/* * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * * Jalview is free software: you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation, either version 3 * of the License, or (at your option) any later version. * * Jalview is distributed in the hope that it will be useful, but * WITHOUT ANY WARRANTY; without even the implied warranty * of MERCHANTABILITY or FITNESS FOR A PARTICULAR * PURPOSE. See the GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with Jalview. If not, see . * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.gui; import static jalview.util.UrlConstants.DB_ACCESSION; import static jalview.util.UrlConstants.SEQUENCE_ID; import static org.testng.AssertJUnit.assertEquals; import static org.testng.AssertJUnit.assertFalse; import static org.testng.AssertJUnit.assertTrue; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; import jalview.datamodel.Annotation; import jalview.datamodel.DBRefEntry; import jalview.datamodel.DBRefSource; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceI; import jalview.io.DataSourceType; import jalview.io.FileFormat; import jalview.io.FormatAdapter; import jalview.util.MessageManager; import java.awt.Component; import java.io.IOException; import java.util.ArrayList; import java.util.List; import javax.swing.JMenu; import javax.swing.JMenuItem; import javax.swing.JPopupMenu; import javax.swing.JSeparator; import org.testng.annotations.BeforeClass; import org.testng.annotations.BeforeMethod; import org.testng.annotations.Test; public class PopupMenuTest { @BeforeClass(alwaysRun = true) public void setUpJvOptionPane() { JvOptionPane.setInteractiveMode(false); JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); } // 4 sequences x 13 positions final static String TEST_DATA = ">FER_CAPAA Ferredoxin\n" + "TIETHKEAELVG-\n" + ">FER_CAPAN Ferredoxin, chloroplast precursor\n" + "TIETHKEAELVG-\n" + ">FER1_SOLLC Ferredoxin-1, chloroplast precursor\n" + "TIETHKEEELTA-\n" + ">Q93XJ9_SOLTU Ferredoxin I precursor\n" + "TIETHKEEELTA-\n"; AlignmentI alignment; AlignmentPanel parentPanel; PopupMenu testee = null; @BeforeMethod(alwaysRun = true) public void setUp() throws IOException { alignment = new FormatAdapter().readFile(TEST_DATA, DataSourceType.PASTE, FileFormat.Fasta); AlignFrame af = new AlignFrame(alignment, 700, 500); parentPanel = new AlignmentPanel(af, af.getViewport()); testee = new PopupMenu(parentPanel, null, null); int i = 0; for (SequenceI seq : alignment.getSequences()) { final AlignmentAnnotation annotation = new AlignmentAnnotation( "label" + i, "desc" + i, i); annotation.setCalcId("calcId" + i); seq.addAlignmentAnnotation(annotation); annotation.setSequenceRef(seq); } } @Test(groups = { "Functional" }) public void testConfigureReferenceAnnotationsMenu_noSequenceSelected() { JMenuItem menu = new JMenuItem(); List seqs = new ArrayList(); testee.configureReferenceAnnotationsMenu(menu, seqs); assertFalse(menu.isEnabled()); // now try null list menu.setEnabled(true); testee.configureReferenceAnnotationsMenu(menu, null); assertFalse(menu.isEnabled()); } /** * Test building the 'add reference annotations' menu for the case where there * are no reference annotations to add to the alignment. The menu item should * be disabled. */ @Test(groups = { "Functional" }) public void testConfigureReferenceAnnotationsMenu_noReferenceAnnotations() { JMenuItem menu = new JMenuItem(); /* * Initial state is that sequences have annotations, and have dataset * sequences, but the dataset sequences have no annotations. Hence nothing * to add. */ List seqs = parentPanel.getAlignment().getSequences(); testee.configureReferenceAnnotationsMenu(menu, seqs); assertFalse(menu.isEnabled()); } /** * Test building the 'add reference annotations' menu for the case where all * reference annotations are already on the alignment. The menu item should be * disabled. */ @Test(groups = { "Functional" }) public void testConfigureReferenceAnnotationsMenu_alreadyAdded() { JMenuItem menu = new JMenuItem(); List seqs = parentPanel.getAlignment().getSequences(); // make up new annotations and add to dataset sequences, sequences and // alignment attachReferenceAnnotations(seqs, true, true); testee.configureReferenceAnnotationsMenu(menu, seqs); assertFalse(menu.isEnabled()); } /** * Test building the 'add reference annotations' menu for the case where * several reference annotations are on the dataset but not on the sequences. * The menu item should be enabled, and acquire a tooltip which lists the * annotation sources (calcIds) and type (labels). */ @Test(groups = { "Functional" }) public void testConfigureReferenceAnnotationsMenu() { JMenuItem menu = new JMenuItem(); List seqs = parentPanel.getAlignment().getSequences(); // make up new annotations and add to dataset sequences attachReferenceAnnotations(seqs, false, false); testee.configureReferenceAnnotationsMenu(menu, seqs); assertTrue(menu.isEnabled()); String s = MessageManager.getString("label.add_annotations_for"); String expected = "

" + s + "
Jmol/secondary structure
PDB/Temp

"; assertEquals(expected, menu.getToolTipText()); } /** * Test building the 'add reference annotations' menu for the case where * several reference annotations are on the dataset and the sequences but not * on the alignment. The menu item should be enabled, and acquire a tooltip * which lists the annotation sources (calcIds) and type (labels). */ @Test(groups = { "Functional" }) public void testConfigureReferenceAnnotationsMenu_notOnAlignment() { JMenuItem menu = new JMenuItem(); List seqs = parentPanel.getAlignment().getSequences(); // make up new annotations and add to dataset sequences and sequences attachReferenceAnnotations(seqs, true, false); testee.configureReferenceAnnotationsMenu(menu, seqs); assertTrue(menu.isEnabled()); String s = MessageManager.getString("label.add_annotations_for"); String expected = "

" + s + "
Jmol/secondary structure
PDB/Temp

"; assertEquals(expected, menu.getToolTipText()); } /** * Generate annotations and add to dataset sequences and (optionally) * sequences and/or alignment * * @param seqs * @param addToSequence * @param addToAlignment */ private void attachReferenceAnnotations(List seqs, boolean addToSequence, boolean addToAlignment) { // PDB.secondary structure on Sequence0 AlignmentAnnotation annotation = new AlignmentAnnotation( "secondary structure", "", 0); annotation.setCalcId("PDB"); seqs.get(0).getDatasetSequence().addAlignmentAnnotation(annotation); if (addToSequence) { seqs.get(0).addAlignmentAnnotation(annotation); } if (addToAlignment) { this.alignment.addAnnotation(annotation); } // PDB.Temp on Sequence1 annotation = new AlignmentAnnotation("Temp", "", 0); annotation.setCalcId("PDB"); seqs.get(1).getDatasetSequence().addAlignmentAnnotation(annotation); if (addToSequence) { seqs.get(1).addAlignmentAnnotation(annotation); } if (addToAlignment) { this.alignment.addAnnotation(annotation); } // JMOL.secondary structure on Sequence0 annotation = new AlignmentAnnotation("secondary structure", "", 0); annotation.setCalcId("Jmol"); seqs.get(0).getDatasetSequence().addAlignmentAnnotation(annotation); if (addToSequence) { seqs.get(0).addAlignmentAnnotation(annotation); } if (addToAlignment) { this.alignment.addAnnotation(annotation); } } /** * Test building the 'add reference annotations' menu for the case where there * are two alignment views: *
    *
  • in one view, reference annotations have been added (are on the * datasets, sequences and alignment)
  • *
  • in the current view, reference annotations are on the dataset and * sequence, but not the alignment
  • *
* The menu item should be enabled, and acquire a tooltip which lists the * annotation sources (calcIds) and type (labels). */ @Test(groups = { "Functional" }) public void testConfigureReferenceAnnotationsMenu_twoViews() { } /** * Test for building menu options including 'show' and 'hide' annotation * types. */ @Test(groups = { "Functional" }) public void testBuildAnnotationTypesMenus() { JMenu showMenu = new JMenu(); JMenu hideMenu = new JMenu(); List seqs = parentPanel.getAlignment().getSequences(); // make up new annotations and add to sequences and to the alignment // PDB.secondary structure on Sequence0 AlignmentAnnotation annotation = new AlignmentAnnotation( "secondary structure", "", new Annotation[] {}); annotation.setCalcId("PDB"); annotation.visible = true; seqs.get(0).addAlignmentAnnotation(annotation); parentPanel.getAlignment().addAnnotation(annotation); // JMOL.secondary structure on Sequence0 - hidden annotation = new AlignmentAnnotation("secondary structure", "", new Annotation[] {}); annotation.setCalcId("JMOL"); annotation.visible = false; seqs.get(0).addAlignmentAnnotation(annotation); parentPanel.getAlignment().addAnnotation(annotation); // Jpred.SSP on Sequence0 - hidden annotation = new AlignmentAnnotation("SSP", "", new Annotation[] {}); annotation.setCalcId("JPred"); annotation.visible = false; seqs.get(0).addAlignmentAnnotation(annotation); parentPanel.getAlignment().addAnnotation(annotation); // PDB.Temp on Sequence1 annotation = new AlignmentAnnotation("Temp", "", new Annotation[] {}); annotation.setCalcId("PDB"); annotation.visible = true; seqs.get(1).addAlignmentAnnotation(annotation); parentPanel.getAlignment().addAnnotation(annotation); /* * Expect menu options to show "secondary structure" and "SSP", and to hide * "secondary structure" and "Temp". Tooltip should be calcId. */ testee.buildAnnotationTypesMenus(showMenu, hideMenu, seqs); assertTrue(showMenu.isEnabled()); assertTrue(hideMenu.isEnabled()); Component[] showOptions = showMenu.getMenuComponents(); Component[] hideOptions = hideMenu.getMenuComponents(); assertEquals(4, showOptions.length); // includes 'All' and separator assertEquals(4, hideOptions.length); String all = MessageManager.getString("label.all"); assertEquals(all, ((JMenuItem) showOptions[0]).getText()); assertTrue(showOptions[1] instanceof JPopupMenu.Separator); assertEquals(JSeparator.HORIZONTAL, ((JSeparator) showOptions[1]).getOrientation()); assertEquals("secondary structure", ((JMenuItem) showOptions[2]).getText()); assertEquals("JMOL", ((JMenuItem) showOptions[2]).getToolTipText()); assertEquals("SSP", ((JMenuItem) showOptions[3]).getText()); assertEquals("JPred", ((JMenuItem) showOptions[3]).getToolTipText()); assertEquals(all, ((JMenuItem) hideOptions[0]).getText()); assertTrue(hideOptions[1] instanceof JPopupMenu.Separator); assertEquals(JSeparator.HORIZONTAL, ((JSeparator) hideOptions[1]).getOrientation()); assertEquals("secondary structure", ((JMenuItem) hideOptions[2]).getText()); assertEquals("PDB", ((JMenuItem) hideOptions[2]).getToolTipText()); assertEquals("Temp", ((JMenuItem) hideOptions[3]).getText()); assertEquals("PDB", ((JMenuItem) hideOptions[3]).getToolTipText()); } /** * Test for building menu options with only 'hide' annotation types enabled. */ @Test(groups = { "Functional" }) public void testBuildAnnotationTypesMenus_showDisabled() { JMenu showMenu = new JMenu(); JMenu hideMenu = new JMenu(); List seqs = parentPanel.getAlignment().getSequences(); // make up new annotations and add to sequences and to the alignment // PDB.secondary structure on Sequence0 AlignmentAnnotation annotation = new AlignmentAnnotation( "secondary structure", "", new Annotation[] {}); annotation.setCalcId("PDB"); annotation.visible = true; seqs.get(0).addAlignmentAnnotation(annotation); parentPanel.getAlignment().addAnnotation(annotation); // PDB.Temp on Sequence1 annotation = new AlignmentAnnotation("Temp", "", new Annotation[] {}); annotation.setCalcId("PDB"); annotation.visible = true; seqs.get(1).addAlignmentAnnotation(annotation); parentPanel.getAlignment().addAnnotation(annotation); /* * Expect menu options to hide "secondary structure" and "Temp". Tooltip * should be calcId. 'Show' menu should be disabled. */ testee.buildAnnotationTypesMenus(showMenu, hideMenu, seqs); assertFalse(showMenu.isEnabled()); assertTrue(hideMenu.isEnabled()); Component[] showOptions = showMenu.getMenuComponents(); Component[] hideOptions = hideMenu.getMenuComponents(); assertEquals(2, showOptions.length); // includes 'All' and separator assertEquals(4, hideOptions.length); String all = MessageManager.getString("label.all"); assertEquals(all, ((JMenuItem) showOptions[0]).getText()); assertTrue(showOptions[1] instanceof JPopupMenu.Separator); assertEquals(JSeparator.HORIZONTAL, ((JSeparator) showOptions[1]).getOrientation()); assertEquals(all, ((JMenuItem) hideOptions[0]).getText()); assertTrue(hideOptions[1] instanceof JPopupMenu.Separator); assertEquals(JSeparator.HORIZONTAL, ((JSeparator) hideOptions[1]).getOrientation()); assertEquals("secondary structure", ((JMenuItem) hideOptions[2]).getText()); assertEquals("PDB", ((JMenuItem) hideOptions[2]).getToolTipText()); assertEquals("Temp", ((JMenuItem) hideOptions[3]).getText()); assertEquals("PDB", ((JMenuItem) hideOptions[3]).getToolTipText()); } /** * Test for building menu options with only 'show' annotation types enabled. */ @Test(groups = { "Functional" }) public void testBuildAnnotationTypesMenus_hideDisabled() { JMenu showMenu = new JMenu(); JMenu hideMenu = new JMenu(); List seqs = parentPanel.getAlignment().getSequences(); // make up new annotations and add to sequences and to the alignment // PDB.secondary structure on Sequence0 AlignmentAnnotation annotation = new AlignmentAnnotation( "secondary structure", "", new Annotation[] {}); annotation.setCalcId("PDB"); annotation.visible = false; seqs.get(0).addAlignmentAnnotation(annotation); parentPanel.getAlignment().addAnnotation(annotation); // PDB.Temp on Sequence1 annotation = new AlignmentAnnotation("Temp", "", new Annotation[] {}); annotation.setCalcId("PDB2"); annotation.visible = false; seqs.get(1).addAlignmentAnnotation(annotation); parentPanel.getAlignment().addAnnotation(annotation); /* * Expect menu options to show "secondary structure" and "Temp". Tooltip * should be calcId. 'hide' menu should be disabled. */ testee.buildAnnotationTypesMenus(showMenu, hideMenu, seqs); assertTrue(showMenu.isEnabled()); assertFalse(hideMenu.isEnabled()); Component[] showOptions = showMenu.getMenuComponents(); Component[] hideOptions = hideMenu.getMenuComponents(); assertEquals(4, showOptions.length); // includes 'All' and separator assertEquals(2, hideOptions.length); String all = MessageManager.getString("label.all"); assertEquals(all, ((JMenuItem) showOptions[0]).getText()); assertTrue(showOptions[1] instanceof JPopupMenu.Separator); assertEquals(JSeparator.HORIZONTAL, ((JSeparator) showOptions[1]).getOrientation()); assertEquals("secondary structure", ((JMenuItem) showOptions[2]).getText()); assertEquals("PDB", ((JMenuItem) showOptions[2]).getToolTipText()); assertEquals("Temp", ((JMenuItem) showOptions[3]).getText()); assertEquals("PDB2", ((JMenuItem) showOptions[3]).getToolTipText()); assertEquals(all, ((JMenuItem) hideOptions[0]).getText()); assertTrue(hideOptions[1] instanceof JPopupMenu.Separator); assertEquals(JSeparator.HORIZONTAL, ((JSeparator) hideOptions[1]).getOrientation()); } /** * Test for adding feature links */ @Test(groups = { "Functional" }) public void testAddFeatureLinks() { // sequences from the alignment List seqs = parentPanel.getAlignment().getSequences(); // create list of links and list of DBRefs List links = new ArrayList(); List refs = new ArrayList(); // links as might be added into Preferences | Connections dialog links.add("EMBL-EBI Search | http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$" + SEQUENCE_ID + "$"); links.add("UNIPROT | http://www.uniprot.org/uniprot/$" + DB_ACCESSION + "$"); links.add("INTERPRO | http://www.ebi.ac.uk/interpro/entry/$" + DB_ACCESSION + "$"); // Gene3D entry tests for case (in)sensitivity links.add("Gene3D | http://gene3d.biochem.ucl.ac.uk/Gene3D/search?sterm=$" + DB_ACCESSION + "$&mode=protein"); // make seq0 dbrefs refs.add(new DBRefEntry(DBRefSource.UNIPROT, "1", "P83527")); refs.add(new DBRefEntry("INTERPRO", "1", "IPR001041")); refs.add(new DBRefEntry("INTERPRO", "1", "IPR006058")); refs.add(new DBRefEntry("INTERPRO", "1", "IPR012675")); // make seq1 dbrefs refs.add(new DBRefEntry(DBRefSource.UNIPROT, "1", "Q9ZTS2")); refs.add(new DBRefEntry("GENE3D", "1", "3.10.20.30")); // add all the dbrefs to the sequences: Uniprot 1 each, Interpro all 3 to // seq0, Gene3D to seq1 seqs.get(0).addDBRef(refs.get(0)); seqs.get(0).addDBRef(refs.get(1)); seqs.get(0).addDBRef(refs.get(2)); seqs.get(0).addDBRef(refs.get(3)); seqs.get(1).addDBRef(refs.get(4)); seqs.get(1).addDBRef(refs.get(5)); // get the Popup Menu for first sequence testee = new PopupMenu(parentPanel, (Sequence) seqs.get(0), links); Component[] seqItems = testee.sequenceMenu.getMenuComponents(); JMenu linkMenu = (JMenu) seqItems[6]; Component[] linkItems = linkMenu.getMenuComponents(); // check the number of links are the expected number assertEquals(5, linkItems.length); // first entry is EMBL-EBI which just uses sequence id not accession id? assertEquals("EMBL-EBI Search", ((JMenuItem) linkItems[0]).getText()); // sequence id for each link should match corresponding DB accession id for (int i = 1; i < 4; i++) { assertEquals(refs.get(i - 1).getSource(), ((JMenuItem) linkItems[i]) .getText().split("\\|")[0]); assertEquals(refs.get(i - 1).getAccessionId(), ((JMenuItem) linkItems[i]) .getText().split("\\|")[1]); } // get the Popup Menu for second sequence testee = new PopupMenu(parentPanel, (Sequence) seqs.get(1), links); seqItems = testee.sequenceMenu.getMenuComponents(); linkMenu = (JMenu) seqItems[6]; linkItems = linkMenu.getMenuComponents(); // check the number of links are the expected number assertEquals(3, linkItems.length); // first entry is EMBL-EBI which just uses sequence id not accession id? assertEquals("EMBL-EBI Search", ((JMenuItem) linkItems[0]).getText()); // sequence id for each link should match corresponding DB accession id for (int i = 1; i < 3; i++) { assertEquals(refs.get(i + 3).getSource(), ((JMenuItem) linkItems[i]) .getText().split("\\|")[0].toUpperCase()); assertEquals(refs.get(i + 3).getAccessionId(), ((JMenuItem) linkItems[i]).getText().split("\\|")[1]); } // if there are no valid links the Links submenu is disabled List nomatchlinks = new ArrayList(); nomatchlinks.add("NOMATCH | http://www.uniprot.org/uniprot/$" + DB_ACCESSION + "$"); testee = new PopupMenu(parentPanel, (Sequence) seqs.get(0), nomatchlinks); seqItems = testee.sequenceMenu.getMenuComponents(); linkMenu = (JMenu) seqItems[6]; assertFalse(linkMenu.isEnabled()); } }