package org.forester.sdi;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+
+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.nhx.NHXParser.TAXONOMY_EXTRACTION;
+import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
+import org.forester.io.parsers.phyloxml.PhyloXmlParser;
+import org.forester.io.parsers.util.ParserUtils;
import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.PhylogenyMethods;
import org.forester.phylogeny.PhylogenyNode;
import org.forester.phylogeny.data.Identifier;
import org.forester.phylogeny.data.Taxonomy;
+import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
+import org.forester.phylogeny.factories.PhylogenyFactory;
import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
import org.forester.util.ForesterUtil;
public class SDIutil {
+ public final static TaxonomyComparisonBase determineTaxonomyComparisonBase( final Phylogeny gene_tree )
+ throws SDIException {
+ int with_id_count = 0;
+ int with_code_count = 0;
+ int with_sn_count = 0;
+ int max = 0;
+ for( final PhylogenyNodeIterator iter = gene_tree.iteratorExternalForward(); iter.hasNext(); ) {
+ final PhylogenyNode g = iter.next();
+ if ( g.getNodeData().isHasTaxonomy() ) {
+ final Taxonomy tax = g.getNodeData().getTaxonomy();
+ if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getValue() ) ) {
+ if ( ++with_id_count > max ) {
+ max = with_id_count;
+ }
+ }
+ if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
+ if ( ++with_code_count > max ) {
+ max = with_code_count;
+ }
+ }
+ if ( !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
+ if ( ++with_sn_count > max ) {
+ max = with_sn_count;
+ }
+ }
+ }
+ }
+ if ( max == 0 ) {
+ throw new SDIException( "gene tree has no taxonomic data" );
+ }
+ else if ( max == 1 ) {
+ throw new SDIException( "gene tree has only one node with taxonomic data" );
+ }
+ else if ( max == with_id_count ) {
+ return TaxonomyComparisonBase.ID;
+ }
+ else if ( max == with_sn_count ) {
+ return TaxonomyComparisonBase.SCIENTIFIC_NAME;
+ }
+ else {
+ return TaxonomyComparisonBase.CODE;
+ }
+ }
+
+ public final static Phylogeny parseSpeciesTree( final Phylogeny gene_tree,
+ final File species_tree_file,
+ final boolean replace_undescores_in_nhx_trees,
+ final boolean ignore_quotes_in_nhx_trees,
+ final TAXONOMY_EXTRACTION taxonomy_extraction_in_nhx_trees )
+ throws FileNotFoundException, PhyloXmlDataFormatException, IOException, SDIException {
+ Phylogeny species_tree;
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ final PhylogenyParser p = ParserUtils.createParserDependingOnFileType( species_tree_file, true );
+ if ( p instanceof PhyloXmlParser ) {
+ species_tree = factory.create( species_tree_file, p )[ 0 ];
+ }
+ else {
+ if ( p instanceof NHXParser ) {
+ final NHXParser nhx = ( NHXParser ) p;
+ nhx.setReplaceUnderscores( replace_undescores_in_nhx_trees );
+ nhx.setIgnoreQuotes( ignore_quotes_in_nhx_trees );
+ nhx.setTaxonomyExtraction( taxonomy_extraction_in_nhx_trees );
+ }
+ else if ( p instanceof NexusPhylogeniesParser ) {
+ final NexusPhylogeniesParser nex = ( NexusPhylogeniesParser ) p;
+ nex.setReplaceUnderscores( replace_undescores_in_nhx_trees );
+ nex.setIgnoreQuotes( ignore_quotes_in_nhx_trees );
+ nex.setTaxonomyExtraction( taxonomy_extraction_in_nhx_trees );
+ }
+ species_tree = factory.create( species_tree_file, p )[ 0 ];
+ species_tree.setRooted( true );
+ final TaxonomyComparisonBase comp_base = determineTaxonomyComparisonBase( gene_tree );
+ switch ( comp_base ) {
+ case SCIENTIFIC_NAME:
+ PhylogenyMethods
+ .transferNodeNameToField( species_tree,
+ PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME,
+ true );
+ break;
+ case CODE:
+ PhylogenyMethods.transferNodeNameToField( species_tree,
+ PhylogenyMethods.PhylogenyNodeField.TAXONOMY_CODE,
+ true );
+ break;
+ case ID:
+ PhylogenyMethods.transferNodeNameToField( species_tree,
+ PhylogenyMethods.PhylogenyNodeField.TAXONOMY_ID,
+ true );
+ break;
+ default:
+ throw new SDIException( "unable to determine comparison base" );
+ }
+ }
+ return species_tree;
+ }
+
static String taxonomyToString( final PhylogenyNode n, final TaxonomyComparisonBase base ) {
switch ( base ) {
case ID:
}
}
}
-
- public final static TaxonomyComparisonBase determineTaxonomyComparisonBase( final Phylogeny gene_tree )
- throws SDIException {
- int with_id_count = 0;
- int with_code_count = 0;
- int with_sn_count = 0;
- int max = 0;
- for( final PhylogenyNodeIterator iter = gene_tree.iteratorExternalForward(); iter.hasNext(); ) {
- final PhylogenyNode g = iter.next();
- if ( g.getNodeData().isHasTaxonomy() ) {
- final Taxonomy tax = g.getNodeData().getTaxonomy();
- if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getValue() ) ) {
- if ( ++with_id_count > max ) {
- max = with_id_count;
- }
- }
- if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
- if ( ++with_code_count > max ) {
- max = with_code_count;
- }
- }
- if ( !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
- if ( ++with_sn_count > max ) {
- max = with_sn_count;
- }
- }
- }
- }
- if ( max == 0 ) {
- throw new SDIException( "gene tree has no taxonomic data" );
- }
- else if ( max == 1 ) {
- throw new SDIException( "gene tree has only one node with taxonomic data" );
- }
- else if ( max == with_id_count ) {
- return TaxonomyComparisonBase.ID;
- }
- else if ( max == with_sn_count ) {
- return TaxonomyComparisonBase.SCIENTIFIC_NAME;
- }
- else {
- return TaxonomyComparisonBase.CODE;
- }
- }
}
git://source.jalview.org / jalview.git / blobdiff