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.iterators.PhylogenyNodeIterator;
import org.forester.util.ForesterUtil;
import org.forester.ws.uniprot.UniProtTaxonomy;
-import org.forester.ws.uniprot.UniProtWsTools;
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();
}
}
- 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" );
|| !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 = TaxonomyDataObtainer.obtainUniProtTaxonomy( desc.getNodeData()
+ .getTaxonomy(), null, null );
if ( ( up_tax == null ) && ForesterUtil.isEmpty( desc.getNodeData().getTaxonomy().getLineage() ) ) {
String desc_str = "";
if ( !ForesterUtil.isEmpty( desc.getName() ) ) {
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 = TaxonomyDataObtainer.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;
- }
-
-
-
}
public class TaxonomyDataObtainer extends RunnableProcess {
+ enum QUERY_TYPE {
+ CODE, SN, CN, ID, LIN;
+ }
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>();
-
- private final Phylogeny _phy;
- private final MainFrameApplication _mf;
- private final TreePanel _treepanel;
- private final boolean _delete;
+ 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();
+ }
+ }
- public TaxonomyDataObtainer( final MainFrameApplication mf,
- final TreePanel treepanel,
- final Phylogeny phy,
- final boolean delete ) {
- _phy = phy;
- _mf = mf;
- _treepanel = treepanel;
- _delete = delete;
+ synchronized static HashMap<String, UniProtTaxonomy> getCnTaxCacheMap() {
+ return _cn_up_cache_map;
}
- public TaxonomyDataObtainer( final MainFrameApplication mf, final TreePanel treepanel, final Phylogeny phy ) {
- _phy = phy;
- _mf = mf;
- _treepanel = treepanel;
- _delete = false;
+ synchronized static HashMap<String, UniProtTaxonomy> getCodeTaxCacheMap() {
+ return _code_up_cache_map;
}
- private String getBaseUrl() {
- return UniProtWsTools.BASE_URL;
+ synchronized static HashMap<String, UniProtTaxonomy> getIdTaxCacheMap() {
+ return _id_up_cache_map;
}
- 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;
+ synchronized static HashMap<String, UniProtTaxonomy> getLineageTaxCacheMap() {
+ return _lineage_up_cache_map;
+ }
+
+ synchronized static HashMap<String, UniProtTaxonomy> getSnTaxCacheMap() {
+ return _sn_up_cache_map;
+ }
+
+ 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();
}
- _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;
+ 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();
}
- 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" );
+ 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 );
}
- else {
- sb.append( "The following taxonomy was not found:\n" );
+ if ( !ForesterUtil.isEmpty( up_tax.getCode() ) ) {
+ TaxonomyDataObtainer.getCodeTaxCacheMap().put( up_tax.getCode(), up_tax );
}
- }
- else {
- if ( _delete ) {
- sb.append( "The following taxonomies were not found and deleted (if external) (total: "
- + not_found.size() + "):\n" );
+ if ( !ForesterUtil.isEmpty( up_tax.getCommonName() ) ) {
+ TaxonomyDataObtainer.getCnTaxCacheMap().put( up_tax.getCommonName(), up_tax );
}
- 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;
+ if ( !ForesterUtil.isEmpty( up_tax.getId() ) ) {
+ TaxonomyDataObtainer.getIdTaxCacheMap().put( up_tax.getId(), up_tax );
}
- 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 );
+ return up_tax;
}
- catch ( final Exception e ) {
- // Not important if this fails, do nothing.
+ else {
+ return null;
}
}
}
-
- 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();
- }
+ 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 );
+ }
+
+ 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 SortedSet<String> obtainDetailedTaxonomicInformation( final Phylogeny phy,
- final boolean delete )
+ final boolean delete )
throws IOException, AncestralTaxonomyInferenceException {
clearCachesIfTooLarge();
final SortedSet<String> not_found = new TreeSet<String>();
}
return not_found;
}
-
-
-
public static UniProtTaxonomy obtainUniProtTaxonomy( final Taxonomy tax, Object query, QUERY_TYPE qt )
throws IOException, AncestralTaxonomyInferenceException {
}
}
-
-
-
- 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" ) ) ) );
+ 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;
}
-
-
+
synchronized private static void updateTaxonomy( final QUERY_TYPE qt,
final PhylogenyNode node,
final Taxonomy tax,
}
}
}
+ private final Phylogeny _phy;
+ private final MainFrameApplication _mf;
+ private final TreePanel _treepanel;
+ private final boolean _delete;
-
- synchronized static HashMap<String, UniProtTaxonomy> getCnTaxCacheMap() {
- return _cn_up_cache_map;
- }
-
- synchronized static HashMap<String, UniProtTaxonomy> getCodeTaxCacheMap() {
- return _code_up_cache_map;
+ public TaxonomyDataObtainer( final MainFrameApplication mf, final TreePanel treepanel, final Phylogeny phy ) {
+ _phy = phy;
+ _mf = mf;
+ _treepanel = treepanel;
+ _delete = false;
}
- synchronized static HashMap<String, UniProtTaxonomy> getIdTaxCacheMap() {
- return _id_up_cache_map;
+ public TaxonomyDataObtainer( final MainFrameApplication mf,
+ final TreePanel treepanel,
+ final Phylogeny phy,
+ final boolean delete ) {
+ _phy = phy;
+ _mf = mf;
+ _treepanel = treepanel;
+ _delete = delete;
}
- synchronized static HashMap<String, UniProtTaxonomy> getSnTaxCacheMap() {
- return _sn_up_cache_map;
+ 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 HashMap<String, UniProtTaxonomy> getLineageTaxCacheMap() {
- return _lineage_up_cache_map;
+ private String getBaseUrl() {
+ return UniProtWsTools.BASE_URL;
}
-
- enum QUERY_TYPE {
- CODE, SN, CN, ID, LIN;
- }
-
@Override
public void run() {
execute();
git://source.jalview.org / jalview.git / commitdiff