import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
+import java.util.Iterator;
import java.util.List;
import java.util.Map;
+import java.util.Map.Entry;
import org.forester.io.parsers.PhylogenyParser;
import org.forester.io.parsers.util.ParserUtils;
import org.forester.io.writers.PhylogenyWriter;
import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.PhylogenyMethods;
+import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;
import org.forester.phylogeny.data.Identifier;
import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
import org.forester.phylogeny.factories.PhylogenyFactory;
final static private String TREE_NAME_OPTION = "pn";
final static private String TREE_ID_OPTION = "pi";
final static private String TREE_DESC_OPTION = "pd";
+ final static private String MIDPOINT_ROOT_OPTION = "mp";
+ 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 KEY_COLUMN = "k";
final static private String VALUE_COLUMN = "v";
final static private String MAPPING_FILE_SEPARATOR_OPTION = "s";
- final static private String MAPPING_FILE_SEPARATOR_DEFAULT = ": ";
+ final static private char MAPPING_FILE_SEPARATOR_DEFAULT = '\t';
final static private String PRG_NAME = "decorator";
- final static private String PRG_VERSION = "1.13";
- final static private String PRG_DATE = "2013.01.19";
+ final static private String PRG_VERSION = "1.14";
+ final static private String PRG_DATE = "130426";
public static void main( final String args[] ) {
ForesterUtil.printProgramInformation( decorator.PRG_NAME, decorator.PRG_VERSION, decorator.PRG_DATE );
allowed_options.add( decorator.TREE_ID_OPTION );
allowed_options.add( decorator.TREE_DESC_OPTION );
allowed_options.add( decorator.TRIM_AFTER_TILDE_OPTION );
+ allowed_options.add( decorator.ORDER_TREE_OPTION );
+ allowed_options.add( decorator.MIDPOINT_ROOT_OPTION );
final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options );
if ( dissallowed_options.length() > 0 ) {
ForesterUtil.fatalError( decorator.PRG_NAME, "unknown option(s): " + dissallowed_options );
}
}
final boolean picky = cla.isOptionSet( decorator.PICKY_OPTION );
- String separator = decorator.MAPPING_FILE_SEPARATOR_DEFAULT;
+ char separator = decorator.MAPPING_FILE_SEPARATOR_DEFAULT;
if ( cla.isOptionSet( decorator.MAPPING_FILE_SEPARATOR_OPTION ) ) {
if ( advanced_table ) {
argumentsError();
}
- separator = cla.getOptionValue( decorator.MAPPING_FILE_SEPARATOR_OPTION );
+ separator = cla.getOptionValueAsChar( decorator.MAPPING_FILE_SEPARATOR_OPTION );
}
int key_column = 0;
int value_column = 1;
boolean extract_bracketed_scientific_name = false;
boolean extract_bracketed_tax_code = false;
boolean trim_after_tilde = false;
+ boolean order_tree = false;
+ boolean midpoint_root = false;
String tree_name = "";
String tree_id = "";
String tree_desc = "";
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;
+ }
+ if ( cla.isOptionSet( decorator.ORDER_TREE_OPTION ) ) {
+ order_tree = true;
+ }
if ( cla.isOptionSet( decorator.FIELD_OPTION ) ) {
field_str = cla.getOptionValue( decorator.FIELD_OPTION );
if ( field_str.equals( NODE_NAME_FIELD ) ) {
if ( !advanced_table ) {
BasicTable<String> mapping_table = null;
try {
- mapping_table = BasicTableParser.parse( mapping_infile, separator, false, true );
+ mapping_table = BasicTableParser.parse( mapping_infile, separator, true, false );
}
catch ( final Exception e ) {
ForesterUtil.fatalError( decorator.PRG_NAME,
if ( ( value_column < 0 ) || ( value_column >= mapping_table.getNumberOfColumns() ) ) {
ForesterUtil.fatalError( decorator.PRG_NAME, "illegal value for value column" );
}
+ if ( mapping_table.isEmpty() || mapping_table.getNumberOfColumns() < 1 ) {
+ ForesterUtil.fatalError( decorator.PRG_NAME, "mapping table is empty" );
+ }
+ if ( mapping_table.getNumberOfColumns() == 1 ) {
+ ForesterUtil.fatalError( decorator.PRG_NAME, "mapping table has only one column" );
+ }
map = mapping_table.getColumnsAsMap( key_column, value_column );
+ Iterator<Entry<String, String>> iter = map.entrySet().iterator();
+ System.out.println();
+ while ( iter.hasNext() ) {
+ Entry<String, String> e = iter.next();
+ System.out.println( e.getKey() + " => " + e.getValue() );
+ }
+ System.out.println();
}
if ( !ForesterUtil.isEmpty( tree_name ) || !ForesterUtil.isEmpty( tree_id )
|| !ForesterUtil.isEmpty( tree_desc ) ) {
catch ( final Exception e ) {
ForesterUtil.fatalError( decorator.PRG_NAME, e.getLocalizedMessage() );
}
+ if ( midpoint_root || order_tree ) {
+ for( final Phylogeny phy : phylogenies ) {
+ if ( midpoint_root ) {
+ PhylogenyMethods.midpointRoot( phy );
+ }
+ if ( order_tree ) {
+ PhylogenyMethods.orderAppearance( phy.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.TAXONOMY );
+ }
+ }
+ }
try {
final PhylogenyWriter w = new PhylogenyWriter();
w.toPhyloXML( phylogenies, 0, phylogenies_outfile, ForesterUtil.getLineSeparator() );
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" );
+ System.out.println( " -" + decorator.MIDPOINT_ROOT_OPTION + " : to midpoint-root the tree" );
+ System.out.println( " -" + decorator.ORDER_TREE_OPTION + " : to order tree branches" );
System.out.println();
System.exit( -1 );
}