From 03683463b01860c61cb869ab5dbb383541ff246c Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Wed, 25 Mar 2009 12:01:17 +0000
Subject: [PATCH] fix formats
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@10274 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
.../digest/CircularGenomeControllerTest.java | 36 ++++++-------
.../digest/EmbossTableParserTest.java | 36 ++++++-------
.../artemis/circular/digest/UtilsTest.java | 50 +++++++++----------
3 files changed, 61 insertions(+), 61 deletions(-)
diff --git a/test/uk/ac/sanger/artemis/circular/digest/CircularGenomeControllerTest.java b/test/uk/ac/sanger/artemis/circular/digest/CircularGenomeControllerTest.java
index e31985198..713162959 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 c23c04465..4ffb1f4c3 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 d6f258431..34be14a8e 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());
+ }
+
}
--
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