// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
//
// Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
package org.forester.analysis;
import java.io.IOException;
import java.util.ArrayList;
-import java.util.HashMap;
import java.util.List;
-import org.forester.analysis.TaxonomyDataObtainer.QUERY_TYPE;
import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyNode;
import org.forester.phylogeny.data.Taxonomy;
import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
import org.forester.util.ForesterUtil;
-import org.forester.ws.uniprot.UniProtTaxonomy;
-import org.forester.ws.uniprot.UniProtWsTools;
+import org.forester.ws.seqdb.UniProtTaxonomy;
public final class AncestralTaxonomyInference {
- private static final int MAX_TAXONOMIES_TO_RETURN = 10;
-
- private static UniProtTaxonomy getTaxonomies( final HashMap<String, UniProtTaxonomy> cache,
- final Object query,
- final QUERY_TYPE qt ) throws IOException,
- AncestralTaxonomyInferenceException {
- if ( cache.containsKey( query ) ) {
- return cache.get( query ).copy();
- }
- else {
- List<UniProtTaxonomy> up_taxonomies = null;
- switch ( qt ) {
- case ID:
- up_taxonomies = getTaxonomiesFromId( ( String ) query );
- break;
- case CODE:
- up_taxonomies = getTaxonomiesFromTaxonomyCode( ( String ) query );
- break;
- case SN:
- up_taxonomies = getTaxonomiesFromScientificName( ( String ) query );
- break;
- case CN:
- up_taxonomies = getTaxonomiesFromCommonName( ( String ) query );
- break;
- case LIN:
- return obtainUniProtTaxonomyFromLineage( ( List<String> ) query );
- default:
- throw new RuntimeException();
- }
- if ( ( up_taxonomies != null ) && ( up_taxonomies.size() == 1 ) ) {
- final UniProtTaxonomy up_tax = up_taxonomies.get( 0 );
- if ( !ForesterUtil.isEmpty( up_tax.getScientificName() ) ) {
- TaxonomyDataObtainer.getSnTaxCacheMap().put( up_tax.getScientificName(), up_tax );
- }
- if ( !ForesterUtil.isEmpty( up_tax.getCode() ) ) {
- TaxonomyDataObtainer.getCodeTaxCacheMap().put( up_tax.getCode(), up_tax );
- }
- if ( !ForesterUtil.isEmpty( up_tax.getCommonName() ) ) {
- TaxonomyDataObtainer.getCnTaxCacheMap().put( up_tax.getCommonName(), up_tax );
- }
- if ( !ForesterUtil.isEmpty( up_tax.getId() ) ) {
- TaxonomyDataObtainer.getIdTaxCacheMap().put( up_tax.getId(), up_tax );
- }
- return up_tax;
- }
- else {
- return null;
- }
- }
- }
-
- private static List<UniProtTaxonomy> getTaxonomiesFromCommonName( final String query )
- throws IOException {
- return UniProtWsTools.getTaxonomiesFromCommonNameStrict( query, MAX_TAXONOMIES_TO_RETURN );
- }
-
- private static List<UniProtTaxonomy> getTaxonomiesFromId( final String query ) throws IOException {
- return UniProtWsTools.getTaxonomiesFromId( query, MAX_TAXONOMIES_TO_RETURN );
- }
-
- private static List<UniProtTaxonomy> getTaxonomiesFromScientificName( final String query )
- throws IOException {
- return UniProtWsTools.getTaxonomiesFromScientificNameStrict( query, MAX_TAXONOMIES_TO_RETURN );
- }
-
- private static List<UniProtTaxonomy> getTaxonomiesFromTaxonomyCode( final String query )
- throws IOException {
- return UniProtWsTools.getTaxonomiesFromTaxonomyCode( query, MAX_TAXONOMIES_TO_RETURN );
- }
-
public static void inferTaxonomyFromDescendents( final Phylogeny phy ) throws IOException,
- AncestralTaxonomyInferenceException {
- TaxonomyDataObtainer.clearCachesIfTooLarge();
+ AncestralTaxonomyInferenceException {
+ TaxonomyDataManager.clearCachesIfTooLarge();
for( final PhylogenyNodeIterator iter = phy.iteratorPostorder(); iter.hasNext(); ) {
final PhylogenyNode node = iter.next();
if ( !node.isExternal() ) {
}
}
- private static void inferTaxonomyFromDescendents( final PhylogenyNode n ) throws IOException,
- AncestralTaxonomyInferenceException {
+ private static void inferTaxonomyFromDescendents( final PhylogenyNode n ) throws IOException,
+ AncestralTaxonomyInferenceException {
if ( n.isExternal() ) {
throw new IllegalArgumentException( "attempt to infer taxonomy from descendants of external node" );
}
int shortest_lin_length = Integer.MAX_VALUE;
for( final PhylogenyNode desc : descs ) {
if ( desc.getNodeData().isHasTaxonomy()
- && ( TaxonomyDataObtainer.isHasAppropriateId( desc.getNodeData().getTaxonomy() )
+ && ( TaxonomyDataManager.isHasAppropriateId( desc.getNodeData().getTaxonomy() )
|| !ForesterUtil.isEmpty( desc.getNodeData().getTaxonomy().getScientificName() )
|| !ForesterUtil.isEmpty( desc.getNodeData().getTaxonomy().getLineage() )
|| !ForesterUtil.isEmpty( desc.getNodeData().getTaxonomy().getTaxonomyCode() ) || !ForesterUtil
.isEmpty( desc.getNodeData().getTaxonomy().getCommonName() ) ) ) {
- final UniProtTaxonomy up_tax = obtainUniProtTaxonomy( desc.getNodeData().getTaxonomy(), null, null );
+ final UniProtTaxonomy up_tax = TaxonomyDataManager.obtainUniProtTaxonomy( desc.getNodeData()
+ .getTaxonomy(), null, null );
if ( ( up_tax == null ) && ForesterUtil.isEmpty( desc.getNodeData().getTaxonomy().getLineage() ) ) {
String desc_str = "";
if ( !ForesterUtil.isEmpty( desc.getName() ) ) {
}
System.out.println( desc.getNodeData().getTaxonomy().toString() );
System.out.println( ForesterUtil.stringListToString( desc.getNodeData().getTaxonomy().getLineage(),
- " > " ) );
+ " > " ) );
throw new AncestralTaxonomyInferenceException( "a taxonomy for node " + desc_str
- + " could not be established from the database" );
+ + " could not be established from the database" );
}
String[] lineage = ForesterUtil.stringListToArray( desc.getNodeData().getTaxonomy().getLineage() );
if ( ( lineage == null ) || ( lineage.length < 1 ) ) {
else {
node = "[" + desc.getId() + "]";
}
- // final List<PhylogenyNode> e = desc.getAllExternalDescendants();
- //TODO remove me!
- // System.out.println();
- // int x = 0;
- // for( final PhylogenyNode object : e ) {
- // System.out.println( x + ":" );
- // System.out.println( object.getName() + " " );
- // x++;
- // }
- // System.out.println();
- //
throw new AncestralTaxonomyInferenceException( "node " + node
- + " has no or inappropriate taxonomic information" );
+ + " has no or inappropriate taxonomic information" );
}
}
final List<String> last_common_lineage = new ArrayList<String>();
if ( last_common_lineage.isEmpty() ) {
boolean saw_viruses = false;
boolean saw_cellular_organism = false;
+ boolean saw_x = false;
for( final String[] lineage : lineages ) {
if ( lineage.length > 0 ) {
if ( lineage[ 0 ].equalsIgnoreCase( UniProtTaxonomy.VIRUSES ) ) {
else if ( lineage[ 0 ].equalsIgnoreCase( UniProtTaxonomy.CELLULAR_ORGANISMS ) ) {
saw_cellular_organism = true;
}
- if ( saw_cellular_organism && saw_viruses ) {
+ else if ( lineage[ 0 ].equalsIgnoreCase( UniProtTaxonomy.X ) ) {
+ saw_x = true;
+ }
+ if ( ( saw_cellular_organism && saw_viruses ) || saw_x ) {
break;
}
}
}
- if ( saw_cellular_organism && saw_viruses ) {
- last_common_lineage.add( UniProtTaxonomy.CELLULAR_ORGANISMS );
- last_common = UniProtTaxonomy.CELLULAR_ORGANISMS;
+ if ( ( saw_cellular_organism && saw_viruses ) || saw_x ) {
+ last_common_lineage.add( UniProtTaxonomy.X );
+ last_common = UniProtTaxonomy.X;
}
else {
String msg = "no common lineage for:\n";
final Taxonomy tax = new Taxonomy();
n.getNodeData().setTaxonomy( tax );
tax.setScientificName( last_common );
- final UniProtTaxonomy up_tax = obtainUniProtTaxonomyFromLineage( last_common_lineage );
+ final UniProtTaxonomy up_tax = TaxonomyDataManager.obtainUniProtTaxonomyFromLineage( last_common_lineage );
if ( up_tax != null ) {
if ( !ForesterUtil.isEmpty( up_tax.getRank() ) ) {
try {
}
}
}
-
-
-
-
- private static UniProtTaxonomy obtainUniProtTaxonomyFromLineage( final List<String> lineage )
- throws AncestralTaxonomyInferenceException, IOException {
- final String lineage_str = ForesterUtil.stringListToString( lineage, ">" );
- UniProtTaxonomy up_tax = null;
- if ( TaxonomyDataObtainer.getLineageTaxCacheMap().containsKey( lineage_str ) ) {
- up_tax = TaxonomyDataObtainer.getLineageTaxCacheMap().get( lineage_str ).copy();
- }
- else {
- final List<UniProtTaxonomy> up_taxonomies = getTaxonomiesFromScientificName( lineage
- .get( lineage.size() - 1 ) );
- if ( ( up_taxonomies != null ) && ( up_taxonomies.size() > 0 ) ) {
- for( final UniProtTaxonomy up_taxonomy : up_taxonomies ) {
- boolean match = true;
- I: for( int i = 0; i < lineage.size(); ++i ) {
- if ( !lineage.get( i ).equalsIgnoreCase( up_taxonomy.getLineage().get( i ) ) ) {
- match = false;
- break I;
- }
- }
- if ( match ) {
- if ( up_tax != null ) {
- throw new AncestralTaxonomyInferenceException( "lineage \""
- + ForesterUtil.stringListToString( lineage, " > " ) + "\" is not unique" );
- }
- up_tax = up_taxonomy;
- }
- }
- if ( up_tax == null ) {
- throw new AncestralTaxonomyInferenceException( "lineage \""
- + ForesterUtil.stringListToString( lineage, " > " ) + "\" not found" );
- }
- TaxonomyDataObtainer.getLineageTaxCacheMap().put( lineage_str, up_tax );
- if ( !ForesterUtil.isEmpty( up_tax.getScientificName() ) ) {
- TaxonomyDataObtainer.getSnTaxCacheMap().put( up_tax.getScientificName(), up_tax );
- }
- if ( !ForesterUtil.isEmpty( up_tax.getCode() ) ) {
- TaxonomyDataObtainer.getCodeTaxCacheMap().put( up_tax.getCode(), up_tax );
- }
- if ( !ForesterUtil.isEmpty( up_tax.getCommonName() ) ) {
- TaxonomyDataObtainer.getCnTaxCacheMap().put( up_tax.getCommonName(), up_tax );
- }
- if ( !ForesterUtil.isEmpty( up_tax.getId() ) ) {
- TaxonomyDataObtainer.getIdTaxCacheMap().put( up_tax.getId(), up_tax );
- }
- }
- }
- return up_tax;
- }
-
-
-
}
git://source.jalview.org / jalview.git / blobdiff