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;
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" );
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;
( ( 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 );
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();
}
}
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";