import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
-import java.util.SortedSet;
-import java.util.TreeSet;
+import org.forester.analysis.TaxonomyDataObtainer.QUERY_TYPE;
import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyNode;
public final class AncestralTaxonomyInference {
- private static final int MAX_CACHE_SIZE = 100000;
private static final int MAX_TAXONOMIES_TO_RETURN = 10;
- private static final HashMap<String, UniProtTaxonomy> _sn_up_cache_map = new HashMap<String, UniProtTaxonomy>();
- private static final HashMap<String, UniProtTaxonomy> _lineage_up_cache_map = new HashMap<String, UniProtTaxonomy>();
- private static final HashMap<String, UniProtTaxonomy> _code_up_cache_map = new HashMap<String, UniProtTaxonomy>();
- private static final HashMap<String, UniProtTaxonomy> _cn_up_cache_map = new HashMap<String, UniProtTaxonomy>();
- private static final HashMap<String, UniProtTaxonomy> _id_up_cache_map = new HashMap<String, UniProtTaxonomy>();
-
- synchronized private static void clearCachesIfTooLarge() {
- if ( getSnTaxCacheMap().size() > MAX_CACHE_SIZE ) {
- getSnTaxCacheMap().clear();
- }
- if ( getLineageTaxCacheMap().size() > MAX_CACHE_SIZE ) {
- getLineageTaxCacheMap().clear();
- }
- if ( getCnTaxCacheMap().size() > MAX_CACHE_SIZE ) {
- getCnTaxCacheMap().clear();
- }
- if ( getCodeTaxCacheMap().size() > MAX_CACHE_SIZE ) {
- getCodeTaxCacheMap().clear();
- }
- if ( getIdTaxCacheMap().size() > MAX_CACHE_SIZE ) {
- getIdTaxCacheMap().clear();
- }
- }
-
- synchronized private static HashMap<String, UniProtTaxonomy> getCnTaxCacheMap() {
- return _cn_up_cache_map;
- }
-
- synchronized private static HashMap<String, UniProtTaxonomy> getCodeTaxCacheMap() {
- return _code_up_cache_map;
- }
-
- synchronized private static HashMap<String, UniProtTaxonomy> getIdTaxCacheMap() {
- return _id_up_cache_map;
- }
-
- synchronized private static HashMap<String, UniProtTaxonomy> getSnTaxCacheMap() {
- return _sn_up_cache_map;
- }
-
- synchronized private static HashMap<String, UniProtTaxonomy> getLineageTaxCacheMap() {
- return _lineage_up_cache_map;
- }
-
- synchronized private static UniProtTaxonomy getTaxonomies( final HashMap<String, UniProtTaxonomy> cache,
+
+ private static UniProtTaxonomy getTaxonomies( final HashMap<String, UniProtTaxonomy> cache,
final Object query,
final QUERY_TYPE qt ) throws IOException,
AncestralTaxonomyInferenceException {
if ( ( up_taxonomies != null ) && ( up_taxonomies.size() == 1 ) ) {
final UniProtTaxonomy up_tax = up_taxonomies.get( 0 );
if ( !ForesterUtil.isEmpty( up_tax.getScientificName() ) ) {
- getSnTaxCacheMap().put( up_tax.getScientificName(), up_tax );
+ TaxonomyDataObtainer.getSnTaxCacheMap().put( up_tax.getScientificName(), up_tax );
}
if ( !ForesterUtil.isEmpty( up_tax.getCode() ) ) {
- getCodeTaxCacheMap().put( up_tax.getCode(), up_tax );
+ TaxonomyDataObtainer.getCodeTaxCacheMap().put( up_tax.getCode(), up_tax );
}
if ( !ForesterUtil.isEmpty( up_tax.getCommonName() ) ) {
- getCnTaxCacheMap().put( up_tax.getCommonName(), up_tax );
+ TaxonomyDataObtainer.getCnTaxCacheMap().put( up_tax.getCommonName(), up_tax );
}
if ( !ForesterUtil.isEmpty( up_tax.getId() ) ) {
- getIdTaxCacheMap().put( up_tax.getId(), up_tax );
+ TaxonomyDataObtainer.getIdTaxCacheMap().put( up_tax.getId(), up_tax );
}
return up_tax;
}
}
}
- synchronized private static List<UniProtTaxonomy> getTaxonomiesFromCommonName( final String query )
+ private static List<UniProtTaxonomy> getTaxonomiesFromCommonName( final String query )
throws IOException {
return UniProtWsTools.getTaxonomiesFromCommonNameStrict( query, MAX_TAXONOMIES_TO_RETURN );
}
- synchronized private static List<UniProtTaxonomy> getTaxonomiesFromId( final String query ) throws IOException {
+ private static List<UniProtTaxonomy> getTaxonomiesFromId( final String query ) throws IOException {
return UniProtWsTools.getTaxonomiesFromId( query, MAX_TAXONOMIES_TO_RETURN );
}
- synchronized private static List<UniProtTaxonomy> getTaxonomiesFromScientificName( final String query )
+ private static List<UniProtTaxonomy> getTaxonomiesFromScientificName( final String query )
throws IOException {
return UniProtWsTools.getTaxonomiesFromScientificNameStrict( query, MAX_TAXONOMIES_TO_RETURN );
}
- synchronized private static List<UniProtTaxonomy> getTaxonomiesFromTaxonomyCode( final String query )
+ private static List<UniProtTaxonomy> getTaxonomiesFromTaxonomyCode( final String query )
throws IOException {
return UniProtWsTools.getTaxonomiesFromTaxonomyCode( query, MAX_TAXONOMIES_TO_RETURN );
}
- synchronized public static void inferTaxonomyFromDescendents( final Phylogeny phy ) throws IOException,
+ public static void inferTaxonomyFromDescendents( final Phylogeny phy ) throws IOException,
AncestralTaxonomyInferenceException {
- clearCachesIfTooLarge();
+ TaxonomyDataObtainer.clearCachesIfTooLarge();
for( final PhylogenyNodeIterator iter = phy.iteratorPostorder(); iter.hasNext(); ) {
final PhylogenyNode node = iter.next();
if ( !node.isExternal() ) {
}
}
- synchronized private static void inferTaxonomyFromDescendents( final PhylogenyNode n ) throws IOException,
+ 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()
- && ( isHasAppropriateId( desc.getNodeData().getTaxonomy() )
+ && ( TaxonomyDataObtainer.isHasAppropriateId( desc.getNodeData().getTaxonomy() )
|| !ForesterUtil.isEmpty( desc.getNodeData().getTaxonomy().getScientificName() )
|| !ForesterUtil.isEmpty( desc.getNodeData().getTaxonomy().getLineage() )
|| !ForesterUtil.isEmpty( desc.getNodeData().getTaxonomy().getTaxonomyCode() ) || !ForesterUtil
}
}
- synchronized private static boolean isHasAppropriateId( final Taxonomy tax ) {
- return ( ( tax.getIdentifier() != null ) && ( !ForesterUtil.isEmpty( tax.getIdentifier().getValue() ) && ( tax
- .getIdentifier().getProvider().equalsIgnoreCase( "ncbi" )
- || tax.getIdentifier().getProvider().equalsIgnoreCase( "uniprot" ) || tax.getIdentifier().getProvider()
- .equalsIgnoreCase( "uniprotkb" ) ) ) );
- }
+
- synchronized public static SortedSet<String> obtainDetailedTaxonomicInformation( final Phylogeny phy,
- final boolean delete )
- throws IOException, AncestralTaxonomyInferenceException {
- clearCachesIfTooLarge();
- final SortedSet<String> not_found = new TreeSet<String>();
- List<PhylogenyNode> not_found_external_nodes = null;
- if ( delete ) {
- not_found_external_nodes = new ArrayList<PhylogenyNode>();
- }
- for( final PhylogenyNodeIterator iter = phy.iteratorPostorder(); iter.hasNext(); ) {
- final PhylogenyNode node = iter.next();
- final QUERY_TYPE qt = null;
- Taxonomy tax = null;
- if ( node.getNodeData().isHasTaxonomy() ) {
- tax = node.getNodeData().getTaxonomy();
- }
- else if ( node.isExternal() ) {
- if ( !ForesterUtil.isEmpty( node.getName() ) ) {
- not_found.add( node.getName() );
- }
- else {
- not_found.add( node.toString() );
- }
- if ( delete ) {
- not_found_external_nodes.add( node );
- }
- }
- UniProtTaxonomy uniprot_tax = null;
- if ( ( tax != null )
- && ( isHasAppropriateId( tax ) || !ForesterUtil.isEmpty( tax.getScientificName() )
- || !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) || !ForesterUtil.isEmpty( tax
- .getCommonName() ) ) ) {
- uniprot_tax = obtainUniProtTaxonomy( tax, null, qt );
- if ( uniprot_tax != null ) {
- updateTaxonomy( qt, node, tax, uniprot_tax );
- }
- else {
- not_found.add( tax.toString() );
- if ( delete && node.isExternal() ) {
- not_found_external_nodes.add( node );
- }
- }
- }
- }
- if ( delete ) {
- for( final PhylogenyNode node : not_found_external_nodes ) {
- phy.deleteSubtree( node, true );
- }
- phy.externalNodesHaveChanged();
- phy.hashIDs();
- phy.recalculateNumberOfExternalDescendants( true );
- }
- return not_found;
- }
-
- synchronized public static UniProtTaxonomy obtainUniProtTaxonomy( final Taxonomy tax, Object query, QUERY_TYPE qt )
- throws IOException, AncestralTaxonomyInferenceException {
- if ( isHasAppropriateId( tax ) ) {
- query = tax.getIdentifier().getValue();
- qt = QUERY_TYPE.ID;
- return getTaxonomies( getIdTaxCacheMap(), query, qt );
- }
- else if ( !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
- if ( !ForesterUtil.isEmpty( tax.getLineage() ) ) {
- query = tax.getLineage();
- qt = QUERY_TYPE.LIN;
- return getTaxonomies( getLineageTaxCacheMap(), query, qt );
- }
- else {
- query = tax.getScientificName();
- qt = QUERY_TYPE.SN;
- return getTaxonomies( getSnTaxCacheMap(), query, qt );
- }
- }
- else if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
- query = tax.getTaxonomyCode();
- qt = QUERY_TYPE.CODE;
- return getTaxonomies( getCodeTaxCacheMap(), query, qt );
- }
- else {
- query = tax.getCommonName();
- qt = QUERY_TYPE.CN;
- return getTaxonomies( getCnTaxCacheMap(), query, qt );
- }
- }
-
- synchronized private static UniProtTaxonomy obtainUniProtTaxonomyFromLineage( final List<String> lineage )
+
+ private static UniProtTaxonomy obtainUniProtTaxonomyFromLineage( final List<String> lineage )
throws AncestralTaxonomyInferenceException, IOException {
final String lineage_str = ForesterUtil.stringListToString( lineage, ">" );
UniProtTaxonomy up_tax = null;
- if ( getLineageTaxCacheMap().containsKey( lineage_str ) ) {
- up_tax = getLineageTaxCacheMap().get( lineage_str ).copy();
+ if ( TaxonomyDataObtainer.getLineageTaxCacheMap().containsKey( lineage_str ) ) {
+ up_tax = TaxonomyDataObtainer.getLineageTaxCacheMap().get( lineage_str ).copy();
}
else {
final List<UniProtTaxonomy> up_taxonomies = getTaxonomiesFromScientificName( lineage
throw new AncestralTaxonomyInferenceException( "lineage \""
+ ForesterUtil.stringListToString( lineage, " > " ) + "\" not found" );
}
- getLineageTaxCacheMap().put( lineage_str, up_tax );
+ TaxonomyDataObtainer.getLineageTaxCacheMap().put( lineage_str, up_tax );
if ( !ForesterUtil.isEmpty( up_tax.getScientificName() ) ) {
- getSnTaxCacheMap().put( up_tax.getScientificName(), up_tax );
+ TaxonomyDataObtainer.getSnTaxCacheMap().put( up_tax.getScientificName(), up_tax );
}
if ( !ForesterUtil.isEmpty( up_tax.getCode() ) ) {
- getCodeTaxCacheMap().put( up_tax.getCode(), up_tax );
+ TaxonomyDataObtainer.getCodeTaxCacheMap().put( up_tax.getCode(), up_tax );
}
if ( !ForesterUtil.isEmpty( up_tax.getCommonName() ) ) {
- getCnTaxCacheMap().put( up_tax.getCommonName(), up_tax );
+ TaxonomyDataObtainer.getCnTaxCacheMap().put( up_tax.getCommonName(), up_tax );
}
if ( !ForesterUtil.isEmpty( up_tax.getId() ) ) {
- getIdTaxCacheMap().put( up_tax.getId(), up_tax );
+ TaxonomyDataObtainer.getIdTaxCacheMap().put( up_tax.getId(), up_tax );
}
}
}
return up_tax;
}
- synchronized private static void updateTaxonomy( final QUERY_TYPE qt,
- final PhylogenyNode node,
- final Taxonomy tax,
- final UniProtTaxonomy up_tax ) {
- if ( ( qt != QUERY_TYPE.SN ) && !ForesterUtil.isEmpty( up_tax.getScientificName() )
- && ForesterUtil.isEmpty( tax.getScientificName() ) ) {
- tax.setScientificName( up_tax.getScientificName() );
- }
- if ( node.isExternal() && ( qt != QUERY_TYPE.CODE ) && !ForesterUtil.isEmpty( up_tax.getCode() )
- && ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
- tax.setTaxonomyCode( up_tax.getCode() );
- }
- if ( ( qt != QUERY_TYPE.CN ) && !ForesterUtil.isEmpty( up_tax.getCommonName() )
- && ForesterUtil.isEmpty( tax.getCommonName() ) ) {
- tax.setCommonName( up_tax.getCommonName() );
- }
- if ( !ForesterUtil.isEmpty( up_tax.getSynonym() ) && !tax.getSynonyms().contains( up_tax.getSynonym() ) ) {
- tax.getSynonyms().add( up_tax.getSynonym() );
- }
- if ( !ForesterUtil.isEmpty( up_tax.getRank() ) && ForesterUtil.isEmpty( tax.getRank() ) ) {
- try {
- tax.setRank( up_tax.getRank().toLowerCase() );
- }
- catch ( final PhyloXmlDataFormatException ex ) {
- tax.setRank( "" );
- }
- }
- if ( ( qt != QUERY_TYPE.ID ) && !ForesterUtil.isEmpty( up_tax.getId() )
- && ( ( tax.getIdentifier() == null ) || ForesterUtil.isEmpty( tax.getIdentifier().getValue() ) ) ) {
- tax.setIdentifier( new Identifier( up_tax.getId(), "uniprot" ) );
- }
- if ( up_tax.getLineage() != null ) {
- tax.setLineage( new ArrayList<String>() );
- for( final String lin : up_tax.getLineage() ) {
- if ( !ForesterUtil.isEmpty( lin ) ) {
- tax.getLineage().add( lin );
- }
- }
- }
- }
-
- private enum QUERY_TYPE {
- CODE, SN, CN, ID, LIN;
- }
+
+
}
--- /dev/null
+// $Id:
+//
+// forester -- software libraries and applications
+// for genomics and evolutionary biology research.
+//
+// Copyright (C) 2010 Christian M Zmasek
+// Copyright (C) 2010 Sanford-Burnham Medical Research Institute
+// All rights reserved
+//
+// This library is free software; you can redistribute it and/or
+// modify it under the terms of the GNU Lesser General Public
+// License as published by the Free Software Foundation; either
+// version 2.1 of the License, or (at your option) any later version.
+//
+// This library is distributed in the hope that it will be useful,
+// but WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+// Lesser General Public License for more details.
+//
+// You should have received a copy of the GNU Lesser General Public
+// License along with this library; if not, write to the Free Software
+// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+//
+// Contact: phylosoft @ gmail . com
+// WWW: www.phylosoft.org/forester
+
+package org.forester.analysis;
+
+import java.io.IOException;
+import java.net.UnknownHostException;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.SortedSet;
+import java.util.TreeSet;
+
+import javax.swing.JOptionPane;
+
+import org.forester.archaeopteryx.MainFrameApplication;
+import org.forester.archaeopteryx.TreePanel;
+import org.forester.archaeopteryx.tools.RunnableProcess;
+import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
+import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.PhylogenyNode;
+import org.forester.phylogeny.data.Identifier;
+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;
+
+public class TaxonomyDataObtainer extends RunnableProcess {
+
+ private static final int MAX_CACHE_SIZE = 100000;
+
+ private static final HashMap<String, UniProtTaxonomy> _sn_up_cache_map = new HashMap<String, UniProtTaxonomy>();
+ private static final HashMap<String, UniProtTaxonomy> _lineage_up_cache_map = new HashMap<String, UniProtTaxonomy>();
+ private static final HashMap<String, UniProtTaxonomy> _code_up_cache_map = new HashMap<String, UniProtTaxonomy>();
+ private static final HashMap<String, UniProtTaxonomy> _cn_up_cache_map = new HashMap<String, UniProtTaxonomy>();
+ private static final HashMap<String, UniProtTaxonomy> _id_up_cache_map = new HashMap<String, UniProtTaxonomy>();
+
+
+ private final Phylogeny _phy;
+ private final MainFrameApplication _mf;
+ private final TreePanel _treepanel;
+ private final boolean _delete;
+
+ public TaxonomyDataObtainer( final MainFrameApplication mf,
+ final TreePanel treepanel,
+ final Phylogeny phy,
+ final boolean delete ) {
+ _phy = phy;
+ _mf = mf;
+ _treepanel = treepanel;
+ _delete = delete;
+ }
+
+ public TaxonomyDataObtainer( final MainFrameApplication mf, final TreePanel treepanel, final Phylogeny phy ) {
+ _phy = phy;
+ _mf = mf;
+ _treepanel = treepanel;
+ _delete = false;
+ }
+
+ private String getBaseUrl() {
+ return UniProtWsTools.BASE_URL;
+ }
+
+ private void execute() {
+ start( _mf, "taxonomy data" );
+ SortedSet<String> not_found = null;
+ try {
+ not_found = obtainDetailedTaxonomicInformation( _phy, _delete );
+ }
+ catch ( final UnknownHostException e ) {
+ JOptionPane.showMessageDialog( _mf,
+ "Could not connect to \"" + getBaseUrl() + "\"",
+ "Network error during taxonomic information gathering",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ catch ( final IOException e ) {
+ e.printStackTrace();
+ JOptionPane.showMessageDialog( _mf,
+ e.toString(),
+ "Failed to obtain taxonomic information",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ catch ( final AncestralTaxonomyInferenceException e ) {
+ e.printStackTrace();
+ JOptionPane.showMessageDialog( _mf,
+ e.toString(),
+ "Failed to obtain taxonomic information",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ finally {
+ end( _mf );
+ }
+ if ( ( _phy == null ) || _phy.isEmpty() ) {
+ try {
+ JOptionPane.showMessageDialog( _mf,
+ "None of the external node taxonomies could be resolved",
+ "Taxonomy Tool Failed",
+ JOptionPane.WARNING_MESSAGE );
+ }
+ catch ( final Exception e ) {
+ // Not important if this fails, do nothing.
+ }
+ return;
+ }
+ _treepanel.setTree( _phy );
+ _mf.showWhole();
+ _treepanel.setEdited( true );
+ if ( ( not_found != null ) && ( not_found.size() > 0 ) ) {
+ int max = not_found.size();
+ boolean more = false;
+ if ( max > 20 ) {
+ more = true;
+ max = 20;
+ }
+ final StringBuffer sb = new StringBuffer();
+ sb.append( "Not all taxonomies could be resolved.\n" );
+ if ( not_found.size() == 1 ) {
+ if ( _delete ) {
+ sb.append( "The following taxonomy was not found and deleted (if external):\n" );
+ }
+ else {
+ sb.append( "The following taxonomy was not found:\n" );
+ }
+ }
+ else {
+ if ( _delete ) {
+ sb.append( "The following taxonomies were not found and deleted (if external) (total: "
+ + not_found.size() + "):\n" );
+ }
+ else {
+ sb.append( "The following taxonomies were not found (total: " + not_found.size() + "):\n" );
+ }
+ }
+ int i = 0;
+ for( final String string : not_found ) {
+ if ( i > 19 ) {
+ break;
+ }
+ sb.append( string );
+ sb.append( "\n" );
+ ++i;
+ }
+ if ( more ) {
+ sb.append( "..." );
+ }
+ try {
+ JOptionPane.showMessageDialog( _mf,
+ sb.toString(),
+ "Taxonomy Tool Completed",
+ JOptionPane.WARNING_MESSAGE );
+ }
+ catch ( final Exception e ) {
+ // Not important if this fails, do nothing.
+ }
+ }
+ else {
+ try {
+ JOptionPane.showMessageDialog( _mf,
+ "Taxonomy tool successfully completed",
+ "Taxonomy Tool Completed",
+ JOptionPane.INFORMATION_MESSAGE );
+ }
+ catch ( final Exception e ) {
+ // Not important if this fails, do nothing.
+ }
+ }
+ }
+
+
+ synchronized static void clearCachesIfTooLarge() {
+ if ( getSnTaxCacheMap().size() > MAX_CACHE_SIZE ) {
+ getSnTaxCacheMap().clear();
+ }
+ if ( getLineageTaxCacheMap().size() > MAX_CACHE_SIZE ) {
+ getLineageTaxCacheMap().clear();
+ }
+ if ( getCnTaxCacheMap().size() > MAX_CACHE_SIZE ) {
+ getCnTaxCacheMap().clear();
+ }
+ if ( getCodeTaxCacheMap().size() > MAX_CACHE_SIZE ) {
+ getCodeTaxCacheMap().clear();
+ }
+ if ( getIdTaxCacheMap().size() > MAX_CACHE_SIZE ) {
+ getIdTaxCacheMap().clear();
+ }
+ }
+
+ synchronized private static SortedSet<String> obtainDetailedTaxonomicInformation( final Phylogeny phy,
+ final boolean delete )
+ throws IOException, AncestralTaxonomyInferenceException {
+ clearCachesIfTooLarge();
+ final SortedSet<String> not_found = new TreeSet<String>();
+ List<PhylogenyNode> not_found_external_nodes = null;
+ if ( delete ) {
+ not_found_external_nodes = new ArrayList<PhylogenyNode>();
+ }
+ for( final PhylogenyNodeIterator iter = phy.iteratorPostorder(); iter.hasNext(); ) {
+ final PhylogenyNode node = iter.next();
+ final QUERY_TYPE qt = null;
+ Taxonomy tax = null;
+ if ( node.getNodeData().isHasTaxonomy() ) {
+ tax = node.getNodeData().getTaxonomy();
+ }
+ else if ( node.isExternal() ) {
+ if ( !ForesterUtil.isEmpty( node.getName() ) ) {
+ not_found.add( node.getName() );
+ }
+ else {
+ not_found.add( node.toString() );
+ }
+ if ( delete ) {
+ not_found_external_nodes.add( node );
+ }
+ }
+ UniProtTaxonomy uniprot_tax = null;
+ if ( ( tax != null )
+ && ( isHasAppropriateId( tax ) || !ForesterUtil.isEmpty( tax.getScientificName() )
+ || !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) || !ForesterUtil.isEmpty( tax
+ .getCommonName() ) ) ) {
+ uniprot_tax = obtainUniProtTaxonomy( tax, null, qt );
+ if ( uniprot_tax != null ) {
+ updateTaxonomy( qt, node, tax, uniprot_tax );
+ }
+ else {
+ not_found.add( tax.toString() );
+ if ( delete && node.isExternal() ) {
+ not_found_external_nodes.add( node );
+ }
+ }
+ }
+ }
+ if ( delete ) {
+ for( final PhylogenyNode node : not_found_external_nodes ) {
+ phy.deleteSubtree( node, true );
+ }
+ phy.externalNodesHaveChanged();
+ phy.hashIDs();
+ phy.recalculateNumberOfExternalDescendants( true );
+ }
+ return not_found;
+ }
+
+
+
+
+ public static UniProtTaxonomy obtainUniProtTaxonomy( final Taxonomy tax, Object query, QUERY_TYPE qt )
+ throws IOException, AncestralTaxonomyInferenceException {
+ if ( TaxonomyDataObtainer.isHasAppropriateId( tax ) ) {
+ query = tax.getIdentifier().getValue();
+ qt = QUERY_TYPE.ID;
+ return getTaxonomies( TaxonomyDataObtainer.getIdTaxCacheMap(), query, qt );
+ }
+ else if ( !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
+ if ( !ForesterUtil.isEmpty( tax.getLineage() ) ) {
+ query = tax.getLineage();
+ qt = QUERY_TYPE.LIN;
+ return getTaxonomies( TaxonomyDataObtainer.getLineageTaxCacheMap(), query, qt );
+ }
+ else {
+ query = tax.getScientificName();
+ qt = QUERY_TYPE.SN;
+ return getTaxonomies( TaxonomyDataObtainer.getSnTaxCacheMap(), query, qt );
+ }
+ }
+ else if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
+ query = tax.getTaxonomyCode();
+ qt = QUERY_TYPE.CODE;
+ return getTaxonomies( TaxonomyDataObtainer.getCodeTaxCacheMap(), query, qt );
+ }
+ else {
+ query = tax.getCommonName();
+ qt = QUERY_TYPE.CN;
+ return getTaxonomies( TaxonomyDataObtainer.getCnTaxCacheMap(), query, qt );
+ }
+ }
+
+
+
+
+ static boolean isHasAppropriateId( final Taxonomy tax ) {
+ return ( ( tax.getIdentifier() != null ) && ( !ForesterUtil.isEmpty( tax.getIdentifier().getValue() ) && ( tax
+ .getIdentifier().getProvider().equalsIgnoreCase( "ncbi" )
+ || tax.getIdentifier().getProvider().equalsIgnoreCase( "uniprot" ) || tax.getIdentifier().getProvider()
+ .equalsIgnoreCase( "uniprotkb" ) ) ) );
+ }
+
+
+ synchronized private static void updateTaxonomy( final QUERY_TYPE qt,
+ final PhylogenyNode node,
+ final Taxonomy tax,
+ final UniProtTaxonomy up_tax ) {
+ if ( ( qt != QUERY_TYPE.SN ) && !ForesterUtil.isEmpty( up_tax.getScientificName() )
+ && ForesterUtil.isEmpty( tax.getScientificName() ) ) {
+ tax.setScientificName( up_tax.getScientificName() );
+ }
+ if ( node.isExternal() && ( qt != QUERY_TYPE.CODE ) && !ForesterUtil.isEmpty( up_tax.getCode() )
+ && ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
+ tax.setTaxonomyCode( up_tax.getCode() );
+ }
+ if ( ( qt != QUERY_TYPE.CN ) && !ForesterUtil.isEmpty( up_tax.getCommonName() )
+ && ForesterUtil.isEmpty( tax.getCommonName() ) ) {
+ tax.setCommonName( up_tax.getCommonName() );
+ }
+ if ( !ForesterUtil.isEmpty( up_tax.getSynonym() ) && !tax.getSynonyms().contains( up_tax.getSynonym() ) ) {
+ tax.getSynonyms().add( up_tax.getSynonym() );
+ }
+ if ( !ForesterUtil.isEmpty( up_tax.getRank() ) && ForesterUtil.isEmpty( tax.getRank() ) ) {
+ try {
+ tax.setRank( up_tax.getRank().toLowerCase() );
+ }
+ catch ( final PhyloXmlDataFormatException ex ) {
+ tax.setRank( "" );
+ }
+ }
+ if ( ( qt != QUERY_TYPE.ID ) && !ForesterUtil.isEmpty( up_tax.getId() )
+ && ( ( tax.getIdentifier() == null ) || ForesterUtil.isEmpty( tax.getIdentifier().getValue() ) ) ) {
+ tax.setIdentifier( new Identifier( up_tax.getId(), "uniprot" ) );
+ }
+ if ( up_tax.getLineage() != null ) {
+ tax.setLineage( new ArrayList<String>() );
+ for( final String lin : up_tax.getLineage() ) {
+ if ( !ForesterUtil.isEmpty( lin ) ) {
+ tax.getLineage().add( lin );
+ }
+ }
+ }
+ }
+
+
+ synchronized static HashMap<String, UniProtTaxonomy> getCnTaxCacheMap() {
+ return _cn_up_cache_map;
+ }
+
+ synchronized static HashMap<String, UniProtTaxonomy> getCodeTaxCacheMap() {
+ return _code_up_cache_map;
+ }
+
+ synchronized static HashMap<String, UniProtTaxonomy> getIdTaxCacheMap() {
+ return _id_up_cache_map;
+ }
+
+ synchronized static HashMap<String, UniProtTaxonomy> getSnTaxCacheMap() {
+ return _sn_up_cache_map;
+ }
+
+ synchronized static HashMap<String, UniProtTaxonomy> getLineageTaxCacheMap() {
+ return _lineage_up_cache_map;
+ }
+
+
+ enum QUERY_TYPE {
+ CODE, SN, CN, ID, LIN;
+ }
+
+ @Override
+ public void run() {
+ execute();
+ }
+}
\ No newline at end of file
import javax.swing.filechooser.FileFilter;
import javax.swing.plaf.synth.SynthLookAndFeel;
+import org.forester.analysis.TaxonomyDataObtainer;
import org.forester.archaeopteryx.AptxUtil.GraphicsExportType;
import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
import org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions;
import org.forester.archaeopteryx.tools.PhylogeneticInferrer;
import org.forester.archaeopteryx.tools.SequenceDataRetriver;
-import org.forester.archaeopteryx.tools.TaxonomyDataObtainer;
import org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient;
import org.forester.archaeopteryx.webservices.WebservicesManager;
import org.forester.io.parsers.FastaParser;
_process_id = process_id;
}
- void start( final MainFrame mf, final String name ) {
+ public void start( final MainFrame mf, final String name ) {
setProcessId( mf.getProcessPool().addProcess( name ) );
mf.updateProcessMenu();
}
- void end( final MainFrame mf ) {
+ public void end( final MainFrame mf ) {
final boolean removed = mf.getProcessPool().removeProcess( getProcessId() );
if ( !removed ) {
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not remove process " + getProcessId()
+++ /dev/null
-// $Id:
-//
-// forester -- software libraries and applications
-// for genomics and evolutionary biology research.
-//
-// Copyright (C) 2010 Christian M Zmasek
-// Copyright (C) 2010 Sanford-Burnham Medical Research Institute
-// All rights reserved
-//
-// This library is free software; you can redistribute it and/or
-// modify it under the terms of the GNU Lesser General Public
-// License as published by the Free Software Foundation; either
-// version 2.1 of the License, or (at your option) any later version.
-//
-// This library is distributed in the hope that it will be useful,
-// but WITHOUT ANY WARRANTY; without even the implied warranty of
-// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
-// Lesser General Public License for more details.
-//
-// You should have received a copy of the GNU Lesser General Public
-// License along with this library; if not, write to the Free Software
-// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-//
-// Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
-
-package org.forester.archaeopteryx.tools;
-
-import java.io.IOException;
-import java.net.UnknownHostException;
-import java.util.SortedSet;
-
-import javax.swing.JOptionPane;
-
-import org.forester.analysis.AncestralTaxonomyInference;
-import org.forester.analysis.AncestralTaxonomyInferenceException;
-import org.forester.archaeopteryx.MainFrameApplication;
-import org.forester.archaeopteryx.TreePanel;
-import org.forester.phylogeny.Phylogeny;
-import org.forester.ws.uniprot.UniProtWsTools;
-
-public class TaxonomyDataObtainer extends RunnableProcess {
-
- private final Phylogeny _phy;
- private final MainFrameApplication _mf;
- private final TreePanel _treepanel;
- private final boolean _delete;
-
- public TaxonomyDataObtainer( final MainFrameApplication mf,
- final TreePanel treepanel,
- final Phylogeny phy,
- final boolean delete ) {
- _phy = phy;
- _mf = mf;
- _treepanel = treepanel;
- _delete = delete;
- }
-
- public TaxonomyDataObtainer( final MainFrameApplication mf, final TreePanel treepanel, final Phylogeny phy ) {
- _phy = phy;
- _mf = mf;
- _treepanel = treepanel;
- _delete = false;
- }
-
- private String getBaseUrl() {
- return UniProtWsTools.BASE_URL;
- }
-
- private void execute() {
- start( _mf, "taxonomy data" );
- SortedSet<String> not_found = null;
- try {
- not_found = AncestralTaxonomyInference.obtainDetailedTaxonomicInformation( _phy, _delete );
- }
- catch ( final UnknownHostException e ) {
- JOptionPane.showMessageDialog( _mf,
- "Could not connect to \"" + getBaseUrl() + "\"",
- "Network error during taxonomic information gathering",
- JOptionPane.ERROR_MESSAGE );
- return;
- }
- catch ( final IOException e ) {
- e.printStackTrace();
- JOptionPane.showMessageDialog( _mf,
- e.toString(),
- "Failed to obtain taxonomic information",
- JOptionPane.ERROR_MESSAGE );
- return;
- }
- catch ( final AncestralTaxonomyInferenceException e ) {
- e.printStackTrace();
- JOptionPane.showMessageDialog( _mf,
- e.toString(),
- "Failed to obtain taxonomic information",
- JOptionPane.ERROR_MESSAGE );
- return;
- }
- finally {
- end( _mf );
- }
- if ( ( _phy == null ) || _phy.isEmpty() ) {
- try {
- JOptionPane.showMessageDialog( _mf,
- "None of the external node taxonomies could be resolved",
- "Taxonomy Tool Failed",
- JOptionPane.WARNING_MESSAGE );
- }
- catch ( final Exception e ) {
- // Not important if this fails, do nothing.
- }
- return;
- }
- _treepanel.setTree( _phy );
- _mf.showWhole();
- _treepanel.setEdited( true );
- if ( ( not_found != null ) && ( not_found.size() > 0 ) ) {
- int max = not_found.size();
- boolean more = false;
- if ( max > 20 ) {
- more = true;
- max = 20;
- }
- final StringBuffer sb = new StringBuffer();
- sb.append( "Not all taxonomies could be resolved.\n" );
- if ( not_found.size() == 1 ) {
- if ( _delete ) {
- sb.append( "The following taxonomy was not found and deleted (if external):\n" );
- }
- else {
- sb.append( "The following taxonomy was not found:\n" );
- }
- }
- else {
- if ( _delete ) {
- sb.append( "The following taxonomies were not found and deleted (if external) (total: "
- + not_found.size() + "):\n" );
- }
- else {
- sb.append( "The following taxonomies were not found (total: " + not_found.size() + "):\n" );
- }
- }
- int i = 0;
- for( final String string : not_found ) {
- if ( i > 19 ) {
- break;
- }
- sb.append( string );
- sb.append( "\n" );
- ++i;
- }
- if ( more ) {
- sb.append( "..." );
- }
- try {
- JOptionPane.showMessageDialog( _mf,
- sb.toString(),
- "Taxonomy Tool Completed",
- JOptionPane.WARNING_MESSAGE );
- }
- catch ( final Exception e ) {
- // Not important if this fails, do nothing.
- }
- }
- else {
- try {
- JOptionPane.showMessageDialog( _mf,
- "Taxonomy tool successfully completed",
- "Taxonomy Tool Completed",
- JOptionPane.INFORMATION_MESSAGE );
- }
- catch ( final Exception e ) {
- // Not important if this fails, do nothing.
- }
- }
- }
-
- @Override
- public void run() {
- execute();
- }
-}
\ No newline at end of file
git://source.jalview.org / jalview.git / commitdiff