+/*
+ * 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.gui;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertTrue;
+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.bin.Cache;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
-import jalview.io.AppletFormatAdapter;
-
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
+import jalview.io.FormatAdapter;
+import jalview.urls.api.UrlProviderFactoryI;
+import jalview.urls.desktop.DesktopUrlProviderFactory;
+import jalview.util.MessageManager;
+import jalview.util.UrlConstants;
+
+import java.awt.Component;
import java.io.IOException;
-import java.util.BitSet;
-import java.util.HashMap;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.Iterator;
import java.util.List;
-import java.util.Map;
-import org.junit.Before;
-import org.junit.Test;
+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;
-/**
- * Unit tests for PopupMenu
- *
- * @author gmcarstairs
- *
- */
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"
+ "TIETHKEEELTA-\n" + ">Q93XJ9_SOLTU Ferredoxin I precursor\n"
+ "TIETHKEEELTA-\n";
- private static final int SEQ_ANN_COUNT = 10;
-
- private static final int AUTO_ANNS = 3;
-
AlignmentI alignment;
AlignmentPanel parentPanel;
- @Before
+ PopupMenu testee = null;
+
+ @BeforeMethod(alwaysRun = true)
public void setUp() throws IOException
{
- AlignmentI al = new jalview.io.FormatAdapter().readFile(TEST_DATA,
- AppletFormatAdapter.PASTE, "FASTA");
- AlignFrame af = new AlignFrame(al, 700, 500);
+ Cache.loadProperties("test/jalview/io/testProps.jvprops");
+ String inMenuString = ("EMBL-EBI Search | http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$"
+ + SEQUENCE_ID
+ + "$"
+ + "|"
+ + "UNIPROT | http://www.uniprot.org/uniprot/$" + DB_ACCESSION + "$")
+ + "|"
+ + ("INTERPRO | http://www.ebi.ac.uk/interpro/entry/$"
+ + DB_ACCESSION + "$")
+ + "|"
+ +
+ // Gene3D entry tests for case (in)sensitivity
+ ("Gene3D | http://gene3d.biochem.ucl.ac.uk/Gene3D/search?sterm=$"
+ + DB_ACCESSION + "$&mode=protein");
+
+ UrlProviderFactoryI factory = new DesktopUrlProviderFactory(
+ UrlConstants.DEFAULT_LABEL, inMenuString, "");
+ Preferences.sequenceUrlLinks = factory.createUrlProvider();
+
+ alignment = new FormatAdapter().readFile(TEST_DATA,
+ DataSourceType.PASTE, FileFormat.Fasta);
+ AlignFrame af = new AlignFrame(alignment, 700, 500);
parentPanel = new AlignmentPanel(af, af.getViewport());
- alignment = parentPanel.getAlignment();
-
- AlignmentAnnotation[] anns = new AlignmentAnnotation[SEQ_ANN_COUNT];
- for (int i = 0; i < anns.length; i++)
+ testee = new PopupMenu(parentPanel, null, null);
+ int i = 0;
+ for (SequenceI seq : alignment.getSequences())
{
- anns[i] = new AlignmentAnnotation("Label" + i, null, 0d);
- anns[i].setCalcId("CalcId" + i);
- anns[i].visible = true;
- alignment.addAnnotation(anns[i]);
+ 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<SequenceI> 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 method that determines visible graph groups.
+ * 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
- public void testGetVisibleGraphGroups()
+ @Test(groups = { "Functional" })
+ public void testConfigureReferenceAnnotationsMenu_noReferenceAnnotations()
{
- AlignmentAnnotation[] anns = alignment.getAlignmentAnnotation();
- /*
- * a bar graph group is not included
- */
- anns[0].graph = AlignmentAnnotation.BAR_GRAPH;
- anns[0].graphGroup = 1;
- anns[0].visible = true;
+ JMenuItem menu = new JMenuItem();
/*
- * a line graph group is included as long as one of its members is visible
+ * Initial state is that sequences have annotations, and have dataset
+ * sequences, but the dataset sequences have no annotations. Hence nothing
+ * to add.
*/
- anns[1].graph = AlignmentAnnotation.LINE_GRAPH;
- anns[1].graphGroup = 5;
- anns[1].visible = false;
- anns[2].graph = AlignmentAnnotation.LINE_GRAPH;
- anns[2].graphGroup = 5;
- anns[2].visible = true;
+ List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
- /*
- * a line graph group with no visible rows is not included
- */
- anns[3].graph = AlignmentAnnotation.LINE_GRAPH;
- anns[3].graphGroup = 3;
- anns[3].visible = false;
-
- // a visible line graph with no graph group is not included
- anns[4].graph = AlignmentAnnotation.LINE_GRAPH;
- anns[4].graphGroup = -1;
- anns[4].visible = true;
-
- BitSet result = PopupMenu.getVisibleLineGraphGroups(anns);
- assertTrue(result.get(5));
- assertFalse(result.get(0));
- assertFalse(result.get(1));
- assertFalse(result.get(2));
- assertFalse(result.get(3));
+ testee.configureReferenceAnnotationsMenu(menu, seqs);
+ assertFalse(menu.isEnabled());
}
/**
- * Test a mixture of show/hidden annotations in/outside selection group.
+ * 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
- public void testGetAnnotationTypesForShowHide_forSelectionGroup()
+ @Test(groups = { "Functional" })
+ public void testConfigureReferenceAnnotationsMenu_alreadyAdded()
{
- Map<String, List<List<String>>> shownTypes = new HashMap<String, List<List<String>>>();
- Map<String, List<List<String>>> hiddenTypes = new HashMap<String, List<List<String>>>();
- AlignmentAnnotation[] anns = alignment.getAlignmentAnnotation();
- BitSet visibleGraphGroups = new BitSet();
- selectSequences(0, 3);
- SequenceI[] seqs = parentPanel.getAlignment().getSequencesArray();
+ JMenuItem menu = new JMenuItem();
+ List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
- /*
- * Configure annotation properties for test (offsetting for auto-calculated
- * rows).
- */
- // not in selection group (should be ignored):
- // hidden annotation Label4 not in selection group
- anns[AUTO_ANNS + 4].sequenceRef = seqs[2];
- anns[AUTO_ANNS + 4].visible = false;
- anns[AUTO_ANNS + 7].sequenceRef = seqs[1];
- anns[AUTO_ANNS + 7].visible = true;
+ // make up new annotations and add to dataset sequences, sequences and
+ // alignment
+ attachReferenceAnnotations(seqs, true, true);
- /*
- * in selection group, hidden:
- */
- anns[AUTO_ANNS + 2].sequenceRef = seqs[3]; // CalcId2/Label2
- anns[AUTO_ANNS + 2].visible = false;
- anns[AUTO_ANNS + 3].sequenceRef = seqs[3]; // CalcId3/Label2
- anns[AUTO_ANNS + 3].visible = false;
- anns[AUTO_ANNS + 3].label = "Label2";
- anns[AUTO_ANNS + 4].sequenceRef = seqs[3]; // CalcId2/Label3
- anns[AUTO_ANNS + 4].visible = false;
- anns[AUTO_ANNS + 4].label = "Label3";
- anns[AUTO_ANNS + 4].setCalcId("CalcId2");
- anns[AUTO_ANNS + 8].sequenceRef = seqs[0]; // CalcId9/Label9
- anns[AUTO_ANNS + 8].visible = false;
- anns[AUTO_ANNS + 8].label = "Label9";
- anns[AUTO_ANNS + 8].setCalcId("CalcId9");
- /*
- * in selection group, visible
- */
- anns[AUTO_ANNS + 6].sequenceRef = seqs[0]; // CalcId6/Label6
- anns[AUTO_ANNS + 6].visible = true;
- anns[AUTO_ANNS + 9].sequenceRef = seqs[3]; // CalcId9/Label9
- anns[AUTO_ANNS + 9].visible = true;
-
- PopupMenu.getAnnotationTypesForShowHide(shownTypes, hiddenTypes,
- visibleGraphGroups, anns, parentPanel.av.getSelectionGroup());
-
- // check results; note CalcId9/Label9 is both hidden and shown (for
- // different sequences) so should be in both
- // shown: CalcId6/Label6 and CalcId9/Label9
- assertEquals(2, shownTypes.size());
- assertEquals(1, shownTypes.get("CalcId6").size());
- assertEquals(1, shownTypes.get("CalcId6").get(0).size());
- assertEquals("Label6", shownTypes.get("CalcId6").get(0).get(0));
- assertEquals(1, shownTypes.get("CalcId9").size());
- assertEquals(1, shownTypes.get("CalcId9").get(0).size());
- assertEquals("Label9", shownTypes.get("CalcId9").get(0).get(0));
-
- // hidden: CalcId2/Label2, CalcId2/Label3, CalcId3/Label2, CalcId9/Label9
- assertEquals(3, hiddenTypes.size());
- assertEquals(2, hiddenTypes.get("CalcId2").size());
- assertEquals(1, hiddenTypes.get("CalcId2").get(0).size());
- assertEquals("Label2", hiddenTypes.get("CalcId2").get(0).get(0));
- assertEquals(1, hiddenTypes.get("CalcId2").get(1).size());
- assertEquals("Label3", hiddenTypes.get("CalcId2").get(1).get(0));
- assertEquals(1, hiddenTypes.get("CalcId3").size());
- assertEquals(1, hiddenTypes.get("CalcId3").get(0).size());
- assertEquals("Label2", hiddenTypes.get("CalcId3").get(0).get(0));
- assertEquals(1, hiddenTypes.get("CalcId9").size());
- assertEquals(1, hiddenTypes.get("CalcId9").get(0).size());
- assertEquals("Label9", hiddenTypes.get("CalcId9").get(0).get(0));
-
- consoleDebug(shownTypes, hiddenTypes);
+ 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<SequenceI> 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 = "<html><style> p.ttip {width: 350; text-align: justify; word-wrap: break-word;}</style><p class=\"ttip\">"
+ + s + "<br/>Jmol/secondary structure<br/>PDB/Temp</p></html>";
+ assertEquals(expected, menu.getToolTipText());
}
/**
- * This output is not part of the test but may help make sense of it...
+ * 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<SequenceI> 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 = "<html><style> p.ttip {width: 350; text-align: justify; word-wrap: break-word;}</style><p class=\"ttip\">"
+ + s + "<br/>Jmol/secondary structure<br/>PDB/Temp</p></html>";
+ assertEquals(expected, menu.getToolTipText());
+ }
+
+ /**
+ * Generate annotations and add to dataset sequences and (optionally)
+ * sequences and/or alignment
*
- * @param shownTypes
- * @param hiddenTypes
+ * @param seqs
+ * @param addToSequence
+ * @param addToAlignment
*/
- protected void consoleDebug(Map<String, List<List<String>>> shownTypes,
- Map<String, List<List<String>>> hiddenTypes)
+ private void attachReferenceAnnotations(List<SequenceI> seqs,
+ boolean addToSequence, boolean addToAlignment)
{
- for (String calcId : shownTypes.keySet())
+ // PDB.secondary structure on Sequence0
+ AlignmentAnnotation annotation = new AlignmentAnnotation(
+ "secondary structure", "", 0);
+ annotation.setCalcId("PDB");
+ seqs.get(0).getDatasetSequence().addAlignmentAnnotation(annotation);
+ if (addToSequence)
{
- System.out.println("Visible annotation types for calcId=" + calcId);
- for (List<String> type : shownTypes.get(calcId))
- {
- System.out.println(" " + type);
- }
+ seqs.get(0).addAlignmentAnnotation(annotation);
}
- for (String calcId : hiddenTypes.keySet())
+ if (addToAlignment)
{
- System.out.println("Hidden annotation types for calcId=" + calcId);
- for (List<String> type : hiddenTypes.get(calcId))
- {
- System.out.println(" " + type);
- }
+ 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:
+ * <ul>
+ * <li>in one view, reference annotations have been added (are on the
+ * datasets, sequences and alignment)</li>
+ * <li>in the current view, reference annotations are on the dataset and
+ * sequence, but not the alignment</li>
+ * </ul>
+ * 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 case where there are 'grouped' annotations, visible and hidden, within
- * and without the selection group.
+ * Test for building menu options including 'show' and 'hide' annotation
+ * types.
*/
- @Test
- public void testGetAnnotationTypesForShowHide_withGraphGroups()
+ @Test(groups = { "Functional" })
+ public void testBuildAnnotationTypesMenus()
{
- final int GROUP_4 = 4;
- final int GROUP_5 = 5;
- final int GROUP_6 = 6;
-
- Map<String, List<List<String>>> shownTypes = new HashMap<String, List<List<String>>>();
- Map<String, List<List<String>>> hiddenTypes = new HashMap<String, List<List<String>>>();
- AlignmentAnnotation[] anns = alignment.getAlignmentAnnotation();
- BitSet visibleGraphGroups = new BitSet();
- visibleGraphGroups.set(GROUP_4);
- visibleGraphGroups.set(GROUP_6);
- selectSequences(0, 3);
- SequenceI[] seqs = parentPanel.getAlignment().getSequencesArray();
+ JMenu showMenu = new JMenu();
+ JMenu hideMenu = new JMenu();
+ List<SequenceI> 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);
/*
- * Configure annotation properties for test (offsetting for auto-calculated
- * rows).
+ * Expect menu options to show "secondary structure" and "SSP", and to hide
+ * "secondary structure" and "Temp". Tooltip should be calcId.
*/
- // annotations for selection group and graph group
- // hidden annotations Label2, Label3, in (hidden) group 5
- anns[AUTO_ANNS + 2].sequenceRef = seqs[3];
- anns[AUTO_ANNS + 2].visible = false;
- anns[AUTO_ANNS + 2].graph = AlignmentAnnotation.LINE_GRAPH;
- anns[AUTO_ANNS + 2].graphGroup = GROUP_5; // not a visible group
- anns[AUTO_ANNS + 3].sequenceRef = seqs[0];
- anns[AUTO_ANNS + 3].visible = false;
- anns[AUTO_ANNS + 3].graph = AlignmentAnnotation.LINE_GRAPH;
- anns[AUTO_ANNS + 3].graphGroup = GROUP_5;
- // need to ensure annotations have the same calcId as well
- anns[AUTO_ANNS + 3].setCalcId("CalcId2");
-
- // annotations Label1 (hidden), Label5 (visible) in group 6 (visible)
- anns[AUTO_ANNS + 1].sequenceRef = seqs[3];
- // being in a visible group should take precedence over this visibility
- anns[AUTO_ANNS + 1].visible = false;
- anns[AUTO_ANNS + 1].graph = AlignmentAnnotation.LINE_GRAPH;
- anns[AUTO_ANNS + 1].graphGroup = GROUP_6;
- anns[AUTO_ANNS + 5].sequenceRef = seqs[0];
- anns[AUTO_ANNS + 5].visible = true; // visibleGraphGroups overrides this
- anns[AUTO_ANNS + 5].graph = AlignmentAnnotation.LINE_GRAPH;
- anns[AUTO_ANNS + 5].graphGroup = GROUP_6;
- anns[AUTO_ANNS + 5].setCalcId("CalcId1");
-
- // annotations outwith selection group - should be ignored
- // hidden grouped annotations
- anns[AUTO_ANNS + 6].sequenceRef = seqs[2];
- anns[AUTO_ANNS + 6].visible = false;
- anns[AUTO_ANNS + 6].graph = AlignmentAnnotation.LINE_GRAPH;
- anns[AUTO_ANNS + 6].graphGroup = GROUP_4;
- anns[AUTO_ANNS + 8].sequenceRef = seqs[1];
- anns[AUTO_ANNS + 8].visible = false;
- anns[AUTO_ANNS + 8].graph = AlignmentAnnotation.LINE_GRAPH;
- anns[AUTO_ANNS + 8].graphGroup = GROUP_4;
- // visible grouped annotations Label7, Label9
- anns[AUTO_ANNS + 7].sequenceRef = seqs[2];
- anns[AUTO_ANNS + 7].visible = true;
- anns[AUTO_ANNS + 7].graph = AlignmentAnnotation.LINE_GRAPH;
- anns[AUTO_ANNS + 7].graphGroup = GROUP_4;
- anns[AUTO_ANNS + 9].sequenceRef = seqs[1];
- anns[AUTO_ANNS + 9].visible = true;
- anns[AUTO_ANNS + 9].graph = AlignmentAnnotation.LINE_GRAPH;
- anns[AUTO_ANNS + 9].graphGroup = GROUP_4;
-
- PopupMenu.getAnnotationTypesForShowHide(shownTypes, hiddenTypes,
- visibleGraphGroups, anns, parentPanel.av.getSelectionGroup());
-
- consoleDebug(shownTypes, hiddenTypes);
-
- // CalcId1 / Label1, Label5 (only) should be 'shown', as a compound type
- assertEquals(1, shownTypes.get("CalcId1").size());
- assertEquals(2, shownTypes.get("CalcId1").get(0).size());
- assertEquals("Label1", shownTypes.get("CalcId1").get(0).get(0));
- assertEquals("Label5", shownTypes.get("CalcId1").get(0).get(1));
-
- // CalcId2 / Label2, Label3 (only) should be 'hidden'
- assertEquals(1, hiddenTypes.get("CalcId2").size());
- assertEquals(2, hiddenTypes.get("CalcId2").get(0).size());
- assertEquals("Label2", hiddenTypes.get("CalcId2").get(0).get(0));
- assertEquals("Label3", hiddenTypes.get("CalcId2").get(0).get(1));
+ 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());
}
/**
- * Add a sequence group to the alignment with the specified sequences (base 0)
- * in it
- *
- * @param i
- * @param more
+ * Test for building menu options with only 'hide' annotation types enabled.
*/
- private void selectSequences(int... selected)
+ @Test(groups = { "Functional" })
+ public void testBuildAnnotationTypesMenus_showDisabled()
{
- SequenceI[] seqs = parentPanel.getAlignment().getSequencesArray();
- SequenceGroup sg = new SequenceGroup();
- for (int i : selected)
+ JMenu showMenu = new JMenu();
+ JMenu hideMenu = new JMenu();
+ List<SequenceI> 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<SequenceI> 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<SequenceI> seqs = parentPanel.getAlignment().getSequences();
+
+ // create list of links and list of DBRefs
+ List<String> links = new ArrayList<>();
+ List<DBRefEntry> 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
+ SequenceI seq = seqs.get(0);
+ seq.addDBRef(refs.get(0));
+
+ seq.addDBRef(refs.get(1));
+ seq.addDBRef(refs.get(2));
+ seq.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
+ List<SequenceFeature> noFeatures = Collections.<SequenceFeature> emptyList();
+ testee = new PopupMenu(parentPanel, seq, noFeatures);
+ 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++)
{
- sg.addSequence(seqs[i], false);
+ String msg = seq.getName() + " link[" + i + "]";
+ assertEquals(msg, refs.get(i - 1).getSource(),
+ ((JMenuItem) linkItems[i])
+ .getText().split("\\|")[0]);
+ assertEquals(msg, refs.get(i - 1).getAccessionId(),
+ ((JMenuItem) linkItems[i])
+ .getText().split("\\|")[1]);
}
+
+ // get the Popup Menu for second sequence
+ seq = seqs.get(1);
+ testee = new PopupMenu(parentPanel, seq, noFeatures);
+ 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++)
+ {
+ String msg = seq.getName() + " link[" + i + "]";
+ assertEquals(msg, refs.get(i + 3).getSource(),
+ ((JMenuItem) linkItems[i])
+ .getText().split("\\|")[0].toUpperCase());
+ assertEquals(msg, refs.get(i + 3).getAccessionId(),
+ ((JMenuItem) linkItems[i]).getText().split("\\|")[1]);
+ }
+
+ // if there are no valid links the Links submenu is disabled
+ List<String> nomatchlinks = new ArrayList<>();
+ nomatchlinks.add("NOMATCH | http://www.uniprot.org/uniprot/$"
+ + DB_ACCESSION + "$");
+
+ testee = new PopupMenu(parentPanel, seq, noFeatures);
+ seqItems = testee.sequenceMenu.getMenuComponents();
+ linkMenu = (JMenu) seqItems[6];
+ assertFalse(linkMenu.isEnabled());
+
+ }
+
+ /**
+ * Test for adding feature links
+ */
+ @Test(groups = { "Functional" })
+ public void testHideInsertions()
+ {
+ // get sequences from the alignment
+ List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
+
+ // add our own seqs to avoid problems with changes to existing sequences
+ // (gap at end of sequences varies depending on how tests are run!)
+ Sequence seqGap1 = new Sequence("GappySeq",
+ "AAAA----AA-AAAAAAA---AAA-----------AAAAAAAAAA--");
+ seqGap1.createDatasetSequence();
+ seqs.add(seqGap1);
+ Sequence seqGap2 = new Sequence("LessGappySeq",
+ "AAAAAA-AAAAA---AAA--AAAAA--AAAAAAA-AAAAAA");
+ seqGap2.createDatasetSequence();
+ seqs.add(seqGap2);
+ Sequence seqGap3 = new Sequence("AnotherGapSeq",
+ "AAAAAA-AAAAAA--AAAAAA-AAAAAAAAAAA---AAAAAAAA");
+ seqGap3.createDatasetSequence();
+ seqs.add(seqGap3);
+ Sequence seqGap4 = new Sequence("NoGaps",
+ "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA");
+ seqGap4.createDatasetSequence();
+ seqs.add(seqGap4);
+
+ ColumnSelection sel = new ColumnSelection();
+ parentPanel.av.getAlignment().getHiddenColumns()
+ .revealAllHiddenColumns(sel);
+
+ // get the Popup Menu for 7th sequence - no insertions
+ testee = new PopupMenu(parentPanel, seqs.get(7), null);
+ testee.hideInsertions_actionPerformed(null);
+
+ HiddenColumns hidden = parentPanel.av.getAlignment().getHiddenColumns();
+ Iterator<int[]> it = hidden.iterator();
+ assertFalse(it.hasNext());
+
+ // get the Popup Menu for GappySeq - this time we have insertions
+ testee = new PopupMenu(parentPanel, seqs.get(4), null);
+ testee.hideInsertions_actionPerformed(null);
+ hidden = parentPanel.av.getAlignment().getHiddenColumns();
+ it = hidden.iterator();
+
+ assertTrue(it.hasNext());
+ int[] region = it.next();
+ assertEquals(region[0], 4);
+ assertEquals(region[1], 7);
+
+ assertTrue(it.hasNext());
+ region = it.next();
+ assertEquals(region[0], 10);
+ assertEquals(region[1], 10);
+
+ assertTrue(it.hasNext());
+ region = it.next();
+ assertEquals(region[0], 18);
+ assertEquals(region[1], 20);
+
+ assertTrue(it.hasNext());
+ region = it.next();
+ assertEquals(region[0], 24);
+ assertEquals(region[1], 34);
+
+ assertTrue(it.hasNext());
+ region = it.next();
+ assertEquals(region[0], 45);
+ assertEquals(region[1], 46);
+
+ assertFalse(it.hasNext());
+
+ sel = new ColumnSelection();
+ hidden.revealAllHiddenColumns(sel);
+
+ // make a sequence group and hide insertions within the group
+ SequenceGroup sg = new SequenceGroup();
+ sg.setStartRes(8);
+ sg.setEndRes(42);
+ sg.addSequence(seqGap2, false);
+ sg.addSequence(seqGap3, false);
parentPanel.av.setSelectionGroup(sg);
+
+ // hide columns outside and within selection
+ // only hidden columns outside the collection will be retained (unless also
+ // gaps in the selection)
+ hidden.hideColumns(1, 10);
+ hidden.hideColumns(31, 40);
+
+ // get the Popup Menu for LessGappySeq in the sequence group
+ testee = new PopupMenu(parentPanel, seqs.get(5), null);
+ testee.hideInsertions_actionPerformed(null);
+ hidden = parentPanel.av.getAlignment().getHiddenColumns();
+ it = hidden.iterator();
+
+ assertTrue(it.hasNext());
+ region = it.next();
+ assertEquals(region[0], 1);
+ assertEquals(region[1], 7);
+
+ assertTrue(it.hasNext());
+ region = it.next();
+ assertEquals(region[0], 13);
+ assertEquals(region[1], 14);
+
+ assertTrue(it.hasNext());
+ region = it.next();
+ assertEquals(region[0], 34);
+ assertEquals(region[1], 34);
}
+
}
git://source.jalview.org / jalview.git / blobdiff