JAL-4090 JAL-1551 spotlessApply

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

diff --git a/test/jalview/datamodel/PAEContactMatrixTest.java b/test/jalview/datamodel/PAEContactMatrixTest.java
index fa7aca5..33f3998 100644 (file)
--- a/test/jalview/datamodel/PAEContactMatrixTest.java
+++ b/test/jalview/datamodel/PAEContactMatrixTest.java
@@ -73,7 +73,8 @@ public class PAEContactMatrixTest
     verifyPAEmatrix(seq, aa, 0, 0, 4);
 
     // test clustering
-    paematrix.setGroupSet(GroupSet.makeGroups(paematrix, false,0.1f, false));
+    paematrix.setGroupSet(
+            GroupSet.makeGroups(paematrix, false, 0.1f, false));
 
     // remap - test the MappableContactMatrix.liftOver method
     SequenceI newseq = new Sequence("Seq", "ASDQEASDQEASDQE");
@@ -117,8 +118,9 @@ public class PAEContactMatrixTest
     newaa = AlignmentUtils.addReferenceAnnotationTo(alForSeq, alseq, newaa,
             null);
     // check for null on out of bounds
-    ContactListI alcl = alForSeq.getContactListFor(newaa, newaa.annotations.length);
-    assertNull(alcl,"Should've gotten null!");
+    ContactListI alcl = alForSeq.getContactListFor(newaa,
+            newaa.annotations.length);
+    assertNull(alcl, "Should've gotten null!");
     // now check for mapping
     alcl = alForSeq.getContactListFor(newaa, 1);
     assertNotNull(alcl);
@@ -213,18 +215,18 @@ public class PAEContactMatrixTest
   /**
    * check mapping and resolution methods work
    */
-  @Test(groups= {"Functional"})
-  public void testMappableContactMatrix() {
+  @Test(groups = { "Functional" })
+  public void testMappableContactMatrix()
+  {
     SequenceI newseq = new Sequence("Seq", "ASDQEASDQEASDQE");
-    MapList map = new MapList(new int[]
-            { 5, 9 }, new int[] { 1, 5 }, 1, 1);
-    AlignmentAnnotation aa = newseq
-            .addContactList(new PAEContactMatrix(newseq,map, PAEdata,null));
+    MapList map = new MapList(new int[] { 5, 9 }, new int[] { 1, 5 }, 1, 1);
+    AlignmentAnnotation aa = newseq.addContactList(
+            new PAEContactMatrix(newseq, map, PAEdata, null));
     ContactListI clist = newseq.getContactListFor(aa, 4);
     assertNotNull(clist);
     clist = newseq.getContactListFor(aa, 3);
     assertNull(clist);
-    
+
     ContactMatrixI cm = newseq.getContactMatrixFor(aa);
     MappableContactMatrixI mcm = (MappableContactMatrixI) cm;
     int[] pos = mcm.getMappedPositionsFor(newseq, 0);
@@ -232,19 +234,18 @@ public class PAEContactMatrixTest
 
     pos = mcm.getMappedPositionsFor(newseq, 1);
     assertNotNull(pos);
-    assertEquals(pos[0],4+newseq.getStart());
-    
+    assertEquals(pos[0], 4 + newseq.getStart());
+
     pos = mcm.getMappedPositionsFor(newseq, 6); // after end of matrix
     assertNull(pos);
     pos = mcm.getMappedPositionsFor(newseq, 5); // at end of matrix
     assertNotNull(pos);
-    assertEquals(pos[0],8+newseq.getStart());
+    assertEquals(pos[0], 8 + newseq.getStart());
     SequenceI alseq = newseq.deriveSequence();
-    alseq.insertCharAt(5,'-');
+    alseq.insertCharAt(5, '-');
     pos = mcm.getMappedPositionsFor(alseq, 5); // at end of matrix
     assertNotNull(pos);
-    assertEquals(pos[0],8+newseq.getStart());
-    
-    
+    assertEquals(pos[0], 8 + newseq.getStart());
+
   }
 }