Clover icon

Coverage Report

  1. Project Clover database Tue Nov 18 2025 10:51:49 GMT
  2. Package jalview.gui

File PopupMenuTest.java

 

Code metrics

16
325
17
1
766
509
26
0.08
19.12
17
1.53

Classes

Class Line # Actions
PopupMenuTest 69 325 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.bin.Console;
50    import jalview.datamodel.AlignmentAnnotation;
51    import jalview.datamodel.AlignmentI;
52    import jalview.datamodel.Annotation;
53    import jalview.datamodel.ColumnSelection;
54    import jalview.datamodel.DBRefEntry;
55    import jalview.datamodel.DBRefSource;
56    import jalview.datamodel.HiddenColumns;
57    import jalview.datamodel.Sequence;
58    import jalview.datamodel.SequenceFeature;
59    import jalview.datamodel.SequenceGroup;
60    import jalview.datamodel.SequenceI;
61    import jalview.io.DataSourceType;
62    import jalview.io.FileFormat;
63    import jalview.io.FormatAdapter;
64    import jalview.urls.api.UrlProviderFactoryI;
65    import jalview.urls.desktop.DesktopUrlProviderFactory;
66    import jalview.util.MessageManager;
67    import jalview.util.UrlConstants;
68   
 
69    public class PopupMenuTest
70    {
71   
 
72  1 toggle @BeforeClass(alwaysRun = true)
73    public void setUpJvOptionPane()
74    {
75  1 JvOptionPane.setInteractiveMode(false);
76  1 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
77    }
78   
79    // 4 sequences x 13 positions
80    final static String TEST_DATA = ">FER_CAPAA Ferredoxin\n"
81    + "TIETHKEAELVG-\n"
82    + ">FER_CAPAN Ferredoxin, chloroplast precursor\n"
83    + "TIETHKEAELVG-\n"
84    + ">FER1_SOLLC Ferredoxin-1, chloroplast precursor\n"
85    + "TIETHKEEELTA-\n" + ">Q93XJ9_SOLTU Ferredoxin I precursor\n"
86    + "TIETHKEEELTA-\n";
87   
88    AlignmentI alignment;
89   
90    AlignmentPanel parentPanel;
91   
92    PopupMenu testee = null;
93   
 
94  13 toggle @BeforeMethod(alwaysRun = true)
95    public void setUp() throws IOException
96    {
97  13 Cache.loadProperties("test/jalview/io/testProps.jvprops");
98  13 Console.initLogger();
99   
100  13 String inMenuString = ("EMBL-EBI Search | http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$"
101    + SEQUENCE_ID + "$" + "|"
102    + "UNIPROT | http://www.uniprot.org/uniprot/$" + DB_ACCESSION
103    + "$") + "|"
104    + ("INTERPRO | http://www.ebi.ac.uk/interpro/entry/$"
105    + DB_ACCESSION + "$")
106    + "|" +
107    // Gene3D entry tests for case (in)sensitivity
108    ("Gene3D | http://gene3d.biochem.ucl.ac.uk/Gene3D/search?sterm=$"
109    + DB_ACCESSION + "$&mode=protein");
110   
111  13 UrlProviderFactoryI factory = new DesktopUrlProviderFactory(
112    UrlConstants.DEFAULT_LABEL, inMenuString, "");
113  13 Preferences.sequenceUrlLinks = factory.createUrlProvider();
114   
115  13 alignment = new FormatAdapter().readFile(TEST_DATA,
116    DataSourceType.PASTE, FileFormat.Fasta);
117  13 AlignFrame af = new AlignFrame(alignment, 700, 500);
118  13 parentPanel = new AlignmentPanel(af, af.getViewport());
119  13 testee = new PopupMenu(parentPanel, alignment.getSequenceAt(0), null);
120  13 int i = 0;
121  13 for (SequenceI seq : alignment.getSequences())
122    {
123  52 final AlignmentAnnotation annotation = new AlignmentAnnotation(
124    "label" + i, "desc" + i, i);
125  52 annotation.setCalcId("calcId" + i);
126  52 seq.addAlignmentAnnotation(annotation);
127  52 annotation.setSequenceRef(seq);
128    }
129    }
130   
 
131  1 toggle @Test(groups = { "Functional" })
132    public void testConfigureReferenceAnnotationsMenu_noSequenceSelected()
133    {
134  1 JMenuItem menu = new JMenuItem();
135  1 List<SequenceI> seqs = new ArrayList<>();
136  1 testee.configureReferenceAnnotationsMenu(menu, seqs);
137  1 assertFalse(menu.isEnabled());
138    // now try null list
139  1 menu.setEnabled(true);
140  1 testee.configureReferenceAnnotationsMenu(menu, null);
141  1 assertFalse(menu.isEnabled());
142    }
143   
144    /**
145    * Test building the 'add reference annotations' menu for the case where there
146    * are no reference annotations to add to the alignment. The menu item should
147    * be disabled.
148    */
 
149  1 toggle @Test(groups = { "Functional" })
150    public void testConfigureReferenceAnnotationsMenu_noReferenceAnnotations()
151    {
152  1 JMenuItem menu = new JMenuItem();
153   
154    /*
155    * Initial state is that sequences have annotations, and have dataset
156    * sequences, but the dataset sequences have no annotations. Hence nothing
157    * to add.
158    */
159  1 List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
160   
161  1 testee.configureReferenceAnnotationsMenu(menu, seqs);
162  1 assertFalse(menu.isEnabled());
163    }
164   
165    /**
166    * Test building the 'add reference annotations' menu for the case where all
167    * reference annotations are already on the alignment. The menu item should be
168    * disabled.
169    */
 
170  1 toggle @Test(groups = { "Functional" })
171    public void testConfigureReferenceAnnotationsMenu_alreadyAdded()
172    {
173  1 JMenuItem menu = new JMenuItem();
174  1 List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
175   
176    // make up new annotations and add to dataset sequences, sequences and
177    // alignment
178  1 attachReferenceAnnotations(seqs, true, true);
179   
180  1 testee.configureReferenceAnnotationsMenu(menu, seqs);
181  1 assertFalse(menu.isEnabled());
182    }
183   
184    /**
185    * Test building the 'add reference annotations' menu for the case where
186    * several reference annotations are on the dataset but not on the sequences.
187    * The menu item should be enabled, and acquire a tooltip which lists the
188    * annotation sources (calcIds) and type (labels).
189    */
 
190  1 toggle @Test(groups = { "Functional" })
191    public void testConfigureReferenceAnnotationsMenu()
192    {
193  1 JMenuItem menu = new JMenuItem();
194  1 List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
195   
196    // make up new annotations and add to dataset sequences
197  1 attachReferenceAnnotations(seqs, false, false);
198   
199  1 testee.configureReferenceAnnotationsMenu(menu, seqs);
200  1 assertTrue(menu.isEnabled());
201  1 String s = MessageManager.getString("label.add_annotations_for");
202  1 String expected = "<html><style> div.ttip {width:350px;white-space:pre-wrap;padding:2px;overflow-wrap:break-word;}</style>"
203    + "<div class=\"ttip\">" + s
204    + "<br/>Jmol/secondary structure<br/>PDB/Temp </div></html>";
205  1 assertEquals(expected, menu.getToolTipText());
206    }
207   
208    /**
209    * Test building the 'add reference annotations' menu for the case where
210    * several reference annotations are on the dataset and the sequences but not
211    * on the alignment. The menu item should be enabled, and acquire a tooltip
212    * which lists the annotation sources (calcIds) and type (labels).
213    */
 
214  1 toggle @Test(groups = { "Functional" })
215    public void testConfigureReferenceAnnotationsMenu_notOnAlignment()
216    {
217  1 JMenuItem menu = new JMenuItem();
218  1 List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
219   
220    // make up new annotations and add to dataset sequences and sequences
221  1 attachReferenceAnnotations(seqs, true, false);
222   
223  1 testee.configureReferenceAnnotationsMenu(menu, seqs);
224  1 assertTrue(menu.isEnabled());
225  1 String s = MessageManager.getString("label.add_annotations_for");
226  1 String expected = "<html><style> div.ttip {width:350px;white-space:pre-wrap;padding:2px;overflow-wrap:break-word;}</style>"
227    + "<div class=\"ttip\">" + s
228    + "<br/>Jmol/secondary structure<br/>PDB/Temp </div></html>";
229  1 assertEquals(expected, menu.getToolTipText());
230    }
231   
232    /**
233    * Generate annotations and add to dataset sequences and (optionally)
234    * sequences and/or alignment
235    *
236    * @param seqs
237    * @param addToSequence
238    * @param addToAlignment
239    */
 
240  3 toggle private void attachReferenceAnnotations(List<SequenceI> seqs,
241    boolean addToSequence, boolean addToAlignment)
242    {
243    // PDB.secondary structure on Sequence0
244  3 AlignmentAnnotation annotation = new AlignmentAnnotation(
245    "secondary structure", "", 0);
246  3 annotation.setCalcId("PDB");
247  3 seqs.get(0).getDatasetSequence().addAlignmentAnnotation(annotation);
248  3 if (addToSequence)
249    {
250  2 seqs.get(0).addAlignmentAnnotation(annotation);
251    }
252  3 if (addToAlignment)
253    {
254  1 this.alignment.addAnnotation(annotation);
255    }
256   
257    // PDB.Temp on Sequence1
258  3 annotation = new AlignmentAnnotation("Temp", "", 0);
259  3 annotation.setCalcId("PDB");
260  3 seqs.get(1).getDatasetSequence().addAlignmentAnnotation(annotation);
261  3 if (addToSequence)
262    {
263  2 seqs.get(1).addAlignmentAnnotation(annotation);
264    }
265  3 if (addToAlignment)
266    {
267  1 this.alignment.addAnnotation(annotation);
268    }
269   
270    // JMOL.secondary structure on Sequence0
271  3 annotation = new AlignmentAnnotation("secondary structure", "", 0);
272  3 annotation.setCalcId("Jmol");
273  3 seqs.get(0).getDatasetSequence().addAlignmentAnnotation(annotation);
274  3 if (addToSequence)
275    {
276  2 seqs.get(0).addAlignmentAnnotation(annotation);
277    }
278  3 if (addToAlignment)
279    {
280  1 this.alignment.addAnnotation(annotation);
281    }
282    }
283   
284    /**
285    * Test building the 'add reference annotations' menu for the case where there
286    * are two alignment views:
287    * <ul>
288    * <li>in one view, reference annotations have been added (are on the
289    * datasets, sequences and alignment)</li>
290    * <li>in the current view, reference annotations are on the dataset and
291    * sequence, but not the alignment</li>
292    * </ul>
293    * The menu item should be enabled, and acquire a tooltip which lists the
294    * annotation sources (calcIds) and type (labels).
295    */
 
296  1 toggle @Test(groups = { "Functional" })
297    public void testConfigureReferenceAnnotationsMenu_twoViews()
298    {
299    }
300   
301    /**
302    * Test for building menu options including 'show' and 'hide' annotation
303    * types.
304    */
 
305  1 toggle @Test(groups = { "Functional" })
306    public void testBuildAnnotationTypesMenus()
307    {
308  1 JMenu showMenu = new JMenu();
309  1 JMenu hideMenu = new JMenu();
310  1 List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
311   
312    // make up new annotations and add to sequences and to the alignment
313   
314    // PDB.secondary structure on Sequence0
315  1 AlignmentAnnotation annotation = new AlignmentAnnotation(
316    "secondary structure", "", new Annotation[] {});
317  1 annotation.setCalcId("PDB");
318  1 annotation.visible = true;
319  1 seqs.get(0).addAlignmentAnnotation(annotation);
320  1 parentPanel.getAlignment().addAnnotation(annotation);
321   
322    // JMOL.secondary structure on Sequence0 - hidden
323  1 annotation = new AlignmentAnnotation("secondary structure", "",
324    new Annotation[] {});
325  1 annotation.setCalcId("JMOL");
326  1 annotation.visible = false;
327  1 seqs.get(0).addAlignmentAnnotation(annotation);
328  1 parentPanel.getAlignment().addAnnotation(annotation);
329   
330    // Jpred.SSP on Sequence0 - hidden
331  1 annotation = new AlignmentAnnotation("SSP", "", new Annotation[] {});
332  1 annotation.setCalcId("JPred");
333  1 annotation.visible = false;
334  1 seqs.get(0).addAlignmentAnnotation(annotation);
335  1 parentPanel.getAlignment().addAnnotation(annotation);
336   
337    // PDB.Temp on Sequence1
338  1 annotation = new AlignmentAnnotation("Temp", "", new Annotation[] {});
339  1 annotation.setCalcId("PDB");
340  1 annotation.visible = true;
341  1 seqs.get(1).addAlignmentAnnotation(annotation);
342  1 parentPanel.getAlignment().addAnnotation(annotation);
343   
344    /*
345    * Expect menu options to show "secondary structure" and "SSP", and to hide
346    * "secondary structure" and "Temp". Tooltip should be calcId.
347    */
348  1 testee.buildAnnotationTypesMenus(showMenu, hideMenu, seqs);
349   
350  1 assertTrue(showMenu.isEnabled());
351  1 assertTrue(hideMenu.isEnabled());
352   
353  1 Component[] showOptions = showMenu.getMenuComponents();
354  1 Component[] hideOptions = hideMenu.getMenuComponents();
355   
356  1 assertEquals(4, showOptions.length); // includes 'All' and separator
357  1 assertEquals(4, hideOptions.length);
358  1 String all = MessageManager.getString("label.all");
359  1 assertEquals(all, ((JMenuItem) showOptions[0]).getText());
360  1 assertTrue(showOptions[1] instanceof JPopupMenu.Separator);
361  1 assertEquals(JSeparator.HORIZONTAL,
362    ((JSeparator) showOptions[1]).getOrientation());
363  1 assertEquals("secondary structure",
364    ((JMenuItem) showOptions[2]).getText());
365  1 assertEquals("JMOL", ((JMenuItem) showOptions[2]).getToolTipText());
366  1 assertEquals("SSP", ((JMenuItem) showOptions[3]).getText());
367  1 assertEquals("JPred", ((JMenuItem) showOptions[3]).getToolTipText());
368   
369  1 assertEquals(all, ((JMenuItem) hideOptions[0]).getText());
370  1 assertTrue(hideOptions[1] instanceof JPopupMenu.Separator);
371  1 assertEquals(JSeparator.HORIZONTAL,
372    ((JSeparator) hideOptions[1]).getOrientation());
373  1 assertEquals("secondary structure",
374    ((JMenuItem) hideOptions[2]).getText());
375  1 assertEquals("PDB", ((JMenuItem) hideOptions[2]).getToolTipText());
376  1 assertEquals("Temp", ((JMenuItem) hideOptions[3]).getText());
377  1 assertEquals("PDB", ((JMenuItem) hideOptions[3]).getToolTipText());
378    }
379   
380    /**
381    * Test for building menu options with only 'hide' annotation types enabled.
382    */
 
383  1 toggle @Test(groups = { "Functional" })
384    public void testBuildAnnotationTypesMenus_showDisabled()
385    {
386  1 JMenu showMenu = new JMenu();
387  1 JMenu hideMenu = new JMenu();
388  1 List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
389   
390    // make up new annotations and add to sequences and to the alignment
391   
392    // PDB.secondary structure on Sequence0
393  1 AlignmentAnnotation annotation = new AlignmentAnnotation(
394    "secondary structure", "", new Annotation[] {});
395  1 annotation.setCalcId("PDB");
396  1 annotation.visible = true;
397  1 seqs.get(0).addAlignmentAnnotation(annotation);
398  1 parentPanel.getAlignment().addAnnotation(annotation);
399   
400    // PDB.Temp on Sequence1
401  1 annotation = new AlignmentAnnotation("Temp", "", new Annotation[] {});
402  1 annotation.setCalcId("PDB");
403  1 annotation.visible = true;
404  1 seqs.get(1).addAlignmentAnnotation(annotation);
405  1 parentPanel.getAlignment().addAnnotation(annotation);
406   
407    /*
408    * Expect menu options to hide "secondary structure" and "Temp". Tooltip
409    * should be calcId. 'Show' menu should be disabled.
410    */
411  1 testee.buildAnnotationTypesMenus(showMenu, hideMenu, seqs);
412   
413  1 assertFalse(showMenu.isEnabled());
414  1 assertTrue(hideMenu.isEnabled());
415   
416  1 Component[] showOptions = showMenu.getMenuComponents();
417  1 Component[] hideOptions = hideMenu.getMenuComponents();
418   
419  1 assertEquals(2, showOptions.length); // includes 'All' and separator
420  1 assertEquals(4, hideOptions.length);
421  1 String all = MessageManager.getString("label.all");
422  1 assertEquals(all, ((JMenuItem) showOptions[0]).getText());
423  1 assertTrue(showOptions[1] instanceof JPopupMenu.Separator);
424  1 assertEquals(JSeparator.HORIZONTAL,
425    ((JSeparator) showOptions[1]).getOrientation());
426   
427  1 assertEquals(all, ((JMenuItem) hideOptions[0]).getText());
428  1 assertTrue(hideOptions[1] instanceof JPopupMenu.Separator);
429  1 assertEquals(JSeparator.HORIZONTAL,
430    ((JSeparator) hideOptions[1]).getOrientation());
431  1 assertEquals("secondary structure",
432    ((JMenuItem) hideOptions[2]).getText());
433  1 assertEquals("PDB", ((JMenuItem) hideOptions[2]).getToolTipText());
434  1 assertEquals("Temp", ((JMenuItem) hideOptions[3]).getText());
435  1 assertEquals("PDB", ((JMenuItem) hideOptions[3]).getToolTipText());
436    }
437   
438    /**
439    * Test for building menu options with only 'show' annotation types enabled.
440    */
 
441  1 toggle @Test(groups = { "Functional" })
442    public void testBuildAnnotationTypesMenus_hideDisabled()
443    {
444  1 JMenu showMenu = new JMenu();
445  1 JMenu hideMenu = new JMenu();
446  1 List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
447   
448    // make up new annotations and add to sequences and to the alignment
449   
450    // PDB.secondary structure on Sequence0
451  1 AlignmentAnnotation annotation = new AlignmentAnnotation(
452    "secondary structure", "", new Annotation[] {});
453  1 annotation.setCalcId("PDB");
454  1 annotation.visible = false;
455  1 seqs.get(0).addAlignmentAnnotation(annotation);
456  1 parentPanel.getAlignment().addAnnotation(annotation);
457   
458    // PDB.Temp on Sequence1
459  1 annotation = new AlignmentAnnotation("Temp", "", new Annotation[] {});
460  1 annotation.setCalcId("PDB2");
461  1 annotation.visible = false;
462  1 seqs.get(1).addAlignmentAnnotation(annotation);
463  1 parentPanel.getAlignment().addAnnotation(annotation);
464   
465    /*
466    * Expect menu options to show "secondary structure" and "Temp". Tooltip
467    * should be calcId. 'hide' menu should be disabled.
468    */
469  1 testee.buildAnnotationTypesMenus(showMenu, hideMenu, seqs);
470   
471  1 assertTrue(showMenu.isEnabled());
472  1 assertFalse(hideMenu.isEnabled());
473   
474  1 Component[] showOptions = showMenu.getMenuComponents();
475  1 Component[] hideOptions = hideMenu.getMenuComponents();
476   
477  1 assertEquals(4, showOptions.length); // includes 'All' and separator
478  1 assertEquals(2, hideOptions.length);
479  1 String all = MessageManager.getString("label.all");
480  1 assertEquals(all, ((JMenuItem) showOptions[0]).getText());
481  1 assertTrue(showOptions[1] instanceof JPopupMenu.Separator);
482  1 assertEquals(JSeparator.HORIZONTAL,
483    ((JSeparator) showOptions[1]).getOrientation());
484  1 assertEquals("secondary structure",
485    ((JMenuItem) showOptions[2]).getText());
486  1 assertEquals("PDB", ((JMenuItem) showOptions[2]).getToolTipText());
487  1 assertEquals("Temp", ((JMenuItem) showOptions[3]).getText());
488  1 assertEquals("PDB2", ((JMenuItem) showOptions[3]).getToolTipText());
489   
490  1 assertEquals(all, ((JMenuItem) hideOptions[0]).getText());
491  1 assertTrue(hideOptions[1] instanceof JPopupMenu.Separator);
492  1 assertEquals(JSeparator.HORIZONTAL,
493    ((JSeparator) hideOptions[1]).getOrientation());
494    }
495   
496    /**
497    * Test for adding sequence id, dbref and feature links
498    */
 
499  1 toggle @Test(groups = { "Functional" })
500    public void testBuildLinkMenu()
501    {
502  1 List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
503  1 final SequenceI seq0 = seqs.get(0);
504  1 final SequenceI seq1 = seqs.get(1);
505  1 final List<SequenceFeature> noFeatures = Collections
506    .<SequenceFeature> emptyList();
507  1 final String linkText = MessageManager.getString("action.link");
508   
509  1 seq0.addDBRef(new DBRefEntry(DBRefSource.UNIPROT, "1", "P83527"));
510  1 seq0.addDBRef(new DBRefEntry("INTERPRO", "1", "IPR001041"));
511  1 seq0.addDBRef(new DBRefEntry("INTERPRO", "1", "IPR012675"));
512  1 seq0.addDBRef(new DBRefEntry("INTERPRO", "1", "IPR006058"));
513  1 seq1.addDBRef(new DBRefEntry(DBRefSource.UNIPROT, "1", "Q9ZTS2"));
514  1 seq1.addDBRef(new DBRefEntry("GENE3D", "1", "3.10.20.30"));
515   
516    /*
517    * check the Link Menu for the first sequence
518    */
519  1 JMenu linkMenu = PopupMenu.buildLinkMenu(seq0, noFeatures);
520  1 assertEquals(linkText, linkMenu.getText());
521  1 Component[] linkItems = linkMenu.getMenuComponents();
522   
523    /*
524    * menu items are ordered: SEQUENCE_ID search first, then dbrefs in order
525    * of database name (and within that by order of dbref addition)
526    */
527  1 assertEquals(5, linkItems.length);
528  1 assertEquals("EMBL-EBI Search", ((JMenuItem) linkItems[0]).getText());
529  1 assertEquals("INTERPRO|IPR001041",
530    ((JMenuItem) linkItems[1]).getText());
531  1 assertEquals("INTERPRO|IPR012675",
532    ((JMenuItem) linkItems[2]).getText());
533  1 assertEquals("INTERPRO|IPR006058",
534    ((JMenuItem) linkItems[3]).getText());
535  1 assertEquals("UNIPROT|P83527", ((JMenuItem) linkItems[4]).getText());
536   
537    /*
538    * check the Link Menu for the second sequence
539    * note dbref GENE3D is matched to link Gene3D, the latter is displayed
540    */
541  1 linkMenu = PopupMenu.buildLinkMenu(seq1, noFeatures);
542  1 linkItems = linkMenu.getMenuComponents();
543  1 assertEquals(3, linkItems.length);
544  1 assertEquals("EMBL-EBI Search", ((JMenuItem) linkItems[0]).getText());
545  1 assertEquals("Gene3D|3.10.20.30", ((JMenuItem) linkItems[1]).getText());
546  1 assertEquals("UNIPROT|Q9ZTS2", ((JMenuItem) linkItems[2]).getText());
547   
548    /*
549    * if there are no valid links the Links submenu is still shown, but
550    * reduced to the EMBL-EBI lookup only (inserted by
551    * CustomUrlProvider.choosePrimaryUrl())
552    */
553  1 String unmatched = "NOMATCH|http://www.uniprot.org/uniprot/$"
554    + DB_ACCESSION + "$";
555  1 UrlProviderFactoryI factory = new DesktopUrlProviderFactory(null,
556    unmatched, "");
557  1 Preferences.sequenceUrlLinks = factory.createUrlProvider();
558   
559  1 linkMenu = PopupMenu.buildLinkMenu(seq1, noFeatures);
560  1 linkItems = linkMenu.getMenuComponents();
561  1 assertEquals(1, linkItems.length);
562  1 assertEquals("EMBL-EBI Search", ((JMenuItem) linkItems[0]).getText());
563   
564    /*
565    * if sequence is null, only feature links are shown (alignment popup submenu)
566    */
567  1 linkMenu = PopupMenu.buildLinkMenu(null, noFeatures);
568  1 linkItems = linkMenu.getMenuComponents();
569  1 assertEquals(0, linkItems.length);
570   
571  1 List<SequenceFeature> features = new ArrayList<>();
572  1 SequenceFeature sf = new SequenceFeature("type", "desc", 1, 20, null);
573  1 features.add(sf);
574  1 linkMenu = PopupMenu.buildLinkMenu(null, features);
575  1 linkItems = linkMenu.getMenuComponents();
576  1 assertEquals(0, linkItems.length); // feature has no links
577   
578  1 sf.addLink("Pfam family|http://pfam.xfam.org/family/PF00111");
579  1 linkMenu = PopupMenu.buildLinkMenu(null, features);
580  1 linkItems = linkMenu.getMenuComponents();
581  1 assertEquals(1, linkItems.length);
582  1 JMenuItem item = (JMenuItem) linkItems[0];
583  1 assertEquals("Pfam family", item.getText());
584    // ? no way to verify URL, compiled into link's actionListener
585    }
586   
 
587  1 toggle @Test(groups = { "Functional" })
588    public void testHideInsertions()
589    {
590    // get sequences from the alignment
591  1 List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
592   
593    // add our own seqs to avoid problems with changes to existing sequences
594    // (gap at end of sequences varies depending on how tests are run!)
595  1 Sequence seqGap1 = new Sequence("GappySeq",
596    "AAAA----AA-AAAAAAA---AAA-----------AAAAAAAAAA--");
597  1 seqGap1.createDatasetSequence();
598  1 seqs.add(seqGap1);
599  1 Sequence seqGap2 = new Sequence("LessGappySeq",
600    "AAAAAA-AAAAA---AAA--AAAAA--AAAAAAA-AAAAAA");
601  1 seqGap2.createDatasetSequence();
602  1 seqs.add(seqGap2);
603  1 Sequence seqGap3 = new Sequence("AnotherGapSeq",
604    "AAAAAA-AAAAAA--AAAAAA-AAAAAAAAAAA---AAAAAAAA");
605  1 seqGap3.createDatasetSequence();
606  1 seqs.add(seqGap3);
607  1 Sequence seqGap4 = new Sequence("NoGaps",
608    "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA");
609  1 seqGap4.createDatasetSequence();
610  1 seqs.add(seqGap4);
611   
612  1 ColumnSelection sel = new ColumnSelection();
613  1 parentPanel.av.getAlignment().getHiddenColumns()
614    .revealAllHiddenColumns(sel);
615   
616    // get the Popup Menu for 7th sequence - no insertions
617  1 testee = new PopupMenu(parentPanel, seqs.get(7), null);
618  1 testee.hideInsertions_actionPerformed(null);
619   
620  1 HiddenColumns hidden = parentPanel.av.getAlignment().getHiddenColumns();
621  1 Iterator<int[]> it = hidden.iterator();
622  1 assertFalse(it.hasNext());
623   
624    // get the Popup Menu for GappySeq - this time we have insertions
625  1 testee = new PopupMenu(parentPanel, seqs.get(4), null);
626  1 testee.hideInsertions_actionPerformed(null);
627  1 hidden = parentPanel.av.getAlignment().getHiddenColumns();
628  1 it = hidden.iterator();
629   
630  1 assertTrue(it.hasNext());
631  1 int[] region = it.next();
632  1 assertEquals(region[0], 4);
633  1 assertEquals(region[1], 7);
634   
635  1 assertTrue(it.hasNext());
636  1 region = it.next();
637  1 assertEquals(region[0], 10);
638  1 assertEquals(region[1], 10);
639   
640  1 assertTrue(it.hasNext());
641  1 region = it.next();
642  1 assertEquals(region[0], 18);
643  1 assertEquals(region[1], 20);
644   
645  1 assertTrue(it.hasNext());
646  1 region = it.next();
647  1 assertEquals(region[0], 24);
648  1 assertEquals(region[1], 34);
649   
650  1 assertTrue(it.hasNext());
651  1 region = it.next();
652  1 assertEquals(region[0], 45);
653  1 assertEquals(region[1], 46);
654   
655  1 assertFalse(it.hasNext());
656   
657  1 sel = new ColumnSelection();
658  1 hidden.revealAllHiddenColumns(sel);
659   
660    // make a sequence group and hide insertions within the group
661  1 SequenceGroup sg = new SequenceGroup();
662  1 sg.setStartRes(8);
663  1 sg.setEndRes(42);
664  1 sg.addSequence(seqGap2, false);
665  1 sg.addSequence(seqGap3, false);
666  1 parentPanel.av.setSelectionGroup(sg);
667   
668    // hide columns outside and within selection
669    // only hidden columns outside the collection will be retained (unless also
670    // gaps in the selection)
671  1 hidden.hideColumns(1, 10);
672  1 hidden.hideColumns(31, 40);
673   
674    // get the Popup Menu for LessGappySeq in the sequence group
675  1 testee = new PopupMenu(parentPanel, seqs.get(5), null);
676  1 testee.hideInsertions_actionPerformed(null);
677  1 hidden = parentPanel.av.getAlignment().getHiddenColumns();
678  1 it = hidden.iterator();
679   
680  1 assertTrue(it.hasNext());
681  1 region = it.next();
682  1 assertEquals(region[0], 1);
683  1 assertEquals(region[1], 7);
684   
685  1 assertTrue(it.hasNext());
686  1 region = it.next();
687  1 assertEquals(region[0], 13);
688  1 assertEquals(region[1], 14);
689   
690  1 assertTrue(it.hasNext());
691  1 region = it.next();
692  1 assertEquals(region[0], 34);
693  1 assertEquals(region[1], 34);
694    }
695   
 
696  1 toggle @Test(groups = { "Functional" })
697    public void testAddFeatureDetails()
698    {
699  1 String menuText = MessageManager.getString("label.feature_details");
700   
701    /*
702    * with no features, sub-menu should not be created
703    */
704  1 List<SequenceFeature> features = new ArrayList<>();
705  1 SequenceI seq = this.alignment.getSequenceAt(0); // FER_CAPAA/1-12
706  1 testee.addFeatureDetails(features, seq, 10);
707  1 JMenu menu = findMenu(testee, menuText);
708  1 assertNull(menu);
709   
710    /*
711    * add some features; the menu item text is wrapped in html, and includes
712    * feature type, position, description, group (if not null)
713    */
714  1 SequenceFeature sf1 = new SequenceFeature("helix", "curly", 2, 6, null);
715  1 SequenceFeature sf2 = new SequenceFeature("chain", "straight", 1, 1,
716    "uniprot");
717  1 features.add(sf1);
718  1 features.add(sf2);
719  1 testee.addFeatureDetails(features, seq, 10);
720  1 menu = findMenu(testee, menuText);
721  1 assertNotNull(menu);
722  1 assertEquals(2, menu.getItemCount());
723  1 JMenuItem item = menu.getItem(0);
724  1 assertEquals("<html>helix 2-6 curly</html>", item.getText());
725  1 item = menu.getItem(1);
726  1 assertEquals("<html>chain 1 straight (uniprot)</html>", item.getText());
727   
728    /*
729    * long feature descriptions are truncated to 40 characters
730    */
731  1 sf1.setDescription("this is a quite extraordinarily long description");
732  1 testee.remove(menu); // don't create the sub-menu twice
733  1 testee.addFeatureDetails(features, seq, 10);
734  1 menu = findMenu(testee, menuText);
735  1 item = menu.getItem(0);
736  1 assertEquals(
737    "<html>helix 2-6 this is a quite extraordinarily long des...</html>",
738    item.getText());
739    }
740   
741    /**
742    * Returns the first component which is a JMenu with the given text
743    *
744    * @param c
745    * @param text
746    * @return
747    */
 
748  3 toggle private JMenu findMenu(Container c, String text)
749    {
750  18 for (int i = 0; i < c.getComponentCount(); i++)
751    {
752  17 Component comp = c.getComponent(i);
753  17 if ((comp instanceof JMenu) && ((JMenu) comp).getText().equals(text))
754    {
755  2 return (JMenu) comp;
756    }
757    }
758  1 return null;
759    }
760   
 
761  1 toggle @Test(groups = { "Functional" })
762    public void testAddFeatureDetails_linkedFeatures()
763    {
764    // todo tests that verify menu items for complement features
765    }
766    }
  • Report generated by OpenClover v 4.4.1 on Tue Nov 18 2025 11:02:12 GMT using coverage data from Tue Nov 18 2025 11:01:58 GMT.
  • OpenClover is free and open-source software.