SimpleFastaCmd implements FastaCmd { @Override public Collection<BioSequence> getBatchAccessions( Collection<String> accessions, String database ) { return this.getBatchAccessions( accessions, database, SimpleFastaCmd.blastDbHome ); } SimpleFastaCmd(); @Override BioSequence getByAccession( String accession, String database ); @Override BioSequence getByIdentifier( int identifier, String database ); @Override Collection<BioSequence> getBatchAccessions( Collection<String> accessions, String database ); @Override Collection<BioSequence> getBatchIdentifiers( Collection<Integer> identifiers, String database ); @Override BioSequence getByAccession( String accession, String database, String blastHome ); @Override BioSequence getByIdentifier( int identifier, String database, String blastHome ); @Override Collection<BioSequence> getBatchAccessions( Collection<String> accessions, String database,
            String blastHome ); @Override Collection<BioSequence> getBatchIdentifiers( Collection<Integer> identifiers, String database,
            String blastHome ); static final String FASTA_CMD_ENV_VAR; }
@Test public void testGetMultipleAcc() { if ( this.fastaCmdExecutableNotExists() ) { return; } SimpleFastaCmd fastaCmd = new SimpleFastaCmd(); Collection<String> input = new ArrayList<>(); input.add( "AA000002.1" ); input.add( "AA000003.1" ); Collection<BioSequence> bs = fastaCmd .getBatchAccessions( input, SimpleFastaCmdTest.TESTBLASTDB, testBlastDbPath ); assertNotNull( bs ); assertEquals( 2, bs.size() ); }
@Test public void testGetMultipleAccSomeNotFound() { if ( this.fastaCmdExecutableNotExists() ) { return; } SimpleFastaCmd fastaCmd = new SimpleFastaCmd(); Collection<String> input = new ArrayList<>(); input.add( "FAKE.2" ); input.add( "AA000002.1" ); input.add( "FAKE.1" ); input.add( "AA000003.1" ); Collection<BioSequence> bs = fastaCmd .getBatchAccessions( input, SimpleFastaCmdTest.TESTBLASTDB, testBlastDbPath ); assertNotNull( bs ); assertEquals( 2, bs.size() ); }