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; word-wrap: break-word;}</style><p class=\"ttip\">"
200 + s + "<br/>Jmol/secondary structure<br/>PDB/Temp</p></html>";
201 assertEquals(expected, menu.getToolTipText());
205 * Test building the 'add reference annotations' menu for the case where
206 * several reference annotations are on the dataset and the sequences but not
207 * on the alignment. The menu item should be enabled, and acquire a tooltip
208 * which lists the annotation sources (calcIds) and type (labels).
210 @Test(groups = { "Functional" })
211 public void testConfigureReferenceAnnotationsMenu_notOnAlignment()
213 JMenuItem menu = new JMenuItem();
214 List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
216 // make up new annotations and add to dataset sequences and sequences
217 attachReferenceAnnotations(seqs, true, false);
219 testee.configureReferenceAnnotationsMenu(menu, seqs);
220 assertTrue(menu.isEnabled());
221 String s = MessageManager.getString("label.add_annotations_for");
222 String expected = "<html><style> p.ttip {width: 350; text-align: justify; word-wrap: break-word;}</style><p class=\"ttip\">"
223 + s + "<br/>Jmol/secondary structure<br/>PDB/Temp</p></html>";
224 assertEquals(expected, menu.getToolTipText());
228 * Generate annotations and add to dataset sequences and (optionally)
229 * sequences and/or alignment
232 * @param addToSequence
233 * @param addToAlignment
235 private void attachReferenceAnnotations(List<SequenceI> seqs,
236 boolean addToSequence, boolean addToAlignment)
238 // PDB.secondary structure on Sequence0
239 AlignmentAnnotation annotation = new AlignmentAnnotation(
240 "secondary structure", "", 0);
241 annotation.setCalcId("PDB");
242 seqs.get(0).getDatasetSequence().addAlignmentAnnotation(annotation);
245 seqs.get(0).addAlignmentAnnotation(annotation);
249 this.alignment.addAnnotation(annotation);
252 // PDB.Temp on Sequence1
253 annotation = new AlignmentAnnotation("Temp", "", 0);
254 annotation.setCalcId("PDB");
255 seqs.get(1).getDatasetSequence().addAlignmentAnnotation(annotation);
258 seqs.get(1).addAlignmentAnnotation(annotation);
262 this.alignment.addAnnotation(annotation);
265 // JMOL.secondary structure on Sequence0
266 annotation = new AlignmentAnnotation("secondary structure", "", 0);
267 annotation.setCalcId("Jmol");
268 seqs.get(0).getDatasetSequence().addAlignmentAnnotation(annotation);
271 seqs.get(0).addAlignmentAnnotation(annotation);
275 this.alignment.addAnnotation(annotation);
280 * Test building the 'add reference annotations' menu for the case where there
281 * are two alignment views:
283 * <li>in one view, reference annotations have been added (are on the
284 * datasets, sequences and alignment)</li>
285 * <li>in the current view, reference annotations are on the dataset and
286 * sequence, but not the alignment</li>
288 * The menu item should be enabled, and acquire a tooltip which lists the
289 * annotation sources (calcIds) and type (labels).
291 @Test(groups = { "Functional" })
292 public void testConfigureReferenceAnnotationsMenu_twoViews()
297 * Test for building menu options including 'show' and 'hide' annotation
300 @Test(groups = { "Functional" })
301 public void testBuildAnnotationTypesMenus()
303 JMenu showMenu = new JMenu();
304 JMenu hideMenu = new JMenu();
305 List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
307 // make up new annotations and add to sequences and to the alignment
309 // PDB.secondary structure on Sequence0
310 AlignmentAnnotation annotation = new AlignmentAnnotation(
311 "secondary structure", "", new Annotation[] {});
312 annotation.setCalcId("PDB");
313 annotation.visible = true;
314 seqs.get(0).addAlignmentAnnotation(annotation);
315 parentPanel.getAlignment().addAnnotation(annotation);
317 // JMOL.secondary structure on Sequence0 - hidden
318 annotation = new AlignmentAnnotation("secondary structure", "",
319 new Annotation[] {});
320 annotation.setCalcId("JMOL");
321 annotation.visible = false;
322 seqs.get(0).addAlignmentAnnotation(annotation);
323 parentPanel.getAlignment().addAnnotation(annotation);
325 // Jpred.SSP on Sequence0 - hidden
326 annotation = new AlignmentAnnotation("SSP", "", new Annotation[] {});
327 annotation.setCalcId("JPred");
328 annotation.visible = false;
329 seqs.get(0).addAlignmentAnnotation(annotation);
330 parentPanel.getAlignment().addAnnotation(annotation);
332 // PDB.Temp on Sequence1
333 annotation = new AlignmentAnnotation("Temp", "", new Annotation[] {});
334 annotation.setCalcId("PDB");
335 annotation.visible = true;
336 seqs.get(1).addAlignmentAnnotation(annotation);
337 parentPanel.getAlignment().addAnnotation(annotation);
340 * Expect menu options to show "secondary structure" and "SSP", and to hide
341 * "secondary structure" and "Temp". Tooltip should be calcId.
343 testee.buildAnnotationTypesMenus(showMenu, hideMenu, seqs);
345 assertTrue(showMenu.isEnabled());
346 assertTrue(hideMenu.isEnabled());
348 Component[] showOptions = showMenu.getMenuComponents();
349 Component[] hideOptions = hideMenu.getMenuComponents();
351 assertEquals(4, showOptions.length); // includes 'All' and separator
352 assertEquals(4, hideOptions.length);
353 String all = MessageManager.getString("label.all");
354 assertEquals(all, ((JMenuItem) showOptions[0]).getText());
355 assertTrue(showOptions[1] instanceof JPopupMenu.Separator);
356 assertEquals(JSeparator.HORIZONTAL,
357 ((JSeparator) showOptions[1]).getOrientation());
358 assertEquals("secondary structure",
359 ((JMenuItem) showOptions[2]).getText());
360 assertEquals("JMOL", ((JMenuItem) showOptions[2]).getToolTipText());
361 assertEquals("SSP", ((JMenuItem) showOptions[3]).getText());
362 assertEquals("JPred", ((JMenuItem) showOptions[3]).getToolTipText());
364 assertEquals(all, ((JMenuItem) hideOptions[0]).getText());
365 assertTrue(hideOptions[1] instanceof JPopupMenu.Separator);
366 assertEquals(JSeparator.HORIZONTAL,
367 ((JSeparator) hideOptions[1]).getOrientation());
368 assertEquals("secondary structure",
369 ((JMenuItem) hideOptions[2]).getText());
370 assertEquals("PDB", ((JMenuItem) hideOptions[2]).getToolTipText());
371 assertEquals("Temp", ((JMenuItem) hideOptions[3]).getText());
372 assertEquals("PDB", ((JMenuItem) hideOptions[3]).getToolTipText());
376 * Test for building menu options with only 'hide' annotation types enabled.
378 @Test(groups = { "Functional" })
379 public void testBuildAnnotationTypesMenus_showDisabled()
381 JMenu showMenu = new JMenu();
382 JMenu hideMenu = new JMenu();
383 List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
385 // make up new annotations and add to sequences and to the alignment
387 // PDB.secondary structure on Sequence0
388 AlignmentAnnotation annotation = new AlignmentAnnotation(
389 "secondary structure", "", new Annotation[] {});
390 annotation.setCalcId("PDB");
391 annotation.visible = true;
392 seqs.get(0).addAlignmentAnnotation(annotation);
393 parentPanel.getAlignment().addAnnotation(annotation);
395 // PDB.Temp on Sequence1
396 annotation = new AlignmentAnnotation("Temp", "", new Annotation[] {});
397 annotation.setCalcId("PDB");
398 annotation.visible = true;
399 seqs.get(1).addAlignmentAnnotation(annotation);
400 parentPanel.getAlignment().addAnnotation(annotation);
403 * Expect menu options to hide "secondary structure" and "Temp". Tooltip
404 * should be calcId. 'Show' menu should be disabled.
406 testee.buildAnnotationTypesMenus(showMenu, hideMenu, seqs);
408 assertFalse(showMenu.isEnabled());
409 assertTrue(hideMenu.isEnabled());
411 Component[] showOptions = showMenu.getMenuComponents();
412 Component[] hideOptions = hideMenu.getMenuComponents();
414 assertEquals(2, showOptions.length); // includes 'All' and separator
415 assertEquals(4, hideOptions.length);
416 String all = MessageManager.getString("label.all");
417 assertEquals(all, ((JMenuItem) showOptions[0]).getText());
418 assertTrue(showOptions[1] instanceof JPopupMenu.Separator);
419 assertEquals(JSeparator.HORIZONTAL,
420 ((JSeparator) showOptions[1]).getOrientation());
422 assertEquals(all, ((JMenuItem) hideOptions[0]).getText());
423 assertTrue(hideOptions[1] instanceof JPopupMenu.Separator);
424 assertEquals(JSeparator.HORIZONTAL,
425 ((JSeparator) hideOptions[1]).getOrientation());
426 assertEquals("secondary structure",
427 ((JMenuItem) hideOptions[2]).getText());
428 assertEquals("PDB", ((JMenuItem) hideOptions[2]).getToolTipText());
429 assertEquals("Temp", ((JMenuItem) hideOptions[3]).getText());
430 assertEquals("PDB", ((JMenuItem) hideOptions[3]).getToolTipText());
434 * Test for building menu options with only 'show' annotation types enabled.
436 @Test(groups = { "Functional" })
437 public void testBuildAnnotationTypesMenus_hideDisabled()
439 JMenu showMenu = new JMenu();
440 JMenu hideMenu = new JMenu();
441 List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
443 // make up new annotations and add to sequences and to the alignment
445 // PDB.secondary structure on Sequence0
446 AlignmentAnnotation annotation = new AlignmentAnnotation(
447 "secondary structure", "", new Annotation[] {});
448 annotation.setCalcId("PDB");
449 annotation.visible = false;
450 seqs.get(0).addAlignmentAnnotation(annotation);
451 parentPanel.getAlignment().addAnnotation(annotation);
453 // PDB.Temp on Sequence1
454 annotation = new AlignmentAnnotation("Temp", "", new Annotation[] {});
455 annotation.setCalcId("PDB2");
456 annotation.visible = false;
457 seqs.get(1).addAlignmentAnnotation(annotation);
458 parentPanel.getAlignment().addAnnotation(annotation);
461 * Expect menu options to show "secondary structure" and "Temp". Tooltip
462 * should be calcId. 'hide' menu should be disabled.
464 testee.buildAnnotationTypesMenus(showMenu, hideMenu, seqs);
466 assertTrue(showMenu.isEnabled());
467 assertFalse(hideMenu.isEnabled());
469 Component[] showOptions = showMenu.getMenuComponents();
470 Component[] hideOptions = hideMenu.getMenuComponents();
472 assertEquals(4, showOptions.length); // includes 'All' and separator
473 assertEquals(2, hideOptions.length);
474 String all = MessageManager.getString("label.all");
475 assertEquals(all, ((JMenuItem) showOptions[0]).getText());
476 assertTrue(showOptions[1] instanceof JPopupMenu.Separator);
477 assertEquals(JSeparator.HORIZONTAL,
478 ((JSeparator) showOptions[1]).getOrientation());
479 assertEquals("secondary structure",
480 ((JMenuItem) showOptions[2]).getText());
481 assertEquals("PDB", ((JMenuItem) showOptions[2]).getToolTipText());
482 assertEquals("Temp", ((JMenuItem) showOptions[3]).getText());
483 assertEquals("PDB2", ((JMenuItem) showOptions[3]).getToolTipText());
485 assertEquals(all, ((JMenuItem) hideOptions[0]).getText());
486 assertTrue(hideOptions[1] instanceof JPopupMenu.Separator);
487 assertEquals(JSeparator.HORIZONTAL,
488 ((JSeparator) hideOptions[1]).getOrientation());
492 * Test for adding sequence id, dbref and feature links
494 @Test(groups = { "Functional" })
495 public void testBuildLinkMenu()
497 List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
498 final SequenceI seq0 = seqs.get(0);
499 final SequenceI seq1 = seqs.get(1);
500 final List<SequenceFeature> noFeatures = Collections
501 .<SequenceFeature> emptyList();
502 final String linkText = MessageManager.getString("action.link");
504 seq0.addDBRef(new DBRefEntry(DBRefSource.UNIPROT, "1", "P83527"));
505 seq0.addDBRef(new DBRefEntry("INTERPRO", "1", "IPR001041"));
506 seq0.addDBRef(new DBRefEntry("INTERPRO", "1", "IPR012675"));
507 seq0.addDBRef(new DBRefEntry("INTERPRO", "1", "IPR006058"));
508 seq1.addDBRef(new DBRefEntry(DBRefSource.UNIPROT, "1", "Q9ZTS2"));
509 seq1.addDBRef(new DBRefEntry("GENE3D", "1", "3.10.20.30"));
512 * check the Link Menu for the first sequence
514 JMenu linkMenu = PopupMenu.buildLinkMenu(seq0, noFeatures);
515 assertEquals(linkText, linkMenu.getText());
516 Component[] linkItems = linkMenu.getMenuComponents();
519 * menu items are ordered: SEQUENCE_ID search first, then dbrefs in order
520 * of database name (and within that by order of dbref addition)
522 assertEquals(5, linkItems.length);
523 assertEquals("EMBL-EBI Search", ((JMenuItem) linkItems[0]).getText());
524 assertEquals("INTERPRO|IPR001041",
525 ((JMenuItem) linkItems[1]).getText());
526 assertEquals("INTERPRO|IPR012675",
527 ((JMenuItem) linkItems[2]).getText());
528 assertEquals("INTERPRO|IPR006058",
529 ((JMenuItem) linkItems[3]).getText());
530 assertEquals("UNIPROT|P83527", ((JMenuItem) linkItems[4]).getText());
533 * check the Link Menu for the second sequence
534 * note dbref GENE3D is matched to link Gene3D, the latter is displayed
536 linkMenu = PopupMenu.buildLinkMenu(seq1, noFeatures);
537 assertEquals(linkText, linkMenu.getText());
538 linkItems = linkMenu.getMenuComponents();
539 assertEquals(3, linkItems.length);
540 assertEquals("EMBL-EBI Search", ((JMenuItem) linkItems[0]).getText());
541 assertEquals("Gene3D|3.10.20.30", ((JMenuItem) linkItems[1]).getText());
542 assertEquals("UNIPROT|Q9ZTS2", ((JMenuItem) linkItems[2]).getText());
545 * if there are no valid links the Links submenu is still shown, but
546 * reduced to the EMBL-EBI lookup only (inserted by
547 * CustomUrlProvider.choosePrimaryUrl())
549 String unmatched = "NOMATCH|http://www.uniprot.org/uniprot/$"
550 + DB_ACCESSION + "$";
551 UrlProviderFactoryI factory = new DesktopUrlProviderFactory(null,
553 Preferences.sequenceUrlLinks = factory.createUrlProvider();
555 linkMenu = PopupMenu.buildLinkMenu(seq1, noFeatures);
556 assertEquals(linkText, linkMenu.getText());
557 linkItems = linkMenu.getMenuComponents();
558 assertEquals(1, linkItems.length);
559 assertEquals("EMBL-EBI Search", ((JMenuItem) linkItems[0]).getText());
562 @Test(groups = { "Functional" })
563 public void testHideInsertions()
565 // get sequences from the alignment
566 List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
568 // add our own seqs to avoid problems with changes to existing sequences
569 // (gap at end of sequences varies depending on how tests are run!)
570 Sequence seqGap1 = new Sequence("GappySeq",
571 "AAAA----AA-AAAAAAA---AAA-----------AAAAAAAAAA--");
572 seqGap1.createDatasetSequence();
574 Sequence seqGap2 = new Sequence("LessGappySeq",
575 "AAAAAA-AAAAA---AAA--AAAAA--AAAAAAA-AAAAAA");
576 seqGap2.createDatasetSequence();
578 Sequence seqGap3 = new Sequence("AnotherGapSeq",
579 "AAAAAA-AAAAAA--AAAAAA-AAAAAAAAAAA---AAAAAAAA");
580 seqGap3.createDatasetSequence();
582 Sequence seqGap4 = new Sequence("NoGaps",
583 "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA");
584 seqGap4.createDatasetSequence();
587 ColumnSelection sel = new ColumnSelection();
588 parentPanel.av.getAlignment().getHiddenColumns()
589 .revealAllHiddenColumns(sel);
591 // get the Popup Menu for 7th sequence - no insertions
592 testee = new PopupMenu(parentPanel, seqs.get(7), null);
593 testee.hideInsertions_actionPerformed(null);
595 HiddenColumns hidden = parentPanel.av.getAlignment().getHiddenColumns();
596 Iterator<int[]> it = hidden.iterator();
597 assertFalse(it.hasNext());
599 // get the Popup Menu for GappySeq - this time we have insertions
600 testee = new PopupMenu(parentPanel, seqs.get(4), null);
601 testee.hideInsertions_actionPerformed(null);
602 hidden = parentPanel.av.getAlignment().getHiddenColumns();
603 it = hidden.iterator();
605 assertTrue(it.hasNext());
606 int[] region = it.next();
607 assertEquals(region[0], 4);
608 assertEquals(region[1], 7);
610 assertTrue(it.hasNext());
612 assertEquals(region[0], 10);
613 assertEquals(region[1], 10);
615 assertTrue(it.hasNext());
617 assertEquals(region[0], 18);
618 assertEquals(region[1], 20);
620 assertTrue(it.hasNext());
622 assertEquals(region[0], 24);
623 assertEquals(region[1], 34);
625 assertTrue(it.hasNext());
627 assertEquals(region[0], 45);
628 assertEquals(region[1], 46);
630 assertFalse(it.hasNext());
632 sel = new ColumnSelection();
633 hidden.revealAllHiddenColumns(sel);
635 // make a sequence group and hide insertions within the group
636 SequenceGroup sg = new SequenceGroup();
639 sg.addSequence(seqGap2, false);
640 sg.addSequence(seqGap3, false);
641 parentPanel.av.setSelectionGroup(sg);
643 // hide columns outside and within selection
644 // only hidden columns outside the collection will be retained (unless also
645 // gaps in the selection)
646 hidden.hideColumns(1, 10);
647 hidden.hideColumns(31, 40);
649 // get the Popup Menu for LessGappySeq in the sequence group
650 testee = new PopupMenu(parentPanel, seqs.get(5), null);
651 testee.hideInsertions_actionPerformed(null);
652 hidden = parentPanel.av.getAlignment().getHiddenColumns();
653 it = hidden.iterator();
655 assertTrue(it.hasNext());
657 assertEquals(region[0], 1);
658 assertEquals(region[1], 7);
660 assertTrue(it.hasNext());
662 assertEquals(region[0], 13);
663 assertEquals(region[1], 14);
665 assertTrue(it.hasNext());
667 assertEquals(region[0], 34);
668 assertEquals(region[1], 34);