Examples with BlastSequenceInput org.nextprot.api.blast.domain.BlastSequenceInput used on opensource projects

Example 6 with BlastSequenceInput

use of org.nextprot.api.blast.domain.BlastSequenceInput in project nextprot-api by calipho-sib.

the class BlastPRunnerTest method testCommandLineBuildingWithParams.

@Test
public void testCommandLineBuildingWithParams() throws Exception {
    config = new BlastSequenceInput(blastBinPath, blastDb);
    config.setBlastSearchParams(BlastSearchParams.valueOf(BlastSearchParams.Matrix.BLOSUM45.toString(), 0.01, 12, 2));
    BlastPRunner runner = new BlastPRunner(config);
    File file = new File("/tmp/input.fasta");
    List<String> cl = runner.buildCommandLine(config, file);
    Assert.assertNotNull(config.getBinPath());
    Assert.assertNotNull(config.getNextprotBlastDbPath());
    Assert.assertEquals(15, cl.size());
    Assert.assertTrue(cl.get(0).endsWith("blastp"));
    Assert.assertEquals("-db", cl.get(1));
    Assert.assertTrue(cl.get(2).endsWith("nextprot"));
    Assert.assertEquals("-query", cl.get(3));
    Assert.assertEquals(file.getAbsolutePath(), cl.get(4));
    Assert.assertEquals("-outfmt", cl.get(5));
    Assert.assertEquals("15", cl.get(6));
    Assert.assertEquals("-matrix", cl.get(7));
    Assert.assertEquals("BLOSUM45", cl.get(8));
    Assert.assertEquals("-evalue", cl.get(9));
    Assert.assertEquals("0.01", cl.get(10));
    Assert.assertEquals("-gapopen", cl.get(11));
    Assert.assertEquals("12", cl.get(12));
    Assert.assertEquals("-gapextend", cl.get(13));
    Assert.assertEquals("2", cl.get(14));
}