private void mapIds ( ) { if ( queryReferences != null ) { queryReferencesMap = new HashMap < String , Sequence > ( queryReferences . size ( ) ) ; for ( int counter = 0 ; counter < queryReferences . size ( ) ; counter ++ ) { String id = "Query_" + ( counter + 1 ) ; queryReferencesMap . put ( id , queryReferences . get ( counter ) ) ; } } if ( databaseReferences != null ) { databaseReferencesMap = new HashMap < String , Sequence > ( databaseReferences . size ( ) ) ; for ( int counter = 0 ; counter < databaseReferences . size ( ) ; counter ++ ) { // this is strange: while Query_id are 1 based, Hit (database) id are 0 based String id = "gnl|BL_ORD_ID|" + ( counter ) ; databaseReferencesMap . put ( id , databaseReferences . get ( counter ) ) ; } } }
fill the map association between sequences an a unique id