import org.forester.io.parsers.PhylogenyParser;
import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
import org.forester.io.parsers.nhx.NHXParser;
+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.iterators.PhylogenyNodeIterator;
import org.forester.util.CommandLineArguments;
import org.forester.util.ForesterUtil;
-import org.forester.util.ForesterUtil.PhylogenyNodeField;
public class phyloxml_converter {
System.exit( -1 );
}
final String field_option_value = cla.getOptionValue( FIELD_OPTION );
- PhylogenyNodeField field = null;
+ PhylogenyMethods.PhylogenyNodeField field = null;
if ( field_option_value.equals( FIELD_CLADE_NAME ) ) {
- field = PhylogenyNodeField.CLADE_NAME;
+ field = PhylogenyMethods.PhylogenyNodeField.CLADE_NAME;
}
else if ( field_option_value.equals( FIELD_TAXONOMY_CODE ) ) {
- field = PhylogenyNodeField.TAXONOMY_CODE;
+ field = PhylogenyMethods.PhylogenyNodeField.TAXONOMY_CODE;
}
else if ( field_option_value.equals( FIELD_TAXONOMY_SCI_NAME ) ) {
- field = PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME;
+ field = PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME;
}
else if ( field_option_value.equals( FIELD_TAXONOMY_COMM_NAME ) ) {
- field = PhylogenyNodeField.TAXONOMY_COMMON_NAME;
+ field = PhylogenyMethods.PhylogenyNodeField.TAXONOMY_COMMON_NAME;
}
else if ( field_option_value.equals( FIELD_SEQUENCE_GENE_NAME ) ) {
- field = PhylogenyNodeField.SEQUENCE_NAME;
+ field = PhylogenyMethods.PhylogenyNodeField.SEQUENCE_NAME;
}
else if ( field_option_value.equals( FIELD_SEQUENCE_SYMBOL ) ) {
- field = PhylogenyNodeField.SEQUENCE_SYMBOL;
+ field = PhylogenyMethods.PhylogenyNodeField.SEQUENCE_SYMBOL;
}
else if ( field_option_value.equals( FIELD_UNIPROT_TAXONOMY_ID_SPLIT_1 ) ) {
- field = PhylogenyNodeField.TAXONOMY_ID_UNIPROT_1;
+ field = PhylogenyMethods.PhylogenyNodeField.TAXONOMY_ID_UNIPROT_1;
}
else if ( field_option_value.equals( FIELD_UNIPROT_TAXONOMY_ID_SPLIT_2 ) ) {
- field = PhylogenyNodeField.TAXONOMY_ID_UNIPROT_2;
+ field = PhylogenyMethods.PhylogenyNodeField.TAXONOMY_ID_UNIPROT_2;
}
else if ( field_option_value.equals( FIELD_DUMMY ) ) {
}
Phylogeny[] phys = null;
try {
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
- final PhylogenyParser parser = ForesterUtil.createParserDependingOnFileType( infile, true );
+ final PhylogenyParser parser = ParserUtils.createParserDependingOnFileType( infile, true );
if ( parser instanceof NHXParser ) {
- if ( ( field != PhylogenyNodeField.TAXONOMY_CODE )
- && ( field != PhylogenyNodeField.TAXONOMY_COMMON_NAME )
- && ( field != PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME ) ) {
+ if ( ( field != PhylogenyMethods.PhylogenyNodeField.TAXONOMY_CODE )
+ && ( field != PhylogenyMethods.PhylogenyNodeField.TAXONOMY_COMMON_NAME )
+ && ( field != PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME ) ) {
if ( extr_taxonomy_pf_only ) {
( ( NHXParser ) parser )
- .setTaxonomyExtraction( ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+ .setTaxonomyExtraction( PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
replace_underscores = false;
}
else if ( extr_taxonomy ) {
- ( ( NHXParser ) parser ).setTaxonomyExtraction( ForesterUtil.TAXONOMY_EXTRACTION.YES );
+ ( ( NHXParser ) parser ).setTaxonomyExtraction( PhylogenyMethods.TAXONOMY_EXTRACTION.YES );
replace_underscores = false;
}
}
else {
- ( ( NHXParser ) parser ).setTaxonomyExtraction( ForesterUtil.TAXONOMY_EXTRACTION.NO );
+ ( ( NHXParser ) parser ).setTaxonomyExtraction( PhylogenyMethods.TAXONOMY_EXTRACTION.NO );
}
( ( NHXParser ) parser ).setReplaceUnderscores( replace_underscores );
( ( NHXParser ) parser ).setIgnoreQuotes( false );
}
if ( int_values_are_boots ) {
for( final Phylogeny phy : phys ) {
- ForesterUtil.transferInternalNamesToBootstrapSupport( phy );
+ PhylogenyMethods.transferInternalNamesToBootstrapSupport( phy );
}
}
if ( field != null ) {
for( final Phylogeny phy : phys ) {
- ForesterUtil.transferNodeNameToField( phy, field );
+ PhylogenyMethods.transferNodeNameToField( phy, field );
}
}
if ( midpoint_reroot ) {