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  1. Project Clover database Wed Oct 31 2018 15:13:58 GMT
  2. Package jalview.gui

File PopupMenuTest.java

 
testAddFeatureLinks: expected:<5> but was:<6>
 

Code metrics

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Classes

Class Line # Actions
PopupMenuTest 65 295 22 53
0.8369230683.7%
 

Contributing tests

This file is covered by 11 tests. .

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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 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.assertTrue;
28   
29    import jalview.bin.Cache;
30    import jalview.datamodel.AlignmentAnnotation;
31    import jalview.datamodel.AlignmentI;
32    import jalview.datamodel.Annotation;
33    import jalview.datamodel.ColumnSelection;
34    import jalview.datamodel.DBRefEntry;
35    import jalview.datamodel.DBRefSource;
36    import jalview.datamodel.HiddenColumns;
37    import jalview.datamodel.Sequence;
38    import jalview.datamodel.SequenceFeature;
39    import jalview.datamodel.SequenceGroup;
40    import jalview.datamodel.SequenceI;
41    import jalview.io.DataSourceType;
42    import jalview.io.FileFormat;
43    import jalview.io.FormatAdapter;
44    import jalview.urls.api.UrlProviderFactoryI;
45    import jalview.urls.desktop.DesktopUrlProviderFactory;
46    import jalview.util.MessageManager;
47    import jalview.util.UrlConstants;
48   
49    import java.awt.Component;
50    import java.io.IOException;
51    import java.util.ArrayList;
52    import java.util.Collections;
53    import java.util.Iterator;
54    import java.util.List;
55   
56    import javax.swing.JMenu;
57    import javax.swing.JMenuItem;
58    import javax.swing.JPopupMenu;
59    import javax.swing.JSeparator;
60   
61    import org.testng.annotations.BeforeClass;
62    import org.testng.annotations.BeforeMethod;
63    import org.testng.annotations.Test;
64   
 
65    public class PopupMenuTest
66    {
67   
 
68  1 toggle @BeforeClass(alwaysRun = true)
69    public void setUpJvOptionPane()
70    {
71  1 JvOptionPane.setInteractiveMode(false);
72  1 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
73    }
74   
75    // 4 sequences x 13 positions
76    final static String TEST_DATA = ">FER_CAPAA Ferredoxin\n"
77    + "TIETHKEAELVG-\n"
78    + ">FER_CAPAN Ferredoxin, chloroplast precursor\n"
79    + "TIETHKEAELVG-\n"
80    + ">FER1_SOLLC Ferredoxin-1, chloroplast precursor\n"
81    + "TIETHKEEELTA-\n" + ">Q93XJ9_SOLTU Ferredoxin I precursor\n"
82    + "TIETHKEEELTA-\n";
83   
84    AlignmentI alignment;
85   
86    AlignmentPanel parentPanel;
87   
88    PopupMenu testee = null;
89   
 
90  11 toggle @BeforeMethod(alwaysRun = true)
91    public void setUp() throws IOException
92    {
93  11 Cache.loadProperties("test/jalview/io/testProps.jvprops");
94  11 String inMenuString = ("EMBL-EBI Search | http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$"
95    + SEQUENCE_ID
96    + "$"
97    + "|"
98    + "UNIPROT | http://www.uniprot.org/uniprot/$" + DB_ACCESSION + "$")
99    + "|"
100    + ("INTERPRO | http://www.ebi.ac.uk/interpro/entry/$"
101    + DB_ACCESSION + "$")
102    + "|"
103    +
104    // Gene3D entry tests for case (in)sensitivity
105    ("Gene3D | http://gene3d.biochem.ucl.ac.uk/Gene3D/search?sterm=$"
106    + DB_ACCESSION + "$&mode=protein");
107   
108  11 UrlProviderFactoryI factory = new DesktopUrlProviderFactory(
109    UrlConstants.DEFAULT_LABEL, inMenuString, "");
110  11 Preferences.sequenceUrlLinks = factory.createUrlProvider();
111   
112  11 alignment = new FormatAdapter().readFile(TEST_DATA,
113    DataSourceType.PASTE, FileFormat.Fasta);
114  11 AlignFrame af = new AlignFrame(alignment, 700, 500);
115  11 parentPanel = new AlignmentPanel(af, af.getViewport());
116  11 testee = new PopupMenu(parentPanel, null, null);
117  11 int i = 0;
118  11 for (SequenceI seq : alignment.getSequences())
119    {
120  44 final AlignmentAnnotation annotation = new AlignmentAnnotation(
121    "label" + i, "desc" + i, i);
122  44 annotation.setCalcId("calcId" + i);
123  44 seq.addAlignmentAnnotation(annotation);
124  44 annotation.setSequenceRef(seq);
125    }
126    }
127   
 
128  1 toggle @Test(groups = { "Functional" })
129    public void testConfigureReferenceAnnotationsMenu_noSequenceSelected()
130    {
131  1 JMenuItem menu = new JMenuItem();
132  1 List<SequenceI> seqs = new ArrayList<>();
133  1 testee.configureReferenceAnnotationsMenu(menu, seqs);
134  1 assertFalse(menu.isEnabled());
135    // now try null list
136  1 menu.setEnabled(true);
137  1 testee.configureReferenceAnnotationsMenu(menu, null);
138  1 assertFalse(menu.isEnabled());
139    }
140   
141    /**
142    * Test building the 'add reference annotations' menu for the case where there
143    * are no reference annotations to add to the alignment. The menu item should
144    * be disabled.
145    */
 
146  1 toggle @Test(groups = { "Functional" })
147    public void testConfigureReferenceAnnotationsMenu_noReferenceAnnotations()
148    {
149  1 JMenuItem menu = new JMenuItem();
150   
151    /*
152    * Initial state is that sequences have annotations, and have dataset
153    * sequences, but the dataset sequences have no annotations. Hence nothing
154    * to add.
155    */
156  1 List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
157   
158  1 testee.configureReferenceAnnotationsMenu(menu, seqs);
159  1 assertFalse(menu.isEnabled());
160    }
161   
162    /**
163    * Test building the 'add reference annotations' menu for the case where all
164    * reference annotations are already on the alignment. The menu item should be
165    * disabled.
166    */
 
167  1 toggle @Test(groups = { "Functional" })
168    public void testConfigureReferenceAnnotationsMenu_alreadyAdded()
169    {
170  1 JMenuItem menu = new JMenuItem();
171  1 List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
172   
173    // make up new annotations and add to dataset sequences, sequences and
174    // alignment
175  1 attachReferenceAnnotations(seqs, true, true);
176   
177  1 testee.configureReferenceAnnotationsMenu(menu, seqs);
178  1 assertFalse(menu.isEnabled());
179    }
180   
181    /**
182    * Test building the 'add reference annotations' menu for the case where
183    * several reference annotations are on the dataset but not on the sequences.
184    * The menu item should be enabled, and acquire a tooltip which lists the
185    * annotation sources (calcIds) and type (labels).
186    */
 
187  1 toggle @Test(groups = { "Functional" })
188    public void testConfigureReferenceAnnotationsMenu()
189    {
190  1 JMenuItem menu = new JMenuItem();
191  1 List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
192   
193    // make up new annotations and add to dataset sequences
194  1 attachReferenceAnnotations(seqs, false, false);
195   
196  1 testee.configureReferenceAnnotationsMenu(menu, seqs);
197  1 assertTrue(menu.isEnabled());
198  1 String s = MessageManager.getString("label.add_annotations_for");
199    // String expected = "<html><style> p.ttip {width: 350; text-align: justify;
200    // word-wrap: break-word;}</style><p class=\"ttip\">"
201    // + s + "<br/>Jmol/secondary structure<br/>PDB/Temp</p></html>";
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    // String expected = "<html><style> p.ttip {width: 350; text-align: justify;
227    // word-wrap: break-word;}</style><p class=\"ttip\">"
228    // + s + "<br/>Jmol/secondary structure<br/>PDB/Temp</p></html>";
229  1 String expected = "<html><style> div.ttip {width:350px;white-space:pre-wrap;padding:2px;overflow-wrap:break-word;}</style>"
230    + "<div class=\"ttip\">Add annotations for<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 feature links
500    */
 
501  0 toggle @Test(groups = { "Functional" })
502    public void testAddFeatureLinks()
503    {
504    // sequences from the alignment
505  0 List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
506   
507    // create list of links and list of DBRefs
508  0 List<String> links = new ArrayList<>();
509  0 List<DBRefEntry> refs = new ArrayList<>();
510   
511    // links as might be added into Preferences | Connections dialog
512  0 links.add("EMBL-EBI Search | http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$"
513    + SEQUENCE_ID + "$");
514  0 links.add("UNIPROT | http://www.uniprot.org/uniprot/$" + DB_ACCESSION
515    + "$");
516  0 links.add("INTERPRO | http://www.ebi.ac.uk/interpro/entry/$"
517    + DB_ACCESSION + "$");
518    // Gene3D entry tests for case (in)sensitivity
519  0 links.add("Gene3D | http://gene3d.biochem.ucl.ac.uk/Gene3D/search?sterm=$"
520    + DB_ACCESSION + "$&mode=protein");
521   
522    // make seq0 dbrefs
523  0 refs.add(new DBRefEntry(DBRefSource.UNIPROT, "1", "P83527"));
524  0 refs.add(new DBRefEntry("INTERPRO", "1", "IPR001041"));
525  0 refs.add(new DBRefEntry("INTERPRO", "1", "IPR006058"));
526  0 refs.add(new DBRefEntry("INTERPRO", "1", "IPR012675"));
527   
528    // make seq1 dbrefs
529  0 refs.add(new DBRefEntry(DBRefSource.UNIPROT, "1", "Q9ZTS2"));
530  0 refs.add(new DBRefEntry("GENE3D", "1", "3.10.20.30"));
531   
532    // add all the dbrefs to the sequences: Uniprot 1 each, Interpro all 3 to
533    // seq0, Gene3D to seq1
534  0 SequenceI seq = seqs.get(0);
535  0 seq.addDBRef(refs.get(0));
536   
537  0 seq.addDBRef(refs.get(1));
538  0 seq.addDBRef(refs.get(2));
539  0 seq.addDBRef(refs.get(3));
540   
541  0 seqs.get(1).addDBRef(refs.get(4));
542  0 seqs.get(1).addDBRef(refs.get(5));
543   
544    // get the Popup Menu for first sequence
545  0 List<SequenceFeature> noFeatures = Collections.<SequenceFeature> emptyList();
546  0 testee = new PopupMenu(parentPanel, seq, noFeatures);
547  0 Component[] seqItems = testee.sequenceMenu.getMenuComponents();
548  0 JMenu linkMenu = (JMenu) seqItems[6];
549  0 Component[] linkItems = linkMenu.getMenuComponents();
550   
551    // check the number of links are the expected number
552  0 Test failure here assertEquals(5, linkItems.length);
553   
554    // first entry is EMBL-EBI which just uses sequence id not accession id?
555  0 assertEquals("EMBL-EBI Search", ((JMenuItem) linkItems[0]).getText());
556   
557    // sequence id for each link should match corresponding DB accession id
558  0 for (int i = 1; i < 4; i++)
559    {
560  0 String msg = seq.getName() + " link[" + i + "]";
561  0 assertEquals(msg, refs.get(i - 1).getSource(),
562    ((JMenuItem) linkItems[i])
563    .getText().split("\\|")[0]);
564  0 assertEquals(msg, refs.get(i - 1).getAccessionId(),
565    ((JMenuItem) linkItems[i])
566    .getText().split("\\|")[1]);
567    }
568   
569    // get the Popup Menu for second sequence
570  0 seq = seqs.get(1);
571  0 testee = new PopupMenu(parentPanel, seq, noFeatures);
572  0 seqItems = testee.sequenceMenu.getMenuComponents();
573  0 linkMenu = (JMenu) seqItems[6];
574  0 linkItems = linkMenu.getMenuComponents();
575   
576    // check the number of links are the expected number
577  0 assertEquals(3, linkItems.length);
578   
579    // first entry is EMBL-EBI which just uses sequence id not accession id?
580  0 assertEquals("EMBL-EBI Search", ((JMenuItem) linkItems[0]).getText());
581   
582    // sequence id for each link should match corresponding DB accession id
583  0 for (int i = 1; i < 3; i++)
584    {
585  0 String msg = seq.getName() + " link[" + i + "]";
586  0 assertEquals(msg, refs.get(i + 3).getSource(),
587    ((JMenuItem) linkItems[i])
588    .getText().split("\\|")[0].toUpperCase());
589  0 assertEquals(msg, refs.get(i + 3).getAccessionId(),
590    ((JMenuItem) linkItems[i]).getText().split("\\|")[1]);
591    }
592   
593    // if there are no valid links the Links submenu is disabled
594  0 List<String> nomatchlinks = new ArrayList<>();
595  0 nomatchlinks.add("NOMATCH | http://www.uniprot.org/uniprot/$"
596    + DB_ACCESSION + "$");
597   
598  0 testee = new PopupMenu(parentPanel, seq, noFeatures);
599  0 seqItems = testee.sequenceMenu.getMenuComponents();
600  0 linkMenu = (JMenu) seqItems[6];
601  0 assertFalse(linkMenu.isEnabled());
602   
603    }
604   
605    /**
606    * Test for adding feature links
607    */
 
608  1 toggle @Test(groups = { "Functional" })
609    public void testHideInsertions()
610    {
611    // get sequences from the alignment
612  1 List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
613   
614    // add our own seqs to avoid problems with changes to existing sequences
615    // (gap at end of sequences varies depending on how tests are run!)
616  1 Sequence seqGap1 = new Sequence("GappySeq",
617    "AAAA----AA-AAAAAAA---AAA-----------AAAAAAAAAA--");
618  1 seqGap1.createDatasetSequence();
619  1 seqs.add(seqGap1);
620  1 Sequence seqGap2 = new Sequence("LessGappySeq",
621    "AAAAAA-AAAAA---AAA--AAAAA--AAAAAAA-AAAAAA");
622  1 seqGap2.createDatasetSequence();
623  1 seqs.add(seqGap2);
624  1 Sequence seqGap3 = new Sequence("AnotherGapSeq",
625    "AAAAAA-AAAAAA--AAAAAA-AAAAAAAAAAA---AAAAAAAA");
626  1 seqGap3.createDatasetSequence();
627  1 seqs.add(seqGap3);
628  1 Sequence seqGap4 = new Sequence("NoGaps",
629    "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA");
630  1 seqGap4.createDatasetSequence();
631  1 seqs.add(seqGap4);
632   
633  1 ColumnSelection sel = new ColumnSelection();
634  1 parentPanel.av.getAlignment().getHiddenColumns()
635    .revealAllHiddenColumns(sel);
636   
637    // get the Popup Menu for 7th sequence - no insertions
638  1 testee = new PopupMenu(parentPanel, seqs.get(7), null);
639  1 testee.hideInsertions_actionPerformed(null);
640   
641  1 HiddenColumns hidden = parentPanel.av.getAlignment().getHiddenColumns();
642  1 Iterator<int[]> it = hidden.iterator();
643  1 assertFalse(it.hasNext());
644   
645    // get the Popup Menu for GappySeq - this time we have insertions
646  1 testee = new PopupMenu(parentPanel, seqs.get(4), null);
647  1 testee.hideInsertions_actionPerformed(null);
648  1 hidden = parentPanel.av.getAlignment().getHiddenColumns();
649  1 it = hidden.iterator();
650   
651  1 assertTrue(it.hasNext());
652  1 int[] region = it.next();
653  1 assertEquals(region[0], 4);
654  1 assertEquals(region[1], 7);
655   
656  1 assertTrue(it.hasNext());
657  1 region = it.next();
658  1 assertEquals(region[0], 10);
659  1 assertEquals(region[1], 10);
660   
661  1 assertTrue(it.hasNext());
662  1 region = it.next();
663  1 assertEquals(region[0], 18);
664  1 assertEquals(region[1], 20);
665   
666  1 assertTrue(it.hasNext());
667  1 region = it.next();
668  1 assertEquals(region[0], 24);
669  1 assertEquals(region[1], 34);
670   
671  1 assertTrue(it.hasNext());
672  1 region = it.next();
673  1 assertEquals(region[0], 45);
674  1 assertEquals(region[1], 46);
675   
676  1 assertFalse(it.hasNext());
677   
678  1 sel = new ColumnSelection();
679  1 hidden.revealAllHiddenColumns(sel);
680   
681    // make a sequence group and hide insertions within the group
682  1 SequenceGroup sg = new SequenceGroup();
683  1 sg.setStartRes(8);
684  1 sg.setEndRes(42);
685  1 sg.addSequence(seqGap2, false);
686  1 sg.addSequence(seqGap3, false);
687  1 parentPanel.av.setSelectionGroup(sg);
688   
689    // hide columns outside and within selection
690    // only hidden columns outside the collection will be retained (unless also
691    // gaps in the selection)
692  1 hidden.hideColumns(1, 10);
693  1 hidden.hideColumns(31, 40);
694   
695    // get the Popup Menu for LessGappySeq in the sequence group
696  1 testee = new PopupMenu(parentPanel, seqs.get(5), null);
697  1 testee.hideInsertions_actionPerformed(null);
698  1 hidden = parentPanel.av.getAlignment().getHiddenColumns();
699  1 it = hidden.iterator();
700   
701  1 assertTrue(it.hasNext());
702  1 region = it.next();
703  1 assertEquals(region[0], 1);
704  1 assertEquals(region[1], 7);
705   
706  1 assertTrue(it.hasNext());
707  1 region = it.next();
708  1 assertEquals(region[0], 13);
709  1 assertEquals(region[1], 14);
710   
711  1 assertTrue(it.hasNext());
712  1 region = it.next();
713  1 assertEquals(region[0], 34);
714  1 assertEquals(region[1], 34);
715    }
716   
717    }
  • Report generated by OpenClover v 4.2.1 on Wed Oct 31 2018 15:15:54 GMT using coverage data from Wed Oct 31 2018 15:15:47 GMT.
  • Clover free edition.