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.bin.Console;
50 import jalview.datamodel.AlignmentAnnotation;
51 import jalview.datamodel.AlignmentI;
52 import jalview.datamodel.Annotation;
53 import jalview.datamodel.ColumnSelection;
54 import jalview.datamodel.DBRefEntry;
55 import jalview.datamodel.DBRefSource;
56 import jalview.datamodel.HiddenColumns;
57 import jalview.datamodel.Sequence;
58 import jalview.datamodel.SequenceFeature;
59 import jalview.datamodel.SequenceGroup;
60 import jalview.datamodel.SequenceI;
61 import jalview.io.DataSourceType;
62 import jalview.io.FileFormat;
63 import jalview.io.FormatAdapter;
64 import jalview.urls.api.UrlProviderFactoryI;
65 import jalview.urls.desktop.DesktopUrlProviderFactory;
66 import jalview.util.MessageManager;
67 import jalview.util.UrlConstants;
69 public class PopupMenuTest
72 @BeforeClass(alwaysRun = true)
73 public void setUpJvOptionPane()
75 JvOptionPane.setInteractiveMode(false);
76 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
79 // 4 sequences x 13 positions
80 final static String TEST_DATA = ">FER_CAPAA Ferredoxin\n"
82 + ">FER_CAPAN Ferredoxin, chloroplast precursor\n"
84 + ">FER1_SOLLC Ferredoxin-1, chloroplast precursor\n"
85 + "TIETHKEEELTA-\n" + ">Q93XJ9_SOLTU Ferredoxin I precursor\n"
90 AlignmentPanel parentPanel;
92 PopupMenu testee = null;
94 @BeforeMethod(alwaysRun = true)
95 public void setUp() throws IOException
97 Cache.loadProperties("test/jalview/io/testProps.jvprops");
100 String inMenuString = ("EMBL-EBI Search | http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$"
101 + SEQUENCE_ID + "$" + "|"
102 + "UNIPROT | http://www.uniprot.org/uniprot/$" + DB_ACCESSION
104 + ("INTERPRO | http://www.ebi.ac.uk/interpro/entry/$"
105 + DB_ACCESSION + "$")
107 // Gene3D entry tests for case (in)sensitivity
108 ("Gene3D | http://gene3d.biochem.ucl.ac.uk/Gene3D/search?sterm=$"
109 + DB_ACCESSION + "$&mode=protein");
111 UrlProviderFactoryI factory = new DesktopUrlProviderFactory(
112 UrlConstants.DEFAULT_LABEL, inMenuString, "");
113 Preferences.sequenceUrlLinks = factory.createUrlProvider();
115 alignment = new FormatAdapter().readFile(TEST_DATA,
116 DataSourceType.PASTE, FileFormat.Fasta);
117 AlignFrame af = new AlignFrame(alignment, 700, 500);
118 parentPanel = new AlignmentPanel(af, af.getViewport());
119 testee = new PopupMenu(parentPanel, alignment.getSequenceAt(0), null);
121 for (SequenceI seq : alignment.getSequences())
123 final AlignmentAnnotation annotation = new AlignmentAnnotation(
124 "label" + i, "desc" + i, i);
125 annotation.setCalcId("calcId" + i);
126 seq.addAlignmentAnnotation(annotation);
127 annotation.setSequenceRef(seq);
131 @Test(groups = { "Functional" })
132 public void testConfigureReferenceAnnotationsMenu_noSequenceSelected()
134 JMenuItem menu = new JMenuItem();
135 List<SequenceI> seqs = new ArrayList<>();
136 testee.configureReferenceAnnotationsMenu(menu, seqs);
137 assertFalse(menu.isEnabled());
139 menu.setEnabled(true);
140 testee.configureReferenceAnnotationsMenu(menu, null);
141 assertFalse(menu.isEnabled());
145 * Test building the 'add reference annotations' menu for the case where there
146 * are no reference annotations to add to the alignment. The menu item should
149 @Test(groups = { "Functional" })
150 public void testConfigureReferenceAnnotationsMenu_noReferenceAnnotations()
152 JMenuItem menu = new JMenuItem();
155 * Initial state is that sequences have annotations, and have dataset
156 * sequences, but the dataset sequences have no annotations. Hence nothing
159 List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
161 testee.configureReferenceAnnotationsMenu(menu, seqs);
162 assertFalse(menu.isEnabled());
166 * Test building the 'add reference annotations' menu for the case where all
167 * reference annotations are already on the alignment. The menu item should be
170 @Test(groups = { "Functional" })
171 public void testConfigureReferenceAnnotationsMenu_alreadyAdded()
173 JMenuItem menu = new JMenuItem();
174 List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
176 // make up new annotations and add to dataset sequences, sequences and
178 attachReferenceAnnotations(seqs, true, true);
180 testee.configureReferenceAnnotationsMenu(menu, seqs);
181 assertFalse(menu.isEnabled());
185 * Test building the 'add reference annotations' menu for the case where
186 * several reference annotations are on the dataset but not on the sequences.
187 * The menu item should be enabled, and acquire a tooltip which lists the
188 * annotation sources (calcIds) and type (labels).
190 @Test(groups = { "Functional" })
191 public void testConfigureReferenceAnnotationsMenu()
193 JMenuItem menu = new JMenuItem();
194 List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
196 // make up new annotations and add to dataset sequences
197 attachReferenceAnnotations(seqs, false, false);
199 testee.configureReferenceAnnotationsMenu(menu, seqs);
200 assertTrue(menu.isEnabled());
201 String s = MessageManager.getString("label.add_annotations_for");
202 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 assertEquals(expected, menu.getToolTipText());
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).
214 @Test(groups = { "Functional" })
215 public void testConfigureReferenceAnnotationsMenu_notOnAlignment()
217 JMenuItem menu = new JMenuItem();
218 List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
220 // make up new annotations and add to dataset sequences and sequences
221 attachReferenceAnnotations(seqs, true, false);
223 testee.configureReferenceAnnotationsMenu(menu, seqs);
224 assertTrue(menu.isEnabled());
225 String s = MessageManager.getString("label.add_annotations_for");
226 String expected = "<html><style> div.ttip {width:350px;white-space:pre-wrap;padding:2px;overflow-wrap:break-word;}</style>"
227 + "<div class=\"ttip\">" + s
228 + "<br/>Jmol/secondary structure<br/>PDB/Temp </div></html>";
229 assertEquals(expected, menu.getToolTipText());
233 * Generate annotations and add to dataset sequences and (optionally)
234 * sequences and/or alignment
237 * @param addToSequence
238 * @param addToAlignment
240 private void attachReferenceAnnotations(List<SequenceI> seqs,
241 boolean addToSequence, boolean addToAlignment)
243 // PDB.secondary structure on Sequence0
244 AlignmentAnnotation annotation = new AlignmentAnnotation(
245 "secondary structure", "", 0);
246 annotation.setCalcId("PDB");
247 seqs.get(0).getDatasetSequence().addAlignmentAnnotation(annotation);
250 seqs.get(0).addAlignmentAnnotation(annotation);
254 this.alignment.addAnnotation(annotation);
257 // PDB.Temp on Sequence1
258 annotation = new AlignmentAnnotation("Temp", "", 0);
259 annotation.setCalcId("PDB");
260 seqs.get(1).getDatasetSequence().addAlignmentAnnotation(annotation);
263 seqs.get(1).addAlignmentAnnotation(annotation);
267 this.alignment.addAnnotation(annotation);
270 // JMOL.secondary structure on Sequence0
271 annotation = new AlignmentAnnotation("secondary structure", "", 0);
272 annotation.setCalcId("Jmol");
273 seqs.get(0).getDatasetSequence().addAlignmentAnnotation(annotation);
276 seqs.get(0).addAlignmentAnnotation(annotation);
280 this.alignment.addAnnotation(annotation);
285 * Test building the 'add reference annotations' menu for the case where there
286 * are two alignment views:
288 * <li>in one view, reference annotations have been added (are on the
289 * datasets, sequences and alignment)</li>
290 * <li>in the current view, reference annotations are on the dataset and
291 * sequence, but not the alignment</li>
293 * The menu item should be enabled, and acquire a tooltip which lists the
294 * annotation sources (calcIds) and type (labels).
296 @Test(groups = { "Functional" })
297 public void testConfigureReferenceAnnotationsMenu_twoViews()
302 * Test for building menu options including 'show' and 'hide' annotation
305 @Test(groups = { "Functional" })
306 public void testBuildAnnotationTypesMenus()
308 JMenu showMenu = new JMenu();
309 JMenu hideMenu = new JMenu();
310 List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
312 // make up new annotations and add to sequences and to the alignment
314 // PDB.secondary structure on Sequence0
315 AlignmentAnnotation annotation = new AlignmentAnnotation(
316 "secondary structure", "", new Annotation[] {});
317 annotation.setCalcId("PDB");
318 annotation.visible = true;
319 seqs.get(0).addAlignmentAnnotation(annotation);
320 parentPanel.getAlignment().addAnnotation(annotation);
322 // JMOL.secondary structure on Sequence0 - hidden
323 annotation = new AlignmentAnnotation("secondary structure", "",
324 new Annotation[] {});
325 annotation.setCalcId("JMOL");
326 annotation.visible = false;
327 seqs.get(0).addAlignmentAnnotation(annotation);
328 parentPanel.getAlignment().addAnnotation(annotation);
330 // Jpred.SSP on Sequence0 - hidden
331 annotation = new AlignmentAnnotation("SSP", "", new Annotation[] {});
332 annotation.setCalcId("JPred");
333 annotation.visible = false;
334 seqs.get(0).addAlignmentAnnotation(annotation);
335 parentPanel.getAlignment().addAnnotation(annotation);
337 // PDB.Temp on Sequence1
338 annotation = new AlignmentAnnotation("Temp", "", new Annotation[] {});
339 annotation.setCalcId("PDB");
340 annotation.visible = true;
341 seqs.get(1).addAlignmentAnnotation(annotation);
342 parentPanel.getAlignment().addAnnotation(annotation);
345 * Expect menu options to show "secondary structure" and "SSP", and to hide
346 * "secondary structure" and "Temp". Tooltip should be calcId.
348 testee.buildAnnotationTypesMenus(showMenu, hideMenu, seqs);
350 assertTrue(showMenu.isEnabled());
351 assertTrue(hideMenu.isEnabled());
353 Component[] showOptions = showMenu.getMenuComponents();
354 Component[] hideOptions = hideMenu.getMenuComponents();
356 assertEquals(4, showOptions.length); // includes 'All' and separator
357 assertEquals(4, hideOptions.length);
358 String all = MessageManager.getString("label.all");
359 assertEquals(all, ((JMenuItem) showOptions[0]).getText());
360 assertTrue(showOptions[1] instanceof JPopupMenu.Separator);
361 assertEquals(JSeparator.HORIZONTAL,
362 ((JSeparator) showOptions[1]).getOrientation());
363 assertEquals("secondary structure",
364 ((JMenuItem) showOptions[2]).getText());
365 assertEquals("JMOL", ((JMenuItem) showOptions[2]).getToolTipText());
366 assertEquals("SSP", ((JMenuItem) showOptions[3]).getText());
367 assertEquals("JPred", ((JMenuItem) showOptions[3]).getToolTipText());
369 assertEquals(all, ((JMenuItem) hideOptions[0]).getText());
370 assertTrue(hideOptions[1] instanceof JPopupMenu.Separator);
371 assertEquals(JSeparator.HORIZONTAL,
372 ((JSeparator) hideOptions[1]).getOrientation());
373 assertEquals("secondary structure",
374 ((JMenuItem) hideOptions[2]).getText());
375 assertEquals("PDB", ((JMenuItem) hideOptions[2]).getToolTipText());
376 assertEquals("Temp", ((JMenuItem) hideOptions[3]).getText());
377 assertEquals("PDB", ((JMenuItem) hideOptions[3]).getToolTipText());
381 * Test for building menu options with only 'hide' annotation types enabled.
383 @Test(groups = { "Functional" })
384 public void testBuildAnnotationTypesMenus_showDisabled()
386 JMenu showMenu = new JMenu();
387 JMenu hideMenu = new JMenu();
388 List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
390 // make up new annotations and add to sequences and to the alignment
392 // PDB.secondary structure on Sequence0
393 AlignmentAnnotation annotation = new AlignmentAnnotation(
394 "secondary structure", "", new Annotation[] {});
395 annotation.setCalcId("PDB");
396 annotation.visible = true;
397 seqs.get(0).addAlignmentAnnotation(annotation);
398 parentPanel.getAlignment().addAnnotation(annotation);
400 // PDB.Temp on Sequence1
401 annotation = new AlignmentAnnotation("Temp", "", new Annotation[] {});
402 annotation.setCalcId("PDB");
403 annotation.visible = true;
404 seqs.get(1).addAlignmentAnnotation(annotation);
405 parentPanel.getAlignment().addAnnotation(annotation);
408 * Expect menu options to hide "secondary structure" and "Temp". Tooltip
409 * should be calcId. 'Show' menu should be disabled.
411 testee.buildAnnotationTypesMenus(showMenu, hideMenu, seqs);
413 assertFalse(showMenu.isEnabled());
414 assertTrue(hideMenu.isEnabled());
416 Component[] showOptions = showMenu.getMenuComponents();
417 Component[] hideOptions = hideMenu.getMenuComponents();
419 assertEquals(2, showOptions.length); // includes 'All' and separator
420 assertEquals(4, hideOptions.length);
421 String all = MessageManager.getString("label.all");
422 assertEquals(all, ((JMenuItem) showOptions[0]).getText());
423 assertTrue(showOptions[1] instanceof JPopupMenu.Separator);
424 assertEquals(JSeparator.HORIZONTAL,
425 ((JSeparator) showOptions[1]).getOrientation());
427 assertEquals(all, ((JMenuItem) hideOptions[0]).getText());
428 assertTrue(hideOptions[1] instanceof JPopupMenu.Separator);
429 assertEquals(JSeparator.HORIZONTAL,
430 ((JSeparator) hideOptions[1]).getOrientation());
431 assertEquals("secondary structure",
432 ((JMenuItem) hideOptions[2]).getText());
433 assertEquals("PDB", ((JMenuItem) hideOptions[2]).getToolTipText());
434 assertEquals("Temp", ((JMenuItem) hideOptions[3]).getText());
435 assertEquals("PDB", ((JMenuItem) hideOptions[3]).getToolTipText());
439 * Test for building menu options with only 'show' annotation types enabled.
441 @Test(groups = { "Functional" })
442 public void testBuildAnnotationTypesMenus_hideDisabled()
444 JMenu showMenu = new JMenu();
445 JMenu hideMenu = new JMenu();
446 List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
448 // make up new annotations and add to sequences and to the alignment
450 // PDB.secondary structure on Sequence0
451 AlignmentAnnotation annotation = new AlignmentAnnotation(
452 "secondary structure", "", new Annotation[] {});
453 annotation.setCalcId("PDB");
454 annotation.visible = false;
455 seqs.get(0).addAlignmentAnnotation(annotation);
456 parentPanel.getAlignment().addAnnotation(annotation);
458 // PDB.Temp on Sequence1
459 annotation = new AlignmentAnnotation("Temp", "", new Annotation[] {});
460 annotation.setCalcId("PDB2");
461 annotation.visible = false;
462 seqs.get(1).addAlignmentAnnotation(annotation);
463 parentPanel.getAlignment().addAnnotation(annotation);
466 * Expect menu options to show "secondary structure" and "Temp". Tooltip
467 * should be calcId. 'hide' menu should be disabled.
469 testee.buildAnnotationTypesMenus(showMenu, hideMenu, seqs);
471 assertTrue(showMenu.isEnabled());
472 assertFalse(hideMenu.isEnabled());
474 Component[] showOptions = showMenu.getMenuComponents();
475 Component[] hideOptions = hideMenu.getMenuComponents();
477 assertEquals(4, showOptions.length); // includes 'All' and separator
478 assertEquals(2, hideOptions.length);
479 String all = MessageManager.getString("label.all");
480 assertEquals(all, ((JMenuItem) showOptions[0]).getText());
481 assertTrue(showOptions[1] instanceof JPopupMenu.Separator);
482 assertEquals(JSeparator.HORIZONTAL,
483 ((JSeparator) showOptions[1]).getOrientation());
484 assertEquals("secondary structure",
485 ((JMenuItem) showOptions[2]).getText());
486 assertEquals("PDB", ((JMenuItem) showOptions[2]).getToolTipText());
487 assertEquals("Temp", ((JMenuItem) showOptions[3]).getText());
488 assertEquals("PDB2", ((JMenuItem) showOptions[3]).getToolTipText());
490 assertEquals(all, ((JMenuItem) hideOptions[0]).getText());
491 assertTrue(hideOptions[1] instanceof JPopupMenu.Separator);
492 assertEquals(JSeparator.HORIZONTAL,
493 ((JSeparator) hideOptions[1]).getOrientation());
497 * Test for adding sequence id, dbref and feature links
499 @Test(groups = { "Functional" })
500 public void testBuildLinkMenu()
502 List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
503 final SequenceI seq0 = seqs.get(0);
504 final SequenceI seq1 = seqs.get(1);
505 final List<SequenceFeature> noFeatures = Collections
506 .<SequenceFeature> emptyList();
507 final String linkText = MessageManager.getString("action.link");
509 seq0.addDBRef(new DBRefEntry(DBRefSource.UNIPROT, "1", "P83527"));
510 seq0.addDBRef(new DBRefEntry("INTERPRO", "1", "IPR001041"));
511 seq0.addDBRef(new DBRefEntry("INTERPRO", "1", "IPR012675"));
512 seq0.addDBRef(new DBRefEntry("INTERPRO", "1", "IPR006058"));
513 seq1.addDBRef(new DBRefEntry(DBRefSource.UNIPROT, "1", "Q9ZTS2"));
514 seq1.addDBRef(new DBRefEntry("GENE3D", "1", "3.10.20.30"));
517 * check the Link Menu for the first sequence
519 JMenu linkMenu = PopupMenu.buildLinkMenu(seq0, noFeatures);
520 assertEquals(linkText, linkMenu.getText());
521 Component[] linkItems = linkMenu.getMenuComponents();
524 * menu items are ordered: SEQUENCE_ID search first, then dbrefs in order
525 * of database name (and within that by order of dbref addition)
527 assertEquals(5, linkItems.length);
528 assertEquals("EMBL-EBI Search", ((JMenuItem) linkItems[0]).getText());
529 assertEquals("INTERPRO|IPR001041",
530 ((JMenuItem) linkItems[1]).getText());
531 assertEquals("INTERPRO|IPR012675",
532 ((JMenuItem) linkItems[2]).getText());
533 assertEquals("INTERPRO|IPR006058",
534 ((JMenuItem) linkItems[3]).getText());
535 assertEquals("UNIPROT|P83527", ((JMenuItem) linkItems[4]).getText());
538 * check the Link Menu for the second sequence
539 * note dbref GENE3D is matched to link Gene3D, the latter is displayed
541 linkMenu = PopupMenu.buildLinkMenu(seq1, noFeatures);
542 linkItems = linkMenu.getMenuComponents();
543 assertEquals(3, linkItems.length);
544 assertEquals("EMBL-EBI Search", ((JMenuItem) linkItems[0]).getText());
545 assertEquals("Gene3D|3.10.20.30", ((JMenuItem) linkItems[1]).getText());
546 assertEquals("UNIPROT|Q9ZTS2", ((JMenuItem) linkItems[2]).getText());
549 * if there are no valid links the Links submenu is still shown, but
550 * reduced to the EMBL-EBI lookup only (inserted by
551 * CustomUrlProvider.choosePrimaryUrl())
553 String unmatched = "NOMATCH|http://www.uniprot.org/uniprot/$"
554 + DB_ACCESSION + "$";
555 UrlProviderFactoryI factory = new DesktopUrlProviderFactory(null,
557 Preferences.sequenceUrlLinks = factory.createUrlProvider();
559 linkMenu = PopupMenu.buildLinkMenu(seq1, noFeatures);
560 linkItems = linkMenu.getMenuComponents();
561 assertEquals(1, linkItems.length);
562 assertEquals("EMBL-EBI Search", ((JMenuItem) linkItems[0]).getText());
565 * if sequence is null, only feature links are shown (alignment popup submenu)
567 linkMenu = PopupMenu.buildLinkMenu(null, noFeatures);
568 linkItems = linkMenu.getMenuComponents();
569 assertEquals(0, linkItems.length);
571 List<SequenceFeature> features = new ArrayList<>();
572 SequenceFeature sf = new SequenceFeature("type", "desc", 1, 20, null);
574 linkMenu = PopupMenu.buildLinkMenu(null, features);
575 linkItems = linkMenu.getMenuComponents();
576 assertEquals(0, linkItems.length); // feature has no links
578 sf.addLink("Pfam family|http://pfam.xfam.org/family/PF00111");
579 linkMenu = PopupMenu.buildLinkMenu(null, features);
580 linkItems = linkMenu.getMenuComponents();
581 assertEquals(1, linkItems.length);
582 JMenuItem item = (JMenuItem) linkItems[0];
583 assertEquals("Pfam family", item.getText());
584 // ? no way to verify URL, compiled into link's actionListener
587 @Test(groups = { "Functional" })
588 public void testHideInsertions()
590 // get sequences from the alignment
591 List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
593 // add our own seqs to avoid problems with changes to existing sequences
594 // (gap at end of sequences varies depending on how tests are run!)
595 Sequence seqGap1 = new Sequence("GappySeq",
596 "AAAA----AA-AAAAAAA---AAA-----------AAAAAAAAAA--");
597 seqGap1.createDatasetSequence();
599 Sequence seqGap2 = new Sequence("LessGappySeq",
600 "AAAAAA-AAAAA---AAA--AAAAA--AAAAAAA-AAAAAA");
601 seqGap2.createDatasetSequence();
603 Sequence seqGap3 = new Sequence("AnotherGapSeq",
604 "AAAAAA-AAAAAA--AAAAAA-AAAAAAAAAAA---AAAAAAAA");
605 seqGap3.createDatasetSequence();
607 Sequence seqGap4 = new Sequence("NoGaps",
608 "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA");
609 seqGap4.createDatasetSequence();
612 ColumnSelection sel = new ColumnSelection();
613 parentPanel.av.getAlignment().getHiddenColumns()
614 .revealAllHiddenColumns(sel);
616 // get the Popup Menu for 7th sequence - no insertions
617 testee = new PopupMenu(parentPanel, seqs.get(7), null);
618 testee.hideInsertions_actionPerformed(null);
620 HiddenColumns hidden = parentPanel.av.getAlignment().getHiddenColumns();
621 Iterator<int[]> it = hidden.iterator();
622 assertFalse(it.hasNext());
624 // get the Popup Menu for GappySeq - this time we have insertions
625 testee = new PopupMenu(parentPanel, seqs.get(4), null);
626 testee.hideInsertions_actionPerformed(null);
627 hidden = parentPanel.av.getAlignment().getHiddenColumns();
628 it = hidden.iterator();
630 assertTrue(it.hasNext());
631 int[] region = it.next();
632 assertEquals(region[0], 4);
633 assertEquals(region[1], 7);
635 assertTrue(it.hasNext());
637 assertEquals(region[0], 10);
638 assertEquals(region[1], 10);
640 assertTrue(it.hasNext());
642 assertEquals(region[0], 18);
643 assertEquals(region[1], 20);
645 assertTrue(it.hasNext());
647 assertEquals(region[0], 24);
648 assertEquals(region[1], 34);
650 assertTrue(it.hasNext());
652 assertEquals(region[0], 45);
653 assertEquals(region[1], 46);
655 assertFalse(it.hasNext());
657 sel = new ColumnSelection();
658 hidden.revealAllHiddenColumns(sel);
660 // make a sequence group and hide insertions within the group
661 SequenceGroup sg = new SequenceGroup();
664 sg.addSequence(seqGap2, false);
665 sg.addSequence(seqGap3, false);
666 parentPanel.av.setSelectionGroup(sg);
668 // hide columns outside and within selection
669 // only hidden columns outside the collection will be retained (unless also
670 // gaps in the selection)
671 hidden.hideColumns(1, 10);
672 hidden.hideColumns(31, 40);
674 // get the Popup Menu for LessGappySeq in the sequence group
675 testee = new PopupMenu(parentPanel, seqs.get(5), null);
676 testee.hideInsertions_actionPerformed(null);
677 hidden = parentPanel.av.getAlignment().getHiddenColumns();
678 it = hidden.iterator();
680 assertTrue(it.hasNext());
682 assertEquals(region[0], 1);
683 assertEquals(region[1], 7);
685 assertTrue(it.hasNext());
687 assertEquals(region[0], 13);
688 assertEquals(region[1], 14);
690 assertTrue(it.hasNext());
692 assertEquals(region[0], 34);
693 assertEquals(region[1], 34);
696 @Test(groups = { "Functional" })
697 public void testAddFeatureDetails()
699 String menuText = MessageManager.getString("label.feature_details");
702 * with no features, sub-menu should not be created
704 List<SequenceFeature> features = new ArrayList<>();
705 SequenceI seq = this.alignment.getSequenceAt(0); // FER_CAPAA/1-12
706 testee.addFeatureDetails(features, seq, 10);
707 JMenu menu = findMenu(testee, menuText);
711 * add some features; the menu item text is wrapped in html, and includes
712 * feature type, position, description, group (if not null)
714 SequenceFeature sf1 = new SequenceFeature("helix", "curly", 2, 6, null);
715 SequenceFeature sf2 = new SequenceFeature("chain", "straight", 1, 1,
719 testee.addFeatureDetails(features, seq, 10);
720 menu = findMenu(testee, menuText);
722 assertEquals(2, menu.getItemCount());
723 JMenuItem item = menu.getItem(0);
724 assertEquals("<html>helix 2-6 curly</html>", item.getText());
725 item = menu.getItem(1);
726 assertEquals("<html>chain 1 straight (uniprot)</html>", item.getText());
729 * long feature descriptions are truncated to 40 characters
731 sf1.setDescription("this is a quite extraordinarily long description");
732 testee.remove(menu); // don't create the sub-menu twice
733 testee.addFeatureDetails(features, seq, 10);
734 menu = findMenu(testee, menuText);
735 item = menu.getItem(0);
737 "<html>helix 2-6 this is a quite extraordinarily long des...</html>",
742 * Returns the first component which is a JMenu with the given text
748 private JMenu findMenu(Container c, String text)
750 for (int i = 0; i < c.getComponentCount(); i++)
752 Component comp = c.getComponent(i);
753 if ((comp instanceof JMenu) && ((JMenu) comp).getText().equals(text))
761 @Test(groups = { "Functional" })
762 public void testAddFeatureDetails_linkedFeatures()
764 // todo tests that verify menu items for complement features