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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
..
d78720c
100644
(file)
--- a/
forester/java/src/org/forester/analysis/TaxonomyDataManager.java
+++ b/
forester/java/src/org/forester/analysis/TaxonomyDataManager.java
@@
-199,7
+199,10
@@
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 );
}
@@
-251,7
+254,7
@@
public final class TaxonomyDataManager extends RunnableProcess {
if ( ( ( tax != null ) && ( isHasAppropriateId( tax )
|| !ForesterUtil.isEmpty( tax.getScientificName() )
|| !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) || !ForesterUtil
if ( ( ( tax != null ) && ( isHasAppropriateId( tax )
|| !ForesterUtil.isEmpty( tax.getScientificName() )
|| !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) || !ForesterUtil
- .isEmpty( tax.getCommonName() ) ) ) ) {
+ .isEmpty( tax.getCommonName() ) ) ) ) {
uniprot_tax = obtainUniProtTaxonomy( tax, null, qt );
}
else {
uniprot_tax = obtainUniProtTaxonomy( tax, null, qt );
}
else {