diff --git a/test/uk/ac/sanger/artemis/circular/digest/CircularGenomeControllerTest.java b/test/uk/ac/sanger/artemis/circular/digest/CircularGenomeControllerTest.java index e31985198a10db730c28f67a7c19e736feff2c93..71316295943e05004b8b81c5d69d51d9939e1a2d 100644 --- a/test/uk/ac/sanger/artemis/circular/digest/CircularGenomeControllerTest.java +++ b/test/uk/ac/sanger/artemis/circular/digest/CircularGenomeControllerTest.java @@ -25,23 +25,23 @@ import org.junit.Test; public class CircularGenomeControllerTest { - /** - * Test that EMBOSS_ROOT is set - */ - @Test - public void testEmbossRoot() - { - assertNotNull("EMBOSS_ROOT not set", System.getProperty("EMBOSS_ROOT")); - } + /** + * Test that EMBOSS_ROOT is set + */ + @Test + public void testEmbossRoot() + { + assertNotNull("EMBOSS_ROOT not set", System.getProperty("EMBOSS_ROOT")); + } - /** - * Test that restrict can be found - */ - @Test - public void testEmbossInstalled() - { - String restrictPath = System.getProperty("EMBOSS_ROOT") + "/bin/restrict"; - File restrict = new File(restrictPath); - assertTrue("restrict not found at: " + restrictPath, restrict.exists()); - } + /** + * Test that restrict can be found + */ + @Test + public void testEmbossInstalled() + { + String restrictPath = System.getProperty("EMBOSS_ROOT") + "/bin/restrict"; + File restrict = new File(restrictPath); + assertTrue("restrict not found at: " + restrictPath, restrict.exists()); + } } \ No newline at end of file diff --git a/test/uk/ac/sanger/artemis/circular/digest/EmbossTableParserTest.java b/test/uk/ac/sanger/artemis/circular/digest/EmbossTableParserTest.java index c23c04465b2156d865cf747b2f6c04dca9c8fca0..4ffb1f4c3e9bc9642d130ccbac175e128ae23bae 100644 --- a/test/uk/ac/sanger/artemis/circular/digest/EmbossTableParserTest.java +++ b/test/uk/ac/sanger/artemis/circular/digest/EmbossTableParserTest.java @@ -35,27 +35,27 @@ import uk.ac.sanger.artemis.circular.digest.EmbossTableParser; public class EmbossTableParserTest { - /** - * Test that restrict output is parsed - */ - @Test - public void testParser() throws IOException - { - final InputStream inputStream = - EmbossTableParserTest.class.getResourceAsStream("/data/foo.restrict"); + /** + * Test that restrict output is parsed + */ + @Test + public void testParser() throws IOException + { + final InputStream inputStream = EmbossTableParserTest.class + .getResourceAsStream("/data/foo.restrict"); InputStreamReader reader = new InputStreamReader(inputStream); EmbossTableParser etp = new EmbossTableParser(); - + List<CutSite> cutSites = etp.parse(new BufferedReader(reader)); CutSite firstCutSite = cutSites.get(0); - - assertEquals("Number of cut sites", cutSites.size(), 4); - assertEquals("Enzyme name", firstCutSite.getEnzymeName(), "HindIII"); - assertEquals("3prime", firstCutSite.getThreePrime(), 85); - assertEquals("5prime", firstCutSite.getFivePrime(), 81); - assertEquals("3prime-rev", firstCutSite.getThreePrimeRev(), 0); - assertEquals("5prime-rev", firstCutSite.getFivePrimeRev(), 0); - assertTrue("Cut site strand", firstCutSite.isForward()); - } + + assertEquals("Number of cut sites", cutSites.size(), 4); + assertEquals("Enzyme name", firstCutSite.getEnzymeName(), "HindIII"); + assertEquals("3prime", firstCutSite.getThreePrime(), 85); + assertEquals("5prime", firstCutSite.getFivePrime(), 81); + assertEquals("3prime-rev", firstCutSite.getThreePrimeRev(), 0); + assertEquals("5prime-rev", firstCutSite.getFivePrimeRev(), 0); + assertTrue("Cut site strand", firstCutSite.isForward()); + } } diff --git a/test/uk/ac/sanger/artemis/circular/digest/UtilsTest.java b/test/uk/ac/sanger/artemis/circular/digest/UtilsTest.java index d6f2584310010de3bfdbda76303abddfbe7e426d..34be14a8e167e1861cccc47ed499467004d09717 100644 --- a/test/uk/ac/sanger/artemis/circular/digest/UtilsTest.java +++ b/test/uk/ac/sanger/artemis/circular/digest/UtilsTest.java @@ -30,32 +30,32 @@ import uk.ac.sanger.artemis.circular.digest.CutSite; public class UtilsTest { - /** - * Test that restrict output is parsed - */ - @Ignore("Use EmbossTableParserTest") - @Test - public void testFindCutSitesFromEmbossReport() - { - final InputStream inputStream = - UtilsTest.class.getResourceAsStream("/data/foo.restrict"); + /** + * Test that restrict output is parsed + */ + @Ignore("Use EmbossTableParserTest") + @Test + public void testFindCutSitesFromEmbossReport() + { + final InputStream inputStream = UtilsTest.class + .getResourceAsStream("/data/foo.restrict"); InputStreamReader reader = new InputStreamReader(inputStream); ReportDetails report = Utils.findCutSitesFromEmbossReport(reader); - - assertNotNull("ReportDetails null",report); - assertEquals("Sequence length",report.length, 41243); - - List<CutSite> cutSites = report.cutSites; - CutSite firstCutSite = cutSites.get(0); - - assertEquals("Number of cut sites", cutSites.size(), 4); - assertEquals("Enzyme name", firstCutSite.getEnzymeName(), "HindIII"); - assertEquals("3prime", firstCutSite.getThreePrime(), 85); - assertEquals("5prime", firstCutSite.getFivePrime(), 81); - assertEquals("3prime-rev", firstCutSite.getThreePrimeRev(), 0); - assertEquals("5prime-rev", firstCutSite.getFivePrimeRev(), 0); - assertTrue("Cut site strand", firstCutSite.isForward()); - } - + + assertNotNull("ReportDetails null", report); + assertEquals("Sequence length", report.length, 41243); + + List<CutSite> cutSites = report.cutSites; + CutSite firstCutSite = cutSites.get(0); + + assertEquals("Number of cut sites", cutSites.size(), 4); + assertEquals("Enzyme name", firstCutSite.getEnzymeName(), "HindIII"); + assertEquals("3prime", firstCutSite.getThreePrime(), 85); + assertEquals("5prime", firstCutSite.getFivePrime(), 81); + assertEquals("3prime-rev", firstCutSite.getThreePrimeRev(), 0); + assertEquals("5prime-rev", firstCutSite.getFivePrimeRev(), 0); + assertTrue("Cut site strand", firstCutSite.isForward()); + } + }