From: cmzmasek@gmail.com Date: Fri, 15 Nov 2013 21:02:55 +0000 (+0000) Subject: inprogress X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=adbb9fb1f03f2de7b7738d433a52a9e69ddcf5bc;p=jalview.git inprogress --- diff --git a/forester/java/src/org/forester/application/decorator.java b/forester/java/src/org/forester/application/decorator.java index 3122b88..54458a3 100644 --- a/forester/java/src/org/forester/application/decorator.java +++ b/forester/java/src/org/forester/application/decorator.java @@ -73,10 +73,7 @@ public final class decorator { final static private String ORDER_TREE_OPTION = "or"; final static private String EXTRACT_BRACKETED_SCIENTIC_NAME_OPTION = "sn"; final static private String EXTRACT_BRACKETED_TAXONOMIC_CODE_OPTION = "tc"; - final static private String PROCESS_NAME_INTELLIGENTLY_OPTION = "x"; - final static private String PROCESS_SIMILAR_TO_OPTION = "xs"; final static private String CUT_NAME_AFTER_FIRST_SPACE_OPTION = "c"; - final static private String ALLOW_REMOVAL_OF_CHARS_OPTION = "r"; final static private String ADVANCED_TABLE_OPTION = "table"; final static private String KEY_COLUMN = "k"; final static private String VALUE_COLUMN = "v"; @@ -88,7 +85,8 @@ public final class decorator { public static void main( final String args[] ) { ForesterUtil.printProgramInformation( decorator.PRG_NAME, decorator.PRG_VERSION, decorator.PRG_DATE ); - if ( ( args.length < 4 ) || ( args.length > 12 ) ) { + System.out.println(); + if ( ( args.length < 4 ) || ( args.length > 13 ) ) { decorator.argumentsError(); } CommandLineArguments cla = null; @@ -107,14 +105,19 @@ public final class decorator { if ( phylogenies_outfile.exists() ) { ForesterUtil.fatalError( PRG_NAME, "[" + phylogenies_outfile + "] already exists" ); } + String err = ForesterUtil.isReadableFile( phylogenies_infile ); + if ( !ForesterUtil.isEmpty( err ) ) { + ForesterUtil.fatalError( PRG_NAME, err ); + } + err = ForesterUtil.isReadableFile( mapping_infile ); + if ( !ForesterUtil.isEmpty( err ) ) { + ForesterUtil.fatalError( PRG_NAME, err ); + } final List allowed_options = new ArrayList(); allowed_options.add( decorator.ADVANCED_TABLE_OPTION ); allowed_options.add( decorator.PICKY_OPTION ); allowed_options.add( decorator.FIELD_OPTION ); - allowed_options.add( decorator.PROCESS_NAME_INTELLIGENTLY_OPTION ); - allowed_options.add( decorator.PROCESS_SIMILAR_TO_OPTION ); allowed_options.add( decorator.CUT_NAME_AFTER_FIRST_SPACE_OPTION ); - allowed_options.add( decorator.ALLOW_REMOVAL_OF_CHARS_OPTION ); allowed_options.add( decorator.KEY_COLUMN ); allowed_options.add( decorator.VALUE_COLUMN ); allowed_options.add( decorator.MAPPING_FILE_SEPARATOR_OPTION ); @@ -152,10 +155,7 @@ public final class decorator { int value_column = 1; String field_str = ""; FIELD field = FIELD.NODE_NAME; - int numbers_of_chars_allowed_to_remove_if_not_found_in_map = -1; boolean cut_name_after_space = false; - boolean process_name_intelligently = false; - boolean process_similar_to = false; boolean extract_bracketed_scientific_name = false; boolean extract_bracketed_tax_code = false; boolean trim_after_tilde = false; @@ -205,28 +205,12 @@ public final class decorator { } cut_name_after_space = true; } - if ( cla.isOptionSet( decorator.PROCESS_NAME_INTELLIGENTLY_OPTION ) ) { - if ( advanced_table ) { - argumentsError(); - } - process_name_intelligently = true; - } - if ( cla.isOptionSet( decorator.PROCESS_SIMILAR_TO_OPTION ) ) { - if ( advanced_table ) { - argumentsError(); - } - process_similar_to = true; - } if ( cla.isOptionSet( decorator.TRIM_AFTER_TILDE_OPTION ) ) { if ( advanced_table ) { argumentsError(); } trim_after_tilde = true; } - if ( cla.isOptionSet( decorator.ALLOW_REMOVAL_OF_CHARS_OPTION ) ) { - numbers_of_chars_allowed_to_remove_if_not_found_in_map = cla - .getOptionValueAsInt( decorator.ALLOW_REMOVAL_OF_CHARS_OPTION ); - } if ( cla.isOptionSet( decorator.MIDPOINT_ROOT_OPTION ) ) { midpoint_root = true; } @@ -272,27 +256,13 @@ public final class decorator { catch ( final Exception e ) { ForesterUtil.fatalError( decorator.PRG_NAME, "error in command line: " + e.getMessage() ); } - if ( ( field != FIELD.NODE_NAME ) && ( cut_name_after_space || process_name_intelligently ) ) { - ForesterUtil.fatalError( decorator.PRG_NAME, "attempt to use -x or -c option without -f=n" ); - } - if ( ( field != FIELD.NODE_NAME ) && process_similar_to ) { - ForesterUtil.fatalError( decorator.PRG_NAME, "attempt to use -" + decorator.PROCESS_SIMILAR_TO_OPTION - + " option without -f=n" ); - } - if ( cut_name_after_space && process_name_intelligently ) { - ForesterUtil.fatalError( decorator.PRG_NAME, "attempt to use -x and -c option together" ); - } - if ( process_similar_to && process_name_intelligently ) { - ForesterUtil.fatalError( decorator.PRG_NAME, "attempt to use -" + decorator.PROCESS_SIMILAR_TO_OPTION - + " and -x option together" ); - } - if ( process_similar_to && cut_name_after_space ) { - ForesterUtil.fatalError( decorator.PRG_NAME, "attempt to use -" + decorator.PROCESS_SIMILAR_TO_OPTION - + " and -c option together" ); - } if ( extract_bracketed_scientific_name && extract_bracketed_tax_code ) { argumentsError(); } + ForesterUtil.programMessage( PRG_NAME, "input tree(s) : " + phylogenies_infile ); + ForesterUtil.programMessage( PRG_NAME, "map : " + mapping_infile ); + ForesterUtil.programMessage( PRG_NAME, "output tree(s): " + phylogenies_outfile ); + System.out.println(); Phylogeny[] phylogenies = null; try { final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); @@ -327,13 +297,23 @@ public final class decorator { ForesterUtil.fatalError( decorator.PRG_NAME, "mapping table has only one column" ); } map = mapping_table.getColumnsAsMap( key_column, value_column ); + final Iterator> iter = map.entrySet().iterator(); if ( verbose ) { - final Iterator> iter = map.entrySet().iterator(); System.out.println(); - while ( iter.hasNext() ) { - final Entry e = iter.next(); + } + while ( iter.hasNext() ) { + final Entry e = iter.next(); + if ( ForesterUtil.isEmpty( e.getKey() ) ) { + ForesterUtil.fatalError( decorator.PRG_NAME, "mapping table contains empty key" ); + } + if ( ForesterUtil.isEmpty( e.getValue() ) ) { + ForesterUtil.fatalError( decorator.PRG_NAME, "mapping table contains empty value" ); + } + if ( verbose ) { System.out.println( e.getKey() + " => " + e.getValue() ); } + } + if ( verbose ) { System.out.println(); } } @@ -371,24 +351,23 @@ public final class decorator { ForesterUtil.fatalError( decorator.PRG_NAME, "failed to read \"" + mapping_infile + "\" [" + e.getMessage() + "]" ); } - PhylogenyDecorator.decorate( phylogenies, - table, - picky, - numbers_of_chars_allowed_to_remove_if_not_found_in_map ); + for( final Phylogeny phylogenie : phylogenies ) { + PhylogenyDecorator.decorate( phylogenie, table, picky ); + } } else { - PhylogenyDecorator.decorate( phylogenies, - map, - field, - extract_bracketed_scientific_name, - extract_bracketed_tax_code, - picky, - cut_name_after_space, - process_name_intelligently, - process_similar_to, - numbers_of_chars_allowed_to_remove_if_not_found_in_map, - trim_after_tilde, - verbose ); + for( final Phylogeny phylogenie : phylogenies ) { + final String msg = PhylogenyDecorator.decorate( phylogenie, + map, + field, + extract_bracketed_scientific_name, + extract_bracketed_tax_code, + picky, + cut_name_after_space, + trim_after_tilde, + verbose ); + ForesterUtil.programMessage( PRG_NAME, msg ); + } } } catch ( final NullPointerException e ) { @@ -456,13 +435,11 @@ public final class decorator { private static void argumentsError() { System.out.println(); System.out.println( decorator.PRG_NAME + " -" + ADVANCED_TABLE_OPTION + " | -f= " - + "[mapping table file|fasta-file] " ); + + " " ); System.out.println(); System.out.println( "options:" ); System.out.println(); System.out.println( " -" + ADVANCED_TABLE_OPTION + " : table instead of one to one map (-f=)" ); - System.out.println( " -r= : allow to remove up to n characters from the end of the names" ); - System.out.println( " in phylogenies infile if not found (in map) otherwise" ); System.out.println( " -p : picky, fails if node name not found in mapping table" ); System.out.println( " -" + TREE_NAME_OPTION + "=: name for the phylogeny" ); System.out.println( " -" + TREE_ID_OPTION + "=: identifier for the phylogeny (in the form provider:value)" ); @@ -489,9 +466,6 @@ public final class decorator { System.out.println( " -" + EXTRACT_BRACKETED_TAXONOMIC_CODE_OPTION + " : to extract bracketed taxonomic codes, e.g. [NEMVE]" ); System.out.println( " -s= : column separator in mapping file, default is tab" ); - System.out.println( " -x : process name \"intelligently\" (only for -f=n)" ); - System.out.println( " -" + decorator.PROCESS_SIMILAR_TO_OPTION - + " : process name \"intelligently\" and process information after \"similar to\" (only for -f=n)" ); System.out.println( " -c : cut name after first space (only for -f=n)" ); System.out.println( " -" + decorator.TRIM_AFTER_TILDE_OPTION + " : trim node name to be replaced after tilde" );