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  1. Project Clover database Thu Aug 13 2020 12:04:21 BST
  2. Package jalview.gui

File PopupMenuTest.java

 

Code metrics

16
325
17
1
769
512
26
0.08
19.12
17
1.53

Classes

Class Line # Actions
PopupMenuTest 68 325 26
1.0100%
 

Contributing tests

This file is covered by 13 tests. .

Source view

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 jalview.util.UrlConstants.DB_ACCESSION;
24    import static jalview.util.UrlConstants.SEQUENCE_ID;
25    import static org.testng.AssertJUnit.assertEquals;
26    import static org.testng.AssertJUnit.assertFalse;
27    import static org.testng.AssertJUnit.assertNotNull;
28    import static org.testng.AssertJUnit.assertNull;
29    import static org.testng.AssertJUnit.assertTrue;
30   
31    import java.awt.Component;
32    import java.awt.Container;
33    import java.io.IOException;
34    import java.util.ArrayList;
35    import java.util.Collections;
36    import java.util.Iterator;
37    import java.util.List;
38   
39    import javax.swing.JMenu;
40    import javax.swing.JMenuItem;
41    import javax.swing.JPopupMenu;
42    import javax.swing.JSeparator;
43   
44    import org.testng.annotations.BeforeClass;
45    import org.testng.annotations.BeforeMethod;
46    import org.testng.annotations.Test;
47   
48    import jalview.bin.Cache;
49    import jalview.datamodel.AlignmentAnnotation;
50    import jalview.datamodel.AlignmentI;
51    import jalview.datamodel.Annotation;
52    import jalview.datamodel.ColumnSelection;
53    import jalview.datamodel.DBRefEntry;
54    import jalview.datamodel.DBRefSource;
55    import jalview.datamodel.HiddenColumns;
56    import jalview.datamodel.Sequence;
57    import jalview.datamodel.SequenceFeature;
58    import jalview.datamodel.SequenceGroup;
59    import jalview.datamodel.SequenceI;
60    import jalview.io.DataSourceType;
61    import jalview.io.FileFormat;
62    import jalview.io.FormatAdapter;
63    import jalview.urls.api.UrlProviderFactoryI;
64    import jalview.urls.desktop.DesktopUrlProviderFactory;
65    import jalview.util.MessageManager;
66    import jalview.util.UrlConstants;
67   
 
68    public class PopupMenuTest
69    {
70   
 
71  1 toggle @BeforeClass(alwaysRun = true)
72    public void setUpJvOptionPane()
73    {
74  1 JvOptionPane.setInteractiveMode(false);
75  1 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
76    }
77   
78    // 4 sequences x 13 positions
79    final static String TEST_DATA = ">FER_CAPAA Ferredoxin\n"
80    + "TIETHKEAELVG-\n"
81    + ">FER_CAPAN Ferredoxin, chloroplast precursor\n"
82    + "TIETHKEAELVG-\n"
83    + ">FER1_SOLLC Ferredoxin-1, chloroplast precursor\n"
84    + "TIETHKEEELTA-\n" + ">Q93XJ9_SOLTU Ferredoxin I precursor\n"
85    + "TIETHKEEELTA-\n";
86   
87    AlignmentI alignment;
88   
89    AlignmentPanel parentPanel;
90   
91    PopupMenu testee = null;
92   
 
93  13 toggle @BeforeMethod(alwaysRun = true)
94    public void setUp() throws IOException
95    {
96  13 Cache.loadProperties("test/jalview/io/testProps.jvprops");
97  13 Cache.initLogger();
98   
99  13 String inMenuString = ("EMBL-EBI Search | http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$"
100    + SEQUENCE_ID
101    + "$"
102    + "|"
103    + "UNIPROT | http://www.uniprot.org/uniprot/$" + DB_ACCESSION + "$")
104    + "|"
105    + ("INTERPRO | http://www.ebi.ac.uk/interpro/entry/$"
106    + DB_ACCESSION + "$")
107    + "|"
108    +
109    // Gene3D entry tests for case (in)sensitivity
110    ("Gene3D | http://gene3d.biochem.ucl.ac.uk/Gene3D/search?sterm=$"
111    + DB_ACCESSION + "$&mode=protein");
112   
113  13 UrlProviderFactoryI factory = new DesktopUrlProviderFactory(
114    UrlConstants.DEFAULT_LABEL, inMenuString, "");
115  13 Preferences.sequenceUrlLinks = factory.createUrlProvider();
116   
117  13 alignment = new FormatAdapter().readFile(TEST_DATA,
118    DataSourceType.PASTE, FileFormat.Fasta);
119  13 AlignFrame af = new AlignFrame(alignment, 700, 500);
120  13 parentPanel = new AlignmentPanel(af, af.getViewport());
121  13 testee = new PopupMenu(parentPanel, alignment.getSequenceAt(0), null);
122  13 int i = 0;
123  13 for (SequenceI seq : alignment.getSequences())
124    {
125  52 final AlignmentAnnotation annotation = new AlignmentAnnotation(
126    "label" + i, "desc" + i, i);
127  52 annotation.setCalcId("calcId" + i);
128  52 seq.addAlignmentAnnotation(annotation);
129  52 annotation.setSequenceRef(seq);
130    }
131    }
132   
 
133  1 toggle @Test(groups = { "Functional" })
134    public void testConfigureReferenceAnnotationsMenu_noSequenceSelected()
135    {
136  1 JMenuItem menu = new JMenuItem();
137  1 List<SequenceI> seqs = new ArrayList<>();
138  1 testee.configureReferenceAnnotationsMenu(menu, seqs);
139  1 assertFalse(menu.isEnabled());
140    // now try null list
141  1 menu.setEnabled(true);
142  1 testee.configureReferenceAnnotationsMenu(menu, null);
143  1 assertFalse(menu.isEnabled());
144    }
145   
146    /**
147    * Test building the 'add reference annotations' menu for the case where there
148    * are no reference annotations to add to the alignment. The menu item should
149    * be disabled.
150    */
 
151  1 toggle @Test(groups = { "Functional" })
152    public void testConfigureReferenceAnnotationsMenu_noReferenceAnnotations()
153    {
154  1 JMenuItem menu = new JMenuItem();
155   
156    /*
157    * Initial state is that sequences have annotations, and have dataset
158    * sequences, but the dataset sequences have no annotations. Hence nothing
159    * to add.
160    */
161  1 List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
162   
163  1 testee.configureReferenceAnnotationsMenu(menu, seqs);
164  1 assertFalse(menu.isEnabled());
165    }
166   
167    /**
168    * Test building the 'add reference annotations' menu for the case where all
169    * reference annotations are already on the alignment. The menu item should be
170    * disabled.
171    */
 
172  1 toggle @Test(groups = { "Functional" })
173    public void testConfigureReferenceAnnotationsMenu_alreadyAdded()
174    {
175  1 JMenuItem menu = new JMenuItem();
176  1 List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
177   
178    // make up new annotations and add to dataset sequences, sequences and
179    // alignment
180  1 attachReferenceAnnotations(seqs, true, true);
181   
182  1 testee.configureReferenceAnnotationsMenu(menu, seqs);
183  1 assertFalse(menu.isEnabled());
184    }
185   
186    /**
187    * Test building the 'add reference annotations' menu for the case where
188    * several reference annotations are on the dataset but not on the sequences.
189    * The menu item should be enabled, and acquire a tooltip which lists the
190    * annotation sources (calcIds) and type (labels).
191    */
 
192  1 toggle @Test(groups = { "Functional" })
193    public void testConfigureReferenceAnnotationsMenu()
194    {
195  1 JMenuItem menu = new JMenuItem();
196  1 List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
197   
198    // make up new annotations and add to dataset sequences
199  1 attachReferenceAnnotations(seqs, false, false);
200   
201  1 testee.configureReferenceAnnotationsMenu(menu, seqs);
202  1 assertTrue(menu.isEnabled());
203  1 String s = MessageManager.getString("label.add_annotations_for");
204  1 String expected = "<html><style> div.ttip {width:350px;white-space:pre-wrap;padding:2px;overflow-wrap:break-word;}</style>"
205    + "<div class=\"ttip\">" + s
206    + "<br/>Jmol/secondary structure<br/>PDB/Temp </div></html>";
207  1 assertEquals(expected, menu.getToolTipText());
208    }
209   
210    /**
211    * Test building the 'add reference annotations' menu for the case where
212    * several reference annotations are on the dataset and the sequences but not
213    * on the alignment. The menu item should be enabled, and acquire a tooltip
214    * which lists the annotation sources (calcIds) and type (labels).
215    */
 
216  1 toggle @Test(groups = { "Functional" })
217    public void testConfigureReferenceAnnotationsMenu_notOnAlignment()
218    {
219  1 JMenuItem menu = new JMenuItem();
220  1 List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
221   
222    // make up new annotations and add to dataset sequences and sequences
223  1 attachReferenceAnnotations(seqs, true, false);
224   
225  1 testee.configureReferenceAnnotationsMenu(menu, seqs);
226  1 assertTrue(menu.isEnabled());
227  1 String s = MessageManager.getString("label.add_annotations_for");
228  1 String expected = "<html><style> div.ttip {width:350px;white-space:pre-wrap;padding:2px;overflow-wrap:break-word;}</style>"
229    + "<div class=\"ttip\">" + s
230    + "<br/>Jmol/secondary structure<br/>PDB/Temp </div></html>";
231  1 assertEquals(expected, menu.getToolTipText());
232    }
233   
234    /**
235    * Generate annotations and add to dataset sequences and (optionally)
236    * sequences and/or alignment
237    *
238    * @param seqs
239    * @param addToSequence
240    * @param addToAlignment
241    */
 
242  3 toggle private void attachReferenceAnnotations(List<SequenceI> seqs,
243    boolean addToSequence, boolean addToAlignment)
244    {
245    // PDB.secondary structure on Sequence0
246  3 AlignmentAnnotation annotation = new AlignmentAnnotation(
247    "secondary structure", "", 0);
248  3 annotation.setCalcId("PDB");
249  3 seqs.get(0).getDatasetSequence().addAlignmentAnnotation(annotation);
250  3 if (addToSequence)
251    {
252  2 seqs.get(0).addAlignmentAnnotation(annotation);
253    }
254  3 if (addToAlignment)
255    {
256  1 this.alignment.addAnnotation(annotation);
257    }
258   
259    // PDB.Temp on Sequence1
260  3 annotation = new AlignmentAnnotation("Temp", "", 0);
261  3 annotation.setCalcId("PDB");
262  3 seqs.get(1).getDatasetSequence().addAlignmentAnnotation(annotation);
263  3 if (addToSequence)
264    {
265  2 seqs.get(1).addAlignmentAnnotation(annotation);
266    }
267  3 if (addToAlignment)
268    {
269  1 this.alignment.addAnnotation(annotation);
270    }
271   
272    // JMOL.secondary structure on Sequence0
273  3 annotation = new AlignmentAnnotation("secondary structure", "", 0);
274  3 annotation.setCalcId("Jmol");
275  3 seqs.get(0).getDatasetSequence().addAlignmentAnnotation(annotation);
276  3 if (addToSequence)
277    {
278  2 seqs.get(0).addAlignmentAnnotation(annotation);
279    }
280  3 if (addToAlignment)
281    {
282  1 this.alignment.addAnnotation(annotation);
283    }
284    }
285   
286    /**
287    * Test building the 'add reference annotations' menu for the case where there
288    * are two alignment views:
289    * <ul>
290    * <li>in one view, reference annotations have been added (are on the
291    * datasets, sequences and alignment)</li>
292    * <li>in the current view, reference annotations are on the dataset and
293    * sequence, but not the alignment</li>
294    * </ul>
295    * The menu item should be enabled, and acquire a tooltip which lists the
296    * annotation sources (calcIds) and type (labels).
297    */
 
298  1 toggle @Test(groups = { "Functional" })
299    public void testConfigureReferenceAnnotationsMenu_twoViews()
300    {
301    }
302   
303    /**
304    * Test for building menu options including 'show' and 'hide' annotation
305    * types.
306    */
 
307  1 toggle @Test(groups = { "Functional" })
308    public void testBuildAnnotationTypesMenus()
309    {
310  1 JMenu showMenu = new JMenu();
311  1 JMenu hideMenu = new JMenu();
312  1 List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
313   
314    // make up new annotations and add to sequences and to the alignment
315   
316    // PDB.secondary structure on Sequence0
317  1 AlignmentAnnotation annotation = new AlignmentAnnotation(
318    "secondary structure", "", new Annotation[] {});
319  1 annotation.setCalcId("PDB");
320  1 annotation.visible = true;
321  1 seqs.get(0).addAlignmentAnnotation(annotation);
322  1 parentPanel.getAlignment().addAnnotation(annotation);
323   
324    // JMOL.secondary structure on Sequence0 - hidden
325  1 annotation = new AlignmentAnnotation("secondary structure", "",
326    new Annotation[] {});
327  1 annotation.setCalcId("JMOL");
328  1 annotation.visible = false;
329  1 seqs.get(0).addAlignmentAnnotation(annotation);
330  1 parentPanel.getAlignment().addAnnotation(annotation);
331   
332    // Jpred.SSP on Sequence0 - hidden
333  1 annotation = new AlignmentAnnotation("SSP", "", new Annotation[] {});
334  1 annotation.setCalcId("JPred");
335  1 annotation.visible = false;
336  1 seqs.get(0).addAlignmentAnnotation(annotation);
337  1 parentPanel.getAlignment().addAnnotation(annotation);
338   
339    // PDB.Temp on Sequence1
340  1 annotation = new AlignmentAnnotation("Temp", "", new Annotation[] {});
341  1 annotation.setCalcId("PDB");
342  1 annotation.visible = true;
343  1 seqs.get(1).addAlignmentAnnotation(annotation);
344  1 parentPanel.getAlignment().addAnnotation(annotation);
345   
346    /*
347    * Expect menu options to show "secondary structure" and "SSP", and to hide
348    * "secondary structure" and "Temp". Tooltip should be calcId.
349    */
350  1 testee.buildAnnotationTypesMenus(showMenu, hideMenu, seqs);
351   
352  1 assertTrue(showMenu.isEnabled());
353  1 assertTrue(hideMenu.isEnabled());
354   
355  1 Component[] showOptions = showMenu.getMenuComponents();
356  1 Component[] hideOptions = hideMenu.getMenuComponents();
357   
358  1 assertEquals(4, showOptions.length); // includes 'All' and separator
359  1 assertEquals(4, hideOptions.length);
360  1 String all = MessageManager.getString("label.all");
361  1 assertEquals(all, ((JMenuItem) showOptions[0]).getText());
362  1 assertTrue(showOptions[1] instanceof JPopupMenu.Separator);
363  1 assertEquals(JSeparator.HORIZONTAL,
364    ((JSeparator) showOptions[1]).getOrientation());
365  1 assertEquals("secondary structure",
366    ((JMenuItem) showOptions[2]).getText());
367  1 assertEquals("JMOL", ((JMenuItem) showOptions[2]).getToolTipText());
368  1 assertEquals("SSP", ((JMenuItem) showOptions[3]).getText());
369  1 assertEquals("JPred", ((JMenuItem) showOptions[3]).getToolTipText());
370   
371  1 assertEquals(all, ((JMenuItem) hideOptions[0]).getText());
372  1 assertTrue(hideOptions[1] instanceof JPopupMenu.Separator);
373  1 assertEquals(JSeparator.HORIZONTAL,
374    ((JSeparator) hideOptions[1]).getOrientation());
375  1 assertEquals("secondary structure",
376    ((JMenuItem) hideOptions[2]).getText());
377  1 assertEquals("PDB", ((JMenuItem) hideOptions[2]).getToolTipText());
378  1 assertEquals("Temp", ((JMenuItem) hideOptions[3]).getText());
379  1 assertEquals("PDB", ((JMenuItem) hideOptions[3]).getToolTipText());
380    }
381   
382    /**
383    * Test for building menu options with only 'hide' annotation types enabled.
384    */
 
385  1 toggle @Test(groups = { "Functional" })
386    public void testBuildAnnotationTypesMenus_showDisabled()
387    {
388  1 JMenu showMenu = new JMenu();
389  1 JMenu hideMenu = new JMenu();
390  1 List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
391   
392    // make up new annotations and add to sequences and to the alignment
393   
394    // PDB.secondary structure on Sequence0
395  1 AlignmentAnnotation annotation = new AlignmentAnnotation(
396    "secondary structure", "", new Annotation[] {});
397  1 annotation.setCalcId("PDB");
398  1 annotation.visible = true;
399  1 seqs.get(0).addAlignmentAnnotation(annotation);
400  1 parentPanel.getAlignment().addAnnotation(annotation);
401   
402    // PDB.Temp on Sequence1
403  1 annotation = new AlignmentAnnotation("Temp", "", new Annotation[] {});
404  1 annotation.setCalcId("PDB");
405  1 annotation.visible = true;
406  1 seqs.get(1).addAlignmentAnnotation(annotation);
407  1 parentPanel.getAlignment().addAnnotation(annotation);
408   
409    /*
410    * Expect menu options to hide "secondary structure" and "Temp". Tooltip
411    * should be calcId. 'Show' menu should be disabled.
412    */
413  1 testee.buildAnnotationTypesMenus(showMenu, hideMenu, seqs);
414   
415  1 assertFalse(showMenu.isEnabled());
416  1 assertTrue(hideMenu.isEnabled());
417   
418  1 Component[] showOptions = showMenu.getMenuComponents();
419  1 Component[] hideOptions = hideMenu.getMenuComponents();
420   
421  1 assertEquals(2, showOptions.length); // includes 'All' and separator
422  1 assertEquals(4, hideOptions.length);
423  1 String all = MessageManager.getString("label.all");
424  1 assertEquals(all, ((JMenuItem) showOptions[0]).getText());
425  1 assertTrue(showOptions[1] instanceof JPopupMenu.Separator);
426  1 assertEquals(JSeparator.HORIZONTAL,
427    ((JSeparator) showOptions[1]).getOrientation());
428   
429  1 assertEquals(all, ((JMenuItem) hideOptions[0]).getText());
430  1 assertTrue(hideOptions[1] instanceof JPopupMenu.Separator);
431  1 assertEquals(JSeparator.HORIZONTAL,
432    ((JSeparator) hideOptions[1]).getOrientation());
433  1 assertEquals("secondary structure",
434    ((JMenuItem) hideOptions[2]).getText());
435  1 assertEquals("PDB", ((JMenuItem) hideOptions[2]).getToolTipText());
436  1 assertEquals("Temp", ((JMenuItem) hideOptions[3]).getText());
437  1 assertEquals("PDB", ((JMenuItem) hideOptions[3]).getToolTipText());
438    }
439   
440    /**
441    * Test for building menu options with only 'show' annotation types enabled.
442    */
 
443  1 toggle @Test(groups = { "Functional" })
444    public void testBuildAnnotationTypesMenus_hideDisabled()
445    {
446  1 JMenu showMenu = new JMenu();
447  1 JMenu hideMenu = new JMenu();
448  1 List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
449   
450    // make up new annotations and add to sequences and to the alignment
451   
452    // PDB.secondary structure on Sequence0
453  1 AlignmentAnnotation annotation = new AlignmentAnnotation(
454    "secondary structure", "", new Annotation[] {});
455  1 annotation.setCalcId("PDB");
456  1 annotation.visible = false;
457  1 seqs.get(0).addAlignmentAnnotation(annotation);
458  1 parentPanel.getAlignment().addAnnotation(annotation);
459   
460    // PDB.Temp on Sequence1
461  1 annotation = new AlignmentAnnotation("Temp", "", new Annotation[] {});
462  1 annotation.setCalcId("PDB2");
463  1 annotation.visible = false;
464  1 seqs.get(1).addAlignmentAnnotation(annotation);
465  1 parentPanel.getAlignment().addAnnotation(annotation);
466   
467    /*
468    * Expect menu options to show "secondary structure" and "Temp". Tooltip
469    * should be calcId. 'hide' menu should be disabled.
470    */
471  1 testee.buildAnnotationTypesMenus(showMenu, hideMenu, seqs);
472   
473  1 assertTrue(showMenu.isEnabled());
474  1 assertFalse(hideMenu.isEnabled());
475   
476  1 Component[] showOptions = showMenu.getMenuComponents();
477  1 Component[] hideOptions = hideMenu.getMenuComponents();
478   
479  1 assertEquals(4, showOptions.length); // includes 'All' and separator
480  1 assertEquals(2, hideOptions.length);
481  1 String all = MessageManager.getString("label.all");
482  1 assertEquals(all, ((JMenuItem) showOptions[0]).getText());
483  1 assertTrue(showOptions[1] instanceof JPopupMenu.Separator);
484  1 assertEquals(JSeparator.HORIZONTAL,
485    ((JSeparator) showOptions[1]).getOrientation());
486  1 assertEquals("secondary structure",
487    ((JMenuItem) showOptions[2]).getText());
488  1 assertEquals("PDB", ((JMenuItem) showOptions[2]).getToolTipText());
489  1 assertEquals("Temp", ((JMenuItem) showOptions[3]).getText());
490  1 assertEquals("PDB2", ((JMenuItem) showOptions[3]).getToolTipText());
491   
492  1 assertEquals(all, ((JMenuItem) hideOptions[0]).getText());
493  1 assertTrue(hideOptions[1] instanceof JPopupMenu.Separator);
494  1 assertEquals(JSeparator.HORIZONTAL,
495    ((JSeparator) hideOptions[1]).getOrientation());
496    }
497   
498    /**
499    * Test for adding sequence id, dbref and feature links
500    */
 
501  1 toggle @Test(groups = { "Functional" })
502    public void testBuildLinkMenu()
503    {
504  1 List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
505  1 final SequenceI seq0 = seqs.get(0);
506  1 final SequenceI seq1 = seqs.get(1);
507  1 final List<SequenceFeature> noFeatures = Collections
508    .<SequenceFeature> emptyList();
509  1 final String linkText = MessageManager.getString("action.link");
510   
511  1 seq0.addDBRef(new DBRefEntry(DBRefSource.UNIPROT, "1", "P83527"));
512  1 seq0.addDBRef(new DBRefEntry("INTERPRO", "1", "IPR001041"));
513  1 seq0.addDBRef(new DBRefEntry("INTERPRO", "1", "IPR012675"));
514  1 seq0.addDBRef(new DBRefEntry("INTERPRO", "1", "IPR006058"));
515  1 seq1.addDBRef(new DBRefEntry(DBRefSource.UNIPROT, "1", "Q9ZTS2"));
516  1 seq1.addDBRef(new DBRefEntry("GENE3D", "1", "3.10.20.30"));
517   
518    /*
519    * check the Link Menu for the first sequence
520    */
521  1 JMenu linkMenu = PopupMenu.buildLinkMenu(seq0, noFeatures);
522  1 assertEquals(linkText, linkMenu.getText());
523  1 Component[] linkItems = linkMenu.getMenuComponents();
524   
525    /*
526    * menu items are ordered: SEQUENCE_ID search first, then dbrefs in order
527    * of database name (and within that by order of dbref addition)
528    */
529  1 assertEquals(5, linkItems.length);
530  1 assertEquals("EMBL-EBI Search", ((JMenuItem) linkItems[0]).getText());
531  1 assertEquals("INTERPRO|IPR001041",
532    ((JMenuItem) linkItems[1]).getText());
533  1 assertEquals("INTERPRO|IPR012675",
534    ((JMenuItem) linkItems[2]).getText());
535  1 assertEquals("INTERPRO|IPR006058",
536    ((JMenuItem) linkItems[3]).getText());
537  1 assertEquals("UNIPROT|P83527", ((JMenuItem) linkItems[4]).getText());
538   
539    /*
540    * check the Link Menu for the second sequence
541    * note dbref GENE3D is matched to link Gene3D, the latter is displayed
542    */
543  1 linkMenu = PopupMenu.buildLinkMenu(seq1, noFeatures);
544  1 linkItems = linkMenu.getMenuComponents();
545  1 assertEquals(3, linkItems.length);
546  1 assertEquals("EMBL-EBI Search", ((JMenuItem) linkItems[0]).getText());
547  1 assertEquals("Gene3D|3.10.20.30", ((JMenuItem) linkItems[1]).getText());
548  1 assertEquals("UNIPROT|Q9ZTS2", ((JMenuItem) linkItems[2]).getText());
549   
550    /*
551    * if there are no valid links the Links submenu is still shown, but
552    * reduced to the EMBL-EBI lookup only (inserted by
553    * CustomUrlProvider.choosePrimaryUrl())
554    */
555  1 String unmatched = "NOMATCH|http://www.uniprot.org/uniprot/$"
556    + DB_ACCESSION + "$";
557  1 UrlProviderFactoryI factory = new DesktopUrlProviderFactory(null,
558    unmatched, "");
559  1 Preferences.sequenceUrlLinks = factory.createUrlProvider();
560   
561  1 linkMenu = PopupMenu.buildLinkMenu(seq1, noFeatures);
562  1 linkItems = linkMenu.getMenuComponents();
563  1 assertEquals(1, linkItems.length);
564  1 assertEquals("EMBL-EBI Search", ((JMenuItem) linkItems[0]).getText());
565   
566    /*
567    * if sequence is null, only feature links are shown (alignment popup submenu)
568    */
569  1 linkMenu = PopupMenu.buildLinkMenu(null, noFeatures);
570  1 linkItems = linkMenu.getMenuComponents();
571  1 assertEquals(0, linkItems.length);
572   
573  1 List<SequenceFeature> features = new ArrayList<>();
574  1 SequenceFeature sf = new SequenceFeature("type", "desc", 1, 20, null);
575  1 features.add(sf);
576  1 linkMenu = PopupMenu.buildLinkMenu(null, features);
577  1 linkItems = linkMenu.getMenuComponents();
578  1 assertEquals(0, linkItems.length); // feature has no links
579   
580  1 sf.addLink("Pfam family|http://pfam.xfam.org/family/PF00111");
581  1 linkMenu = PopupMenu.buildLinkMenu(null, features);
582  1 linkItems = linkMenu.getMenuComponents();
583  1 assertEquals(1, linkItems.length);
584  1 JMenuItem item = (JMenuItem) linkItems[0];
585  1 assertEquals("Pfam family", item.getText());
586    // ? no way to verify URL, compiled into link's actionListener
587    }
588   
 
589  1 toggle @Test(groups = { "Functional" })
590    public void testHideInsertions()
591    {
592    // get sequences from the alignment
593  1 List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
594   
595    // add our own seqs to avoid problems with changes to existing sequences
596    // (gap at end of sequences varies depending on how tests are run!)
597  1 Sequence seqGap1 = new Sequence("GappySeq",
598    "AAAA----AA-AAAAAAA---AAA-----------AAAAAAAAAA--");
599  1 seqGap1.createDatasetSequence();
600  1 seqs.add(seqGap1);
601  1 Sequence seqGap2 = new Sequence("LessGappySeq",
602    "AAAAAA-AAAAA---AAA--AAAAA--AAAAAAA-AAAAAA");
603  1 seqGap2.createDatasetSequence();
604  1 seqs.add(seqGap2);
605  1 Sequence seqGap3 = new Sequence("AnotherGapSeq",
606    "AAAAAA-AAAAAA--AAAAAA-AAAAAAAAAAA---AAAAAAAA");
607  1 seqGap3.createDatasetSequence();
608  1 seqs.add(seqGap3);
609  1 Sequence seqGap4 = new Sequence("NoGaps",
610    "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA");
611  1 seqGap4.createDatasetSequence();
612  1 seqs.add(seqGap4);
613   
614  1 ColumnSelection sel = new ColumnSelection();
615  1 parentPanel.av.getAlignment().getHiddenColumns()
616    .revealAllHiddenColumns(sel);
617   
618    // get the Popup Menu for 7th sequence - no insertions
619  1 testee = new PopupMenu(parentPanel, seqs.get(7), null);
620  1 testee.hideInsertions_actionPerformed(null);
621   
622  1 HiddenColumns hidden = parentPanel.av.getAlignment().getHiddenColumns();
623  1 Iterator<int[]> it = hidden.iterator();
624  1 assertFalse(it.hasNext());
625   
626    // get the Popup Menu for GappySeq - this time we have insertions
627  1 testee = new PopupMenu(parentPanel, seqs.get(4), null);
628  1 testee.hideInsertions_actionPerformed(null);
629  1 hidden = parentPanel.av.getAlignment().getHiddenColumns();
630  1 it = hidden.iterator();
631   
632  1 assertTrue(it.hasNext());
633  1 int[] region = it.next();
634  1 assertEquals(region[0], 4);
635  1 assertEquals(region[1], 7);
636   
637  1 assertTrue(it.hasNext());
638  1 region = it.next();
639  1 assertEquals(region[0], 10);
640  1 assertEquals(region[1], 10);
641   
642  1 assertTrue(it.hasNext());
643  1 region = it.next();
644  1 assertEquals(region[0], 18);
645  1 assertEquals(region[1], 20);
646   
647  1 assertTrue(it.hasNext());
648  1 region = it.next();
649  1 assertEquals(region[0], 24);
650  1 assertEquals(region[1], 34);
651   
652  1 assertTrue(it.hasNext());
653  1 region = it.next();
654  1 assertEquals(region[0], 45);
655  1 assertEquals(region[1], 46);
656   
657  1 assertFalse(it.hasNext());
658   
659  1 sel = new ColumnSelection();
660  1 hidden.revealAllHiddenColumns(sel);
661   
662    // make a sequence group and hide insertions within the group
663  1 SequenceGroup sg = new SequenceGroup();
664  1 sg.setStartRes(8);
665  1 sg.setEndRes(42);
666  1 sg.addSequence(seqGap2, false);
667  1 sg.addSequence(seqGap3, false);
668  1 parentPanel.av.setSelectionGroup(sg);
669   
670    // hide columns outside and within selection
671    // only hidden columns outside the collection will be retained (unless also
672    // gaps in the selection)
673  1 hidden.hideColumns(1, 10);
674  1 hidden.hideColumns(31, 40);
675   
676    // get the Popup Menu for LessGappySeq in the sequence group
677  1 testee = new PopupMenu(parentPanel, seqs.get(5), null);
678  1 testee.hideInsertions_actionPerformed(null);
679  1 hidden = parentPanel.av.getAlignment().getHiddenColumns();
680  1 it = hidden.iterator();
681   
682  1 assertTrue(it.hasNext());
683  1 region = it.next();
684  1 assertEquals(region[0], 1);
685  1 assertEquals(region[1], 7);
686   
687  1 assertTrue(it.hasNext());
688  1 region = it.next();
689  1 assertEquals(region[0], 13);
690  1 assertEquals(region[1], 14);
691   
692  1 assertTrue(it.hasNext());
693  1 region = it.next();
694  1 assertEquals(region[0], 34);
695  1 assertEquals(region[1], 34);
696    }
697   
 
698  1 toggle @Test(groups = { "Functional" })
699    public void testAddFeatureDetails()
700    {
701  1 String menuText = MessageManager.getString("label.feature_details");
702   
703    /*
704    * with no features, sub-menu should not be created
705    */
706  1 List<SequenceFeature> features = new ArrayList<>();
707  1 SequenceI seq = this.alignment.getSequenceAt(0); // FER_CAPAA/1-12
708  1 testee.addFeatureDetails(features, seq, 10);
709  1 JMenu menu = findMenu(testee, menuText);
710  1 assertNull(menu);
711   
712    /*
713    * add some features; the menu item text is wrapped in html, and includes
714    * feature type, position, description, group (if not null)
715    */
716  1 SequenceFeature sf1 = new SequenceFeature("helix", "curly", 2, 6, null);
717  1 SequenceFeature sf2 = new SequenceFeature("chain", "straight", 1, 1,
718    "uniprot");
719  1 features.add(sf1);
720  1 features.add(sf2);
721  1 testee.addFeatureDetails(features, seq, 10);
722  1 menu = findMenu(testee, menuText);
723  1 assertNotNull(menu);
724  1 assertEquals(2, menu.getItemCount());
725  1 JMenuItem item = menu.getItem(0);
726  1 assertEquals("<html>helix 2-6 curly</html>", item.getText());
727  1 item = menu.getItem(1);
728  1 assertEquals("<html>chain 1 straight (uniprot)</html>", item.getText());
729   
730    /*
731    * long feature descriptions are truncated to 40 characters
732    */
733  1 sf1.setDescription(
734    "this is a quite extraordinarily long description");
735  1 testee.remove(menu); // don't create the sub-menu twice
736  1 testee.addFeatureDetails(features, seq, 10);
737  1 menu = findMenu(testee, menuText);
738  1 item = menu.getItem(0);
739  1 assertEquals(
740    "<html>helix 2-6 this is a quite extraordinarily long des...</html>",
741    item.getText());
742    }
743   
744    /**
745    * Returns the first component which is a JMenu with the given text
746    *
747    * @param c
748    * @param text
749    * @return
750    */
 
751  3 toggle private JMenu findMenu(Container c, String text)
752    {
753  18 for (int i = 0; i < c.getComponentCount(); i++)
754    {
755  17 Component comp = c.getComponent(i);
756  17 if ((comp instanceof JMenu) && ((JMenu) comp).getText().equals(text))
757    {
758  2 return (JMenu) comp;
759    }
760    }
761  1 return null;
762    }
763   
 
764  1 toggle @Test(groups = { "Functional" })
765    public void testAddFeatureDetails_linkedFeatures()
766    {
767    // todo tests that verify menu items for complement features
768    }
769    }
  • Report generated by OpenClover v 4.4.1 on Thu Aug 13 2020 12:06:48 BST using coverage data from Thu Aug 13 2020 12:06:40 BST.
  • OpenClover is free and open-source software.