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.assertTrue;
29 import jalview.bin.Cache;
30 import jalview.datamodel.AlignmentAnnotation;
31 import jalview.datamodel.AlignmentI;
32 import jalview.datamodel.Annotation;
33 import jalview.datamodel.ColumnSelection;
34 import jalview.datamodel.DBRefEntry;
35 import jalview.datamodel.DBRefSource;
36 import jalview.datamodel.HiddenColumns;
37 import jalview.datamodel.Sequence;
38 import jalview.datamodel.SequenceFeature;
39 import jalview.datamodel.SequenceGroup;
40 import jalview.datamodel.SequenceI;
41 import jalview.io.DataSourceType;
42 import jalview.io.FileFormat;
43 import jalview.io.FormatAdapter;
44 import jalview.urls.api.UrlProviderFactoryI;
45 import jalview.urls.desktop.DesktopUrlProviderFactory;
46 import jalview.util.MessageManager;
47 import jalview.util.UrlConstants;
49 import java.awt.Component;
50 import java.io.IOException;
51 import java.util.ArrayList;
52 import java.util.Collections;
53 import java.util.Iterator;
54 import java.util.List;
56 import javax.swing.JMenu;
57 import javax.swing.JMenuItem;
58 import javax.swing.JPopupMenu;
59 import javax.swing.JSeparator;
61 import org.testng.annotations.BeforeClass;
62 import org.testng.annotations.BeforeMethod;
63 import org.testng.annotations.Test;
65 public class PopupMenuTest
68 @BeforeClass(alwaysRun = true)
69 public void setUpJvOptionPane()
71 JvOptionPane.setInteractiveMode(false);
72 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
75 // 4 sequences x 13 positions
76 final static String TEST_DATA = ">FER_CAPAA Ferredoxin\n"
78 + ">FER_CAPAN Ferredoxin, chloroplast precursor\n"
80 + ">FER1_SOLLC Ferredoxin-1, chloroplast precursor\n"
81 + "TIETHKEEELTA-\n" + ">Q93XJ9_SOLTU Ferredoxin I precursor\n"
86 AlignmentPanel parentPanel;
88 PopupMenu testee = null;
90 @BeforeMethod(alwaysRun = true)
91 public void setUp() throws IOException
93 Cache.loadProperties("test/jalview/io/testProps.jvprops");
94 String inMenuString = ("EMBL-EBI Search | http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$"
98 + "UNIPROT | http://www.uniprot.org/uniprot/$" + DB_ACCESSION + "$")
100 + ("INTERPRO | http://www.ebi.ac.uk/interpro/entry/$"
101 + DB_ACCESSION + "$")
104 // Gene3D entry tests for case (in)sensitivity
105 ("Gene3D | http://gene3d.biochem.ucl.ac.uk/Gene3D/search?sterm=$"
106 + DB_ACCESSION + "$&mode=protein");
108 UrlProviderFactoryI factory = new DesktopUrlProviderFactory(
109 UrlConstants.DEFAULT_LABEL, inMenuString, "");
110 Preferences.sequenceUrlLinks = factory.createUrlProvider();
112 alignment = new FormatAdapter().readFile(TEST_DATA,
113 DataSourceType.PASTE, FileFormat.Fasta);
114 AlignFrame af = new AlignFrame(alignment, 700, 500);
115 parentPanel = new AlignmentPanel(af, af.getViewport());
116 testee = new PopupMenu(parentPanel, null, null);
118 for (SequenceI seq : alignment.getSequences())
120 final AlignmentAnnotation annotation = new AlignmentAnnotation(
121 "label" + i, "desc" + i, i);
122 annotation.setCalcId("calcId" + i);
123 seq.addAlignmentAnnotation(annotation);
124 annotation.setSequenceRef(seq);
128 @Test(groups = { "Functional" })
129 public void testConfigureReferenceAnnotationsMenu_noSequenceSelected()
131 JMenuItem menu = new JMenuItem();
132 List<SequenceI> seqs = new ArrayList<>();
133 testee.configureReferenceAnnotationsMenu(menu, seqs);
134 assertFalse(menu.isEnabled());
136 menu.setEnabled(true);
137 testee.configureReferenceAnnotationsMenu(menu, null);
138 assertFalse(menu.isEnabled());
142 * Test building the 'add reference annotations' menu for the case where there
143 * are no reference annotations to add to the alignment. The menu item should
146 @Test(groups = { "Functional" })
147 public void testConfigureReferenceAnnotationsMenu_noReferenceAnnotations()
149 JMenuItem menu = new JMenuItem();
152 * Initial state is that sequences have annotations, and have dataset
153 * sequences, but the dataset sequences have no annotations. Hence nothing
156 List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
158 testee.configureReferenceAnnotationsMenu(menu, seqs);
159 assertFalse(menu.isEnabled());
163 * Test building the 'add reference annotations' menu for the case where all
164 * reference annotations are already on the alignment. The menu item should be
167 @Test(groups = { "Functional" })
168 public void testConfigureReferenceAnnotationsMenu_alreadyAdded()
170 JMenuItem menu = new JMenuItem();
171 List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
173 // make up new annotations and add to dataset sequences, sequences and
175 attachReferenceAnnotations(seqs, true, true);
177 testee.configureReferenceAnnotationsMenu(menu, seqs);
178 assertFalse(menu.isEnabled());
182 * Test building the 'add reference annotations' menu for the case where
183 * several reference annotations are on the dataset but not on the sequences.
184 * The menu item should be enabled, and acquire a tooltip which lists the
185 * annotation sources (calcIds) and type (labels).
187 @Test(groups = { "Functional" })
188 public void testConfigureReferenceAnnotationsMenu()
190 JMenuItem menu = new JMenuItem();
191 List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
193 // make up new annotations and add to dataset sequences
194 attachReferenceAnnotations(seqs, false, false);
196 testee.configureReferenceAnnotationsMenu(menu, seqs);
197 assertTrue(menu.isEnabled());
198 String s = MessageManager.getString("label.add_annotations_for");
199 // String expected = "<html><style> p.ttip {width: 350; text-align: justify;
200 // word-wrap: break-word;}</style><p class=\"ttip\">"
201 // + s + "<br/>Jmol/secondary structure<br/>PDB/Temp</p></html>";
202 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> p.ttip {width: 350; text-align: justify;
227 // word-wrap: break-word;}</style><p class=\"ttip\">"
228 // + s + "<br/>Jmol/secondary structure<br/>PDB/Temp</p></html>";
229 String expected = "<html><style> div.ttip {width:350px;white-space:pre-wrap;padding:2px;overflow-wrap:break-word;}</style>"
230 + "<div class=\"ttip\">Add annotations for<br/>Jmol/secondary structure<br/>PDB/Temp </div></html>";
231 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.setCalcId("PDB");
249 seqs.get(0).getDatasetSequence().addAlignmentAnnotation(annotation);
252 seqs.get(0).addAlignmentAnnotation(annotation);
256 this.alignment.addAnnotation(annotation);
259 // PDB.Temp on Sequence1
260 annotation = new AlignmentAnnotation("Temp", "", 0);
261 annotation.setCalcId("PDB");
262 seqs.get(1).getDatasetSequence().addAlignmentAnnotation(annotation);
265 seqs.get(1).addAlignmentAnnotation(annotation);
269 this.alignment.addAnnotation(annotation);
272 // JMOL.secondary structure on Sequence0
273 annotation = new AlignmentAnnotation("secondary structure", "", 0);
274 annotation.setCalcId("Jmol");
275 seqs.get(0).getDatasetSequence().addAlignmentAnnotation(annotation);
278 seqs.get(0).addAlignmentAnnotation(annotation);
282 this.alignment.addAnnotation(annotation);
287 * Test building the 'add reference annotations' menu for the case where there
288 * are two alignment views:
290 * <li>in one view, reference annotations have been added (are on the
291 * datasets, sequences and alignment)</li>
292 * <li>in the current view, reference annotations are on the dataset and
293 * sequence, but not the alignment</li>
295 * The menu item should be enabled, and acquire a tooltip which lists the
296 * annotation sources (calcIds) and type (labels).
298 @Test(groups = { "Functional" })
299 public void testConfigureReferenceAnnotationsMenu_twoViews()
304 * Test for building menu options including 'show' and 'hide' annotation
307 @Test(groups = { "Functional" })
308 public void testBuildAnnotationTypesMenus()
310 JMenu showMenu = new JMenu();
311 JMenu hideMenu = new JMenu();
312 List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
314 // make up new annotations and add to sequences and to the alignment
316 // PDB.secondary structure on Sequence0
317 AlignmentAnnotation annotation = new AlignmentAnnotation(
318 "secondary structure", "", new Annotation[] {});
319 annotation.setCalcId("PDB");
320 annotation.visible = true;
321 seqs.get(0).addAlignmentAnnotation(annotation);
322 parentPanel.getAlignment().addAnnotation(annotation);
324 // JMOL.secondary structure on Sequence0 - hidden
325 annotation = new AlignmentAnnotation("secondary structure", "",
326 new Annotation[] {});
327 annotation.setCalcId("JMOL");
328 annotation.visible = false;
329 seqs.get(0).addAlignmentAnnotation(annotation);
330 parentPanel.getAlignment().addAnnotation(annotation);
332 // Jpred.SSP on Sequence0 - hidden
333 annotation = new AlignmentAnnotation("SSP", "", new Annotation[] {});
334 annotation.setCalcId("JPred");
335 annotation.visible = false;
336 seqs.get(0).addAlignmentAnnotation(annotation);
337 parentPanel.getAlignment().addAnnotation(annotation);
339 // PDB.Temp on Sequence1
340 annotation = new AlignmentAnnotation("Temp", "", new Annotation[] {});
341 annotation.setCalcId("PDB");
342 annotation.visible = true;
343 seqs.get(1).addAlignmentAnnotation(annotation);
344 parentPanel.getAlignment().addAnnotation(annotation);
347 * Expect menu options to show "secondary structure" and "SSP", and to hide
348 * "secondary structure" and "Temp". Tooltip should be calcId.
350 testee.buildAnnotationTypesMenus(showMenu, hideMenu, seqs);
352 assertTrue(showMenu.isEnabled());
353 assertTrue(hideMenu.isEnabled());
355 Component[] showOptions = showMenu.getMenuComponents();
356 Component[] hideOptions = hideMenu.getMenuComponents();
358 assertEquals(4, showOptions.length); // includes 'All' and separator
359 assertEquals(4, hideOptions.length);
360 String all = MessageManager.getString("label.all");
361 assertEquals(all, ((JMenuItem) showOptions[0]).getText());
362 assertTrue(showOptions[1] instanceof JPopupMenu.Separator);
363 assertEquals(JSeparator.HORIZONTAL,
364 ((JSeparator) showOptions[1]).getOrientation());
365 assertEquals("secondary structure",
366 ((JMenuItem) showOptions[2]).getText());
367 assertEquals("JMOL", ((JMenuItem) showOptions[2]).getToolTipText());
368 assertEquals("SSP", ((JMenuItem) showOptions[3]).getText());
369 assertEquals("JPred", ((JMenuItem) showOptions[3]).getToolTipText());
371 assertEquals(all, ((JMenuItem) hideOptions[0]).getText());
372 assertTrue(hideOptions[1] instanceof JPopupMenu.Separator);
373 assertEquals(JSeparator.HORIZONTAL,
374 ((JSeparator) hideOptions[1]).getOrientation());
375 assertEquals("secondary structure",
376 ((JMenuItem) hideOptions[2]).getText());
377 assertEquals("PDB", ((JMenuItem) hideOptions[2]).getToolTipText());
378 assertEquals("Temp", ((JMenuItem) hideOptions[3]).getText());
379 assertEquals("PDB", ((JMenuItem) hideOptions[3]).getToolTipText());
383 * Test for building menu options with only 'hide' annotation types enabled.
385 @Test(groups = { "Functional" })
386 public void testBuildAnnotationTypesMenus_showDisabled()
388 JMenu showMenu = new JMenu();
389 JMenu hideMenu = new JMenu();
390 List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
392 // make up new annotations and add to sequences and to the alignment
394 // PDB.secondary structure on Sequence0
395 AlignmentAnnotation annotation = new AlignmentAnnotation(
396 "secondary structure", "", new Annotation[] {});
397 annotation.setCalcId("PDB");
398 annotation.visible = true;
399 seqs.get(0).addAlignmentAnnotation(annotation);
400 parentPanel.getAlignment().addAnnotation(annotation);
402 // PDB.Temp on Sequence1
403 annotation = new AlignmentAnnotation("Temp", "", new Annotation[] {});
404 annotation.setCalcId("PDB");
405 annotation.visible = true;
406 seqs.get(1).addAlignmentAnnotation(annotation);
407 parentPanel.getAlignment().addAnnotation(annotation);
410 * Expect menu options to hide "secondary structure" and "Temp". Tooltip
411 * should be calcId. 'Show' menu should be disabled.
413 testee.buildAnnotationTypesMenus(showMenu, hideMenu, seqs);
415 assertFalse(showMenu.isEnabled());
416 assertTrue(hideMenu.isEnabled());
418 Component[] showOptions = showMenu.getMenuComponents();
419 Component[] hideOptions = hideMenu.getMenuComponents();
421 assertEquals(2, showOptions.length); // includes 'All' and separator
422 assertEquals(4, hideOptions.length);
423 String all = MessageManager.getString("label.all");
424 assertEquals(all, ((JMenuItem) showOptions[0]).getText());
425 assertTrue(showOptions[1] instanceof JPopupMenu.Separator);
426 assertEquals(JSeparator.HORIZONTAL,
427 ((JSeparator) showOptions[1]).getOrientation());
429 assertEquals(all, ((JMenuItem) hideOptions[0]).getText());
430 assertTrue(hideOptions[1] instanceof JPopupMenu.Separator);
431 assertEquals(JSeparator.HORIZONTAL,
432 ((JSeparator) hideOptions[1]).getOrientation());
433 assertEquals("secondary structure",
434 ((JMenuItem) hideOptions[2]).getText());
435 assertEquals("PDB", ((JMenuItem) hideOptions[2]).getToolTipText());
436 assertEquals("Temp", ((JMenuItem) hideOptions[3]).getText());
437 assertEquals("PDB", ((JMenuItem) hideOptions[3]).getToolTipText());
441 * Test for building menu options with only 'show' annotation types enabled.
443 @Test(groups = { "Functional" })
444 public void testBuildAnnotationTypesMenus_hideDisabled()
446 JMenu showMenu = new JMenu();
447 JMenu hideMenu = new JMenu();
448 List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
450 // make up new annotations and add to sequences and to the alignment
452 // PDB.secondary structure on Sequence0
453 AlignmentAnnotation annotation = new AlignmentAnnotation(
454 "secondary structure", "", new Annotation[] {});
455 annotation.setCalcId("PDB");
456 annotation.visible = false;
457 seqs.get(0).addAlignmentAnnotation(annotation);
458 parentPanel.getAlignment().addAnnotation(annotation);
460 // PDB.Temp on Sequence1
461 annotation = new AlignmentAnnotation("Temp", "", new Annotation[] {});
462 annotation.setCalcId("PDB2");
463 annotation.visible = false;
464 seqs.get(1).addAlignmentAnnotation(annotation);
465 parentPanel.getAlignment().addAnnotation(annotation);
468 * Expect menu options to show "secondary structure" and "Temp". Tooltip
469 * should be calcId. 'hide' menu should be disabled.
471 testee.buildAnnotationTypesMenus(showMenu, hideMenu, seqs);
473 assertTrue(showMenu.isEnabled());
474 assertFalse(hideMenu.isEnabled());
476 Component[] showOptions = showMenu.getMenuComponents();
477 Component[] hideOptions = hideMenu.getMenuComponents();
479 assertEquals(4, showOptions.length); // includes 'All' and separator
480 assertEquals(2, hideOptions.length);
481 String all = MessageManager.getString("label.all");
482 assertEquals(all, ((JMenuItem) showOptions[0]).getText());
483 assertTrue(showOptions[1] instanceof JPopupMenu.Separator);
484 assertEquals(JSeparator.HORIZONTAL,
485 ((JSeparator) showOptions[1]).getOrientation());
486 assertEquals("secondary structure",
487 ((JMenuItem) showOptions[2]).getText());
488 assertEquals("PDB", ((JMenuItem) showOptions[2]).getToolTipText());
489 assertEquals("Temp", ((JMenuItem) showOptions[3]).getText());
490 assertEquals("PDB2", ((JMenuItem) showOptions[3]).getToolTipText());
492 assertEquals(all, ((JMenuItem) hideOptions[0]).getText());
493 assertTrue(hideOptions[1] instanceof JPopupMenu.Separator);
494 assertEquals(JSeparator.HORIZONTAL,
495 ((JSeparator) hideOptions[1]).getOrientation());
499 * Test for adding sequence id, dbref and feature links
501 @Test(groups = { "Functional" })
502 public void testBuildLinkMenu()
504 List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
505 final SequenceI seq0 = seqs.get(0);
506 final SequenceI seq1 = seqs.get(1);
507 final List<SequenceFeature> noFeatures = Collections
508 .<SequenceFeature> emptyList();
509 final String linkText = MessageManager.getString("action.link");
511 seq0.addDBRef(new DBRefEntry(DBRefSource.UNIPROT, "1", "P83527"));
512 seq0.addDBRef(new DBRefEntry("INTERPRO", "1", "IPR001041"));
513 seq0.addDBRef(new DBRefEntry("INTERPRO", "1", "IPR012675"));
514 seq0.addDBRef(new DBRefEntry("INTERPRO", "1", "IPR006058"));
515 seq1.addDBRef(new DBRefEntry(DBRefSource.UNIPROT, "1", "Q9ZTS2"));
516 seq1.addDBRef(new DBRefEntry("GENE3D", "1", "3.10.20.30"));
519 * check the Link Menu for the first sequence
521 JMenu linkMenu = PopupMenu.buildLinkMenu(seq0, noFeatures);
522 assertEquals(linkText, linkMenu.getText());
523 Component[] linkItems = linkMenu.getMenuComponents();
526 * menu items are ordered: SEQUENCE_ID search first, then dbrefs in order
527 * of database name (and within that by order of dbref addition)
529 assertEquals(5, linkItems.length);
530 assertEquals("EMBL-EBI Search", ((JMenuItem) linkItems[0]).getText());
531 assertEquals("INTERPRO|IPR001041",
532 ((JMenuItem) linkItems[1]).getText());
533 assertEquals("INTERPRO|IPR012675",
534 ((JMenuItem) linkItems[2]).getText());
535 assertEquals("INTERPRO|IPR006058",
536 ((JMenuItem) linkItems[3]).getText());
537 assertEquals("UNIPROT|P83527", ((JMenuItem) linkItems[4]).getText());
540 * check the Link Menu for the second sequence
541 * note dbref GENE3D is matched to link Gene3D, the latter is displayed
543 linkMenu = PopupMenu.buildLinkMenu(seq1, noFeatures);
544 assertEquals(linkText, linkMenu.getText());
545 linkItems = linkMenu.getMenuComponents();
546 assertEquals(3, linkItems.length);
547 assertEquals("EMBL-EBI Search", ((JMenuItem) linkItems[0]).getText());
548 assertEquals("Gene3D|3.10.20.30", ((JMenuItem) linkItems[1]).getText());
549 assertEquals("UNIPROT|Q9ZTS2", ((JMenuItem) linkItems[2]).getText());
552 * if there are no valid links the Links submenu is still shown, but
553 * reduced to the EMBL-EBI lookup only (inserted by
554 * CustomUrlProvider.choosePrimaryUrl())
556 String unmatched = "NOMATCH|http://www.uniprot.org/uniprot/$"
557 + DB_ACCESSION + "$";
558 UrlProviderFactoryI factory = new DesktopUrlProviderFactory(null,
560 Preferences.sequenceUrlLinks = factory.createUrlProvider();
562 linkMenu = PopupMenu.buildLinkMenu(seq1, noFeatures);
563 assertEquals(linkText, linkMenu.getText());
564 linkItems = linkMenu.getMenuComponents();
565 assertEquals(1, linkItems.length);
566 assertEquals("EMBL-EBI Search", ((JMenuItem) linkItems[0]).getText());
569 @Test(groups = { "Functional" })
570 public void testHideInsertions()
572 // get sequences from the alignment
573 List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
575 // add our own seqs to avoid problems with changes to existing sequences
576 // (gap at end of sequences varies depending on how tests are run!)
577 Sequence seqGap1 = new Sequence("GappySeq",
578 "AAAA----AA-AAAAAAA---AAA-----------AAAAAAAAAA--");
579 seqGap1.createDatasetSequence();
581 Sequence seqGap2 = new Sequence("LessGappySeq",
582 "AAAAAA-AAAAA---AAA--AAAAA--AAAAAAA-AAAAAA");
583 seqGap2.createDatasetSequence();
585 Sequence seqGap3 = new Sequence("AnotherGapSeq",
586 "AAAAAA-AAAAAA--AAAAAA-AAAAAAAAAAA---AAAAAAAA");
587 seqGap3.createDatasetSequence();
589 Sequence seqGap4 = new Sequence("NoGaps",
590 "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA");
591 seqGap4.createDatasetSequence();
594 ColumnSelection sel = new ColumnSelection();
595 parentPanel.av.getAlignment().getHiddenColumns()
596 .revealAllHiddenColumns(sel);
598 // get the Popup Menu for 7th sequence - no insertions
599 testee = new PopupMenu(parentPanel, seqs.get(7), null);
600 testee.hideInsertions_actionPerformed(null);
602 HiddenColumns hidden = parentPanel.av.getAlignment().getHiddenColumns();
603 Iterator<int[]> it = hidden.iterator();
604 assertFalse(it.hasNext());
606 // get the Popup Menu for GappySeq - this time we have insertions
607 testee = new PopupMenu(parentPanel, seqs.get(4), null);
608 testee.hideInsertions_actionPerformed(null);
609 hidden = parentPanel.av.getAlignment().getHiddenColumns();
610 it = hidden.iterator();
612 assertTrue(it.hasNext());
613 int[] region = it.next();
614 assertEquals(region[0], 4);
615 assertEquals(region[1], 7);
617 assertTrue(it.hasNext());
619 assertEquals(region[0], 10);
620 assertEquals(region[1], 10);
622 assertTrue(it.hasNext());
624 assertEquals(region[0], 18);
625 assertEquals(region[1], 20);
627 assertTrue(it.hasNext());
629 assertEquals(region[0], 24);
630 assertEquals(region[1], 34);
632 assertTrue(it.hasNext());
634 assertEquals(region[0], 45);
635 assertEquals(region[1], 46);
637 assertFalse(it.hasNext());
639 sel = new ColumnSelection();
640 hidden.revealAllHiddenColumns(sel);
642 // make a sequence group and hide insertions within the group
643 SequenceGroup sg = new SequenceGroup();
646 sg.addSequence(seqGap2, false);
647 sg.addSequence(seqGap3, false);
648 parentPanel.av.setSelectionGroup(sg);
650 // hide columns outside and within selection
651 // only hidden columns outside the collection will be retained (unless also
652 // gaps in the selection)
653 hidden.hideColumns(1, 10);
654 hidden.hideColumns(31, 40);
656 // get the Popup Menu for LessGappySeq in the sequence group
657 testee = new PopupMenu(parentPanel, seqs.get(5), null);
658 testee.hideInsertions_actionPerformed(null);
659 hidden = parentPanel.av.getAlignment().getHiddenColumns();
660 it = hidden.iterator();
662 assertTrue(it.hasNext());
664 assertEquals(region[0], 1);
665 assertEquals(region[1], 7);
667 assertTrue(it.hasNext());
669 assertEquals(region[0], 13);
670 assertEquals(region[1], 14);
672 assertTrue(it.hasNext());
674 assertEquals(region[0], 34);
675 assertEquals(region[1], 34);