import org.forester.phylogeny.data.Identifier;
import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
import org.forester.phylogeny.factories.PhylogenyFactory;
import org.forester.phylogeny.data.Identifier;
import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
import org.forester.phylogeny.factories.PhylogenyFactory;
import org.forester.tools.PhylogenyDecorator;
import org.forester.tools.PhylogenyDecorator.FIELD;
import org.forester.util.BasicTable;
import org.forester.tools.PhylogenyDecorator;
import org.forester.tools.PhylogenyDecorator.FIELD;
import org.forester.util.BasicTable;
}
catch ( final Exception e ) {
ForesterUtil.fatalError( decorator.PRG_NAME, "failed to read phylgenies from [" + phylogenies_infile
}
catch ( final Exception e ) {
ForesterUtil.fatalError( decorator.PRG_NAME, "failed to read phylgenies from [" + phylogenies_infile
if ( ( phylogenies.length > 1 )
&& ( !ForesterUtil.isEmpty( tree_name ) || !ForesterUtil.isEmpty( tree_id ) ) ) {
ForesterUtil.fatalError( decorator.PRG_NAME,
if ( ( phylogenies.length > 1 )
&& ( !ForesterUtil.isEmpty( tree_name ) || !ForesterUtil.isEmpty( tree_id ) ) ) {
ForesterUtil.fatalError( decorator.PRG_NAME,
}
private static Map<String, String> readFastaFileIntoMap( final File mapping_infile, final boolean verbose ) {
}
private static Map<String, String> readFastaFileIntoMap( final File mapping_infile, final boolean verbose ) {
}
if ( ForesterUtil.isEmpty( seqs ) ) {
ForesterUtil.fatalError( decorator.PRG_NAME, "fasta-file [" + mapping_infile
}
if ( ForesterUtil.isEmpty( seqs ) ) {
ForesterUtil.fatalError( decorator.PRG_NAME, "fasta-file [" + mapping_infile
if ( ForesterUtil.isEmpty( seq.getIdentifier() ) ) {
ForesterUtil.fatalError( decorator.PRG_NAME, "fasta-file [" + mapping_infile
if ( ForesterUtil.isEmpty( seq.getIdentifier() ) ) {
ForesterUtil.fatalError( decorator.PRG_NAME, "fasta-file [" + mapping_infile
}
if ( map.containsKey( seq.getIdentifier() ) ) {
ForesterUtil.fatalError( decorator.PRG_NAME, "sequence identifier [" + seq.getIdentifier()
}
if ( map.containsKey( seq.getIdentifier() ) ) {
ForesterUtil.fatalError( decorator.PRG_NAME, "sequence identifier [" + seq.getIdentifier()
}
if ( seq.getLength() < 1 ) {
ForesterUtil.fatalError( decorator.PRG_NAME, "sequence [" + seq.getIdentifier() + "] is empty" );
}
if ( seq.getLength() < 1 ) {
ForesterUtil.fatalError( decorator.PRG_NAME, "sequence [" + seq.getIdentifier() + "] is empty" );
System.out.println();
System.out.println( " -f=<c> : field to be replaced: " + NODE_NAME_FIELD + " : node name" );
System.out.println( " " + SEQUENCE_ANNOTATION_DESC
System.out.println();
System.out.println( " -f=<c> : field to be replaced: " + NODE_NAME_FIELD + " : node name" );
System.out.println( " " + SEQUENCE_ANNOTATION_DESC
System.out.println( " " + DS_FILED + " : domain structure" );
System.out.println( " " + TAXONOMY_CODE_FIELD + " : taxonomy code" );
System.out.println( " " + TAXONOMY_SCIENTIFIC_NAME_FIELD
System.out.println( " " + DS_FILED + " : domain structure" );
System.out.println( " " + TAXONOMY_CODE_FIELD + " : taxonomy code" );
System.out.println( " " + TAXONOMY_SCIENTIFIC_NAME_FIELD
System.out.println( " " + SEQUENCE_NAME_FIELD + " : sequence name" );
System.out.println( " " + MOL_SEQ + " : molecular sequence" );
System.out.println( " -k=<n> : key column in mapping table (0 based)," );
System.out.println( " " + SEQUENCE_NAME_FIELD + " : sequence name" );
System.out.println( " " + MOL_SEQ + " : molecular sequence" );
System.out.println( " -k=<n> : key column in mapping table (0 based)," );
System.out.println( " -v=<n> : value column in mapping table (0 based)," );
System.out.println( " data which with to decorate - default is 1" );
System.out.println( " -" + EXTRACT_BRACKETED_SCIENTIC_NAME_OPTION
System.out.println( " -v=<n> : value column in mapping table (0 based)," );
System.out.println( " data which with to decorate - default is 1" );
System.out.println( " -" + EXTRACT_BRACKETED_SCIENTIC_NAME_OPTION
System.out.println( " -s=<c> : column separator in mapping file, default is tab" );
System.out.println( " -c : cut name after first space (only for -f=n)" );
System.out.println( " -" + decorator.TRIM_AFTER_TILDE_OPTION
System.out.println( " -s=<c> : column separator in mapping file, default is tab" );
System.out.println( " -c : cut name after first space (only for -f=n)" );
System.out.println( " -" + decorator.TRIM_AFTER_TILDE_OPTION
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( " -" + decorator.VERBOSE_OPTION + " : verbose" );
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( " -" + decorator.VERBOSE_OPTION + " : verbose" );