1. Project Clover database Fri Dec 6 2024 13:47:14 GMT
  2. Package jalview.gui

File AnnotationColumnChooserTest.java

 

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Classes

Class
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Actions
AnnotationColumnChooserTest 50 67 4
1.0100%
 

Contributing tests

This file is covered by 1 test. .

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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.gui;
22   
23    import static org.testng.Assert.assertFalse;
24    import static org.testng.AssertJUnit.assertEquals;
25   
26    import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
27    import jalview.bin.Cache;
28    import jalview.datamodel.AlignmentAnnotation;
29    import jalview.datamodel.AlignmentI;
30    import jalview.datamodel.Annotation;
31    import jalview.datamodel.HiddenColumns;
32    import jalview.datamodel.SequenceI;
33    import jalview.io.DataSourceType;
34    import jalview.io.FileFormat;
35    import jalview.io.FormatAdapter;
36   
37    import java.io.IOException;
38    import java.util.Iterator;
39   
40    import org.testng.annotations.BeforeClass;
41    import org.testng.annotations.BeforeMethod;
42    import org.testng.annotations.Test;
43   
44    /**
45    * Unit tests for AnnotationChooser
46    *
47    * @author kmourao
48    *
49    */
 
50    public class AnnotationColumnChooserTest
51    {
 
52  1 toggle @BeforeClass(alwaysRun = true)
53    public void setUpJvOptionPane()
54    {
55  1 JvOptionPane.setInteractiveMode(false);
56  1 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
57    }
58   
59    // 4 sequences x 13 positions
60    final static String TEST_DATA = ">FER_CAPAA Ferredoxin\n"
61    + "TIETHKEAELVG-\n"
62    + ">FER_CAPAN Ferredoxin, chloroplast precursor\n"
63    + "TIETHKEAELVG-\n"
64    + ">FER1_SOLLC Ferredoxin-1, chloroplast precursor\n"
65    + "TIETHKEEELTA-\n" + ">Q93XJ9_SOLTU Ferredoxin I precursor\n"
66    + "TIETHKEEELTA-\n";
67   
68    AnnotationChooser testee;
69   
70    AlignmentPanel parentPanel;
71   
72    AlignFrame af;
73   
 
74  1 toggle @BeforeMethod(alwaysRun = true)
75    public void setUp() throws IOException
76    {
77  1 Cache.loadProperties("test/jalview/io/testProps.jvprops");
78    // pin down annotation sort order for test
79  1 Cache.applicationProperties.setProperty(Preferences.SORT_ANNOTATIONS,
80    SequenceAnnotationOrder.NONE.name());
81  1 final String TRUE = Boolean.TRUE.toString();
82  1 Cache.applicationProperties.setProperty(Preferences.SHOW_AUTOCALC_ABOVE,
83    TRUE);
84  1 Cache.applicationProperties.setProperty("SHOW_QUALITY", TRUE);
85  1 Cache.applicationProperties.setProperty("SHOW_CONSERVATION", TRUE);
86  1 Cache.applicationProperties.setProperty("SHOW_IDENTITY", TRUE);
87   
88  1 AlignmentI al = new FormatAdapter().readFile(TEST_DATA,
89    DataSourceType.PASTE, FileFormat.Fasta);
90  1 af = new AlignFrame(al, 700, 500);
91  1 parentPanel = new AlignmentPanel(af, af.getViewport());
92  1 addAnnotations();
93    }
94   
95    /**
96    * Add 4 annotations, 3 of them sequence-specific.
97    *
98    * <PRE>
99    * ann1 - for sequence 0 - label 'IUPRED' ann2 - not sequence related - label
100    * 'Beauty' ann3 - for sequence 3 - label 'JMol' ann4 - for sequence 2 - label
101    * 'IUPRED' ann5 - for sequence 1 - label 'JMol'
102    */
 
103  1 toggle private void addAnnotations()
104    {
105  1 Annotation an = new Annotation(2f);
106  1 Annotation[] anns = new Annotation[] { an, an, an };
107  1 AlignmentAnnotation ann0 = new AlignmentAnnotation("IUPRED", "", anns);
108  1 AlignmentAnnotation ann1 = new AlignmentAnnotation("Beauty", "", anns);
109  1 AlignmentAnnotation ann2 = new AlignmentAnnotation("JMol", "", anns);
110  1 AlignmentAnnotation ann3 = new AlignmentAnnotation("IUPRED", "", anns);
111  1 AlignmentAnnotation ann4 = new AlignmentAnnotation("JMol", "", anns);
112  1 SequenceI[] seqs = parentPanel.getAlignment().getSequencesArray();
113  1 ann0.setSequenceRef(seqs[0]);
114  1 ann2.setSequenceRef(seqs[3]);
115  1 ann3.setSequenceRef(seqs[2]);
116  1 ann4.setSequenceRef(seqs[1]);
117  1 parentPanel.getAlignment().addAnnotation(ann0);
118  1 parentPanel.getAlignment().addAnnotation(ann1);
119  1 parentPanel.getAlignment().addAnnotation(ann2);
120  1 parentPanel.getAlignment().addAnnotation(ann3);
121  1 parentPanel.getAlignment().addAnnotation(ann4);
122    }
123   
124    /**
125    * Test reset
126    */
 
127  1 toggle @Test(groups = { "Functional" })
128    public void testReset()
129    {
130  1 AnnotationColumnChooser acc = new AnnotationColumnChooser(
131    af.getViewport(), af.alignPanel);
132   
133  1 HiddenColumns oldhidden = new HiddenColumns();
134  1 oldhidden.hideColumns(10, 20);
135  1 acc.setOldHiddenColumns(oldhidden);
136   
137  1 HiddenColumns newHidden = new HiddenColumns();
138  1 newHidden.hideColumns(0, 3);
139  1 newHidden.hideColumns(22, 25);
140  1 af.getViewport().setHiddenColumns(newHidden);
141   
142  1 HiddenColumns currentHidden = af.getViewport().getAlignment()
143    .getHiddenColumns();
144  1 Iterator<int[]> regions = currentHidden.iterator();
145  1 int[] next = regions.next();
146  1 assertEquals(0, next[0]);
147  1 assertEquals(3, next[1]);
148  1 next = regions.next();
149  1 assertEquals(22, next[0]);
150  1 assertEquals(25, next[1]);
151   
152    // now reset hidden columns
153  1 acc.reset();
154  1 currentHidden = af.getViewport().getAlignment().getHiddenColumns();
155  1 regions = currentHidden.iterator();
156  1 next = regions.next();
157  1 assertEquals(10, next[0]);
158  1 assertEquals(20, next[1]);
159   
160    // check works with empty hidden columns as old columns
161  1 oldhidden = new HiddenColumns();
162  1 acc.setOldHiddenColumns(oldhidden);
163  1 acc.reset();
164  1 currentHidden = af.getViewport().getAlignment().getHiddenColumns();
165  1 assertFalse(currentHidden.hasHiddenColumns());
166   
167    // check works with empty hidden columns as new columns
168  1 oldhidden.hideColumns(10, 20);
169  1 acc.setOldHiddenColumns(oldhidden);
170  1 currentHidden = af.getViewport().getAlignment().getHiddenColumns();
171  1 assertFalse(currentHidden.hasHiddenColumns());
172   
173  1 acc.reset();
174  1 currentHidden = af.getViewport().getAlignment().getHiddenColumns();
175  1 regions = currentHidden.iterator();
176  1 next = regions.next();
177  1 assertEquals(10, next[0]);
178  1 assertEquals(20, next[1]);
179    }
180    }