X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fanalysis%2FAlignmentUtilsTests.java;h=f017662081eda164e5a0605f6c28743c97d82ec5;hb=56d72101b0584635cf539d5413db27abc8deb575;hp=0f3ea960a6f5a622cff1be6092cedf2bdfe8ec39;hpb=57924096fd7009330b3d879874f7d42874b4f416;p=jalview.git

diff --git a/test/jalview/analysis/AlignmentUtilsTests.java b/test/jalview/analysis/AlignmentUtilsTests.java
index 0f3ea96..f017662 100644
--- a/test/jalview/analysis/AlignmentUtilsTests.java
+++ b/test/jalview/analysis/AlignmentUtilsTests.java
@@ -2605,25 +2605,29 @@ public class AlignmentUtilsTests
     assertSame(seq, cds1.getDatasetSequence());
   }
 
-
   @Test(groups = "Functional")
   public void testAddReferenceAnnotations()
   {
-    SequenceI longseq= new Sequence("longA","ASDASDASDASDAASDASDASDASDA");
+    SequenceI longseq = new Sequence("longA", "ASDASDASDASDAASDASDASDASDA");
     Annotation[] aa = new Annotation[longseq.getLength()];
-    
-    for (int p=0;p<aa.length; p++)
+
+    for (int p = 0; p < aa.length; p++)
     {
-      aa[p] = new Annotation("P", "pos "+(p+1), (char)0, (float)p+1);
+      aa[p] = new Annotation("P", "pos " + (p + 1), (char) 0,
+              (float) p + 1);
     }
-    AlignmentAnnotation refAnnot=new AlignmentAnnotation("LongSeqAnnot","Annotations",aa);
+    AlignmentAnnotation refAnnot = new AlignmentAnnotation("LongSeqAnnot",
+            "Annotations", aa);
     refAnnot.setCalcId("Test");
     longseq.addAlignmentAnnotation(refAnnot);
     verifyExpectedSequenceAnnotation(refAnnot);
 
-    Alignment ourAl = new Alignment(new SequenceI[] { longseq.getSubSequence(5, 10),longseq.getSubSequence(7, 12)});
+    Alignment ourAl = new Alignment(
+            new SequenceI[]
+            { longseq.getSubSequence(5, 10),
+                longseq.getSubSequence(7, 12) });
     ourAl.createDatasetAlignment();
-    
+
     // transfer annotation
     SortedMap<String, String> tipEntries = new TreeMap<>();
     Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<>();
@@ -2633,9 +2637,9 @@ public class AlignmentUtilsTests
     AlignmentUtils.addReferenceAnnotations(candidates, ourAl, null);
 
     assertNotNull(ourAl.getAlignmentAnnotation());
-    assertEquals(ourAl.getAlignmentAnnotation().length,2);
-    
-    for (AlignmentAnnotation alan:ourAl.getAlignmentAnnotation())
+    assertEquals(ourAl.getAlignmentAnnotation().length, 2);
+
+    for (AlignmentAnnotation alan : ourAl.getAlignmentAnnotation())
     {
       verifyExpectedSequenceAnnotation(alan);
     }
@@ -2643,12 +2647,14 @@ public class AlignmentUtilsTests
     // now simulate copy/paste to new alignment
     SequenceI[] newSeqAl = new SequenceI[2];
     // copy sequences but no annotation
-    newSeqAl[0]=new Sequence(ourAl.getSequenceAt(0),ourAl.getSequenceAt(0).getAnnotation());
-    newSeqAl[1]=new Sequence(ourAl.getSequenceAt(1),ourAl.getSequenceAt(1).getAnnotation());
-    
+    newSeqAl[0] = new Sequence(ourAl.getSequenceAt(0),
+            ourAl.getSequenceAt(0).getAnnotation());
+    newSeqAl[1] = new Sequence(ourAl.getSequenceAt(1),
+            ourAl.getSequenceAt(1).getAnnotation());
+
     Alignment newAl = new Alignment(newSeqAl);
     // delete annotation
-    for (SequenceI sq:newAl.getSequences())
+    for (SequenceI sq : newAl.getSequences())
     {
       sq.setAlignmentAnnotation(new AlignmentAnnotation[0]);
     }
@@ -2656,28 +2662,37 @@ public class AlignmentUtilsTests
     SequenceGroup sg = new SequenceGroup(Arrays.asList(newSeqAl));
     sg.setStartRes(0);
     sg.setEndRes(newAl.getWidth());
-    AlignmentUtils.addReferenceAnnotationTo(newAl, newSeqAl[0], newSeqAl[0].getDatasetSequence().getAnnotation()[0], sg);
-    AlignmentUtils.addReferenceAnnotationTo(newAl, newSeqAl[1], newSeqAl[1].getDatasetSequence().getAnnotation()[0], sg);
-    for (AlignmentAnnotation alan:newAl.getAlignmentAnnotation())
+    AlignmentUtils.addReferenceAnnotationTo(newAl, newSeqAl[0],
+            newSeqAl[0].getDatasetSequence().getAnnotation()[0], sg);
+    AlignmentUtils.addReferenceAnnotationTo(newAl, newSeqAl[1],
+            newSeqAl[1].getDatasetSequence().getAnnotation()[0], sg);
+    for (AlignmentAnnotation alan : newAl.getAlignmentAnnotation())
     {
       verifyExpectedSequenceAnnotation(alan);
     }
   }
-  
+
   /**
-   * helper - tests annotation is mapped to position it was originally created for
+   * helper - tests annotation is mapped to position it was originally created
+   * for
+   * 
    * @param alan
    */
   private void verifyExpectedSequenceAnnotation(AlignmentAnnotation alan)
   {
-    for (int c=0;c<alan.annotations.length;c++)
+    for (int c = 0; c < alan.annotations.length; c++)
     {
       Annotation a = alan.annotations[c];
-      if (a!=null)
+      if (a != null)
       {
-        assertEquals("Misaligned annotation at "+c,(float)alan.sequenceRef.findPosition(c),a.value);
-      } else {
-        assertTrue("Unexpected Null at position "+c,c>=alan.sequenceRef.getLength() || Comparison.isGap(alan.sequenceRef.getCharAt(c)));
+        assertEquals("Misaligned annotation at " + c,
+                (float) alan.sequenceRef.findPosition(c), a.value);
+      }
+      else
+      {
+        assertTrue("Unexpected Null at position " + c,
+                c >= alan.sequenceRef.getLength()
+                        || Comparison.isGap(alan.sequenceRef.getCharAt(c)));
       }
     }
   }
@@ -2707,15 +2722,17 @@ public class AlignmentUtilsTests
     AlignmentAnnotation alan = al.findAnnotations(sq, null, cm_aan.label)
             .iterator().next();
     ContactMatrixI t_cm = al.getContactMatrixFor(alan);
-    assertNotNull("No contact map for the transferred annotation row.",t_cm);
+    assertNotNull("No contact map for the transferred annotation row.",
+            t_cm);
     assertTrue(t_cm instanceof SeqDistanceContactMatrix);
-    assertTrue(((SeqDistanceContactMatrix)t_cm).hasReferenceSeq());
-    
+    assertTrue(((SeqDistanceContactMatrix) t_cm).hasReferenceSeq());
+
     ContactListI cl = al.getContactListFor(alan, 1);
     assertNotNull(
             "No contact matrix recovered after reference annotation transfer",
             cl);
-    // semantics of sequence associated contact list is slightly tricky - column 3 in alignment should have data
+    // semantics of sequence associated contact list is slightly tricky - column
+    // 3 in alignment should have data
     cl = al.getContactListFor(alan, 3);
     assertNotNull(
             "Contact matrix should have data for last position in sequence",