import org.forester.util.ForesterUtil;
import org.forester.util.GeneralTable;
import org.forester.util.SequenceIdParser;
-import org.forester.ws.uniprot.DatabaseTools;
-import org.forester.ws.uniprot.SequenceDatabaseEntry;
-import org.forester.ws.uniprot.UniProtTaxonomy;
-import org.forester.ws.uniprot.UniProtWsTools;
+import org.forester.ws.seqdb.DatabaseTools;
+import org.forester.ws.seqdb.SequenceDatabaseEntry;
+import org.forester.ws.seqdb.SequenceDbWsTools;
+import org.forester.ws.seqdb.UniProtTaxonomy;
import org.forester.ws.wabi.TxSearch;
import org.forester.ws.wabi.TxSearch.RANKS;
import org.forester.ws.wabi.TxSearch.TAX_NAME_CLASS;
private static boolean testUniprotTaxonomySearch() {
try {
- List<UniProtTaxonomy> results = UniProtWsTools
+ List<UniProtTaxonomy> results = SequenceDbWsTools
.getTaxonomiesFromCommonNameStrict( "starlet sea anemone", 10 );
if ( results.size() != 1 ) {
return false;
return false;
}
results = null;
- results = UniProtWsTools.getTaxonomiesFromScientificNameStrict( "Nematostella vectensis", 10 );
+ results = SequenceDbWsTools.getTaxonomiesFromScientificNameStrict( "Nematostella vectensis", 10 );
if ( results.size() != 1 ) {
return false;
}
return false;
}
results = null;
- results = UniProtWsTools.getTaxonomiesFromId( "45351", 10 );
+ results = SequenceDbWsTools.getTaxonomiesFromId( "45351", 10 );
if ( results.size() != 1 ) {
return false;
}
return false;
}
results = null;
- results = UniProtWsTools.getTaxonomiesFromTaxonomyCode( "NEMVE", 10 );
+ results = SequenceDbWsTools.getTaxonomiesFromTaxonomyCode( "NEMVE", 10 );
if ( results.size() != 1 ) {
return false;
}
}
private static boolean testUniprotEntryRetrieval() {
- if ( !UniProtWsTools.parseUniProtAccessor( "P12345" ).equals( "P12345" ) ) {
+ if ( !SequenceDbWsTools.parseUniProtAccessor( "P12345" ).equals( "P12345" ) ) {
return false;
}
- if ( UniProtWsTools.parseUniProtAccessor( "EP12345" ) != null ) {
+ if ( SequenceDbWsTools.parseUniProtAccessor( "EP12345" ) != null ) {
return false;
}
- if ( UniProtWsTools.parseUniProtAccessor( "3 4P12345" ) != null ) {
+ if ( SequenceDbWsTools.parseUniProtAccessor( "3 4P12345" ) != null ) {
return false;
}
- if ( UniProtWsTools.parseUniProtAccessor( "P12345E" ) != null ) {
+ if ( SequenceDbWsTools.parseUniProtAccessor( "P12345E" ) != null ) {
return false;
}
- if ( UniProtWsTools.parseUniProtAccessor( "P123455" ) != null ) {
+ if ( SequenceDbWsTools.parseUniProtAccessor( "P123455" ) != null ) {
return false;
}
- if ( UniProtWsTools.parseUniProtAccessor( "EP12345E" ) != null ) {
+ if ( SequenceDbWsTools.parseUniProtAccessor( "EP12345E" ) != null ) {
return false;
}
- if ( UniProtWsTools.parseUniProtAccessor( "AY423861" ) != null ) {
+ if ( SequenceDbWsTools.parseUniProtAccessor( "AY423861" ) != null ) {
return false;
}
- if ( !UniProtWsTools.parseUniProtAccessor( "P1DDD5" ).equals( "P1DDD5" ) ) {
+ if ( !SequenceDbWsTools.parseUniProtAccessor( "P1DDD5" ).equals( "P1DDD5" ) ) {
return false;
}
- if ( UniProtWsTools.parseUniProtAccessor( "P1DDDD" ) != null ) {
+ if ( SequenceDbWsTools.parseUniProtAccessor( "P1DDDD" ) != null ) {
return false;
}
- if ( !UniProtWsTools.parseUniProtAccessor( "P1234X/P12345/12-42" ).equals( "P12345" ) ) {
+ if ( !SequenceDbWsTools.parseUniProtAccessor( "P1234X/P12345/12-42" ).equals( "P12345" ) ) {
return false;
}
- if ( !UniProtWsTools.parseUniProtAccessor( "P1234X P12345 12-42" ).equals( "P12345" ) ) {
+ if ( !SequenceDbWsTools.parseUniProtAccessor( "P1234X P12345 12-42" ).equals( "P12345" ) ) {
return false;
}
- if ( !UniProtWsTools.parseUniProtAccessor( "P12345/12-42" ).equals( "P12345" ) ) {
+ if ( !SequenceDbWsTools.parseUniProtAccessor( "P12345/12-42" ).equals( "P12345" ) ) {
return false;
}
- if ( !UniProtWsTools.parseUniProtAccessor( "P1234X/P12345" ).equals( "P12345" ) ) {
+ if ( !SequenceDbWsTools.parseUniProtAccessor( "P1234X/P12345" ).equals( "P12345" ) ) {
return false;
}
try {
- final SequenceDatabaseEntry entry = UniProtWsTools.obtainUniProtEntry( "P12345", 200 );
+ final SequenceDatabaseEntry entry = SequenceDbWsTools.obtainUniProtEntry( "P12345", 200 );
if ( !entry.getAccession().equals( "P12345" ) ) {
return false;
}
|| ForesterUtil.isEmpty( id.getValue() )
|| ForesterUtil.isEmpty( id.getProvider() )
|| !id.getValue().equals( "XP_002434188" )
- || !id.getProvider().equals( "ncbi" ) ) {
+ || !id.getProvider().equals( "refseq" ) ) {
if ( id != null ) {
System.out.println( "value =" + id.getValue() );
System.out.println( "provider=" + id.getProvider() );
|| ForesterUtil.isEmpty( id.getValue() )
|| ForesterUtil.isEmpty( id.getProvider() )
|| !id.getValue().equals( "XP_002434188" )
- || !id.getProvider().equals( "ncbi" ) ) {
+ || !id.getProvider().equals( "refseq" ) ) {
if ( id != null ) {
System.out.println( "value =" + id.getValue() );
System.out.println( "provider=" + id.getProvider() );