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;
}
//Nucleotide: 1 letter + 5 numerals OR 2 letters + 6 numerals
//Protein: 3 letters + 5 numerals
//http://www.ncbi.nlm.nih.gov/Sequin/acc.html
- if ( !DatabaseTools.parseGenbankAccessor( "AY423861" ).equals( "AY423861" ) ) {
+ if ( !SequenceIdParser.parseGenbankAccessor( "AY423861" ).equals( "AY423861" ) ) {
return false;
}
- if ( !DatabaseTools.parseGenbankAccessor( ".AY423861." ).equals( "AY423861" ) ) {
+ if ( !SequenceIdParser.parseGenbankAccessor( ".AY423861." ).equals( "AY423861" ) ) {
return false;
}
- if ( DatabaseTools.parseGenbankAccessor( "AAY423861" ) != null ) {
+ if ( SequenceIdParser.parseGenbankAccessor( "AAY423861" ) != null ) {
return false;
}
- if ( DatabaseTools.parseGenbankAccessor( "AY4238612" ) != null ) {
+ if ( SequenceIdParser.parseGenbankAccessor( "AY4238612" ) != null ) {
return false;
}
- if ( DatabaseTools.parseGenbankAccessor( "AAY4238612" ) != null ) {
+ if ( SequenceIdParser.parseGenbankAccessor( "AAY4238612" ) != null ) {
return false;
}
- if ( DatabaseTools.parseGenbankAccessor( "Y423861" ) != null ) {
+ if ( SequenceIdParser.parseGenbankAccessor( "Y423861" ) != null ) {
return false;
}
- if ( !DatabaseTools.parseGenbankAccessor( "S12345" ).equals( "S12345" ) ) {
+ if ( !SequenceIdParser.parseGenbankAccessor( "S12345" ).equals( "S12345" ) ) {
return false;
}
- if ( !DatabaseTools.parseGenbankAccessor( "|S12345|" ).equals( "S12345" ) ) {
+ if ( !SequenceIdParser.parseGenbankAccessor( "|S12345|" ).equals( "S12345" ) ) {
return false;
}
- if ( DatabaseTools.parseGenbankAccessor( "|S123456" ) != null ) {
+ if ( SequenceIdParser.parseGenbankAccessor( "|S123456" ) != null ) {
return false;
}
- if ( DatabaseTools.parseGenbankAccessor( "ABC123456" ) != null ) {
+ if ( SequenceIdParser.parseGenbankAccessor( "ABC123456" ) != null ) {
return false;
}
- if ( !DatabaseTools.parseGenbankAccessor( "ABC12345" ).equals( "ABC12345" ) ) {
+ if ( !SequenceIdParser.parseGenbankAccessor( "ABC12345" ).equals( "ABC12345" ) ) {
return false;
}
- if ( !DatabaseTools.parseGenbankAccessor( "&ABC12345&" ).equals( "ABC12345" ) ) {
+ if ( !SequenceIdParser.parseGenbankAccessor( "&ABC12345&" ).equals( "ABC12345" ) ) {
return false;
}
- if ( DatabaseTools.parseGenbankAccessor( "ABCD12345" ) != null ) {
+ if ( SequenceIdParser.parseGenbankAccessor( "ABCD12345" ) != null ) {
return false;
}
return true;
}
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;
}
private static boolean testSequenceIdParsing() {
try {
- Identifier id = SequenceIdParser.parse( "mites|ref_XP_002434188_1" );
- if ( id == null || ForesterUtil.isEmpty( id.getValue() ) || !id.getValue().equals( "002434188_1" ) ) {
+ Identifier id = SequenceIdParser.parse( "gb_ADF31344_segmented_worms_" );
+ if ( id == null
+ || ForesterUtil.isEmpty( id.getValue() )
+ || ForesterUtil.isEmpty( id.getProvider() )
+ || !id.getValue().equals( "ADF31344" )
+ || !id.getProvider().equals( "ncbi" ) ) {
+ if ( id != null ) {
+ System.out.println( "value =" + id.getValue() );
+ System.out.println( "provider=" + id.getProvider() );
+ }
+ return false;
+ }
+ //
+ id = SequenceIdParser.parse( "segmented worms|gb_ADF31344" );
+ if ( id == null
+ || ForesterUtil.isEmpty( id.getValue() )
+ || ForesterUtil.isEmpty( id.getProvider() )
+ || !id.getValue().equals( "ADF31344" )
+ || !id.getProvider().equals( "ncbi" ) ) {
+ if ( id != null ) {
+ System.out.println( "value =" + id.getValue() );
+ System.out.println( "provider=" + id.getProvider() );
+ }
+ return false;
+ }
+ //
+ id = SequenceIdParser.parse( "segmented worms gb_ADF31344 and more" );
+ if ( id == null
+ || ForesterUtil.isEmpty( id.getValue() )
+ || ForesterUtil.isEmpty( id.getProvider() )
+ || !id.getValue().equals( "ADF31344" )
+ || !id.getProvider().equals( "ncbi" ) ) {
+ if ( id != null ) {
+ System.out.println( "value =" + id.getValue() );
+ System.out.println( "provider=" + id.getProvider() );
+ }
+ return false;
+ }
+
+ //
+ id = SequenceIdParser.parse( "gb_AAA96518_1" );
+ if ( id == null
+ || ForesterUtil.isEmpty( id.getValue() )
+ || ForesterUtil.isEmpty( id.getProvider() )
+ || !id.getValue().equals( "AAA96518" )
+ || !id.getProvider().equals( "ncbi" ) ) {
+ if ( id != null ) {
+ System.out.println( "value =" + id.getValue() );
+ System.out.println( "provider=" + id.getProvider() );
+ }
+ return false;
+ }
+ //
+ id = SequenceIdParser.parse( "gb_EHB07727_1_rodents_" );
+ if ( id == null
+ || ForesterUtil.isEmpty( id.getValue() )
+ || ForesterUtil.isEmpty( id.getProvider() )
+ || !id.getValue().equals( "EHB07727" )
+ || !id.getProvider().equals( "ncbi" ) ) {
+ if ( id != null ) {
+ System.out.println( "value =" + id.getValue() );
+ System.out.println( "provider=" + id.getProvider() );
+ }
+ return false;
+ }
+ //
+ id = SequenceIdParser.parse( "dbj_BAF37827_1_turtles_" );
+ if ( id == null
+ || ForesterUtil.isEmpty( id.getValue() )
+ || ForesterUtil.isEmpty( id.getProvider() )
+ || !id.getValue().equals( "BAF37827" )
+ || !id.getProvider().equals( "ncbi" ) ) {
+ if ( id != null ) {
+ System.out.println( "value =" + id.getValue() );
+ System.out.println( "provider=" + id.getProvider() );
+ }
+ return false;
+ }
+ //
+ id = SequenceIdParser.parse( "emb_CAA73223_1_primates_" );
+ if ( id == null
+ || ForesterUtil.isEmpty( id.getValue() )
+ || ForesterUtil.isEmpty( id.getProvider() )
+ || !id.getValue().equals( "CAA73223" )
+ || !id.getProvider().equals( "ncbi" ) ) {
+ if ( id != null ) {
+ System.out.println( "value =" + id.getValue() );
+ System.out.println( "provider=" + id.getProvider() );
+ }
+ return false;
+ }
+ //
+ id = SequenceIdParser.parse( "mites|ref_XP_002434188_1" );
+ if ( id == null
+ || ForesterUtil.isEmpty( id.getValue() )
+ || ForesterUtil.isEmpty( id.getProvider() )
+ || !id.getValue().equals( "XP_002434188" )
+ || !id.getProvider().equals( "refseq" ) ) {
+ if ( id != null ) {
+ System.out.println( "value =" + id.getValue() );
+ System.out.println( "provider=" + id.getProvider() );
+ }
+ return false;
+ }
+ //
+ id = SequenceIdParser.parse( "mites_ref_XP_002434188_1_bla_XP_12345" );
+ if ( id == null
+ || ForesterUtil.isEmpty( id.getValue() )
+ || ForesterUtil.isEmpty( id.getProvider() )
+ || !id.getValue().equals( "XP_002434188" )
+ || !id.getProvider().equals( "refseq" ) ) {
+ if ( id != null ) {
+ System.out.println( "value =" + id.getValue() );
+ System.out.println( "provider=" + id.getProvider() );
+ }
+ return false;
+ }
+ //
+ id = SequenceIdParser.parse( "XP_12345" );
+ if ( id != null ) {
return false;
}
+
+ // lcl_91970_unknown_
}
catch ( final Exception e ) {
e.printStackTrace( System.out );