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.annotations = new Annotation[] { new Annotation(2f) };
242 annotation.setCalcId("PDB");
243 seqs.get(0).getDatasetSequence().addAlignmentAnnotation(annotation);
246 seqs.get(0).addAlignmentAnnotation(annotation);
250 this.alignment.addAnnotation(annotation);
253 // PDB.Temp on Sequence1
254 annotation = new AlignmentAnnotation("Temp", "", 0);
255 annotation.setCalcId("PDB");
256 annotation.annotations = new Annotation[] { new Annotation(2f) };
257 seqs.get(1).getDatasetSequence().addAlignmentAnnotation(annotation);
260 seqs.get(1).addAlignmentAnnotation(annotation);
264 this.alignment.addAnnotation(annotation);
267 // JMOL.secondary structure on Sequence0
268 annotation = new AlignmentAnnotation("secondary structure", "", 0);
269 annotation.setCalcId("Jmol");
270 annotation.annotations = new Annotation[] { new Annotation(2f) };
271 seqs.get(0).getDatasetSequence().addAlignmentAnnotation(annotation);
274 seqs.get(0).addAlignmentAnnotation(annotation);
278 this.alignment.addAnnotation(annotation);
283 * Test building the 'add reference annotations' menu for the case where there
284 * are two alignment views:
286 * <li>in one view, reference annotations have been added (are on the
287 * datasets, sequences and alignment)</li>
288 * <li>in the current view, reference annotations are on the dataset and
289 * sequence, but not the alignment</li>
291 * The menu item should be enabled, and acquire a tooltip which lists the
292 * annotation sources (calcIds) and type (labels).
294 @Test(groups = { "Functional" })
295 public void testConfigureReferenceAnnotationsMenu_twoViews()
300 * Test for building menu options including 'show' and 'hide' annotation
303 @Test(groups = { "Functional" })
304 public void testBuildAnnotationTypesMenus()
306 JMenu showMenu = new JMenu();
307 JMenu hideMenu = new JMenu();
308 List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
310 // make up new annotations and add to sequences and to the alignment
312 // PDB.secondary structure on Sequence0
313 AlignmentAnnotation annotation = new AlignmentAnnotation(
314 "secondary structure", "", new Annotation[] {});
315 annotation.setCalcId("PDB");
316 annotation.visible = true;
317 seqs.get(0).addAlignmentAnnotation(annotation);
318 parentPanel.getAlignment().addAnnotation(annotation);
320 // JMOL.secondary structure on Sequence0 - hidden
321 annotation = new AlignmentAnnotation("secondary structure", "",
322 new Annotation[] {});
323 annotation.setCalcId("JMOL");
324 annotation.visible = false;
325 seqs.get(0).addAlignmentAnnotation(annotation);
326 parentPanel.getAlignment().addAnnotation(annotation);
328 // Jpred.SSP on Sequence0 - hidden
329 annotation = new AlignmentAnnotation("SSP", "", new Annotation[] {});
330 annotation.setCalcId("JPred");
331 annotation.visible = false;
332 seqs.get(0).addAlignmentAnnotation(annotation);
333 parentPanel.getAlignment().addAnnotation(annotation);
335 // PDB.Temp on Sequence1
336 annotation = new AlignmentAnnotation("Temp", "", new Annotation[] {});
337 annotation.setCalcId("PDB");
338 annotation.visible = true;
339 seqs.get(1).addAlignmentAnnotation(annotation);
340 parentPanel.getAlignment().addAnnotation(annotation);
343 * Expect menu options to show "secondary structure" and "SSP", and to hide
344 * "secondary structure" and "Temp". Tooltip should be calcId.
346 testee.buildAnnotationTypesMenus(showMenu, hideMenu, seqs);
348 assertTrue(showMenu.isEnabled());
349 assertTrue(hideMenu.isEnabled());
351 Component[] showOptions = showMenu.getMenuComponents();
352 Component[] hideOptions = hideMenu.getMenuComponents();
354 assertEquals(4, showOptions.length); // includes 'All' and separator
355 assertEquals(4, hideOptions.length);
356 String all = MessageManager.getString("label.all");
357 assertEquals(all, ((JMenuItem) showOptions[0]).getText());
358 assertTrue(showOptions[1] instanceof JPopupMenu.Separator);
359 assertEquals(JSeparator.HORIZONTAL,
360 ((JSeparator) showOptions[1]).getOrientation());
361 assertEquals("secondary structure",
362 ((JMenuItem) showOptions[2]).getText());
363 assertEquals("JMOL", ((JMenuItem) showOptions[2]).getToolTipText());
364 assertEquals("SSP", ((JMenuItem) showOptions[3]).getText());
365 assertEquals("JPred", ((JMenuItem) showOptions[3]).getToolTipText());
367 assertEquals(all, ((JMenuItem) hideOptions[0]).getText());
368 assertTrue(hideOptions[1] instanceof JPopupMenu.Separator);
369 assertEquals(JSeparator.HORIZONTAL,
370 ((JSeparator) hideOptions[1]).getOrientation());
371 assertEquals("secondary structure",
372 ((JMenuItem) hideOptions[2]).getText());
373 assertEquals("PDB", ((JMenuItem) hideOptions[2]).getToolTipText());
374 assertEquals("Temp", ((JMenuItem) hideOptions[3]).getText());
375 assertEquals("PDB", ((JMenuItem) hideOptions[3]).getToolTipText());
379 * Test for building menu options with only 'hide' annotation types enabled.
381 @Test(groups = { "Functional" })
382 public void testBuildAnnotationTypesMenus_showDisabled()
384 JMenu showMenu = new JMenu();
385 JMenu hideMenu = new JMenu();
386 List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
388 // make up new annotations and add to sequences and to the alignment
390 // PDB.secondary structure on Sequence0
391 AlignmentAnnotation annotation = new AlignmentAnnotation(
392 "secondary structure", "", new Annotation[] {});
393 annotation.setCalcId("PDB");
394 annotation.visible = true;
395 seqs.get(0).addAlignmentAnnotation(annotation);
396 parentPanel.getAlignment().addAnnotation(annotation);
398 // PDB.Temp on Sequence1
399 annotation = new AlignmentAnnotation("Temp", "", new Annotation[] {});
400 annotation.setCalcId("PDB");
401 annotation.visible = true;
402 seqs.get(1).addAlignmentAnnotation(annotation);
403 parentPanel.getAlignment().addAnnotation(annotation);
406 * Expect menu options to hide "secondary structure" and "Temp". Tooltip
407 * should be calcId. 'Show' menu should be disabled.
409 testee.buildAnnotationTypesMenus(showMenu, hideMenu, seqs);
411 assertFalse(showMenu.isEnabled());
412 assertTrue(hideMenu.isEnabled());
414 Component[] showOptions = showMenu.getMenuComponents();
415 Component[] hideOptions = hideMenu.getMenuComponents();
417 assertEquals(2, showOptions.length); // includes 'All' and separator
418 assertEquals(4, hideOptions.length);
419 String all = MessageManager.getString("label.all");
420 assertEquals(all, ((JMenuItem) showOptions[0]).getText());
421 assertTrue(showOptions[1] instanceof JPopupMenu.Separator);
422 assertEquals(JSeparator.HORIZONTAL,
423 ((JSeparator) showOptions[1]).getOrientation());
425 assertEquals(all, ((JMenuItem) hideOptions[0]).getText());
426 assertTrue(hideOptions[1] instanceof JPopupMenu.Separator);
427 assertEquals(JSeparator.HORIZONTAL,
428 ((JSeparator) hideOptions[1]).getOrientation());
429 assertEquals("secondary structure",
430 ((JMenuItem) hideOptions[2]).getText());
431 assertEquals("PDB", ((JMenuItem) hideOptions[2]).getToolTipText());
432 assertEquals("Temp", ((JMenuItem) hideOptions[3]).getText());
433 assertEquals("PDB", ((JMenuItem) hideOptions[3]).getToolTipText());
437 * Test for building menu options with only 'show' annotation types enabled.
439 @Test(groups = { "Functional" })
440 public void testBuildAnnotationTypesMenus_hideDisabled()
442 JMenu showMenu = new JMenu();
443 JMenu hideMenu = new JMenu();
444 List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
446 // make up new annotations and add to sequences and to the alignment
448 // PDB.secondary structure on Sequence0
449 AlignmentAnnotation annotation = new AlignmentAnnotation(
450 "secondary structure", "", new Annotation[] {});
451 annotation.setCalcId("PDB");
452 annotation.visible = false;
453 seqs.get(0).addAlignmentAnnotation(annotation);
454 parentPanel.getAlignment().addAnnotation(annotation);
456 // PDB.Temp on Sequence1
457 annotation = new AlignmentAnnotation("Temp", "", new Annotation[] {});
458 annotation.setCalcId("PDB2");
459 annotation.visible = false;
460 seqs.get(1).addAlignmentAnnotation(annotation);
461 parentPanel.getAlignment().addAnnotation(annotation);
464 * Expect menu options to show "secondary structure" and "Temp". Tooltip
465 * should be calcId. 'hide' menu should be disabled.
467 testee.buildAnnotationTypesMenus(showMenu, hideMenu, seqs);
469 assertTrue(showMenu.isEnabled());
470 assertFalse(hideMenu.isEnabled());
472 Component[] showOptions = showMenu.getMenuComponents();
473 Component[] hideOptions = hideMenu.getMenuComponents();
475 assertEquals(4, showOptions.length); // includes 'All' and separator
476 assertEquals(2, hideOptions.length);
477 String all = MessageManager.getString("label.all");
478 assertEquals(all, ((JMenuItem) showOptions[0]).getText());
479 assertTrue(showOptions[1] instanceof JPopupMenu.Separator);
480 assertEquals(JSeparator.HORIZONTAL,
481 ((JSeparator) showOptions[1]).getOrientation());
482 assertEquals("secondary structure",
483 ((JMenuItem) showOptions[2]).getText());
484 assertEquals("PDB", ((JMenuItem) showOptions[2]).getToolTipText());
485 assertEquals("Temp", ((JMenuItem) showOptions[3]).getText());
486 assertEquals("PDB2", ((JMenuItem) showOptions[3]).getToolTipText());
488 assertEquals(all, ((JMenuItem) hideOptions[0]).getText());
489 assertTrue(hideOptions[1] instanceof JPopupMenu.Separator);
490 assertEquals(JSeparator.HORIZONTAL,
491 ((JSeparator) hideOptions[1]).getOrientation());
495 * Test for adding feature links
497 @Test(groups = { "Functional" })
498 public void testAddFeatureLinks()
500 // sequences from the alignment
501 List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
503 // create list of links and list of DBRefs
504 List<String> links = new ArrayList<>();
505 List<DBRefEntry> refs = new ArrayList<>();
507 // links as might be added into Preferences | Connections dialog
508 links.add("EMBL-EBI Search | http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$"
509 + SEQUENCE_ID + "$");
510 links.add("UNIPROT | http://www.uniprot.org/uniprot/$" + DB_ACCESSION
512 links.add("INTERPRO | http://www.ebi.ac.uk/interpro/entry/$"
513 + DB_ACCESSION + "$");
514 // Gene3D entry tests for case (in)sensitivity
515 links.add("Gene3D | http://gene3d.biochem.ucl.ac.uk/Gene3D/search?sterm=$"
516 + DB_ACCESSION + "$&mode=protein");
519 refs.add(new DBRefEntry(DBRefSource.UNIPROT, "1", "P83527"));
520 refs.add(new DBRefEntry("INTERPRO", "1", "IPR001041"));
521 refs.add(new DBRefEntry("INTERPRO", "1", "IPR006058"));
522 refs.add(new DBRefEntry("INTERPRO", "1", "IPR012675"));
525 refs.add(new DBRefEntry(DBRefSource.UNIPROT, "1", "Q9ZTS2"));
526 refs.add(new DBRefEntry("GENE3D", "1", "3.10.20.30"));
528 // add all the dbrefs to the sequences: Uniprot 1 each, Interpro all 3 to
529 // seq0, Gene3D to seq1
530 SequenceI seq = seqs.get(0);
531 seq.addDBRef(refs.get(0));
533 seq.addDBRef(refs.get(1));
534 seq.addDBRef(refs.get(2));
535 seq.addDBRef(refs.get(3));
537 seqs.get(1).addDBRef(refs.get(4));
538 seqs.get(1).addDBRef(refs.get(5));
540 // get the Popup Menu for first sequence
541 List<SequenceFeature> noFeatures = Collections.<SequenceFeature> emptyList();
542 testee = new PopupMenu(parentPanel, seq, noFeatures);
543 Component[] seqItems = testee.sequenceMenu.getMenuComponents();
544 JMenu linkMenu = (JMenu) seqItems[6];
545 Component[] linkItems = linkMenu.getMenuComponents();
547 // check the number of links are the expected number
548 assertEquals(5, linkItems.length);
550 // first entry is EMBL-EBI which just uses sequence id not accession id?
551 assertEquals("EMBL-EBI Search", ((JMenuItem) linkItems[0]).getText());
553 // sequence id for each link should match corresponding DB accession id
554 for (int i = 1; i < 4; i++)
556 String msg = seq.getName() + " link[" + i + "]";
557 assertEquals(msg, refs.get(i - 1).getSource(),
558 ((JMenuItem) linkItems[i])
559 .getText().split("\\|")[0]);
560 assertEquals(msg, refs.get(i - 1).getAccessionId(),
561 ((JMenuItem) linkItems[i])
562 .getText().split("\\|")[1]);
565 // get the Popup Menu for second sequence
567 testee = new PopupMenu(parentPanel, seq, noFeatures);
568 seqItems = testee.sequenceMenu.getMenuComponents();
569 linkMenu = (JMenu) seqItems[6];
570 linkItems = linkMenu.getMenuComponents();
572 // check the number of links are the expected number
573 assertEquals(3, linkItems.length);
575 // first entry is EMBL-EBI which just uses sequence id not accession id?
576 assertEquals("EMBL-EBI Search", ((JMenuItem) linkItems[0]).getText());
578 // sequence id for each link should match corresponding DB accession id
579 for (int i = 1; i < 3; i++)
581 String msg = seq.getName() + " link[" + i + "]";
582 assertEquals(msg, refs.get(i + 3).getSource(),
583 ((JMenuItem) linkItems[i])
584 .getText().split("\\|")[0].toUpperCase());
585 assertEquals(msg, refs.get(i + 3).getAccessionId(),
586 ((JMenuItem) linkItems[i]).getText().split("\\|")[1]);
589 // if there are no valid links the Links submenu is disabled
590 List<String> nomatchlinks = new ArrayList<>();
591 nomatchlinks.add("NOMATCH | http://www.uniprot.org/uniprot/$"
592 + DB_ACCESSION + "$");
594 testee = new PopupMenu(parentPanel, seq, noFeatures);
595 seqItems = testee.sequenceMenu.getMenuComponents();
596 linkMenu = (JMenu) seqItems[6];
597 assertFalse(linkMenu.isEnabled());
602 * Test for adding feature links
604 @Test(groups = { "Functional" })
605 public void testHideInsertions()
607 // get sequences from the alignment
608 List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
610 // add our own seqs to avoid problems with changes to existing sequences
611 // (gap at end of sequences varies depending on how tests are run!)
612 Sequence seqGap1 = new Sequence("GappySeq",
613 "AAAA----AA-AAAAAAA---AAA-----------AAAAAAAAAA--");
614 seqGap1.createDatasetSequence();
616 Sequence seqGap2 = new Sequence("LessGappySeq",
617 "AAAAAA-AAAAA---AAA--AAAAA--AAAAAAA-AAAAAA");
618 seqGap2.createDatasetSequence();
620 Sequence seqGap3 = new Sequence("AnotherGapSeq",
621 "AAAAAA-AAAAAA--AAAAAA-AAAAAAAAAAA---AAAAAAAA");
622 seqGap3.createDatasetSequence();
624 Sequence seqGap4 = new Sequence("NoGaps",
625 "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA");
626 seqGap4.createDatasetSequence();
629 ColumnSelection sel = new ColumnSelection();
630 parentPanel.av.getAlignment().getHiddenColumns()
631 .revealAllHiddenColumns(sel);
633 // get the Popup Menu for 7th sequence - no insertions
634 testee = new PopupMenu(parentPanel, seqs.get(7), null);
635 testee.hideInsertions_actionPerformed(null);
637 HiddenColumns hidden = parentPanel.av.getAlignment().getHiddenColumns();
638 Iterator<int[]> it = hidden.iterator();
639 assertFalse(it.hasNext());
641 // get the Popup Menu for GappySeq - this time we have insertions
642 testee = new PopupMenu(parentPanel, seqs.get(4), null);
643 testee.hideInsertions_actionPerformed(null);
644 hidden = parentPanel.av.getAlignment().getHiddenColumns();
645 it = hidden.iterator();
647 assertTrue(it.hasNext());
648 int[] region = it.next();
649 assertEquals(region[0], 4);
650 assertEquals(region[1], 7);
652 assertTrue(it.hasNext());
654 assertEquals(region[0], 10);
655 assertEquals(region[1], 10);
657 assertTrue(it.hasNext());
659 assertEquals(region[0], 18);
660 assertEquals(region[1], 20);
662 assertTrue(it.hasNext());
664 assertEquals(region[0], 24);
665 assertEquals(region[1], 34);
667 assertTrue(it.hasNext());
669 assertEquals(region[0], 45);
670 assertEquals(region[1], 46);
672 assertFalse(it.hasNext());
674 sel = new ColumnSelection();
675 hidden.revealAllHiddenColumns(sel);
677 // make a sequence group and hide insertions within the group
678 SequenceGroup sg = new SequenceGroup();
681 sg.addSequence(seqGap2, false);
682 sg.addSequence(seqGap3, false);
683 parentPanel.av.setSelectionGroup(sg);
685 // hide columns outside and within selection
686 // only hidden columns outside the collection will be retained (unless also
687 // gaps in the selection)
688 hidden.hideColumns(1, 10);
689 hidden.hideColumns(31, 40);
691 // get the Popup Menu for LessGappySeq in the sequence group
692 testee = new PopupMenu(parentPanel, seqs.get(5), null);
693 testee.hideInsertions_actionPerformed(null);
694 hidden = parentPanel.av.getAlignment().getHiddenColumns();
695 it = hidden.iterator();
697 assertTrue(it.hasNext());
699 assertEquals(region[0], 1);
700 assertEquals(region[1], 7);
702 assertTrue(it.hasNext());
704 assertEquals(region[0], 13);
705 assertEquals(region[1], 14);
707 assertTrue(it.hasNext());
709 assertEquals(region[0], 34);
710 assertEquals(region[1], 34);