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 assertEquals(expected, menu.getToolTipText());
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).
216 @Test(groups = { "Functional" })
217 public void testConfigureReferenceAnnotationsMenu_notOnAlignment()
219 JMenuItem menu = new JMenuItem();
220 List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
222 // make up new annotations and add to dataset sequences and sequences
223 attachReferenceAnnotations(seqs, true, false);
225 testee.configureReferenceAnnotationsMenu(menu, seqs);
226 assertTrue(menu.isEnabled());
227 String s = MessageManager.getString("label.add_annotations_for");
228 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 assertEquals(expected, menu.getToolTipText());
235 * Generate annotations and add to dataset sequences and (optionally)
236 * sequences and/or alignment
239 * @param addToSequence
240 * @param addToAlignment
242 private void attachReferenceAnnotations(List<SequenceI> seqs,
243 boolean addToSequence, boolean addToAlignment)
245 // PDB.secondary structure on Sequence0
246 AlignmentAnnotation annotation = new AlignmentAnnotation(
247 "secondary structure", "", 0);
248 annotation.annotations = new Annotation[] { new Annotation(2f) };
249 annotation.setCalcId("PDB");
250 seqs.get(0).getDatasetSequence().addAlignmentAnnotation(annotation);
253 seqs.get(0).addAlignmentAnnotation(annotation);
257 this.alignment.addAnnotation(annotation);
260 // PDB.Temp on Sequence1
261 annotation = new AlignmentAnnotation("Temp", "", 0);
262 annotation.setCalcId("PDB");
263 annotation.annotations = new Annotation[] { new Annotation(2f) };
264 seqs.get(1).getDatasetSequence().addAlignmentAnnotation(annotation);
267 seqs.get(1).addAlignmentAnnotation(annotation);
271 this.alignment.addAnnotation(annotation);
274 // JMOL.secondary structure on Sequence0
275 annotation = new AlignmentAnnotation("secondary structure", "", 0);
276 annotation.setCalcId("Jmol");
277 annotation.annotations = new Annotation[] { new Annotation(2f) };
278 seqs.get(0).getDatasetSequence().addAlignmentAnnotation(annotation);
281 seqs.get(0).addAlignmentAnnotation(annotation);
285 this.alignment.addAnnotation(annotation);
290 * Test building the 'add reference annotations' menu for the case where there
291 * are two alignment views:
293 * <li>in one view, reference annotations have been added (are on the
294 * datasets, sequences and alignment)</li>
295 * <li>in the current view, reference annotations are on the dataset and
296 * sequence, but not the alignment</li>
298 * The menu item should be enabled, and acquire a tooltip which lists the
299 * annotation sources (calcIds) and type (labels).
301 @Test(groups = { "Functional" })
302 public void testConfigureReferenceAnnotationsMenu_twoViews()
307 * Test for building menu options including 'show' and 'hide' annotation
310 @Test(groups = { "Functional" })
311 public void testBuildAnnotationTypesMenus()
313 JMenu showMenu = new JMenu();
314 JMenu hideMenu = new JMenu();
315 List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
317 // make up new annotations and add to sequences and to the alignment
319 // PDB.secondary structure on Sequence0
320 AlignmentAnnotation annotation = new AlignmentAnnotation(
321 "secondary structure", "", new Annotation[] {});
322 annotation.setCalcId("PDB");
323 annotation.visible = true;
324 seqs.get(0).addAlignmentAnnotation(annotation);
325 parentPanel.getAlignment().addAnnotation(annotation);
327 // JMOL.secondary structure on Sequence0 - hidden
328 annotation = new AlignmentAnnotation("secondary structure", "",
329 new Annotation[] {});
330 annotation.setCalcId("JMOL");
331 annotation.visible = false;
332 seqs.get(0).addAlignmentAnnotation(annotation);
333 parentPanel.getAlignment().addAnnotation(annotation);
335 // Jpred.SSP on Sequence0 - hidden
336 annotation = new AlignmentAnnotation("SSP", "", new Annotation[] {});
337 annotation.setCalcId("JPred");
338 annotation.visible = false;
339 seqs.get(0).addAlignmentAnnotation(annotation);
340 parentPanel.getAlignment().addAnnotation(annotation);
342 // PDB.Temp on Sequence1
343 annotation = new AlignmentAnnotation("Temp", "", new Annotation[] {});
344 annotation.setCalcId("PDB");
345 annotation.visible = true;
346 seqs.get(1).addAlignmentAnnotation(annotation);
347 parentPanel.getAlignment().addAnnotation(annotation);
350 * Expect menu options to show "secondary structure" and "SSP", and to hide
351 * "secondary structure" and "Temp". Tooltip should be calcId.
353 testee.buildAnnotationTypesMenus(showMenu, hideMenu, seqs);
355 assertTrue(showMenu.isEnabled());
356 assertTrue(hideMenu.isEnabled());
358 Component[] showOptions = showMenu.getMenuComponents();
359 Component[] hideOptions = hideMenu.getMenuComponents();
361 assertEquals(4, showOptions.length); // includes 'All' and separator
362 assertEquals(4, hideOptions.length);
363 String all = MessageManager.getString("label.all");
364 assertEquals(all, ((JMenuItem) showOptions[0]).getText());
365 assertTrue(showOptions[1] instanceof JPopupMenu.Separator);
366 assertEquals(JSeparator.HORIZONTAL,
367 ((JSeparator) showOptions[1]).getOrientation());
368 assertEquals("secondary structure",
369 ((JMenuItem) showOptions[2]).getText());
370 assertEquals("JMOL", ((JMenuItem) showOptions[2]).getToolTipText());
371 assertEquals("SSP", ((JMenuItem) showOptions[3]).getText());
372 assertEquals("JPred", ((JMenuItem) showOptions[3]).getToolTipText());
374 assertEquals(all, ((JMenuItem) hideOptions[0]).getText());
375 assertTrue(hideOptions[1] instanceof JPopupMenu.Separator);
376 assertEquals(JSeparator.HORIZONTAL,
377 ((JSeparator) hideOptions[1]).getOrientation());
378 assertEquals("secondary structure",
379 ((JMenuItem) hideOptions[2]).getText());
380 assertEquals("PDB", ((JMenuItem) hideOptions[2]).getToolTipText());
381 assertEquals("Temp", ((JMenuItem) hideOptions[3]).getText());
382 assertEquals("PDB", ((JMenuItem) hideOptions[3]).getToolTipText());
386 * Test for building menu options with only 'hide' annotation types enabled.
388 @Test(groups = { "Functional" })
389 public void testBuildAnnotationTypesMenus_showDisabled()
391 JMenu showMenu = new JMenu();
392 JMenu hideMenu = new JMenu();
393 List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
395 // make up new annotations and add to sequences and to the alignment
397 // PDB.secondary structure on Sequence0
398 AlignmentAnnotation annotation = new AlignmentAnnotation(
399 "secondary structure", "", new Annotation[] {});
400 annotation.setCalcId("PDB");
401 annotation.visible = true;
402 seqs.get(0).addAlignmentAnnotation(annotation);
403 parentPanel.getAlignment().addAnnotation(annotation);
405 // PDB.Temp on Sequence1
406 annotation = new AlignmentAnnotation("Temp", "", new Annotation[] {});
407 annotation.setCalcId("PDB");
408 annotation.visible = true;
409 seqs.get(1).addAlignmentAnnotation(annotation);
410 parentPanel.getAlignment().addAnnotation(annotation);
413 * Expect menu options to hide "secondary structure" and "Temp". Tooltip
414 * should be calcId. 'Show' menu should be disabled.
416 testee.buildAnnotationTypesMenus(showMenu, hideMenu, seqs);
418 assertFalse(showMenu.isEnabled());
419 assertTrue(hideMenu.isEnabled());
421 Component[] showOptions = showMenu.getMenuComponents();
422 Component[] hideOptions = hideMenu.getMenuComponents();
424 assertEquals(2, showOptions.length); // includes 'All' and separator
425 assertEquals(4, hideOptions.length);
426 String all = MessageManager.getString("label.all");
427 assertEquals(all, ((JMenuItem) showOptions[0]).getText());
428 assertTrue(showOptions[1] instanceof JPopupMenu.Separator);
429 assertEquals(JSeparator.HORIZONTAL,
430 ((JSeparator) showOptions[1]).getOrientation());
432 assertEquals(all, ((JMenuItem) hideOptions[0]).getText());
433 assertTrue(hideOptions[1] instanceof JPopupMenu.Separator);
434 assertEquals(JSeparator.HORIZONTAL,
435 ((JSeparator) hideOptions[1]).getOrientation());
436 assertEquals("secondary structure",
437 ((JMenuItem) hideOptions[2]).getText());
438 assertEquals("PDB", ((JMenuItem) hideOptions[2]).getToolTipText());
439 assertEquals("Temp", ((JMenuItem) hideOptions[3]).getText());
440 assertEquals("PDB", ((JMenuItem) hideOptions[3]).getToolTipText());
444 * Test for building menu options with only 'show' annotation types enabled.
446 @Test(groups = { "Functional" })
447 public void testBuildAnnotationTypesMenus_hideDisabled()
449 JMenu showMenu = new JMenu();
450 JMenu hideMenu = new JMenu();
451 List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
453 // make up new annotations and add to sequences and to the alignment
455 // PDB.secondary structure on Sequence0
456 AlignmentAnnotation annotation = new AlignmentAnnotation(
457 "secondary structure", "", new Annotation[] {});
458 annotation.setCalcId("PDB");
459 annotation.visible = false;
460 seqs.get(0).addAlignmentAnnotation(annotation);
461 parentPanel.getAlignment().addAnnotation(annotation);
463 // PDB.Temp on Sequence1
464 annotation = new AlignmentAnnotation("Temp", "", new Annotation[] {});
465 annotation.setCalcId("PDB2");
466 annotation.visible = false;
467 seqs.get(1).addAlignmentAnnotation(annotation);
468 parentPanel.getAlignment().addAnnotation(annotation);
471 * Expect menu options to show "secondary structure" and "Temp". Tooltip
472 * should be calcId. 'hide' menu should be disabled.
474 testee.buildAnnotationTypesMenus(showMenu, hideMenu, seqs);
476 assertTrue(showMenu.isEnabled());
477 assertFalse(hideMenu.isEnabled());
479 Component[] showOptions = showMenu.getMenuComponents();
480 Component[] hideOptions = hideMenu.getMenuComponents();
482 assertEquals(4, showOptions.length); // includes 'All' and separator
483 assertEquals(2, hideOptions.length);
484 String all = MessageManager.getString("label.all");
485 assertEquals(all, ((JMenuItem) showOptions[0]).getText());
486 assertTrue(showOptions[1] instanceof JPopupMenu.Separator);
487 assertEquals(JSeparator.HORIZONTAL,
488 ((JSeparator) showOptions[1]).getOrientation());
489 assertEquals("secondary structure",
490 ((JMenuItem) showOptions[2]).getText());
491 assertEquals("PDB", ((JMenuItem) showOptions[2]).getToolTipText());
492 assertEquals("Temp", ((JMenuItem) showOptions[3]).getText());
493 assertEquals("PDB2", ((JMenuItem) showOptions[3]).getToolTipText());
495 assertEquals(all, ((JMenuItem) hideOptions[0]).getText());
496 assertTrue(hideOptions[1] instanceof JPopupMenu.Separator);
497 assertEquals(JSeparator.HORIZONTAL,
498 ((JSeparator) hideOptions[1]).getOrientation());
502 * Test for adding sequence id, dbref and feature links
504 @Test(groups = { "Functional" })
505 public void testBuildLinkMenu()
507 List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
508 final SequenceI seq0 = seqs.get(0);
509 final SequenceI seq1 = seqs.get(1);
510 final List<SequenceFeature> noFeatures = Collections
511 .<SequenceFeature> emptyList();
512 final String linkText = MessageManager.getString("action.link");
514 seq0.addDBRef(new DBRefEntry(DBRefSource.UNIPROT, "1", "P83527"));
515 seq0.addDBRef(new DBRefEntry("INTERPRO", "1", "IPR001041"));
516 seq0.addDBRef(new DBRefEntry("INTERPRO", "1", "IPR012675"));
517 seq0.addDBRef(new DBRefEntry("INTERPRO", "1", "IPR006058"));
518 seq1.addDBRef(new DBRefEntry(DBRefSource.UNIPROT, "1", "Q9ZTS2"));
519 seq1.addDBRef(new DBRefEntry("GENE3D", "1", "3.10.20.30"));
522 * check the Link Menu for the first sequence
524 JMenu linkMenu = PopupMenu.buildLinkMenu(seq0, noFeatures);
525 assertEquals(linkText, linkMenu.getText());
526 Component[] linkItems = linkMenu.getMenuComponents();
529 * menu items are ordered: SEQUENCE_ID search first, then dbrefs in order
530 * of database name (and within that by order of dbref addition)
532 assertEquals(5, linkItems.length);
533 assertEquals("EMBL-EBI Search", ((JMenuItem) linkItems[0]).getText());
534 assertEquals("INTERPRO|IPR001041",
535 ((JMenuItem) linkItems[1]).getText());
536 assertEquals("INTERPRO|IPR012675",
537 ((JMenuItem) linkItems[2]).getText());
538 assertEquals("INTERPRO|IPR006058",
539 ((JMenuItem) linkItems[3]).getText());
540 assertEquals("UNIPROT|P83527", ((JMenuItem) linkItems[4]).getText());
543 * check the Link Menu for the second sequence
544 * note dbref GENE3D is matched to link Gene3D, the latter is displayed
546 linkMenu = PopupMenu.buildLinkMenu(seq1, noFeatures);
547 linkItems = linkMenu.getMenuComponents();
548 assertEquals(3, linkItems.length);
549 assertEquals("EMBL-EBI Search", ((JMenuItem) linkItems[0]).getText());
550 assertEquals("Gene3D|3.10.20.30", ((JMenuItem) linkItems[1]).getText());
551 assertEquals("UNIPROT|Q9ZTS2", ((JMenuItem) linkItems[2]).getText());
554 * if there are no valid links the Links submenu is still shown, but
555 * reduced to the EMBL-EBI lookup only (inserted by
556 * CustomUrlProvider.choosePrimaryUrl())
558 String unmatched = "NOMATCH|http://www.uniprot.org/uniprot/$"
559 + DB_ACCESSION + "$";
560 UrlProviderFactoryI factory = new DesktopUrlProviderFactory(null,
562 Preferences.sequenceUrlLinks = factory.createUrlProvider();
564 linkMenu = PopupMenu.buildLinkMenu(seq1, noFeatures);
565 linkItems = linkMenu.getMenuComponents();
566 assertEquals(1, linkItems.length);
567 assertEquals("EMBL-EBI Search", ((JMenuItem) linkItems[0]).getText());
570 * if sequence is null, only feature links are shown (alignment popup submenu)
572 linkMenu = PopupMenu.buildLinkMenu(null, noFeatures);
573 linkItems = linkMenu.getMenuComponents();
574 assertEquals(0, linkItems.length);
576 List<SequenceFeature> features = new ArrayList<>();
577 SequenceFeature sf = new SequenceFeature("type", "desc", 1, 20, null);
579 linkMenu = PopupMenu.buildLinkMenu(null, features);
580 linkItems = linkMenu.getMenuComponents();
581 assertEquals(0, linkItems.length); // feature has no links
583 sf.addLink("Pfam family|http://pfam.xfam.org/family/PF00111");
584 linkMenu = PopupMenu.buildLinkMenu(null, features);
585 linkItems = linkMenu.getMenuComponents();
586 assertEquals(1, linkItems.length);
587 JMenuItem item = (JMenuItem) linkItems[0];
588 assertEquals("Pfam family", item.getText());
589 // ? no way to verify URL, compiled into link's actionListener
592 @Test(groups = { "Functional" })
593 public void testHideInsertions()
595 // get sequences from the alignment
596 List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
598 // add our own seqs to avoid problems with changes to existing sequences
599 // (gap at end of sequences varies depending on how tests are run!)
600 Sequence seqGap1 = new Sequence("GappySeq",
601 "AAAA----AA-AAAAAAA---AAA-----------AAAAAAAAAA--");
602 seqGap1.createDatasetSequence();
604 Sequence seqGap2 = new Sequence("LessGappySeq",
605 "AAAAAA-AAAAA---AAA--AAAAA--AAAAAAA-AAAAAA");
606 seqGap2.createDatasetSequence();
608 Sequence seqGap3 = new Sequence("AnotherGapSeq",
609 "AAAAAA-AAAAAA--AAAAAA-AAAAAAAAAAA---AAAAAAAA");
610 seqGap3.createDatasetSequence();
612 Sequence seqGap4 = new Sequence("NoGaps",
613 "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA");
614 seqGap4.createDatasetSequence();
617 ColumnSelection sel = new ColumnSelection();
618 parentPanel.av.getAlignment().getHiddenColumns()
619 .revealAllHiddenColumns(sel);
621 // get the Popup Menu for 7th sequence - no insertions
622 testee = new PopupMenu(parentPanel, seqs.get(7), null);
623 testee.hideInsertions_actionPerformed(null);
625 HiddenColumns hidden = parentPanel.av.getAlignment().getHiddenColumns();
626 Iterator<int[]> it = hidden.iterator();
627 assertFalse(it.hasNext());
629 // get the Popup Menu for GappySeq - this time we have insertions
630 testee = new PopupMenu(parentPanel, seqs.get(4), null);
631 testee.hideInsertions_actionPerformed(null);
632 hidden = parentPanel.av.getAlignment().getHiddenColumns();
633 it = hidden.iterator();
635 assertTrue(it.hasNext());
636 int[] region = it.next();
637 assertEquals(region[0], 4);
638 assertEquals(region[1], 7);
640 assertTrue(it.hasNext());
642 assertEquals(region[0], 10);
643 assertEquals(region[1], 10);
645 assertTrue(it.hasNext());
647 assertEquals(region[0], 18);
648 assertEquals(region[1], 20);
650 assertTrue(it.hasNext());
652 assertEquals(region[0], 24);
653 assertEquals(region[1], 34);
655 assertTrue(it.hasNext());
657 assertEquals(region[0], 45);
658 assertEquals(region[1], 46);
660 assertFalse(it.hasNext());
662 sel = new ColumnSelection();
663 hidden.revealAllHiddenColumns(sel);
665 // make a sequence group and hide insertions within the group
666 SequenceGroup sg = new SequenceGroup();
669 sg.addSequence(seqGap2, false);
670 sg.addSequence(seqGap3, false);
671 parentPanel.av.setSelectionGroup(sg);
673 // hide columns outside and within selection
674 // only hidden columns outside the collection will be retained (unless also
675 // gaps in the selection)
676 hidden.hideColumns(1, 10);
677 hidden.hideColumns(31, 40);
679 // get the Popup Menu for LessGappySeq in the sequence group
680 testee = new PopupMenu(parentPanel, seqs.get(5), null);
681 testee.hideInsertions_actionPerformed(null);
682 hidden = parentPanel.av.getAlignment().getHiddenColumns();
683 it = hidden.iterator();
685 assertTrue(it.hasNext());
687 assertEquals(region[0], 1);
688 assertEquals(region[1], 7);
690 assertTrue(it.hasNext());
692 assertEquals(region[0], 13);
693 assertEquals(region[1], 14);
695 assertTrue(it.hasNext());
697 assertEquals(region[0], 34);
698 assertEquals(region[1], 34);
701 @Test(groups = { "Functional" })
702 public void testAddFeatureDetails()
704 String menuText = MessageManager.getString("label.feature_details");
707 * with no features, sub-menu should not be created
709 List<SequenceFeature> features = new ArrayList<>();
710 SequenceI seq = this.alignment.getSequenceAt(0); // FER_CAPAA/1-12
711 testee.addFeatureDetails(features, seq, 10);
712 JMenu menu = findMenu(testee, menuText);
716 * add some features; the menu item text is wrapped in html, and includes
717 * feature type, position, description, group (if not null)
719 SequenceFeature sf1 = new SequenceFeature("helix", "curly", 2, 6, null);
720 SequenceFeature sf2 = new SequenceFeature("chain", "straight", 1, 1,
724 testee.addFeatureDetails(features, seq, 10);
725 menu = findMenu(testee, menuText);
727 assertEquals(2, menu.getItemCount());
728 JMenuItem item = menu.getItem(0);
729 assertEquals("<html>helix 2-6 curly</html>", item.getText());
730 item = menu.getItem(1);
731 assertEquals("<html>chain 1 straight (uniprot)</html>", item.getText());
734 * long feature descriptions are truncated to 40 characters
737 "this is a quite extraordinarily long description");
738 testee.remove(menu); // don't create the sub-menu twice
739 testee.addFeatureDetails(features, seq, 10);
740 menu = findMenu(testee, menuText);
741 item = menu.getItem(0);
743 "<html>helix 2-6 this is a quite extraordinarily long des...</html>",
748 * Returns the first component which is a JMenu with the given text
754 private JMenu findMenu(Container c, String text)
756 for (int i = 0; i < c.getComponentCount(); i++)
758 Component comp = c.getComponent(i);
759 if ((comp instanceof JMenu) && ((JMenu) comp).getText().equals(text))
767 @Test(groups = { "Functional" })
768 public void testAddFeatureDetails_linkedFeatures()
770 // todo tests that verify menu items for complement features