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 feature links
501 @Test(groups = { "Functional" })
502 public void testAddFeatureLinks()
504 // sequences from the alignment
505 List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
507 // create list of links and list of DBRefs
508 List<String> links = new ArrayList<>();
509 List<DBRefEntry> refs = new ArrayList<>();
511 // links as might be added into Preferences | Connections dialog
512 links.add("EMBL-EBI Search | http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$"
513 + SEQUENCE_ID + "$");
514 links.add("UNIPROT | http://www.uniprot.org/uniprot/$" + DB_ACCESSION
516 links.add("INTERPRO | http://www.ebi.ac.uk/interpro/entry/$"
517 + DB_ACCESSION + "$");
518 // Gene3D entry tests for case (in)sensitivity
519 links.add("Gene3D | http://gene3d.biochem.ucl.ac.uk/Gene3D/search?sterm=$"
520 + DB_ACCESSION + "$&mode=protein");
523 refs.add(new DBRefEntry(DBRefSource.UNIPROT, "1", "P83527"));
524 refs.add(new DBRefEntry("INTERPRO", "1", "IPR001041"));
525 refs.add(new DBRefEntry("INTERPRO", "1", "IPR006058"));
526 refs.add(new DBRefEntry("INTERPRO", "1", "IPR012675"));
529 refs.add(new DBRefEntry(DBRefSource.UNIPROT, "1", "Q9ZTS2"));
530 refs.add(new DBRefEntry("GENE3D", "1", "3.10.20.30"));
532 // add all the dbrefs to the sequences: Uniprot 1 each, Interpro all 3 to
533 // seq0, Gene3D to seq1
534 SequenceI seq = seqs.get(0);
535 seq.addDBRef(refs.get(0));
537 seq.addDBRef(refs.get(1));
538 seq.addDBRef(refs.get(2));
539 seq.addDBRef(refs.get(3));
541 seqs.get(1).addDBRef(refs.get(4));
542 seqs.get(1).addDBRef(refs.get(5));
544 // get the Popup Menu for first sequence
545 List<SequenceFeature> noFeatures = Collections.<SequenceFeature> emptyList();
546 testee = new PopupMenu(parentPanel, seq, noFeatures);
547 Component[] seqItems = testee.sequenceMenu.getMenuComponents();
548 JMenu linkMenu = (JMenu) seqItems[6];
549 Component[] linkItems = linkMenu.getMenuComponents();
551 // check the number of links are the expected number
552 assertEquals(5, linkItems.length);
554 // first entry is EMBL-EBI which just uses sequence id not accession id?
555 assertEquals("EMBL-EBI Search", ((JMenuItem) linkItems[0]).getText());
557 // sequence id for each link should match corresponding DB accession id
558 for (int i = 1; i < 4; i++)
560 String msg = seq.getName() + " link[" + i + "]";
561 assertEquals(msg, refs.get(i - 1).getSource(),
562 ((JMenuItem) linkItems[i])
563 .getText().split("\\|")[0]);
564 assertEquals(msg, refs.get(i - 1).getAccessionId(),
565 ((JMenuItem) linkItems[i])
566 .getText().split("\\|")[1]);
569 // get the Popup Menu for second sequence
571 testee = new PopupMenu(parentPanel, seq, noFeatures);
572 seqItems = testee.sequenceMenu.getMenuComponents();
573 linkMenu = (JMenu) seqItems[6];
574 linkItems = linkMenu.getMenuComponents();
576 // check the number of links are the expected number
577 assertEquals(3, linkItems.length);
579 // first entry is EMBL-EBI which just uses sequence id not accession id?
580 assertEquals("EMBL-EBI Search", ((JMenuItem) linkItems[0]).getText());
582 // sequence id for each link should match corresponding DB accession id
583 for (int i = 1; i < 3; i++)
585 String msg = seq.getName() + " link[" + i + "]";
586 assertEquals(msg, refs.get(i + 3).getSource(),
587 ((JMenuItem) linkItems[i])
588 .getText().split("\\|")[0].toUpperCase());
589 assertEquals(msg, refs.get(i + 3).getAccessionId(),
590 ((JMenuItem) linkItems[i]).getText().split("\\|")[1]);
593 // if there are no valid links the Links submenu is disabled
594 List<String> nomatchlinks = new ArrayList<>();
595 nomatchlinks.add("NOMATCH | http://www.uniprot.org/uniprot/$"
596 + DB_ACCESSION + "$");
598 testee = new PopupMenu(parentPanel, seq, noFeatures);
599 seqItems = testee.sequenceMenu.getMenuComponents();
600 linkMenu = (JMenu) seqItems[6];
601 assertFalse(linkMenu.isEnabled());
606 * Test for adding feature links
608 @Test(groups = { "Functional" })
609 public void testHideInsertions()
611 // get sequences from the alignment
612 List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
614 // add our own seqs to avoid problems with changes to existing sequences
615 // (gap at end of sequences varies depending on how tests are run!)
616 Sequence seqGap1 = new Sequence("GappySeq",
617 "AAAA----AA-AAAAAAA---AAA-----------AAAAAAAAAA--");
618 seqGap1.createDatasetSequence();
620 Sequence seqGap2 = new Sequence("LessGappySeq",
621 "AAAAAA-AAAAA---AAA--AAAAA--AAAAAAA-AAAAAA");
622 seqGap2.createDatasetSequence();
624 Sequence seqGap3 = new Sequence("AnotherGapSeq",
625 "AAAAAA-AAAAAA--AAAAAA-AAAAAAAAAAA---AAAAAAAA");
626 seqGap3.createDatasetSequence();
628 Sequence seqGap4 = new Sequence("NoGaps",
629 "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA");
630 seqGap4.createDatasetSequence();
633 ColumnSelection sel = new ColumnSelection();
634 parentPanel.av.getAlignment().getHiddenColumns()
635 .revealAllHiddenColumns(sel);
637 // get the Popup Menu for 7th sequence - no insertions
638 testee = new PopupMenu(parentPanel, seqs.get(7), null);
639 testee.hideInsertions_actionPerformed(null);
641 HiddenColumns hidden = parentPanel.av.getAlignment().getHiddenColumns();
642 Iterator<int[]> it = hidden.iterator();
643 assertFalse(it.hasNext());
645 // get the Popup Menu for GappySeq - this time we have insertions
646 testee = new PopupMenu(parentPanel, seqs.get(4), null);
647 testee.hideInsertions_actionPerformed(null);
648 hidden = parentPanel.av.getAlignment().getHiddenColumns();
649 it = hidden.iterator();
651 assertTrue(it.hasNext());
652 int[] region = it.next();
653 assertEquals(region[0], 4);
654 assertEquals(region[1], 7);
656 assertTrue(it.hasNext());
658 assertEquals(region[0], 10);
659 assertEquals(region[1], 10);
661 assertTrue(it.hasNext());
663 assertEquals(region[0], 18);
664 assertEquals(region[1], 20);
666 assertTrue(it.hasNext());
668 assertEquals(region[0], 24);
669 assertEquals(region[1], 34);
671 assertTrue(it.hasNext());
673 assertEquals(region[0], 45);
674 assertEquals(region[1], 46);
676 assertFalse(it.hasNext());
678 sel = new ColumnSelection();
679 hidden.revealAllHiddenColumns(sel);
681 // make a sequence group and hide insertions within the group
682 SequenceGroup sg = new SequenceGroup();
685 sg.addSequence(seqGap2, false);
686 sg.addSequence(seqGap3, false);
687 parentPanel.av.setSelectionGroup(sg);
689 // hide columns outside and within selection
690 // only hidden columns outside the collection will be retained (unless also
691 // gaps in the selection)
692 hidden.hideColumns(1, 10);
693 hidden.hideColumns(31, 40);
695 // get the Popup Menu for LessGappySeq in the sequence group
696 testee = new PopupMenu(parentPanel, seqs.get(5), null);
697 testee.hideInsertions_actionPerformed(null);
698 hidden = parentPanel.av.getAlignment().getHiddenColumns();
699 it = hidden.iterator();
701 assertTrue(it.hasNext());
703 assertEquals(region[0], 1);
704 assertEquals(region[1], 7);
706 assertTrue(it.hasNext());
708 assertEquals(region[0], 13);
709 assertEquals(region[1], 14);
711 assertTrue(it.hasNext());
713 assertEquals(region[0], 34);
714 assertEquals(region[1], 34);