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[jalview.git]
/
forester
/
java
/
src
/
org
/
forester
/
analysis
/
TaxonomyDataManager.java
diff --git
a/forester/java/src/org/forester/analysis/TaxonomyDataManager.java
b/forester/java/src/org/forester/analysis/TaxonomyDataManager.java
index
6301504
..
78c75f9
100644
(file)
--- a/
forester/java/src/org/forester/analysis/TaxonomyDataManager.java
+++ b/
forester/java/src/org/forester/analysis/TaxonomyDataManager.java
@@
-130,10
+130,12
@@
public final class TaxonomyDataManager extends RunnableProcess {
return _sn_up_cache_map;
}
return _sn_up_cache_map;
}
+
+ @SuppressWarnings("unchecked")
private final static UniProtTaxonomy obtainTaxonomy( final HashMap<String, UniProtTaxonomy> cache,
final Object query,
final QUERY_TYPE qt ) throws IOException,
private final static UniProtTaxonomy obtainTaxonomy( final HashMap<String, UniProtTaxonomy> cache,
final Object query,
final QUERY_TYPE qt ) throws IOException,
- AncestralTaxonomyInferenceException {
+ AncestralTaxonomyInferenceException {
if ( cache.containsKey( query ) ) {
return cache.get( query ).copy();
}
if ( cache.containsKey( query ) ) {
return cache.get( query ).copy();
}
@@
-154,6
+156,7
@@
public final class TaxonomyDataManager extends RunnableProcess {
break;
case LIN:
return obtainUniProtTaxonomyFromLineage( ( List<String> ) query );
break;
case LIN:
return obtainUniProtTaxonomyFromLineage( ( List<String> ) query );
+
default:
throw new RuntimeException();
}
default:
throw new RuntimeException();
}
@@
-199,7
+202,10
@@
public final class TaxonomyDataManager extends RunnableProcess {
}
private final static List<UniProtTaxonomy> getTaxonomiesFromTaxonomyCode( final String query ) throws IOException {
}
private final static List<UniProtTaxonomy> getTaxonomiesFromTaxonomyCode( final String query ) throws IOException {
- if ( ( query.indexOf( "XX" ) == 3 ) && TaxonomyUtil.isHasTaxIdFromFakeTaxCode( query ) ) {
+ //FIXME fix "SPHAR" issue
+ if ( ( ( query.indexOf( "XX" ) == 3 ) && TaxonomyUtil.isHasTaxIdFromFakeTaxCode( query ) )
+ || query.equals( "SPHAR" ) /* TODO remove me, is same as Sphingomonas aromaticivorans */
+ ) {
final int id = TaxonomyUtil.getTaxIdFromFakeTaxCode( query );
return SequenceDbWsTools.getTaxonomiesFromId( String.valueOf( id ), MAX_TAXONOMIES_TO_RETURN );
}
final int id = TaxonomyUtil.getTaxIdFromFakeTaxCode( query );
return SequenceDbWsTools.getTaxonomiesFromId( String.valueOf( id ), MAX_TAXONOMIES_TO_RETURN );
}
@@
-216,7
+222,7
@@
public final class TaxonomyDataManager extends RunnableProcess {
synchronized final private static SortedSet<String> obtainDetailedTaxonomicInformation( final Phylogeny phy,
final boolean delete,
final boolean allow_to_use_basic_node_names )
synchronized final private static SortedSet<String> obtainDetailedTaxonomicInformation( final Phylogeny phy,
final boolean delete,
final boolean allow_to_use_basic_node_names )
- throws IOException, AncestralTaxonomyInferenceException {
+ throws IOException, AncestralTaxonomyInferenceException {
clearCachesIfTooLarge();
final SortedSet<String> not_found = new TreeSet<String>();
List<PhylogenyNode> not_found_external_nodes = null;
clearCachesIfTooLarge();
final SortedSet<String> not_found = new TreeSet<String>();
List<PhylogenyNode> not_found_external_nodes = null;
@@
-373,7
+379,7
@@
public final class TaxonomyDataManager extends RunnableProcess {
else {
final List<UniProtTaxonomy> matching_taxonomies = new ArrayList<UniProtTaxonomy>();
final List<UniProtTaxonomy> up_taxonomies = getTaxonomiesFromScientificName( lineage
else {
final List<UniProtTaxonomy> matching_taxonomies = new ArrayList<UniProtTaxonomy>();
final List<UniProtTaxonomy> up_taxonomies = getTaxonomiesFromScientificName( lineage
- .get( lineage.size() - 1 ) );
+ .get( lineage.size() - 1 ) );
if ( ( up_taxonomies != null ) && ( up_taxonomies.size() > 0 ) ) {
for( final UniProtTaxonomy up_taxonomy : up_taxonomies ) {
boolean match = true;
if ( ( up_taxonomies != null ) && ( up_taxonomies.size() > 0 ) ) {
for( final UniProtTaxonomy up_taxonomy : up_taxonomies ) {
boolean match = true;
@@
-422,7
+428,7
@@
public final class TaxonomyDataManager extends RunnableProcess {
}
else {
throw new AncestralTaxonomyInferenceException( "taxonomy \"" + ( lineage.get( lineage.size() - 1 ) )
}
else {
throw new AncestralTaxonomyInferenceException( "taxonomy \"" + ( lineage.get( lineage.size() - 1 ) )
- + "\" not found" );
+ + "\" not found" );
}
}
}
}
}
}
@@
-431,7
+437,7
@@
public final class TaxonomyDataManager extends RunnableProcess {
final PhylogenyNode node,
final Taxonomy tax,
final UniProtTaxonomy up_tax )
final PhylogenyNode node,
final Taxonomy tax,
final UniProtTaxonomy up_tax )
- throws PhyloXmlDataFormatException {
+ throws PhyloXmlDataFormatException {
if ( ( qt != QUERY_TYPE.SN ) && !ForesterUtil.isEmpty( up_tax.getScientificName() )
&& ForesterUtil.isEmpty( tax.getScientificName() ) ) {
tax.setScientificName( up_tax.getScientificName() );
if ( ( qt != QUERY_TYPE.SN ) && !ForesterUtil.isEmpty( up_tax.getScientificName() )
&& ForesterUtil.isEmpty( tax.getScientificName() ) ) {
tax.setScientificName( up_tax.getScientificName() );
@@
-509,7
+515,7
@@
public final class TaxonomyDataManager extends RunnableProcess {
JOptionPane.WARNING_MESSAGE );
}
catch ( final Exception e ) {
JOptionPane.WARNING_MESSAGE );
}
catch ( final Exception e ) {
- // Not important if this fails, do nothing.
+ // Not important if this fails, do nothing.
}
return;
}
}
return;
}
@@
-561,7
+567,7
@@
public final class TaxonomyDataManager extends RunnableProcess {
JOptionPane.WARNING_MESSAGE );
}
catch ( final Exception e ) {
JOptionPane.WARNING_MESSAGE );
}
catch ( final Exception e ) {
- // Not important if this fails, do nothing.
+ // Not important if this fails, do nothing.
}
}
else {
}
}
else {