X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fdatamodel%2FSequenceGroupTest.java;h=622ebb9c3a5a6a3ff087c7ed1bb04d13b5127b16;hb=3659ecfe7bb17dd25a0a6b5c94a7d9dab4525136;hp=80790ed5e441558e1a217b9fa208f007236ed3da;hpb=42498abb930c08393b09fc7af2564b7f210ac294;p=jalview.git

diff --git a/test/jalview/datamodel/SequenceGroupTest.java b/test/jalview/datamodel/SequenceGroupTest.java
index 80790ed..622ebb9 100644
--- a/test/jalview/datamodel/SequenceGroupTest.java
+++ b/test/jalview/datamodel/SequenceGroupTest.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.assertEquals;
@@ -9,18 +29,22 @@ import static org.testng.Assert.assertSame;
 import static org.testng.Assert.assertTrue;
 import static org.testng.Assert.fail;
 
+import jalview.analysis.Conservation;
 import jalview.schemes.NucleotideColourScheme;
 import jalview.schemes.PIDColourScheme;
 
 import java.awt.Color;
-
-import junit.extensions.PA;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
 
 import org.testng.annotations.Test;
 
+import junit.extensions.PA;
+
 public class SequenceGroupTest
 {
-  @Test(groups={"Functional"})
+  @Test(groups = { "Functional" })
   public void testAddSequence()
   {
     SequenceGroup sg = new SequenceGroup();
@@ -48,16 +72,16 @@ public class SequenceGroupTest
     assertTrue(sg.getSequences().contains(seq3));
   }
 
-  @Test(groups={"Functional"})
+  @Test(groups = { "Functional" })
   public void testAddOrRemove()
   {
     SequenceGroup sg = new SequenceGroup();
     assertTrue(sg.getSequences().isEmpty());
-  
+
     SequenceI seq1 = new Sequence("seq1", "abc");
     SequenceI seq2 = new Sequence("seq2", "abc");
     SequenceI seq3 = new Sequence(seq1);
-  
+
     sg.addOrRemove(seq1, false);
     assertEquals(sg.getSequences().size(), 1);
     sg.addOrRemove(seq2, false);
@@ -72,7 +96,7 @@ public class SequenceGroupTest
     assertFalse(sg.getSequences().contains(seq1));
   }
 
-  @Test(groups={"Functional"})
+  @Test(groups = { "Functional" })
   public void testGetColourScheme()
   {
     SequenceGroup sg = new SequenceGroup();
@@ -87,7 +111,7 @@ public class SequenceGroupTest
     assertSame(scheme, sg.getColourScheme());
   }
 
-  @Test(groups={"Functional"})
+  @Test(groups = { "Functional" })
   public void testSetContext()
   {
     SequenceGroup sg1 = new SequenceGroup();
@@ -232,6 +256,11 @@ public class SequenceGroupTest
     sg.setName("g1");
     sg.setDescription("desc");
     sg.setColourScheme(new PIDColourScheme());
+    Conservation cons = new Conservation("Cons", 2,
+            Collections.<SequenceI> emptyList(), 3, 12);
+    PA.setValue(cons, "consSequence", new Sequence("s", "abc"));
+    sg.getGroupColourScheme().setConservation(cons);
+    sg.getGroupColourScheme().setConsensus(new Profiles(null));
     sg.setDisplayBoxes(false);
     sg.setDisplayText(false);
     sg.setColourText(true);
@@ -253,8 +282,12 @@ public class SequenceGroupTest
     SequenceGroup sg2 = new SequenceGroup(sg);
     assertEquals(sg2.getName(), sg.getName());
     assertEquals(sg2.getDescription(), sg.getDescription());
-    assertSame(sg2.getGroupColourScheme(), sg.getGroupColourScheme());
+    assertNotSame(sg2.getGroupColourScheme(), sg.getGroupColourScheme());
     assertSame(sg2.getColourScheme(), sg.getColourScheme());
+    assertSame(PA.getValue(sg2.getGroupColourScheme(), "consensus"),
+            PA.getValue(sg.getGroupColourScheme(), "consensus"));
+    assertSame(PA.getValue(sg2.getGroupColourScheme(), "conservation"),
+            PA.getValue(sg.getGroupColourScheme(), "conservation"));
     assertEquals(sg2.getDisplayBoxes(), sg.getDisplayBoxes());
     assertEquals(sg2.getDisplayText(), sg.getDisplayText());
     assertEquals(sg2.getColourText(), sg.getColourText());
@@ -290,4 +323,36 @@ public class SequenceGroupTest
      */
     assertNull(sg2.getContext());
   }
+
+  @Test(groups = { "Functional" })
+  public void testConstructor_list()
+  {
+    SequenceI s1 = new Sequence("abcde", "fg");
+    SequenceI s2 = new Sequence("foo", "bar");
+    List<SequenceI> seqs = new ArrayList<SequenceI>();
+    seqs.add(s1);
+    seqs.add(s2);
+    SequenceGroup sg = new SequenceGroup(seqs);
+
+    /*
+     * verify sg has a copy of the original list
+     */
+    List<SequenceI> sgList = sg.getSequences();
+    assertNotSame(sgList, seqs);
+    assertEquals(sgList, seqs);
+
+    /*
+     * add to sgList, original is unchanged
+     */
+    sg.addSequence(new Sequence("bar", "foo"), false);
+    assertEquals(sgList.size(), 3);
+    assertEquals(seqs.size(), 2);
+
+    /*
+     * delete from original, sgList is unchanged
+     */
+    seqs.remove(s1);
+    assertEquals(sgList.size(), 3);
+    assertEquals(seqs.size(), 1);
+  }
 }