public final class UniProtTaxonomy {
- public static final String ARCHAEA = "Archaea";
- public static final String BACTERIA = "Bacteria";
- public static final String EUKARYOTA = "Eukaryota";
- private final List<String> _lineage;
- private final String _code;
- private final String _scientific_name;
- private final String _common_name;
- private final String _synonym;
- private final String _rank;
- private final String _id;
- public final static String CELLULAR_ORGANISMS = "cellular organisms";
- public final static String VIRUSES = "Viruses";
+ public static final String ARCHAEA = "Archaea";
+ public static final String BACTERIA = "Bacteria";
+ public static final String EUKARYOTA = "Eukaryota";
+ private final List<String> _lineage;
+ private final String _code;
+ private final String _scientific_name;
+ private final String _common_name;
+ private final String _synonym;
+ private final String _rank;
+ private final String _id;
+ public final static String CELLULAR_ORGANISMS = "cellular organisms";
+ public final static String VIRUSES = "Viruses";
+ public static final String X = "x";
public UniProtTaxonomy( final String line ) {
final String[] items = line.split( "\t" );
_synonym = synonym;
_rank = rank;
_id = id;
- if ( ( _lineage != null && _lineage.isEmpty() ) || ( ( !ForesterUtil.isEmpty( _lineage ) ) && !_lineage.get( _lineage.size() - 1 ).equalsIgnoreCase( _scientific_name ) ) ) {
+ if ( ( ( _lineage != null ) && _lineage.isEmpty() )
+ || ( ( !ForesterUtil.isEmpty( _lineage ) ) && !_lineage.get( _lineage.size() - 1 )
+ .equalsIgnoreCase( _scientific_name ) ) ) {
_lineage.add( _scientific_name );
}
-
}
-
-
/**
* Creates deep copy for all fields, except lineage.
*
public String getSynonym() {
return _synonym;
}
-
+
public final static UniProtTaxonomy createSpecialFromScientificName( final String sn ) {
-
- List<String> lineage = new ArrayList<String>();
- String code = "";
- String common_name = "";
+ final List<String> lineage = new ArrayList<String>();
+ final String code = "";
+ final String common_name = "";
String scientific_name = "";
- String synonym = "";
+ final String synonym = "";
String rank = "";
String id = "";
-
if ( sn.equalsIgnoreCase( BACTERIA ) ) {
scientific_name = BACTERIA;
lineage.add( "cellular organisms" );
else if ( sn.equalsIgnoreCase( ARCHAEA ) ) {
scientific_name = ARCHAEA;
lineage.add( "cellular organisms" );
-
rank = "superkingdom";
id = "2157";
}
rank = "superkingdom";
id = "10239";
}
+ else if ( sn.equalsIgnoreCase( X ) ) {
+ scientific_name = X;
+ }
else {
throw new IllegalArgumentException( "illegal attempt to make UniProt taxonomy for :" + sn );
}
return new UniProtTaxonomy( lineage, code, common_name, scientific_name, synonym, rank, id );
-
-
}
}