X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FAnnotationFileIOTest.java;h=18e008ec823a91c96d5341f95f4ce8d0d0de7813;hb=7ab5d6b0ba5fec1ea4a4239e79c476d841622485;hp=64ca141039611bcd32ee2102d02937aa9d502a56;hpb=1889827c44c51f6353fe8619e5d44b421158af23;p=jalview.git

diff --git a/test/jalview/io/AnnotationFileIOTest.java b/test/jalview/io/AnnotationFileIOTest.java
index 64ca141..18e008e 100644
--- a/test/jalview/io/AnnotationFileIOTest.java
+++ b/test/jalview/io/AnnotationFileIOTest.java
@@ -49,9 +49,10 @@ public class AnnotationFileIOTest
   @Test
   public void exampleAnnotationFileIO() throws Exception
   {
-    for (String[] testPair:TestFiles)
+    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]));
     }
   }
 
@@ -65,11 +66,12 @@ public class AnnotationFileIOTest
 
       AlignmentI al = rf.readFile(ff, AppletFormatAdapter.FILE,
               new IdentifyFile().Identify(ff, AppletFormatAdapter.FILE));
-      
+
       // make sure dataset is initialised ? not sure about this
       for (int i = 0; i < al.getSequencesArray().length; ++i)
       {
-        al.getSequenceAt(i).setDatasetSequence(al.getSequenceAt(i).createDatasetSequence());
+        al.getSequenceAt(i).setDatasetSequence(
+                al.getSequenceAt(i).createDatasetSequence());
       }
       assertNotNull("Couldn't read supplied alignment data.", al);
       return al;
@@ -77,9 +79,10 @@ public class AnnotationFileIOTest
     {
       e.printStackTrace();
     }
-    fail("Couln't read the alignment in file '"+f.toString()+"'");
+    fail("Couln't read the alignment in file '" + f.toString() + "'");
     return null;
   }
+
   /**
    * test alignment data in given file can be imported, exported and reimported
    * with no dataloss
@@ -90,25 +93,48 @@ public class AnnotationFileIOTest
    *          - label for IO class used to write and read back in the data from
    *          f
    */
-  public static void testAnnotationFileIO(String testname, File f, File annotFile)
+  public static void testAnnotationFileIO(String testname, File f,
+          File annotFile)
   {
-    System.out.println("Test: "+testname+"\nReading annotation file '"+annotFile+"' onto : " + f);
+    System.out.println("Test: " + testname + "\nReading annotation file '"
+            + annotFile + "' onto : " + f);
     String af = annotFile.getPath();
     try
     {
       AlignmentI al = readAlignmentFile(f);
-      
-      assertTrue("Test "+testname+"\nAlignment was not annotated - annotation file not imported.",new AnnotationFile().readAnnotationFile(al, af, FormatAdapter.FILE));
-      
-      String anfileout = new AnnotationFile().printAnnotations(al.getAlignmentAnnotation(), al.getGroups(), al.getProperties());
-      assertTrue("Test "+testname+"\nAlignment annotation file was not regenerated. Null string",anfileout!=null);
-      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");
-      
+      assertTrue(
+              "Test "
+                      + testname
+                      + "\nAlignment was not annotated - annotation file not imported.",
+              new AnnotationFile().readAnnotationFile(al, af,
+                      FormatAdapter.FILE));
+
+      String anfileout = new AnnotationFile().printAnnotations(
+              al.getAlignmentAnnotation(), al.getGroups(),
+              al.getProperties());
+      assertTrue(
+              "Test "
+                      + testname
+                      + "\nAlignment annotation file was not regenerated. Null string",
+              anfileout != null);
+      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");
+
       AlignmentI al_new = readAlignmentFile(f);
-      assertTrue("Test "+testname+"\nregenerated annotation file did not annotate alignment.",new AnnotationFile().readAnnotationFile(al_new, anfileout, FormatAdapter.PASTE));
-      
+      assertTrue(
+              "Test "
+                      + testname
+                      + "\nregenerated annotation file did not annotate alignment.",
+              new AnnotationFile().readAnnotationFile(al_new, anfileout,
+                      FormatAdapter.PASTE));
+
       // test for consistency in io
       StockholmFileTest.testAlignmentEquivalence(al, al_new);
       return;
@@ -116,6 +142,9 @@ public class AnnotationFileIOTest
     {
       e.printStackTrace();
     }
-    fail("Test "+testname+"\nCouldn't complete Annotation file roundtrip input/output/input test for '"+annotFile+"'.");
+    fail("Test "
+            + testname
+            + "\nCouldn't complete Annotation file roundtrip input/output/input test for '"
+            + annotFile + "'.");
   }
 }