2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
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.
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.
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.
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;
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;
39 import javax.swing.JMenu;
40 import javax.swing.JMenuItem;
41 import javax.swing.JPopupMenu;
42 import javax.swing.JSeparator;
44 import org.testng.annotations.BeforeClass;
45 import org.testng.annotations.BeforeMethod;
46 import org.testng.annotations.Test;
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;
68 public class PopupMenuTest
71 @BeforeClass(alwaysRun = true)
72 public void setUpJvOptionPane()
74 JvOptionPane.setInteractiveMode(false);
75 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
78 // 4 sequences x 13 positions
79 final static String TEST_DATA = ">FER_CAPAA Ferredoxin\n"
81 + ">FER_CAPAN Ferredoxin, chloroplast precursor\n"
83 + ">FER1_SOLLC Ferredoxin-1, chloroplast precursor\n"
84 + "TIETHKEEELTA-\n" + ">Q93XJ9_SOLTU Ferredoxin I precursor\n"
89 AlignmentPanel parentPanel;
91 PopupMenu testee = null;
93 @BeforeMethod(alwaysRun = true)
94 public void setUp() throws IOException
96 Cache.loadProperties("test/jalview/io/testProps.jvprops");
99 String inMenuString = ("EMBL-EBI Search | http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$"
103 + "UNIPROT | http://www.uniprot.org/uniprot/$" + DB_ACCESSION + "$")
105 + ("INTERPRO | http://www.ebi.ac.uk/interpro/entry/$"
106 + DB_ACCESSION + "$")
109 // Gene3D entry tests for case (in)sensitivity
110 ("Gene3D | http://gene3d.biochem.ucl.ac.uk/Gene3D/search?sterm=$"
111 + DB_ACCESSION + "$&mode=protein");
113 UrlProviderFactoryI factory = new DesktopUrlProviderFactory(
114 UrlConstants.DEFAULT_LABEL, inMenuString, "");
115 Preferences.sequenceUrlLinks = factory.createUrlProvider();
117 alignment = new FormatAdapter().readFile(TEST_DATA,
118 DataSourceType.PASTE, FileFormat.Fasta);
119 AlignFrame af = new AlignFrame(alignment, 700, 500);
120 parentPanel = new AlignmentPanel(af, af.getViewport());
121 testee = new PopupMenu(parentPanel, alignment.getSequenceAt(0), null);
123 for (SequenceI seq : alignment.getSequences())
125 final AlignmentAnnotation annotation = new AlignmentAnnotation(
126 "label" + i, "desc" + i, i);
127 annotation.setCalcId("calcId" + i);
128 seq.addAlignmentAnnotation(annotation);
129 annotation.setSequenceRef(seq);
133 @Test(groups = { "Functional" })
134 public void testConfigureReferenceAnnotationsMenu_noSequenceSelected()
136 JMenuItem menu = new JMenuItem();
137 List<SequenceI> seqs = new ArrayList<>();
138 testee.configureReferenceAnnotationsMenu(menu, seqs);
139 assertFalse(menu.isEnabled());
141 menu.setEnabled(true);
142 testee.configureReferenceAnnotationsMenu(menu, null);
143 assertFalse(menu.isEnabled());
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
151 @Test(groups = { "Functional" })
152 public void testConfigureReferenceAnnotationsMenu_noReferenceAnnotations()
154 JMenuItem menu = new JMenuItem();
157 * Initial state is that sequences have annotations, and have dataset
158 * sequences, but the dataset sequences have no annotations. Hence nothing
161 List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
163 testee.configureReferenceAnnotationsMenu(menu, seqs);
164 assertFalse(menu.isEnabled());
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
172 @Test(groups = { "Functional" })
173 public void testConfigureReferenceAnnotationsMenu_alreadyAdded()
175 JMenuItem menu = new JMenuItem();
176 List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
178 // make up new annotations and add to dataset sequences, sequences and
180 attachReferenceAnnotations(seqs, true, true);
182 testee.configureReferenceAnnotationsMenu(menu, seqs);
183 assertFalse(menu.isEnabled());
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).
192 @Test(groups = { "Functional" })
193 public void testConfigureReferenceAnnotationsMenu()
195 JMenuItem menu = new JMenuItem();
196 List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
198 // make up new annotations and add to dataset sequences
199 attachReferenceAnnotations(seqs, false, false);
201 testee.configureReferenceAnnotationsMenu(menu, seqs);
202 assertTrue(menu.isEnabled());
203 String s = MessageManager.getString("label.add_annotations_for");
204 // 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 String expected = "<html>" + s + "<br>Jmol/secondary structure<br>PDB/Temp</html>";
208 assertEquals(expected, menu.getToolTipText());
212 * Test building the 'add reference annotations' menu for the case where
213 * several reference annotations are on the dataset and the sequences but not
214 * on the alignment. The menu item should be enabled, and acquire a tooltip
215 * which lists the annotation sources (calcIds) and type (labels).
217 @Test(groups = { "Functional" })
218 public void testConfigureReferenceAnnotationsMenu_notOnAlignment()
220 JMenuItem menu = new JMenuItem();
221 List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
223 // make up new annotations and add to dataset sequences and sequences
224 attachReferenceAnnotations(seqs, true, false);
226 testee.configureReferenceAnnotationsMenu(menu, seqs);
227 assertTrue(menu.isEnabled());
228 String s = MessageManager.getString("label.add_annotations_for");
229 // String expected = "<html><style> div.ttip {width:350px;white-space:pre-wrap;padding:2px;overflow-wrap:break-word;}</style>"
230 // + "<div class=\"ttip\">" + s
231 // + "<br/>Jmol/secondary structure<br/>PDB/Temp</html>";
232 String expected = "<html>" + s
233 + "<br>Jmol/secondary structure<br>PDB/Temp</html>";
234 s = menu.getToolTipText();
235 assertEquals(expected, s);
239 * Generate annotations and add to dataset sequences and (optionally)
240 * sequences and/or alignment
243 * @param addToSequence
244 * @param addToAlignment
246 private void attachReferenceAnnotations(List<SequenceI> seqs,
247 boolean addToSequence, boolean addToAlignment)
249 // PDB.secondary structure on Sequence0
250 AlignmentAnnotation annotation = new AlignmentAnnotation(
251 "secondary structure", "", 0);
252 annotation.annotations = new Annotation[] { new Annotation(2f) };
253 annotation.setCalcId("PDB");
254 seqs.get(0).getDatasetSequence().addAlignmentAnnotation(annotation);
257 seqs.get(0).addAlignmentAnnotation(annotation);
261 this.alignment.addAnnotation(annotation);
264 // PDB.Temp on Sequence1
265 annotation = new AlignmentAnnotation("Temp", "", 0);
266 annotation.setCalcId("PDB");
267 annotation.annotations = new Annotation[] { new Annotation(2f) };
268 seqs.get(1).getDatasetSequence().addAlignmentAnnotation(annotation);
271 seqs.get(1).addAlignmentAnnotation(annotation);
275 this.alignment.addAnnotation(annotation);
278 // JMOL.secondary structure on Sequence0
279 annotation = new AlignmentAnnotation("secondary structure", "", 0);
280 annotation.setCalcId("Jmol");
281 annotation.annotations = new Annotation[] { new Annotation(2f) };
282 seqs.get(0).getDatasetSequence().addAlignmentAnnotation(annotation);
285 seqs.get(0).addAlignmentAnnotation(annotation);
289 this.alignment.addAnnotation(annotation);
294 * Test building the 'add reference annotations' menu for the case where there
295 * are two alignment views:
297 * <li>in one view, reference annotations have been added (are on the
298 * datasets, sequences and alignment)</li>
299 * <li>in the current view, reference annotations are on the dataset and
300 * sequence, but not the alignment</li>
302 * The menu item should be enabled, and acquire a tooltip which lists the
303 * annotation sources (calcIds) and type (labels).
305 @Test(groups = { "Functional" })
306 public void testConfigureReferenceAnnotationsMenu_twoViews()
311 * Test for building menu options including 'show' and 'hide' annotation
314 @Test(groups = { "Functional" })
315 public void testBuildAnnotationTypesMenus()
317 JMenu showMenu = new JMenu();
318 JMenu hideMenu = new JMenu();
319 List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
321 // make up new annotations and add to sequences and to the alignment
323 // PDB.secondary structure on Sequence0
324 AlignmentAnnotation annotation = new AlignmentAnnotation(
325 "secondary structure", "", new Annotation[] {});
326 annotation.setCalcId("PDB");
327 annotation.visible = true;
328 seqs.get(0).addAlignmentAnnotation(annotation);
329 parentPanel.getAlignment().addAnnotation(annotation);
331 // JMOL.secondary structure on Sequence0 - hidden
332 annotation = new AlignmentAnnotation("secondary structure", "",
333 new Annotation[] {});
334 annotation.setCalcId("JMOL");
335 annotation.visible = false;
336 seqs.get(0).addAlignmentAnnotation(annotation);
337 parentPanel.getAlignment().addAnnotation(annotation);
339 // Jpred.SSP on Sequence0 - hidden
340 annotation = new AlignmentAnnotation("SSP", "", new Annotation[] {});
341 annotation.setCalcId("JPred");
342 annotation.visible = false;
343 seqs.get(0).addAlignmentAnnotation(annotation);
344 parentPanel.getAlignment().addAnnotation(annotation);
346 // PDB.Temp on Sequence1
347 annotation = new AlignmentAnnotation("Temp", "", new Annotation[] {});
348 annotation.setCalcId("PDB");
349 annotation.visible = true;
350 seqs.get(1).addAlignmentAnnotation(annotation);
351 parentPanel.getAlignment().addAnnotation(annotation);
354 * Expect menu options to show "secondary structure" and "SSP", and to hide
355 * "secondary structure" and "Temp". Tooltip should be calcId.
357 testee.buildAnnotationTypesMenus(showMenu, hideMenu, seqs);
359 assertTrue(showMenu.isEnabled());
360 assertTrue(hideMenu.isEnabled());
362 Component[] showOptions = showMenu.getMenuComponents();
363 Component[] hideOptions = hideMenu.getMenuComponents();
365 assertEquals(4, showOptions.length); // includes 'All' and separator
366 assertEquals(4, hideOptions.length);
367 String all = MessageManager.getString("label.all");
368 assertEquals(all, ((JMenuItem) showOptions[0]).getText());
369 assertTrue(showOptions[1] instanceof JPopupMenu.Separator);
370 assertEquals(JSeparator.HORIZONTAL,
371 ((JSeparator) showOptions[1]).getOrientation());
372 assertEquals("secondary structure",
373 ((JMenuItem) showOptions[2]).getText());
374 assertEquals("JMOL", ((JMenuItem) showOptions[2]).getToolTipText());
375 assertEquals("SSP", ((JMenuItem) showOptions[3]).getText());
376 assertEquals("JPred", ((JMenuItem) showOptions[3]).getToolTipText());
378 assertEquals(all, ((JMenuItem) hideOptions[0]).getText());
379 assertTrue(hideOptions[1] instanceof JPopupMenu.Separator);
380 assertEquals(JSeparator.HORIZONTAL,
381 ((JSeparator) hideOptions[1]).getOrientation());
382 assertEquals("secondary structure",
383 ((JMenuItem) hideOptions[2]).getText());
384 assertEquals("PDB", ((JMenuItem) hideOptions[2]).getToolTipText());
385 assertEquals("Temp", ((JMenuItem) hideOptions[3]).getText());
386 assertEquals("PDB", ((JMenuItem) hideOptions[3]).getToolTipText());
390 * Test for building menu options with only 'hide' annotation types enabled.
392 @Test(groups = { "Functional" })
393 public void testBuildAnnotationTypesMenus_showDisabled()
395 JMenu showMenu = new JMenu();
396 JMenu hideMenu = new JMenu();
397 List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
399 // make up new annotations and add to sequences and to the alignment
401 // PDB.secondary structure on Sequence0
402 AlignmentAnnotation annotation = new AlignmentAnnotation(
403 "secondary structure", "", new Annotation[] {});
404 annotation.setCalcId("PDB");
405 annotation.visible = true;
406 seqs.get(0).addAlignmentAnnotation(annotation);
407 parentPanel.getAlignment().addAnnotation(annotation);
409 // PDB.Temp on Sequence1
410 annotation = new AlignmentAnnotation("Temp", "", new Annotation[] {});
411 annotation.setCalcId("PDB");
412 annotation.visible = true;
413 seqs.get(1).addAlignmentAnnotation(annotation);
414 parentPanel.getAlignment().addAnnotation(annotation);
417 * Expect menu options to hide "secondary structure" and "Temp". Tooltip
418 * should be calcId. 'Show' menu should be disabled.
420 testee.buildAnnotationTypesMenus(showMenu, hideMenu, seqs);
422 assertFalse(showMenu.isEnabled());
423 assertTrue(hideMenu.isEnabled());
425 Component[] showOptions = showMenu.getMenuComponents();
426 Component[] hideOptions = hideMenu.getMenuComponents();
428 assertEquals(2, showOptions.length); // includes 'All' and separator
429 assertEquals(4, hideOptions.length);
430 String all = MessageManager.getString("label.all");
431 assertEquals(all, ((JMenuItem) showOptions[0]).getText());
432 assertTrue(showOptions[1] instanceof JPopupMenu.Separator);
433 assertEquals(JSeparator.HORIZONTAL,
434 ((JSeparator) showOptions[1]).getOrientation());
436 assertEquals(all, ((JMenuItem) hideOptions[0]).getText());
437 assertTrue(hideOptions[1] instanceof JPopupMenu.Separator);
438 assertEquals(JSeparator.HORIZONTAL,
439 ((JSeparator) hideOptions[1]).getOrientation());
440 assertEquals("secondary structure",
441 ((JMenuItem) hideOptions[2]).getText());
442 assertEquals("PDB", ((JMenuItem) hideOptions[2]).getToolTipText());
443 assertEquals("Temp", ((JMenuItem) hideOptions[3]).getText());
444 assertEquals("PDB", ((JMenuItem) hideOptions[3]).getToolTipText());
448 * Test for building menu options with only 'show' annotation types enabled.
450 @Test(groups = { "Functional" })
451 public void testBuildAnnotationTypesMenus_hideDisabled()
453 JMenu showMenu = new JMenu();
454 JMenu hideMenu = new JMenu();
455 List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
457 // make up new annotations and add to sequences and to the alignment
459 // PDB.secondary structure on Sequence0
460 AlignmentAnnotation annotation = new AlignmentAnnotation(
461 "secondary structure", "", new Annotation[] {});
462 annotation.setCalcId("PDB");
463 annotation.visible = false;
464 seqs.get(0).addAlignmentAnnotation(annotation);
465 parentPanel.getAlignment().addAnnotation(annotation);
467 // PDB.Temp on Sequence1
468 annotation = new AlignmentAnnotation("Temp", "", new Annotation[] {});
469 annotation.setCalcId("PDB2");
470 annotation.visible = false;
471 seqs.get(1).addAlignmentAnnotation(annotation);
472 parentPanel.getAlignment().addAnnotation(annotation);
475 * Expect menu options to show "secondary structure" and "Temp". Tooltip
476 * should be calcId. 'hide' menu should be disabled.
478 testee.buildAnnotationTypesMenus(showMenu, hideMenu, seqs);
480 assertTrue(showMenu.isEnabled());
481 assertFalse(hideMenu.isEnabled());
483 Component[] showOptions = showMenu.getMenuComponents();
484 Component[] hideOptions = hideMenu.getMenuComponents();
486 assertEquals(4, showOptions.length); // includes 'All' and separator
487 assertEquals(2, hideOptions.length);
488 String all = MessageManager.getString("label.all");
489 assertEquals(all, ((JMenuItem) showOptions[0]).getText());
490 assertTrue(showOptions[1] instanceof JPopupMenu.Separator);
491 assertEquals(JSeparator.HORIZONTAL,
492 ((JSeparator) showOptions[1]).getOrientation());
493 assertEquals("secondary structure",
494 ((JMenuItem) showOptions[2]).getText());
495 assertEquals("PDB", ((JMenuItem) showOptions[2]).getToolTipText());
496 assertEquals("Temp", ((JMenuItem) showOptions[3]).getText());
497 assertEquals("PDB2", ((JMenuItem) showOptions[3]).getToolTipText());
499 assertEquals(all, ((JMenuItem) hideOptions[0]).getText());
500 assertTrue(hideOptions[1] instanceof JPopupMenu.Separator);
501 assertEquals(JSeparator.HORIZONTAL,
502 ((JSeparator) hideOptions[1]).getOrientation());
506 * Test for adding sequence id, dbref and feature links
508 @Test(groups = { "Functional" })
509 public void testBuildLinkMenu()
511 List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
512 final SequenceI seq0 = seqs.get(0);
513 final SequenceI seq1 = seqs.get(1);
514 final List<SequenceFeature> noFeatures = Collections
515 .<SequenceFeature> emptyList();
516 final String linkText = MessageManager.getString("action.link");
518 seq0.addDBRef(new DBRefEntry(DBRefSource.UNIPROT, "1", "P83527"));
519 seq0.addDBRef(new DBRefEntry("INTERPRO", "1", "IPR001041"));
520 seq0.addDBRef(new DBRefEntry("INTERPRO", "1", "IPR012675"));
521 seq0.addDBRef(new DBRefEntry("INTERPRO", "1", "IPR006058"));
522 seq1.addDBRef(new DBRefEntry(DBRefSource.UNIPROT, "1", "Q9ZTS2"));
523 seq1.addDBRef(new DBRefEntry("GENE3D", "1", "3.10.20.30"));
526 * check the Link Menu for the first sequence
528 JMenu linkMenu = PopupMenu.buildLinkMenu(seq0, noFeatures);
529 assertEquals(linkText, linkMenu.getText());
530 Component[] linkItems = linkMenu.getMenuComponents();
533 * menu items are ordered: SEQUENCE_ID search first, then dbrefs in order
534 * of database name (and within that by order of dbref addition)
536 assertEquals(5, linkItems.length);
537 assertEquals("EMBL-EBI Search", ((JMenuItem) linkItems[0]).getText());
538 assertEquals("INTERPRO|IPR001041",
539 ((JMenuItem) linkItems[1]).getText());
540 assertEquals("INTERPRO|IPR012675",
541 ((JMenuItem) linkItems[2]).getText());
542 assertEquals("INTERPRO|IPR006058",
543 ((JMenuItem) linkItems[3]).getText());
544 assertEquals("UNIPROT|P83527", ((JMenuItem) linkItems[4]).getText());
547 * check the Link Menu for the second sequence
548 * note dbref GENE3D is matched to link Gene3D, the latter is displayed
550 linkMenu = PopupMenu.buildLinkMenu(seq1, noFeatures);
551 linkItems = linkMenu.getMenuComponents();
552 assertEquals(3, linkItems.length);
553 assertEquals("EMBL-EBI Search", ((JMenuItem) linkItems[0]).getText());
554 assertEquals("Gene3D|3.10.20.30", ((JMenuItem) linkItems[1]).getText());
555 assertEquals("UNIPROT|Q9ZTS2", ((JMenuItem) linkItems[2]).getText());
558 * if there are no valid links the Links submenu is still shown, but
559 * reduced to the EMBL-EBI lookup only (inserted by
560 * CustomUrlProvider.choosePrimaryUrl())
562 String unmatched = "NOMATCH|http://www.uniprot.org/uniprot/$"
563 + DB_ACCESSION + "$";
564 UrlProviderFactoryI factory = new DesktopUrlProviderFactory(null,
566 Preferences.sequenceUrlLinks = factory.createUrlProvider();
568 linkMenu = PopupMenu.buildLinkMenu(seq1, noFeatures);
569 linkItems = linkMenu.getMenuComponents();
570 assertEquals(1, linkItems.length);
571 assertEquals("EMBL-EBI Search", ((JMenuItem) linkItems[0]).getText());
574 * if sequence is null, only feature links are shown (alignment popup submenu)
576 linkMenu = PopupMenu.buildLinkMenu(null, noFeatures);
577 linkItems = linkMenu.getMenuComponents();
578 assertEquals(0, linkItems.length);
580 List<SequenceFeature> features = new ArrayList<>();
581 SequenceFeature sf = new SequenceFeature("type", "desc", 1, 20, null);
583 linkMenu = PopupMenu.buildLinkMenu(null, features);
584 linkItems = linkMenu.getMenuComponents();
585 assertEquals(0, linkItems.length); // feature has no links
587 sf.addLink("Pfam family|http://pfam.xfam.org/family/PF00111");
588 linkMenu = PopupMenu.buildLinkMenu(null, features);
589 linkItems = linkMenu.getMenuComponents();
590 assertEquals(1, linkItems.length);
591 JMenuItem item = (JMenuItem) linkItems[0];
592 assertEquals("Pfam family", item.getText());
593 // ? no way to verify URL, compiled into link's actionListener
596 @Test(groups = { "Functional" })
597 public void testHideInsertions()
599 // get sequences from the alignment
600 List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
602 // add our own seqs to avoid problems with changes to existing sequences
603 // (gap at end of sequences varies depending on how tests are run!)
604 Sequence seqGap1 = new Sequence("GappySeq",
605 "AAAA----AA-AAAAAAA---AAA-----------AAAAAAAAAA--");
606 seqGap1.createDatasetSequence();
608 Sequence seqGap2 = new Sequence("LessGappySeq",
609 "AAAAAA-AAAAA---AAA--AAAAA--AAAAAAA-AAAAAA");
610 seqGap2.createDatasetSequence();
612 Sequence seqGap3 = new Sequence("AnotherGapSeq",
613 "AAAAAA-AAAAAA--AAAAAA-AAAAAAAAAAA---AAAAAAAA");
614 seqGap3.createDatasetSequence();
616 Sequence seqGap4 = new Sequence("NoGaps",
617 "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA");
618 seqGap4.createDatasetSequence();
621 ColumnSelection sel = new ColumnSelection();
622 parentPanel.av.getAlignment().getHiddenColumns()
623 .revealAllHiddenColumns(sel);
625 // get the Popup Menu for 7th sequence - no insertions
626 testee = new PopupMenu(parentPanel, seqs.get(7), null);
627 testee.hideInsertions_actionPerformed(null);
629 HiddenColumns hidden = parentPanel.av.getAlignment().getHiddenColumns();
630 Iterator<int[]> it = hidden.iterator();
631 assertFalse(it.hasNext());
633 // get the Popup Menu for GappySeq - this time we have insertions
634 testee = new PopupMenu(parentPanel, seqs.get(4), null);
635 testee.hideInsertions_actionPerformed(null);
636 hidden = parentPanel.av.getAlignment().getHiddenColumns();
637 it = hidden.iterator();
639 assertTrue(it.hasNext());
640 int[] region = it.next();
641 assertEquals(region[0], 4);
642 assertEquals(region[1], 7);
644 assertTrue(it.hasNext());
646 assertEquals(region[0], 10);
647 assertEquals(region[1], 10);
649 assertTrue(it.hasNext());
651 assertEquals(region[0], 18);
652 assertEquals(region[1], 20);
654 assertTrue(it.hasNext());
656 assertEquals(region[0], 24);
657 assertEquals(region[1], 34);
659 assertTrue(it.hasNext());
661 assertEquals(region[0], 45);
662 assertEquals(region[1], 46);
664 assertFalse(it.hasNext());
666 sel = new ColumnSelection();
667 hidden.revealAllHiddenColumns(sel);
669 // make a sequence group and hide insertions within the group
670 SequenceGroup sg = new SequenceGroup();
673 sg.addSequence(seqGap2, false);
674 sg.addSequence(seqGap3, false);
675 parentPanel.av.setSelectionGroup(sg);
677 // hide columns outside and within selection
678 // only hidden columns outside the collection will be retained (unless also
679 // gaps in the selection)
680 hidden.hideColumns(1, 10);
681 hidden.hideColumns(31, 40);
683 // get the Popup Menu for LessGappySeq in the sequence group
684 testee = new PopupMenu(parentPanel, seqs.get(5), null);
685 testee.hideInsertions_actionPerformed(null);
686 hidden = parentPanel.av.getAlignment().getHiddenColumns();
687 it = hidden.iterator();
689 assertTrue(it.hasNext());
691 assertEquals(region[0], 1);
692 assertEquals(region[1], 7);
694 assertTrue(it.hasNext());
696 assertEquals(region[0], 13);
697 assertEquals(region[1], 14);
699 assertTrue(it.hasNext());
701 assertEquals(region[0], 34);
702 assertEquals(region[1], 34);
705 @Test(groups = { "Functional" })
706 public void testAddFeatureDetails()
708 String menuText = MessageManager.getString("label.feature_details");
711 * with no features, sub-menu should not be created
713 List<SequenceFeature> features = new ArrayList<>();
714 SequenceI seq = this.alignment.getSequenceAt(0); // FER_CAPAA/1-12
715 testee.addFeatureDetails(features, seq, 10);
716 JMenu menu = findMenu(testee, menuText);
720 * add some features; the menu item text is wrapped in html, and includes
721 * feature type, position, description, group (if not null)
723 SequenceFeature sf1 = new SequenceFeature("helix", "curly", 2, 6, null);
724 SequenceFeature sf2 = new SequenceFeature("chain", "straight", 1, 1,
728 testee.addFeatureDetails(features, seq, 10);
729 menu = findMenu(testee, menuText);
731 assertEquals(2, menu.getItemCount());
732 JMenuItem item = menu.getItem(0);
733 assertEquals("<html>helix 2-6 curly</html>", item.getText());
734 item = menu.getItem(1);
735 assertEquals("<html>chain 1 straight (uniprot)</html>", item.getText());
738 * long feature descriptions are truncated to 40 characters
741 "this is a quite extraordinarily long description");
742 testee.remove(menu); // don't create the sub-menu twice
743 testee.addFeatureDetails(features, seq, 10);
744 menu = findMenu(testee, menuText);
745 item = menu.getItem(0);
747 "<html>helix 2-6 this is a quite extraordinarily long des...</html>",
752 * Returns the first component which is a JMenu with the given text
758 private JMenu findMenu(Container c, String text)
760 for (int i = 0; i < c.getComponentCount(); i++)
762 Component comp = c.getComponent(i);
763 if ((comp instanceof JMenu) && ((JMenu) comp).getText().equals(text))
771 @Test(groups = { "Functional" })
772 public void testAddFeatureDetails_linkedFeatures()
774 // todo tests that verify menu items for complement features