X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FAnnotationFileIOTest.java;fp=test%2Fjalview%2Fio%2FAnnotationFileIOTest.java;h=de78aa1e871a7645425962d9ffd53187e2894265;hb=3659ecfe7bb17dd25a0a6b5c94a7d9dab4525136;hp=9c4be2dcfa7b21e2a443a084b86913a55ab4ea77;hpb=5d49f772d8dd53aba8907f37a244b00ed8f86a87;p=jalview.git

diff --git a/test/jalview/io/AnnotationFileIOTest.java b/test/jalview/io/AnnotationFileIOTest.java
index 9c4be2d..de78aa1 100644
--- a/test/jalview/io/AnnotationFileIOTest.java
+++ b/test/jalview/io/AnnotationFileIOTest.java
@@ -50,28 +50,26 @@ public class AnnotationFileIOTest
     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
   }
 
-  static String TestFiles[][] = {
-      { "Test example annotation import/export", "examples/uniref50.fa",
-          "examples/testdata/example_annot_file.jva" },
+  static String TestFiles[][] = { { "Test example annotation import/export",
+      "examples/uniref50.fa", "examples/testdata/example_annot_file.jva" },
       { "Test multiple combine annotation statements import/export",
           "examples/uniref50.fa",
           "examples/testdata/test_combine_annot.jva" },
-      {
-          "Test multiple combine annotation statements with sequence_ref import/export",
+      { "Test multiple combine annotation statements with sequence_ref import/export",
           "examples/uniref50.fa", "examples/testdata/uniref50_iupred.jva" },
-      {
-          "Test group only annotation file parsing results in parser indicating annotation was parsed",
+      { "Test group only annotation file parsing results in parser indicating annotation was parsed",
           "examples/uniref50.fa", "examples/testdata/test_grpannot.jva" },
       { "Test hiding/showing of insertions on sequence_ref",
-          "examples/uniref50.fa", "examples/testdata/uniref50_seqref.jva" } };
+          "examples/uniref50.fa",
+          "examples/testdata/uniref50_seqref.jva" } };
 
   @Test(groups = { "Functional" })
   public void exampleAnnotationFileIO() throws Exception
   {
     for (String[] testPair : TestFiles)
     {
-      testAnnotationFileIO(testPair[0], new File(testPair[1]), new File(
-              testPair[2]));
+      testAnnotationFileIO(testPair[0], new File(testPair[1]),
+              new File(testPair[2]));
     }
   }
 
@@ -97,7 +95,8 @@ public class AnnotationFileIOTest
     {
       e.printStackTrace();
     }
-    Assert.fail("Couln't read the alignment in file '" + f.toString() + "'");
+    Assert.fail(
+            "Couln't read the alignment in file '" + f.toString() + "'");
     return null;
   }
 
@@ -111,8 +110,7 @@ public class AnnotationFileIOTest
    *          - label for IO class used to write and read back in the data from
    *          f
    */
-  void testAnnotationFileIO(String testname, File f,
-          File annotFile)
+  void testAnnotationFileIO(String testname, File f, File annotFile)
   {
     System.out.println("Test: " + testname + "\nReading annotation file '"
             + annotFile + "' onto : " + f);
@@ -121,10 +119,8 @@ public class AnnotationFileIOTest
     {
       AlignmentI al = readAlignmentFile(f);
       HiddenColumns cs = new HiddenColumns();
-      assertTrue(
-              "Test "
-                      + testname
-                      + "\nAlignment was not annotated - annotation file not imported.",
+      assertTrue("Test " + testname
+              + "\nAlignment was not annotated - annotation file not imported.",
               new AnnotationFile().readAnnotationFile(al, cs, af,
                       DataSourceType.FILE));
 
@@ -135,25 +131,19 @@ public class AnnotationFileIOTest
       String anfileout = new AnnotationFile().printAnnotations(
               al.getAlignmentAnnotation(), al.getGroups(),
               al.getProperties(), null, al, v);
-      assertTrue(
-              "Test "
-                      + testname
-                      + "\nAlignment annotation file was not regenerated. Null string",
+      assertTrue("Test " + testname
+              + "\nAlignment annotation file was not regenerated. Null string",
               anfileout != null);
-      assertTrue(
-              "Test "
-                      + testname
-                      + "\nAlignment annotation file was not regenerated. Empty string",
+      assertTrue("Test " + testname
+              + "\nAlignment annotation file was not regenerated. Empty string",
               anfileout.length() > "JALVIEW_ANNOTATION".length());
 
-      System.out.println("Output annotation file:\n" + anfileout
-              + "\n<<EOF\n");
+      System.out.println(
+              "Output annotation file:\n" + anfileout + "\n<<EOF\n");
 
       AlignmentI al_new = readAlignmentFile(f);
-      assertTrue(
-              "Test "
-                      + testname
-                      + "\nregenerated annotation file did not annotate alignment.",
+      assertTrue("Test " + testname
+              + "\nregenerated annotation file did not annotate alignment.",
               new AnnotationFile().readAnnotationFile(al_new, anfileout,
                       DataSourceType.PASTE));
 
@@ -165,13 +155,12 @@ public class AnnotationFileIOTest
     {
       e.printStackTrace();
     }
-    Assert.fail("Test "
-            + testname
+    Assert.fail("Test " + testname
             + "\nCouldn't complete Annotation file roundtrip input/output/input test for '"
             + annotFile + "'.");
   }
-  
-  @Test(groups="Functional")
+
+  @Test(groups = "Functional")
   public void testAnnotateAlignmentView()
   {
     long t1 = System.currentTimeMillis();
@@ -188,8 +177,9 @@ public class AnnotationFileIOTest
             + "SEQUENCE_GROUP\tGroup2\t*\t*\t2\n"
             + "SEQUENCE_GROUP\tGroup1\t*\t*\t3\n"
             + "PROPERTIES\tGroup1\toutlineColour=blue\tidColour=red\n";
-    new AnnotationFile().annotateAlignmentView(af.getViewport(), annotationFile, DataSourceType.PASTE);
-    
+    new AnnotationFile().annotateAlignmentView(af.getViewport(),
+            annotationFile, DataSourceType.PASTE);
+
     AlignmentI al = af.getViewport().getAlignment();
     List<SequenceGroup> groups = al.getGroups();
     assertEquals(3, groups.size());
@@ -201,7 +191,7 @@ public class AnnotationFileIOTest
     sg = groups.get(1);
     assertEquals("Group2", sg.getName());
     assertTrue(sg.contains(al.getSequenceAt(1)));
-    
+
     /*
      * the bug fix: a second group of the same name is also given properties
      */