X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fdatamodel%2FAlignmentTest.java;h=1c27420c21aea5abd091c0e7542b708782dfbc0c;hb=a0ccef9cc78fffa7be85f3b658a5768958a301ce;hp=d00abb13e8f9b77437446282b2ddffca7cf33f77;hpb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;p=jalview.git

diff --git a/test/jalview/datamodel/AlignmentTest.java b/test/jalview/datamodel/AlignmentTest.java
index d00abb1..1c27420 100644
--- a/test/jalview/datamodel/AlignmentTest.java
+++ b/test/jalview/datamodel/AlignmentTest.java
@@ -27,16 +27,6 @@ import static org.testng.AssertJUnit.assertNull;
 import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
 
-import jalview.analysis.AlignmentGenerator;
-import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping;
-import jalview.gui.JvOptionPane;
-import jalview.io.DataSourceType;
-import jalview.io.FileFormat;
-import jalview.io.FileFormatI;
-import jalview.io.FormatAdapter;
-import jalview.util.Comparison;
-import jalview.util.MapList;
-
 import java.io.IOException;
 import java.util.Arrays;
 import java.util.Iterator;
@@ -47,6 +37,16 @@ import org.testng.annotations.BeforeClass;
 import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
 
+import jalview.analysis.AlignmentGenerator;
+import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping;
+import jalview.gui.JvOptionPane;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
+import jalview.io.FileFormatI;
+import jalview.io.FormatAdapter;
+import jalview.util.Comparison;
+import jalview.util.MapList;
+
 /**
  * Unit tests for Alignment datamodel.
  * 
@@ -1578,4 +1578,28 @@ public class AlignmentTest
     a.getHiddenColumns().hideColumns(2, 5);
     assertEquals(5, a.getVisibleWidth());
   }
+
+  @Test(groups = { "Functional" })
+  public void testGetContactMap()
+  {
+    // TODO
+    // 1. test adding/removing/manipulating contact maps with/without associated
+    // sequence(s) or groups
+    // 2. For sequence associated - ensure that inserting a gap in sequence
+    // results in the contact map being relocated accordingly
+    // 3. RENDERER QUESTION - should contact maps reflect gaps in the alignment
+    // ?
+
+  }
+
+  @Test(groups = { "Functional" })
+  public void testEquals()
+  {
+    SequenceI seq1 = new Sequence("seq1", "ABCDEF--");
+    SequenceI seq2 = new Sequence("seq2", "-JKLMNO--");
+    SequenceI seq3 = new Sequence("seq2", "-PQR");
+    AlignmentI a = new Alignment(new SequenceI[] { seq1, seq2, seq3 });
+    a.setDataset(null);
+    assertEquals(a.getDataset(), a.getDataset());
+  }
 }