+/*
+ * 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 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 javax.swing.JPopupMenu;
import javax.swing.JSeparator;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.Annotation;
-import jalview.datamodel.SequenceI;
-import jalview.io.AppletFormatAdapter;
-import jalview.io.FormatAdapter;
-
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"
PopupMenu testee = null;
- @BeforeMethod
+ @BeforeMethod(alwaysRun = true)
public void setUp() throws IOException
{
alignment = new FormatAdapter().readFile(TEST_DATA,
- AppletFormatAdapter.PASTE, "FASTA");
+ 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);
+ final AlignmentAnnotation annotation = new AlignmentAnnotation(
+ "label" + i, "desc" + i, i);
annotation.setCalcId("calcId" + i);
seq.addAlignmentAnnotation(annotation);
annotation.setSequenceRef(seq);
}
}
- @Test
+ @Test(groups = { "Functional" })
public void testConfigureReferenceAnnotationsMenu_noSequenceSelected()
{
JMenuItem menu = new JMenuItem();
* are no reference annotations to add to the alignment. The menu item should
* be disabled.
*/
- @Test
+ @Test(groups = { "Functional" })
public void testConfigureReferenceAnnotationsMenu_noReferenceAnnotations()
{
JMenuItem menu = new JMenuItem();
* reference annotations are already on the alignment. The menu item should be
* disabled.
*/
- @Test
+ @Test(groups = { "Functional" })
public void testConfigureReferenceAnnotationsMenu_alreadyAdded()
{
JMenuItem menu = new JMenuItem();
* The menu item should be enabled, and acquire a tooltip which lists the
* annotation sources (calcIds) and type (labels).
*/
- @Test
+ @Test(groups = { "Functional" })
public void testConfigureReferenceAnnotationsMenu()
{
JMenuItem menu = new JMenuItem();
testee.configureReferenceAnnotationsMenu(menu, seqs);
assertTrue(menu.isEnabled());
- String expected = "<html><table width=350 border=0><tr><td align=justify>Add annotations for<br/>JMOL/secondary structure<br/>PBD/Temp</td></tr></table></html>";
+ 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());
}
* on the alignment. The menu item should be enabled, and acquire a tooltip
* which lists the annotation sources (calcIds) and type (labels).
*/
- @Test
+ @Test(groups = { "Functional" })
public void testConfigureReferenceAnnotationsMenu_notOnAlignment()
{
JMenuItem menu = new JMenuItem();
testee.configureReferenceAnnotationsMenu(menu, seqs);
assertTrue(menu.isEnabled());
- String expected = "<html><table width=350 border=0><tr><td align=justify>Add annotations for<br/>JMOL/secondary structure<br/>PBD/Temp</td></tr></table></html>";
+ 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());
}
// PDB.secondary structure on Sequence0
AlignmentAnnotation annotation = new AlignmentAnnotation(
"secondary structure", "", 0);
- annotation.setCalcId("PBD");
+ annotation.setCalcId("PDB");
seqs.get(0).getDatasetSequence().addAlignmentAnnotation(annotation);
if (addToSequence)
{
// PDB.Temp on Sequence1
annotation = new AlignmentAnnotation("Temp", "", 0);
- annotation.setCalcId("PBD");
+ annotation.setCalcId("PDB");
seqs.get(1).getDatasetSequence().addAlignmentAnnotation(annotation);
if (addToSequence)
{
// JMOL.secondary structure on Sequence0
annotation = new AlignmentAnnotation("secondary structure", "", 0);
- annotation.setCalcId("JMOL");
+ annotation.setCalcId("Jmol");
seqs.get(0).getDatasetSequence().addAlignmentAnnotation(annotation);
if (addToSequence)
{
* The menu item should be enabled, and acquire a tooltip which lists the
* annotation sources (calcIds) and type (labels).
*/
- @Test
+ @Test(groups = { "Functional" })
public void testConfigureReferenceAnnotationsMenu_twoViews()
{
}
* Test for building menu options including 'show' and 'hide' annotation
* types.
*/
- @Test
+ @Test(groups = { "Functional" })
public void testBuildAnnotationTypesMenus()
{
JMenu showMenu = new JMenu();
// PDB.secondary structure on Sequence0
AlignmentAnnotation annotation = new AlignmentAnnotation(
- "secondary structure", "", new Annotation[]
- {});
+ "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 = 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 = 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 = new AlignmentAnnotation("Temp", "", new Annotation[] {});
annotation.setCalcId("PDB");
annotation.visible = true;
seqs.get(1).addAlignmentAnnotation(annotation);
assertEquals(4, showOptions.length); // includes 'All' and separator
assertEquals(4, hideOptions.length);
- assertEquals("All",
- ((JMenuItem) showOptions[0]).getText());
+ assertEquals("All", ((JMenuItem) showOptions[0]).getText());
assertTrue(showOptions[1] instanceof JPopupMenu.Separator);
assertEquals(JSeparator.HORIZONTAL,
((JSeparator) showOptions[1]).getOrientation());
assertEquals("SSP", ((JMenuItem) showOptions[3]).getText());
assertEquals("JPred", ((JMenuItem) showOptions[3]).getToolTipText());
- assertEquals("All",
- ((JMenuItem) hideOptions[0]).getText());
+ assertEquals("All", ((JMenuItem) hideOptions[0]).getText());
assertTrue(hideOptions[1] instanceof JPopupMenu.Separator);
assertEquals(JSeparator.HORIZONTAL,
((JSeparator) hideOptions[1]).getOrientation());
/**
* Test for building menu options with only 'hide' annotation types enabled.
*/
- @Test
+ @Test(groups = { "Functional" })
public void testBuildAnnotationTypesMenus_showDisabled()
{
JMenu showMenu = new JMenu();
// PDB.secondary structure on Sequence0
AlignmentAnnotation annotation = new AlignmentAnnotation(
- "secondary structure", "", new Annotation[]
- {});
+ "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 = new AlignmentAnnotation("Temp", "", new Annotation[] {});
annotation.setCalcId("PDB");
annotation.visible = true;
seqs.get(1).addAlignmentAnnotation(annotation);
/**
* Test for building menu options with only 'show' annotation types enabled.
*/
- @Test
+ @Test(groups = { "Functional" })
public void testBuildAnnotationTypesMenus_hideDisabled()
{
JMenu showMenu = new JMenu();
// PDB.secondary structure on Sequence0
AlignmentAnnotation annotation = new AlignmentAnnotation(
- "secondary structure", "", new Annotation[]
- {});
+ "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 = new AlignmentAnnotation("Temp", "", new Annotation[] {});
annotation.setCalcId("PDB2");
annotation.visible = false;
seqs.get(1).addAlignmentAnnotation(annotation);
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<String>();
+ List<DBRefEntry> refs = new ArrayList<DBRefEntry>();
+
+ // 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<String> nomatchlinks = new ArrayList<String>();
+ 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());
+
+ }
}
git://source.jalview.org / jalview.git / blobdiff