UtilsΒΆ
Class ReadMSA provides methods to read one or multiple sequences from a .fasta file. The main method is readSequenceFromFastaFile() , which takes a path to the .fasta file as a parameter and returns an array of arrays of chars, containing the sequences from the file (one array for each sequence), and its adjacent method seqAlignedCorrectly(), which is used to determine whether or not the sequences in the file are aligned correctly (in this case, if all sequences in the file are of equal length (including gaps as chars), they will be considered correctly aligned).
| Method Summary | |
|---|---|
| Modifier and Type | Method and Description |
| public static char[][] | readSequenceFromFastaFile(String filepath) Returns sequences from the file specified by filepath one array per sequence |
| private static boolean | seqAlignedCorrectly(List<List<Character>> theList) Returns true if all List<Character> in theList are of the same size |
Class ReadMSATest contains methods for unit testing of the code in class ReadMSA. The tests were written to cover 100% of the code in ReadMSA. Following is the Method Summary for the class.
| Method Summary | |
|---|---|
| Modifier and Type | Method and Description |
@BeforeEach public void |
init() Initializes seqReader (the instance of ReadMSA) before each Test |
@Test public void |
correctSequenceHandlingTest() Unit testing for correctly aligned sequences. Fails if the length of returned array does not fit the number of sequences in the input file, or if any of the sequences has been read wrong |
@Test public void |
correctHandlingOfBlankLinesTest() Unit testing for files that have blank lines (if not handled correctly, blank lines will cause the program to throw exception) |
@Test public void |
invalidFilePathTest() Unit testing for invalid filepaths. Fails if no FileNotFoundException is raised in case of passing an invalid filepath as a parameter |
@Test public void |
incorrectSequenceTest() Unit testing for incorrectly aligned sequences. The test fails if a file with incorrectly aligned (not equal in size) sequences is passed as a parameter in method call, and no RuntimeException is thrown |
@AfterEach public void |
fin() Sets seqReader to null after each test |