JAL-2189 format tests

[jalview.git] / test / jalview / datamodel / AlignmentTest.java

diff --git a/test/jalview/datamodel/AlignmentTest.java b/test/jalview/datamodel/AlignmentTest.java
index fcf724a..7958e9b 100644 (file)
--- a/test/jalview/datamodel/AlignmentTest.java
+++ b/test/jalview/datamodel/AlignmentTest.java
@@ -134,19 +134,23 @@ public class AlignmentTest
    *          - the alignmentI object to verify (either alignment or dataset)
    * @param raiseAssert
    *          - when set, testng assertions are raised.
-   *          @param message
-   *          - null or a string message to prepend to the assert failed messages.
+   * @param message
+   *          - null or a string message to prepend to the assert failed
+   *          messages.
    * @return true if alignment references were in order, otherwise false.
    */
   public static boolean verifyAlignmentDatasetRefs(AlignmentI alignment,
           boolean raiseAssert, String message)
   {
-    if (message==null) { message = ""; }
+    if (message == null)
+    {
+      message = "";
+    }
     if (alignment == null)
     {
       if (raiseAssert)
       {
-        Assert.fail(message+"Alignment for verification was null.");
+        Assert.fail(message + "Alignment for verification was null.");
       }
       return false;
     }
@@ -161,7 +165,8 @@ public class AlignmentTest
         {
           if (raiseAssert)
           {
-            Assert.fail(message+" Alignment contained a sequence who's dataset sequence has a second dataset reference.");
+            Assert.fail(message
+                    + " Alignment contained a sequence who's dataset sequence has a second dataset reference.");
           }
           return false;
         }
@@ -169,12 +174,14 @@ public class AlignmentTest
         {
           if (raiseAssert)
           {
-            Assert.fail(message+" Alignment contained a sequence who's dataset sequence was not in the dataset.");
+            Assert.fail(message
+                    + " Alignment contained a sequence who's dataset sequence was not in the dataset.");
           }
           return false;
         }
       }
-      return verifyAlignmentDatasetRefs(alignment.getDataset(), raiseAssert, message);
+      return verifyAlignmentDatasetRefs(alignment.getDataset(),
+              raiseAssert, message);
     }
     else
     {
@@ -187,7 +194,8 @@ public class AlignmentTest
         {
           if (raiseAssert)
           {
-            Assert.fail(message+" Dataset contained a sequence with non-null dataset reference (ie not a dataset sequence!)");
+            Assert.fail(message
+                    + " Dataset contained a sequence with non-null dataset reference (ie not a dataset sequence!)");
           }
           return false;
         }
@@ -216,7 +224,8 @@ public class AlignmentTest
                 {
                   if (raiseAssert)
                   {
-                    Assert.fail(message+" DBRefEntry for sequence in alignment had map to sequence which was not a dataset sequence");
+                    Assert.fail(message
+                            + " DBRefEntry for sequence in alignment had map to sequence which was not a dataset sequence");
                   }
                   return false;
 
@@ -225,7 +234,8 @@ public class AlignmentTest
                 {
                   if (raiseAssert)
                   {
-                    Assert.fail(message+" DBRefEntry for sequence in alignment had map to sequence not in dataset");
+                    Assert.fail(message
+                            + " DBRefEntry for sequence in alignment had map to sequence not in dataset");
                   }
                   return false;
                 }
@@ -245,7 +255,8 @@ public class AlignmentTest
             {
               if (raiseAssert)
               {
-                Assert.fail(message+" CodonFrame-SSM-FromSeq is not a dataset sequence");
+                Assert.fail(message
+                        + " CodonFrame-SSM-FromSeq is not a dataset sequence");
               }
               return false;
             }
@@ -254,7 +265,8 @@ public class AlignmentTest
 
               if (raiseAssert)
               {
-                Assert.fail(message+" CodonFrame-SSM-FromSeq is not contained in dataset");
+                Assert.fail(message
+                        + " CodonFrame-SSM-FromSeq is not contained in dataset");
               }
               return false;
             }
@@ -262,7 +274,8 @@ public class AlignmentTest
             {
               if (raiseAssert)
               {
-                Assert.fail(message+" CodonFrame-SSM-Mapping-ToSeq is not a dataset sequence");
+                Assert.fail(message
+                        + " CodonFrame-SSM-Mapping-ToSeq is not a dataset sequence");
               }
               return false;
             }
@@ -271,7 +284,8 @@ public class AlignmentTest
 
               if (raiseAssert)
               {
-                Assert.fail(message+" CodonFrame-SSM-Mapping-ToSeq is not contained in dataset");
+                Assert.fail(message
+                        + " CodonFrame-SSM-Mapping-ToSeq is not contained in dataset");
               }
               return false;
             }
@@ -335,6 +349,7 @@ public class AlignmentTest
                       + msg);
     }
   }
+
   @Test(groups = { "Functional" })
   public void testVerifyAlignmentDatasetRefs()
   {
@@ -342,16 +357,13 @@ public class AlignmentTest
             "TTTTTT");
 
     // construct simple valid alignment dataset
-    Alignment al = new Alignment(new SequenceI[] {
-        sq1, sq2 });
+    Alignment al = new Alignment(new SequenceI[] { sq1, sq2 });
     // expect this to pass
     assertVerifyAlignment(al, true, "Simple valid alignment didn't verify");
 
     // check test for sequence->datasetSequence validity
     sq1.setDatasetSequence(sq2);
-    assertVerifyAlignment(
-            al,
-            false,
+    assertVerifyAlignment(al, false,
             "didn't detect dataset sequence with a dataset sequence reference.");
 
     sq1.setDatasetSequence(null);
@@ -445,7 +457,7 @@ public class AlignmentTest
    */
   public static void assertDatasetIsNormalised(AlignmentI al, String message)
   {
-    if (al.getDataset()!=null)
+    if (al.getDataset() != null)
     {
       assertDatasetIsNormalised(al.getDataset(), message);
       return;
@@ -454,17 +466,17 @@ public class AlignmentTest
      * look for pairs of sequences with same ID, start, end, and sequence
      */
     List<SequenceI> seqSet = al.getSequences();
-    for (int p=0;p<seqSet.size(); p++)
+    for (int p = 0; p < seqSet.size(); p++)
     {
       SequenceI pSeq = seqSet.get(p);
-      for (int q=p+1; q<seqSet.size(); q++)
+      for (int q = p + 1; q < seqSet.size(); q++)
       {
         SequenceI qSeq = seqSet.get(q);
-        if (pSeq.getStart()!=qSeq.getStart())
+        if (pSeq.getStart() != qSeq.getStart())
         {
           continue;
         }
-        if (pSeq.getEnd()!=qSeq.getEnd())
+        if (pSeq.getEnd() != qSeq.getEnd())
         {
           continue;
         }
@@ -482,7 +494,7 @@ public class AlignmentTest
       }
     }
   }
-  
+
   @Test(groups = { "Functional", "Asserts" })
   public void testAssertDatasetIsNormalised()
   {
@@ -557,6 +569,7 @@ public class AlignmentTest
       Assert.fail("Expected identical sequence to raise exception.");
     }
   }
+
   /*
    * Read in Stockholm format test data including secondary structure
    * annotations.
@@ -1013,6 +1026,7 @@ public class AlignmentTest
     assertAlignmentDatasetRefs(align,
             "addSequence broke dataset reference integrity");
   }
+
   @Test(groups = "Functional")
   public void getVisibleStartAndEndIndexTest()
   {
@@ -1052,7 +1066,7 @@ public class AlignmentTest
     SequenceI pep = new Sequence("pep", "ASD");
     SequenceI dna = new Sequence("dna", "aaaGCCTCGGATggg");
     SequenceI cds = new Sequence("cds", "GCCTCGGAT");
-  
+
     // add dbref from dna to peptide
     DBRefEntry dbr = new DBRefEntry("UNIPROT", "", "pep");
     dbr.setMap(new Mapping(pep, new MapList(new int[] { 4, 15 }, new int[] {
@@ -1078,14 +1092,14 @@ public class AlignmentTest
     pep.addDBRef(dbr4);
 
     AlignmentI protein = new Alignment(new SequenceI[] { pep });
-  
+
     /*
      * create the alignment dataset
      */
     ((Alignment) protein).createDatasetAlignment();
-  
+
     AlignmentI ds = protein.getDataset();
-  
+
     // should be 3 sequences in dataset
     assertEquals(3, ds.getHeight());
     assertTrue(ds.getSequences().contains(pep.getDatasetSequence()));