JAL-4090 JAL-1551 source license

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

diff --git a/test/jalview/datamodel/PAEContactMatrixTest.java b/test/jalview/datamodel/PAEContactMatrixTest.java
index 67edb37..e4bb000 100644 (file)
--- a/test/jalview/datamodel/PAEContactMatrixTest.java
+++ b/test/jalview/datamodel/PAEContactMatrixTest.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.datamodel;
 
 import static org.testng.Assert.*;
@@ -73,7 +93,8 @@ public class PAEContactMatrixTest
     verifyPAEmatrix(seq, aa, 0, 0, 4);
 
     // test clustering
-    paematrix.setGroupSet(GroupSet.makeGroups(paematrix, 0.1f, false));
+    paematrix.setGroupSet(
+            GroupSet.makeGroups(paematrix, false, 0.1f, false));
 
     // remap - test the MappableContactMatrix.liftOver method
     SequenceI newseq = new Sequence("Seq", "ASDQEASDQEASDQE");
@@ -116,7 +137,12 @@ public class PAEContactMatrixTest
     AlignmentI alForSeq = new Alignment(new SequenceI[] { alseq });
     newaa = AlignmentUtils.addReferenceAnnotationTo(alForSeq, alseq, newaa,
             null);
-    ContactListI alcl = alForSeq.getContactListFor(newaa, 1);
+    // check for null on out of bounds
+    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);
     mappedCl = alcl.getMappedPositionsFor(0, 4);
     assertNotNull(mappedCl);
@@ -209,18 +235,18 @@ 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);
@@ -228,19 +254,18 @@ 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());
+
   }
 }