surfacing { final static private long JACKNIFE_RANDOM_SEED_DEFAULT = 19; final static private double JACKNIFE_RATIO_DEFAULT = 0.5; //final static private String INFER_SPECIES_TREES_OPTION = "species_tree_inference"; - final static private String FILTER_POSITIVE_OPTION = "pos_filter"; + final static private String FILTER_POSITIVE_OPTION = "pos_filter"; final static private String FILTER_NEGATIVE_OPTION = "neg_filter"; final static private String FILTER_NEGATIVE_DOMAINS_OPTION = "neg_dom_filter"; final static private String INPUT_FILES_FROM_FILE_OPTION = "input"; @@ -252,9 +251,7 @@ public class surfacing { private static final String PLUS_MINUS_ALL_GO_IDS_DOM_SUFFIX = "_plus_minus_go_ids_all.txt"; private static final String PLUS_MINUS_PASSING_GO_IDS_DOM_SUFFIX = "_plus_minus_go_ids_passing.txt"; private static final String OUTPUT_LIST_OF_ALL_PROTEINS_OPTIONS = "all_prot"; - final static private String OUTPUT_LIST_OF_ALL_PROTEINS_PER_DOMAIN_E_VALUE_OPTION = "all_prot_e"; - - + final static private String OUTPUT_LIST_OF_ALL_PROTEINS_PER_DOMAIN_E_VALUE_OPTION = "all_prot_e"; private static final boolean VERBOSE = false; private static final String OUTPUT_DOMAIN_COMBINATIONS_GAINED_MORE_THAN_ONCE_ANALYSIS_SUFFIX = "_fitch_dc_gains_counts"; private static final String OUTPUT_DOMAIN_COMBINATIONS_LOST_MORE_THAN_ONCE_ANALYSIS_SUFFIX = "_fitch_dc_losses_counts"; @@ -273,7 +270,7 @@ public class surfacing { private static final String LOG_FILE_SUFFIX = "_log.txt"; private static final String DATA_FILE_SUFFIX = "_domain_combination_data.txt"; private static final String DATA_FILE_DESC = "#SPECIES\tPRTEIN_ID\tN_TERM_DOMAIN\tC_TERM_DOMAIN\tN_TERM_DOMAIN_PER_DOMAIN_E_VALUE\tC_TERM_DOMAIN_PER_DOMAIN_E_VALUE\tN_TERM_DOMAIN_COUNTS_PER_PROTEIN\tC_TERM_DOMAIN_COUNTS_PER_PROTEIN"; - private static final INDIVIDUAL_SCORE_CUTOFF INDIVIDUAL_SCORE_CUTOFF_DEFAULT = INDIVIDUAL_SCORE_CUTOFF.FULL_SEQUENCE; + private static final INDIVIDUAL_SCORE_CUTOFF INDIVIDUAL_SCORE_CUTOFF_DEFAULT = INDIVIDUAL_SCORE_CUTOFF.FULL_SEQUENCE; //TODO look at me! change? public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_OUTPUT_SUFFIX = "_indep_dc_gains_fitch_counts.txt"; public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_DC_OUTPUT_SUFFIX = "_indep_dc_gains_fitch_lists.txt"; public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_SUFFIX = "_indep_dc_gains_fitch_lists_for_go_mapping.txt"; @@ -545,8 +542,6 @@ public class surfacing { return intrees; } - - private static void log( final String msg, final Writer w ) { try { w.write( msg ); @@ -861,7 +856,8 @@ public class surfacing { // if ( cla.isOptionSet( surfacing.OUTPUT_LIST_OF_ALL_PROTEINS_PER_DOMAIN_E_VALUE_OPTION ) ) { try { - output_list_of_all_proteins_per_domain_e_value_max = cla.getOptionValueAsDouble( surfacing.OUTPUT_LIST_OF_ALL_PROTEINS_PER_DOMAIN_E_VALUE_OPTION ); + output_list_of_all_proteins_per_domain_e_value_max = cla + .getOptionValueAsDouble( surfacing.OUTPUT_LIST_OF_ALL_PROTEINS_PER_DOMAIN_E_VALUE_OPTION ); } catch ( final Exception e ) { ForesterUtil.fatalError( surfacing.PRG_NAME, "no acceptable value for per domain E-value maximum" ); @@ -916,7 +912,6 @@ public class surfacing { + "=" ); } query_domain_ids = cla.getOptionValue( surfacing.SEQ_EXTRACT_OPTION ); - } DomainSimilarity.DomainSimilaritySortField domain_similarity_sort_field = DOMAIN_SORT_FILD_DEFAULT; DomainSimilarity.DomainSimilaritySortField domain_similarity_sort_field_for_automated_pwc = DOMAIN_SORT_FILD_DEFAULT; @@ -1389,9 +1384,10 @@ public class surfacing { System.out.println( "E-value maximum (inclusive) : " + e_value_max ); html_desc.append( "E-value maximum (inclusive):" + e_value_max + "" + nl ); } - if ( output_protein_lists_for_all_domains ) { + if ( output_protein_lists_for_all_domains ) { System.out.println( "Domain E-value max : " + output_list_of_all_proteins_per_domain_e_value_max ); - html_desc.append( "Protein lists: E-value maximum per domain (inclusive):" + output_list_of_all_proteins_per_domain_e_value_max + "" + nl ); + html_desc.append( "Protein lists: E-value maximum per domain (inclusive):" + + output_list_of_all_proteins_per_domain_e_value_max + "" + nl ); } System.out.println( "Ignore DUFs : " + ignore_dufs ); if ( ignore_virus_like_ids ) { @@ -2331,13 +2327,14 @@ public class surfacing { protein_lists_per_species, domain_id_to_go_ids_map, go_id_to_term_map, - plus_minus_analysis_numbers - ); + plus_minus_analysis_numbers ); } if ( output_protein_lists_for_all_domains ) { - writeProteinListsForAllSpecies( out_dir, protein_lists_per_species, gwcd_list, output_list_of_all_proteins_per_domain_e_value_max ); + writeProteinListsForAllSpecies( out_dir, + protein_lists_per_species, + gwcd_list, + output_list_of_all_proteins_per_domain_e_value_max ); } - if ( all_bin_domain_combinations_gained_fitch != null ) { try { executeFitchGainsAnalysis( new File( output_file @@ -2502,7 +2499,6 @@ public class surfacing { } } - private static void printHelp() { System.out.println(); System.out.println( "Usage:" ); @@ -2590,8 +2586,8 @@ public class surfacing { System.out.println( surfacing.DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_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" ); - + 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" ); System.out.println(); System.out.println( "Example 1: java -Xms128m -Xmx512m -cp path/to/forester.jar" + " org.forester.application.surfacing p2g=pfam2go_2012_02_07.txt -dufs -cos=Pfam_260_NC1" @@ -2787,7 +2783,7 @@ public class surfacing { proteins_file_writer, "\t", LIMIT_SPEC_FOR_PROT_EX, - domain_e_cutoff ); + domain_e_cutoff ); proteins_file_writer.close(); } catch ( final IOException e ) {