1 /*
2  * Jalview - A Sequence Alignment Editor and Viewer (2.11.1.4)
3  * Copyright (C) 2021 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.Assert.assertTrue;
24 
25 import jalview.analysis.AlignmentGenerator;
26 
27 import java.util.Hashtable;
28 import java.util.NoSuchElementException;
29 
30 import org.testng.annotations.BeforeClass;
31 import org.testng.annotations.Test;
32 
33 public class AllRowsIteratorTest
34 {
35   AlignmentI al;
36 
37   Hashtable<SequenceI, SequenceCollectionI> hiddenRepSequences = new Hashtable<>();
38 
39   @BeforeClass(alwaysRun = true)
setup()40   public void setup()
41   {
42     // create random alignment
43     AlignmentGenerator gen = new AlignmentGenerator(false);
44     al = gen.generate(20, 15, 123, 5, 5);
45     if (!hiddenRepSequences.isEmpty())
46     {
47       al.getHiddenSequences().showAll(hiddenRepSequences);
48     }
49     hideSequences(2, 4);
50   }
51 
52   /*
53    * Test iterator iterates through collection correctly
54    */
55   @Test(groups = { "Functional" })
testHasNextAndNext()56   public void testHasNextAndNext()
57   {
58     AllRowsIterator it = new AllRowsIterator(0, 3, al);
59     int count = 0;
60     while (it.hasNext())
61     {
62       it.next();
63       count++;
64     }
65     assertTrue(count == 4, "hasNext() is false after 4 iterations");
66   }
67 
68   /*
69    * Test iterator throws NoSuchElementException at end of iteration
70    */
71   @Test(
72     groups = { "Functional" },
73     expectedExceptions = { NoSuchElementException.class })
testLastNext()74   public void testLastNext() throws NoSuchElementException
75   {
76     AllRowsIterator it = new AllRowsIterator(0, 3, al);
77     while (it.hasNext())
78     {
79       it.next();
80     }
81     it.next();
82   }
83 
84   /*
85    * Test iterator throws UnsupportedOperationException on call to remove
86    */
87   @Test(
88     groups = { "Functional" },
89     expectedExceptions = { UnsupportedOperationException.class })
testRemove()90   public void testRemove() throws UnsupportedOperationException
91   {
92     AllRowsIterator it = new AllRowsIterator(0, 3, al);
93     it.remove();
94   }
95 
96 
97   /*
98    * Hide sequences between start and end
99    */
hideSequences(int start, int end)100   private void hideSequences(int start, int end)
101   {
102     SequenceI[] allseqs = al.getSequencesArray();
103     SequenceGroup theseSeqs = new SequenceGroup();
104 
105     for (int i = start; i <= end; i++)
106     {
107       theseSeqs.addSequence(allseqs[i], false);
108       al.getHiddenSequences().hideSequence(allseqs[i]);
109     }
110 
111     hiddenRepSequences.put(allseqs[start], theseSeqs);
112   }
113 
114   /*
115    * Test iterator behaves correctly when there is only one element in the collection
116    */
117   @Test(groups = { "Functional" })
testOneElement()118   public void testOneElement()
119   {
120     AllRowsIterator it = new AllRowsIterator(0, 0, al);
121     int count = 0;
122     while (it.hasNext())
123     {
124       it.next();
125       count++;
126     }
127     assertTrue(count == 1, "hasNext() is false after 1 iteration");
128   }
129 
130 }
131