From: cmzmasek@gmail.com Date: Sat, 1 Sep 2012 00:08:03 +0000 (+0000) Subject: in progress X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=8161eb0ffe094f29eeefbb4e71eabcd0884c5e63;p=jalview.git in progress --- diff --git a/forester/java/src/org/forester/application/phyloxml_converter.java b/forester/java/src/org/forester/application/phyloxml_converter.java index 25497ec..8951e18 100644 --- a/forester/java/src/org/forester/application/phyloxml_converter.java +++ b/forester/java/src/org/forester/application/phyloxml_converter.java @@ -68,9 +68,10 @@ public class phyloxml_converter { final static private String ORDER_SUBTREES = "o"; final static private String NO_TREE_LEVEL_INDENDATION = "ni"; final static private String REPLACE_UNDER_SCORES = "ru"; + final static private String IGNORE_QUOTES = "iqs"; final static private String PRG_NAME = "phyloxml_converter"; - final static private String PRG_VERSION = "1.30"; - final static private String PRG_DATE = "2011.03.01"; + final static private String PRG_VERSION = "1.301"; + final static private String PRG_DATE = "2012.08.31"; final static private String E_MAIL = "phylosoft@gmail.com"; final static private String WWW = "www.phylosoft.org/forester/"; final static private boolean SPECIAL = false; @@ -104,6 +105,7 @@ public class phyloxml_converter { allowed_options.add( REPLACE_UNDER_SCORES ); allowed_options.add( EXTRACT_TAXONOMY ); allowed_options.add( EXTRACT_TAXONOMY_PF ); + allowed_options.add( IGNORE_QUOTES ); if ( cla.getNumberOfNames() != 2 ) { System.out.println(); System.out.println( "[" + PRG_NAME + "] incorrect number of arguments" ); @@ -158,6 +160,10 @@ public class phyloxml_converter { ForesterUtil.fatalError( PRG_NAME, "unknown value for -\"" + FIELD_OPTION + "\" option: \"" + field_option_value + "\"" ); } + boolean ignore_quotes = false; + if ( cla.isOptionSet( IGNORE_QUOTES ) ) { + ignore_quotes = true; + } boolean int_values_are_boots = false; if ( cla.isOptionSet( INTERNAL_NAMES_ARE_BOOT_SUPPPORT ) ) { int_values_are_boots = true; @@ -216,7 +222,7 @@ public class phyloxml_converter { ( ( NHXParser ) parser ).setTaxonomyExtraction( PhylogenyMethods.TAXONOMY_EXTRACTION.NO ); } ( ( NHXParser ) parser ).setReplaceUnderscores( replace_underscores ); - ( ( NHXParser ) parser ).setIgnoreQuotes( false ); + ( ( NHXParser ) parser ).setIgnoreQuotes( ignore_quotes ); } else if ( parser instanceof NexusPhylogeniesParser ) { ( ( NexusPhylogeniesParser ) parser ).setReplaceUnderscores( replace_underscores ); @@ -377,21 +383,22 @@ public class phyloxml_converter { System.out.println(); System.out.println( " options: " ); System.out.println( " -" + INTERNAL_NAMES_ARE_BOOT_SUPPPORT - + " : internal names in NH or NHX tree are bootstrap support values" ); - System.out.println( " -" + REPLACE_UNDER_SCORES + ": replace all underscores with spaces" ); - System.out.println( " -" + MIDPOINT_REROOT + " : midpoint reroot" ); - System.out.println( " -" + ORDER_SUBTREES + " : order subtrees" ); + + " : internal names in NH or NHX tree are bootstrap support values" ); + System.out.println( " -" + REPLACE_UNDER_SCORES + " : replace all underscores with spaces" ); + System.out.println( " -" + MIDPOINT_REROOT + " : midpoint reroot" ); + System.out.println( " -" + ORDER_SUBTREES + " : order subtrees" ); System.out .println( " -" + EXTRACT_TAXONOMY - + ": extract taxonomy to taxonomy code from \"seqname_TAXON\"-style names (cannot be used with the following field options: " + + " : extract taxonomy to taxonomy code from \"seqname_TAXON\"-style names (cannot be used with the following field options: " + FIELD_TAXONOMY_CODE + ", " + FIELD_TAXONOMY_COMM_NAME + ", " + FIELD_TAXONOMY_SCI_NAME + ")" ); System.out .println( " -" + EXTRACT_TAXONOMY_PF - + ": extract taxonomy to taxonomy code from Pfam (\"seqname_TAXON/x-y\") style names only (cannot be used with the following field options: " + + " : extract taxonomy to taxonomy code from Pfam (\"seqname_TAXON/x-y\") style names only (cannot be used with the following field options: " + FIELD_TAXONOMY_CODE + ", " + FIELD_TAXONOMY_COMM_NAME + ", " + FIELD_TAXONOMY_SCI_NAME + ")" ); - System.out.println( " -" + NO_TREE_LEVEL_INDENDATION + ": no tree level indendation in phyloXML output" ); + System.out.println( " -" + NO_TREE_LEVEL_INDENDATION + " : no tree level indendation in phyloXML output" ); + System.out.println( " -" + IGNORE_QUOTES + ": ignore quotes and whitespace (e.g. \"a b\" becomes ab)" ); System.out.println(); } } diff --git a/forester/java/src/org/forester/application/surfacing.java b/forester/java/src/org/forester/application/surfacing.java index 2ef8817..99e946c 100644 --- a/forester/java/src/org/forester/application/surfacing.java +++ b/forester/java/src/org/forester/application/surfacing.java @@ -270,7 +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; //TODO look at me! change? + 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";