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.setCalcId("PDB");
253 seqs.get(0).getDatasetSequence().addAlignmentAnnotation(annotation);
256 seqs.get(0).addAlignmentAnnotation(annotation);
260 this.alignment.addAnnotation(annotation);
263 // PDB.Temp on Sequence1
264 annotation = new AlignmentAnnotation("Temp", "", 0);
265 annotation.setCalcId("PDB");
266 seqs.get(1).getDatasetSequence().addAlignmentAnnotation(annotation);
269 seqs.get(1).addAlignmentAnnotation(annotation);
273 this.alignment.addAnnotation(annotation);
276 // JMOL.secondary structure on Sequence0
277 annotation = new AlignmentAnnotation("secondary structure", "", 0);
278 annotation.setCalcId("Jmol");
279 seqs.get(0).getDatasetSequence().addAlignmentAnnotation(annotation);
282 seqs.get(0).addAlignmentAnnotation(annotation);
286 this.alignment.addAnnotation(annotation);
291 * Test building the 'add reference annotations' menu for the case where there
292 * are two alignment views:
294 * <li>in one view, reference annotations have been added (are on the
295 * datasets, sequences and alignment)</li>
296 * <li>in the current view, reference annotations are on the dataset and
297 * sequence, but not the alignment</li>
299 * The menu item should be enabled, and acquire a tooltip which lists the
300 * annotation sources (calcIds) and type (labels).
302 @Test(groups = { "Functional" })
303 public void testConfigureReferenceAnnotationsMenu_twoViews()
308 * Test for building menu options including 'show' and 'hide' annotation
311 @Test(groups = { "Functional" })
312 public void testBuildAnnotationTypesMenus()
314 JMenu showMenu = new JMenu();
315 JMenu hideMenu = new JMenu();
316 List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
318 // make up new annotations and add to sequences and to the alignment
320 // PDB.secondary structure on Sequence0
321 AlignmentAnnotation annotation = new AlignmentAnnotation(
322 "secondary structure", "", new Annotation[] {});
323 annotation.setCalcId("PDB");
324 annotation.visible = true;
325 seqs.get(0).addAlignmentAnnotation(annotation);
326 parentPanel.getAlignment().addAnnotation(annotation);
328 // JMOL.secondary structure on Sequence0 - hidden
329 annotation = new AlignmentAnnotation("secondary structure", "",
330 new Annotation[] {});
331 annotation.setCalcId("JMOL");
332 annotation.visible = false;
333 seqs.get(0).addAlignmentAnnotation(annotation);
334 parentPanel.getAlignment().addAnnotation(annotation);
336 // Jpred.SSP on Sequence0 - hidden
337 annotation = new AlignmentAnnotation("SSP", "", new Annotation[] {});
338 annotation.setCalcId("JPred");
339 annotation.visible = false;
340 seqs.get(0).addAlignmentAnnotation(annotation);
341 parentPanel.getAlignment().addAnnotation(annotation);
343 // PDB.Temp on Sequence1
344 annotation = new AlignmentAnnotation("Temp", "", new Annotation[] {});
345 annotation.setCalcId("PDB");
346 annotation.visible = true;
347 seqs.get(1).addAlignmentAnnotation(annotation);
348 parentPanel.getAlignment().addAnnotation(annotation);
351 * Expect menu options to show "secondary structure" and "SSP", and to hide
352 * "secondary structure" and "Temp". Tooltip should be calcId.
354 testee.buildAnnotationTypesMenus(showMenu, hideMenu, seqs);
356 assertTrue(showMenu.isEnabled());
357 assertTrue(hideMenu.isEnabled());
359 Component[] showOptions = showMenu.getMenuComponents();
360 Component[] hideOptions = hideMenu.getMenuComponents();
362 assertEquals(4, showOptions.length); // includes 'All' and separator
363 assertEquals(4, hideOptions.length);
364 String all = MessageManager.getString("label.all");
365 assertEquals(all, ((JMenuItem) showOptions[0]).getText());
366 assertTrue(showOptions[1] instanceof JPopupMenu.Separator);
367 assertEquals(JSeparator.HORIZONTAL,
368 ((JSeparator) showOptions[1]).getOrientation());
369 assertEquals("secondary structure",
370 ((JMenuItem) showOptions[2]).getText());
371 assertEquals("JMOL", ((JMenuItem) showOptions[2]).getToolTipText());
372 assertEquals("SSP", ((JMenuItem) showOptions[3]).getText());
373 assertEquals("JPred", ((JMenuItem) showOptions[3]).getToolTipText());
375 assertEquals(all, ((JMenuItem) hideOptions[0]).getText());
376 assertTrue(hideOptions[1] instanceof JPopupMenu.Separator);
377 assertEquals(JSeparator.HORIZONTAL,
378 ((JSeparator) hideOptions[1]).getOrientation());
379 assertEquals("secondary structure",
380 ((JMenuItem) hideOptions[2]).getText());
381 assertEquals("PDB", ((JMenuItem) hideOptions[2]).getToolTipText());
382 assertEquals("Temp", ((JMenuItem) hideOptions[3]).getText());
383 assertEquals("PDB", ((JMenuItem) hideOptions[3]).getToolTipText());
387 * Test for building menu options with only 'hide' annotation types enabled.
389 @Test(groups = { "Functional" })
390 public void testBuildAnnotationTypesMenus_showDisabled()
392 JMenu showMenu = new JMenu();
393 JMenu hideMenu = new JMenu();
394 List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
396 // make up new annotations and add to sequences and to the alignment
398 // PDB.secondary structure on Sequence0
399 AlignmentAnnotation annotation = new AlignmentAnnotation(
400 "secondary structure", "", new Annotation[] {});
401 annotation.setCalcId("PDB");
402 annotation.visible = true;
403 seqs.get(0).addAlignmentAnnotation(annotation);
404 parentPanel.getAlignment().addAnnotation(annotation);
406 // PDB.Temp on Sequence1
407 annotation = new AlignmentAnnotation("Temp", "", new Annotation[] {});
408 annotation.setCalcId("PDB");
409 annotation.visible = true;
410 seqs.get(1).addAlignmentAnnotation(annotation);
411 parentPanel.getAlignment().addAnnotation(annotation);
414 * Expect menu options to hide "secondary structure" and "Temp". Tooltip
415 * should be calcId. 'Show' menu should be disabled.
417 testee.buildAnnotationTypesMenus(showMenu, hideMenu, seqs);
419 assertFalse(showMenu.isEnabled());
420 assertTrue(hideMenu.isEnabled());
422 Component[] showOptions = showMenu.getMenuComponents();
423 Component[] hideOptions = hideMenu.getMenuComponents();
425 assertEquals(2, showOptions.length); // includes 'All' and separator
426 assertEquals(4, hideOptions.length);
427 String all = MessageManager.getString("label.all");
428 assertEquals(all, ((JMenuItem) showOptions[0]).getText());
429 assertTrue(showOptions[1] instanceof JPopupMenu.Separator);
430 assertEquals(JSeparator.HORIZONTAL,
431 ((JSeparator) showOptions[1]).getOrientation());
433 assertEquals(all, ((JMenuItem) hideOptions[0]).getText());
434 assertTrue(hideOptions[1] instanceof JPopupMenu.Separator);
435 assertEquals(JSeparator.HORIZONTAL,
436 ((JSeparator) hideOptions[1]).getOrientation());
437 assertEquals("secondary structure",
438 ((JMenuItem) hideOptions[2]).getText());
439 assertEquals("PDB", ((JMenuItem) hideOptions[2]).getToolTipText());
440 assertEquals("Temp", ((JMenuItem) hideOptions[3]).getText());
441 assertEquals("PDB", ((JMenuItem) hideOptions[3]).getToolTipText());
445 * Test for building menu options with only 'show' annotation types enabled.
447 @Test(groups = { "Functional" })
448 public void testBuildAnnotationTypesMenus_hideDisabled()
450 JMenu showMenu = new JMenu();
451 JMenu hideMenu = new JMenu();
452 List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
454 // make up new annotations and add to sequences and to the alignment
456 // PDB.secondary structure on Sequence0
457 AlignmentAnnotation annotation = new AlignmentAnnotation(
458 "secondary structure", "", new Annotation[] {});
459 annotation.setCalcId("PDB");
460 annotation.visible = false;
461 seqs.get(0).addAlignmentAnnotation(annotation);
462 parentPanel.getAlignment().addAnnotation(annotation);
464 // PDB.Temp on Sequence1
465 annotation = new AlignmentAnnotation("Temp", "", new Annotation[] {});
466 annotation.setCalcId("PDB2");
467 annotation.visible = false;
468 seqs.get(1).addAlignmentAnnotation(annotation);
469 parentPanel.getAlignment().addAnnotation(annotation);
472 * Expect menu options to show "secondary structure" and "Temp". Tooltip
473 * should be calcId. 'hide' menu should be disabled.
475 testee.buildAnnotationTypesMenus(showMenu, hideMenu, seqs);
477 assertTrue(showMenu.isEnabled());
478 assertFalse(hideMenu.isEnabled());
480 Component[] showOptions = showMenu.getMenuComponents();
481 Component[] hideOptions = hideMenu.getMenuComponents();
483 assertEquals(4, showOptions.length); // includes 'All' and separator
484 assertEquals(2, hideOptions.length);
485 String all = MessageManager.getString("label.all");
486 assertEquals(all, ((JMenuItem) showOptions[0]).getText());
487 assertTrue(showOptions[1] instanceof JPopupMenu.Separator);
488 assertEquals(JSeparator.HORIZONTAL,
489 ((JSeparator) showOptions[1]).getOrientation());
490 assertEquals("secondary structure",
491 ((JMenuItem) showOptions[2]).getText());
492 assertEquals("PDB", ((JMenuItem) showOptions[2]).getToolTipText());
493 assertEquals("Temp", ((JMenuItem) showOptions[3]).getText());
494 assertEquals("PDB2", ((JMenuItem) showOptions[3]).getToolTipText());
496 assertEquals(all, ((JMenuItem) hideOptions[0]).getText());
497 assertTrue(hideOptions[1] instanceof JPopupMenu.Separator);
498 assertEquals(JSeparator.HORIZONTAL,
499 ((JSeparator) hideOptions[1]).getOrientation());
503 * Test for adding sequence id, dbref and feature links
505 @Test(groups = { "Functional" })
506 public void testBuildLinkMenu()
508 List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
509 final SequenceI seq0 = seqs.get(0);
510 final SequenceI seq1 = seqs.get(1);
511 final List<SequenceFeature> noFeatures = Collections
512 .<SequenceFeature> emptyList();
513 final String linkText = MessageManager.getString("action.link");
515 seq0.addDBRef(new DBRefEntry(DBRefSource.UNIPROT, "1", "P83527"));
516 seq0.addDBRef(new DBRefEntry("INTERPRO", "1", "IPR001041"));
517 seq0.addDBRef(new DBRefEntry("INTERPRO", "1", "IPR012675"));
518 seq0.addDBRef(new DBRefEntry("INTERPRO", "1", "IPR006058"));
519 seq1.addDBRef(new DBRefEntry(DBRefSource.UNIPROT, "1", "Q9ZTS2"));
520 seq1.addDBRef(new DBRefEntry("GENE3D", "1", "3.10.20.30"));
523 * check the Link Menu for the first sequence
525 JMenu linkMenu = PopupMenu.buildLinkMenu(seq0, noFeatures);
526 assertEquals(linkText, linkMenu.getText());
527 Component[] linkItems = linkMenu.getMenuComponents();
530 * menu items are ordered: SEQUENCE_ID search first, then dbrefs in order
531 * of database name (and within that by order of dbref addition)
533 assertEquals(5, linkItems.length);
534 assertEquals("EMBL-EBI Search", ((JMenuItem) linkItems[0]).getText());
535 assertEquals("INTERPRO|IPR001041",
536 ((JMenuItem) linkItems[1]).getText());
537 assertEquals("INTERPRO|IPR012675",
538 ((JMenuItem) linkItems[2]).getText());
539 assertEquals("INTERPRO|IPR006058",
540 ((JMenuItem) linkItems[3]).getText());
541 assertEquals("UNIPROT|P83527", ((JMenuItem) linkItems[4]).getText());
544 * check the Link Menu for the second sequence
545 * note dbref GENE3D is matched to link Gene3D, the latter is displayed
547 linkMenu = PopupMenu.buildLinkMenu(seq1, noFeatures);
548 linkItems = linkMenu.getMenuComponents();
549 assertEquals(3, linkItems.length);
550 assertEquals("EMBL-EBI Search", ((JMenuItem) linkItems[0]).getText());
551 assertEquals("Gene3D|3.10.20.30", ((JMenuItem) linkItems[1]).getText());
552 assertEquals("UNIPROT|Q9ZTS2", ((JMenuItem) linkItems[2]).getText());
555 * if there are no valid links the Links submenu is still shown, but
556 * reduced to the EMBL-EBI lookup only (inserted by
557 * CustomUrlProvider.choosePrimaryUrl())
559 String unmatched = "NOMATCH|http://www.uniprot.org/uniprot/$"
560 + DB_ACCESSION + "$";
561 UrlProviderFactoryI factory = new DesktopUrlProviderFactory(null,
563 Preferences.sequenceUrlLinks = factory.createUrlProvider();
565 linkMenu = PopupMenu.buildLinkMenu(seq1, noFeatures);
566 linkItems = linkMenu.getMenuComponents();
567 assertEquals(1, linkItems.length);
568 assertEquals("EMBL-EBI Search", ((JMenuItem) linkItems[0]).getText());
571 * if sequence is null, only feature links are shown (alignment popup submenu)
573 linkMenu = PopupMenu.buildLinkMenu(null, noFeatures);
574 linkItems = linkMenu.getMenuComponents();
575 assertEquals(0, linkItems.length);
577 List<SequenceFeature> features = new ArrayList<>();
578 SequenceFeature sf = new SequenceFeature("type", "desc", 1, 20, null);
580 linkMenu = PopupMenu.buildLinkMenu(null, features);
581 linkItems = linkMenu.getMenuComponents();
582 assertEquals(0, linkItems.length); // feature has no links
584 sf.addLink("Pfam family|http://pfam.xfam.org/family/PF00111");
585 linkMenu = PopupMenu.buildLinkMenu(null, features);
586 linkItems = linkMenu.getMenuComponents();
587 assertEquals(1, linkItems.length);
588 JMenuItem item = (JMenuItem) linkItems[0];
589 assertEquals("Pfam family", item.getText());
590 // ? no way to verify URL, compiled into link's actionListener
593 @Test(groups = { "Functional" })
594 public void testHideInsertions()
596 // get sequences from the alignment
597 List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
599 // add our own seqs to avoid problems with changes to existing sequences
600 // (gap at end of sequences varies depending on how tests are run!)
601 Sequence seqGap1 = new Sequence("GappySeq",
602 "AAAA----AA-AAAAAAA---AAA-----------AAAAAAAAAA--");
603 seqGap1.createDatasetSequence();
605 Sequence seqGap2 = new Sequence("LessGappySeq",
606 "AAAAAA-AAAAA---AAA--AAAAA--AAAAAAA-AAAAAA");
607 seqGap2.createDatasetSequence();
609 Sequence seqGap3 = new Sequence("AnotherGapSeq",
610 "AAAAAA-AAAAAA--AAAAAA-AAAAAAAAAAA---AAAAAAAA");
611 seqGap3.createDatasetSequence();
613 Sequence seqGap4 = new Sequence("NoGaps",
614 "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA");
615 seqGap4.createDatasetSequence();
618 ColumnSelection sel = new ColumnSelection();
619 parentPanel.av.getAlignment().getHiddenColumns()
620 .revealAllHiddenColumns(sel);
622 // get the Popup Menu for 7th sequence - no insertions
623 testee = new PopupMenu(parentPanel, seqs.get(7), null);
624 testee.hideInsertions_actionPerformed(null);
626 HiddenColumns hidden = parentPanel.av.getAlignment().getHiddenColumns();
627 Iterator<int[]> it = hidden.iterator();
628 assertFalse(it.hasNext());
630 // get the Popup Menu for GappySeq - this time we have insertions
631 testee = new PopupMenu(parentPanel, seqs.get(4), null);
632 testee.hideInsertions_actionPerformed(null);
633 hidden = parentPanel.av.getAlignment().getHiddenColumns();
634 it = hidden.iterator();
636 assertTrue(it.hasNext());
637 int[] region = it.next();
638 assertEquals(region[0], 4);
639 assertEquals(region[1], 7);
641 assertTrue(it.hasNext());
643 assertEquals(region[0], 10);
644 assertEquals(region[1], 10);
646 assertTrue(it.hasNext());
648 assertEquals(region[0], 18);
649 assertEquals(region[1], 20);
651 assertTrue(it.hasNext());
653 assertEquals(region[0], 24);
654 assertEquals(region[1], 34);
656 assertTrue(it.hasNext());
658 assertEquals(region[0], 45);
659 assertEquals(region[1], 46);
661 assertFalse(it.hasNext());
663 sel = new ColumnSelection();
664 hidden.revealAllHiddenColumns(sel);
666 // make a sequence group and hide insertions within the group
667 SequenceGroup sg = new SequenceGroup();
670 sg.addSequence(seqGap2, false);
671 sg.addSequence(seqGap3, false);
672 parentPanel.av.setSelectionGroup(sg);
674 // hide columns outside and within selection
675 // only hidden columns outside the collection will be retained (unless also
676 // gaps in the selection)
677 hidden.hideColumns(1, 10);
678 hidden.hideColumns(31, 40);
680 // get the Popup Menu for LessGappySeq in the sequence group
681 testee = new PopupMenu(parentPanel, seqs.get(5), null);
682 testee.hideInsertions_actionPerformed(null);
683 hidden = parentPanel.av.getAlignment().getHiddenColumns();
684 it = hidden.iterator();
686 assertTrue(it.hasNext());
688 assertEquals(region[0], 1);
689 assertEquals(region[1], 7);
691 assertTrue(it.hasNext());
693 assertEquals(region[0], 13);
694 assertEquals(region[1], 14);
696 assertTrue(it.hasNext());
698 assertEquals(region[0], 34);
699 assertEquals(region[1], 34);
702 @Test(groups = { "Functional" })
703 public void testAddFeatureDetails()
705 String menuText = MessageManager.getString("label.feature_details");
708 * with no features, sub-menu should not be created
710 List<SequenceFeature> features = new ArrayList<>();
711 SequenceI seq = this.alignment.getSequenceAt(0); // FER_CAPAA/1-12
712 testee.addFeatureDetails(features, seq, 10);
713 JMenu menu = findMenu(testee, menuText);
717 * add some features; the menu item text is wrapped in html, and includes
718 * feature type, position, description, group (if not null)
720 SequenceFeature sf1 = new SequenceFeature("helix", "curly", 2, 6, null);
721 SequenceFeature sf2 = new SequenceFeature("chain", "straight", 1, 1,
725 testee.addFeatureDetails(features, seq, 10);
726 menu = findMenu(testee, menuText);
728 assertEquals(2, menu.getItemCount());
729 JMenuItem item = menu.getItem(0);
730 assertEquals("<html>helix 2-6 curly</html>", item.getText());
731 item = menu.getItem(1);
732 assertEquals("<html>chain 1 straight (uniprot)</html>", item.getText());
735 * long feature descriptions are truncated to 40 characters
738 "this is a quite extraordinarily long description");
739 testee.remove(menu); // don't create the sub-menu twice
740 testee.addFeatureDetails(features, seq, 10);
741 menu = findMenu(testee, menuText);
742 item = menu.getItem(0);
744 "<html>helix 2-6 this is a quite extraordinarily long des...</html>",
749 * Returns the first component which is a JMenu with the given text
755 private JMenu findMenu(Container c, String text)
757 for (int i = 0; i < c.getComponentCount(); i++)
759 Component comp = c.getComponent(i);
760 if ((comp instanceof JMenu) && ((JMenu) comp).getText().equals(text))
768 @Test(groups = { "Functional" })
769 public void testAddFeatureDetails_linkedFeatures()
771 // todo tests that verify menu items for complement features