@Test public void testLoadFastaSequences() { BiojavaSequence seq = null; try { // Test read Protein as fasta seq = biojava.loadSequence(TestData.getPathToAAFastaSequence()); assertNotNull(seq); assertEquals("SEQUENCE", seq.getPlainSequence().trim().toUpperCase()); // Test read DNA as fasta seq = biojava.loadSequence(TestData.getPathToDNAFastaSequence()); assertNotNull(seq); assertEquals("GATTACA", seq.getPlainSequence().trim().toUpperCase()); /* //Test read RNA as fasta seq = biojava.loadSequence( TestData.getPathToRNAFastaSequence() ); assertNotNull( seq ); assertEquals( "GAUUACA", seq.getPlainSequence().trim().toUpperCase() ); */ } catch (IOException e) { fail(e.getMessage()); } catch (Exception e) { LogUtils.debugTrace(logger, e); fail(e.getMessage()); } }
@Test public void testToFasta() { BiojavaSequence seq = null; try { seq = biojava.loadSequence(TestData.getPathToAAFastaSequence()); // seq = biojava.loadSequence( TestData.getPathToFosbFastaSequence() ); } catch (IOException e) { LogUtils.debugTrace(logger, e); fail(e.getMessage()); } catch (Exception e) { LogUtils.debugTrace(logger, e); fail(e.getMessage()); } assertNotNull(seq); // assertEquals( "Sequence", seq.getName()); try { assertEquals("SEQUENCE", seq.getPlainSequence().trim()); } catch (IOException e) { LogUtils.debugTrace(logger, e); fail(e.getMessage()); } }