create method to test HMM model as string
[jalview.git] / test / jalview / datamodel / SequenceDummyTest.java
1 /*
2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
4  * 
5  * This file is part of Jalview.
6  * 
7  * Jalview is free software: you can redistribute it and/or
8  * modify it under the terms of the GNU General Public License 
9  * as published by the Free Software Foundation, either version 3
10  * of the License, or (at your option) any later version.
11  *  
12  * Jalview is distributed in the hope that it will be useful, but 
13  * WITHOUT ANY WARRANTY; without even the implied warranty 
14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
15  * PURPOSE.  See the GNU General Public License for more details.
16  * 
17  * You should have received a copy of the GNU General Public License
18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
19  * The Jalview Authors are detailed in the 'AUTHORS' file.
20  */
21 package jalview.datamodel;
22
23 import static org.testng.AssertJUnit.assertFalse;
24 import static org.testng.AssertJUnit.assertTrue;
25
26 import jalview.gui.JvOptionPane;
27
28 import org.testng.annotations.BeforeClass;
29 import org.testng.annotations.Test;
30
31 @Test
32 public class SequenceDummyTest
33 {
34
35   @BeforeClass(alwaysRun = true)
36   public void setUpJvOptionPane()
37   {
38     JvOptionPane.setInteractiveMode(false);
39     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
40   }
41
42   /**
43    * test for become method
44    */
45   @Test(groups = { "Functional" })
46   public void testBecome()
47   {
48     SequenceI seq = new Sequence("OrigSeq", "ASEQUENCE");
49     SequenceFeature ofeat = new SequenceFeature("NewFeat", "somedesc", 3,
50             12, 2.3f, "none");
51
52     SequenceDummy dummySeq = new SequenceDummy("OrigSeq");
53     dummySeq.addSequenceFeature(ofeat);
54     dummySeq.become(seq);
55     assertFalse("Dummy sequence did not become a full sequence",
56             dummySeq.isDummy());
57     assertTrue("Sequence was not updated from template", seq
58             .getSequenceAsString().equals(dummySeq.getSequenceAsString()));
59     boolean found = false;
60     for (SequenceFeature sf : dummySeq.getSequenceFeatures())
61     {
62       if (sf == ofeat)
63       {
64         found = true;
65         break;
66       }
67     }
68     assertTrue("Didn't retain original sequence feature", found);
69
70     // todo - should test all aspect of copy constructor
71   }
72 }