*/
package jalview.gui;
+import static jalview.util.UrlConstants.DB_ACCESSION;
import static jalview.util.UrlConstants.SEQUENCE_ID;
-import static jalview.util.UrlConstants.SEQUENCE_NAME;
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.DBRefEntry;
import jalview.datamodel.DBRefSource;
-import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
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.ArrayList;
+import java.util.Collections;
import java.util.List;
import javax.swing.JMenu;
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"
@BeforeMethod(alwaysRun = true)
public void setUp() throws IOException
{
+ 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,
- 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);
assertEquals(4, showOptions.length); // includes 'All' and separator
assertEquals(4, hideOptions.length);
- assertEquals("All", ((JMenuItem) showOptions[0]).getText());
+ 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("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());
assertEquals(2, showOptions.length); // includes 'All' and separator
assertEquals(4, hideOptions.length);
- assertEquals("All", ((JMenuItem) showOptions[0]).getText());
+ 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());
+ assertEquals(all, ((JMenuItem) hideOptions[0]).getText());
assertTrue(hideOptions[1] instanceof JPopupMenu.Separator);
assertEquals(JSeparator.HORIZONTAL,
((JSeparator) hideOptions[1]).getOrientation());
assertEquals(4, showOptions.length); // includes 'All' and separator
assertEquals(2, hideOptions.length);
- assertEquals("All", ((JMenuItem) showOptions[0]).getText());
+ 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("Temp", ((JMenuItem) showOptions[3]).getText());
assertEquals("PDB2", ((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());
// 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=$"
- + SEQUENCE_NAME + "$");
- links.add("UNIPROT | http://www.uniprot.org/uniprot/$" + SEQUENCE_ID
+ + SEQUENCE_ID + "$");
+ links.add("UNIPROT | http://www.uniprot.org/uniprot/$" + DB_ACCESSION
+ "$");
links.add("INTERPRO | http://www.ebi.ac.uk/interpro/entry/$"
- + SEQUENCE_ID + "$");
+ + DB_ACCESSION + "$");
// Gene3D entry tests for case (in)sensitivity
links.add("Gene3D | http://gene3d.biochem.ucl.ac.uk/Gene3D/search?sterm=$"
- + SEQUENCE_ID + "$&mode=protein");
+ + DB_ACCESSION + "$&mode=protein");
// make seq0 dbrefs
refs.add(new DBRefEntry(DBRefSource.UNIPROT, "1", "P83527"));
// 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));
+ SequenceI seq = seqs.get(0);
+ seq.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));
+ 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
- testee = new PopupMenu(parentPanel, (Sequence) seqs.get(0), links);
+ 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();
// 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])
+ String msg = seq.getName() + " link[" + i + "]";
+ assertEquals(msg, refs.get(i - 1).getSource(),
+ ((JMenuItem) linkItems[i])
.getText().split("\\|")[0]);
- assertEquals(refs.get(i - 1).getAccessionId(),
+ assertEquals(msg, 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);
+ seq = seqs.get(1);
+ testee = new PopupMenu(parentPanel, seq, noFeatures);
seqItems = testee.sequenceMenu.getMenuComponents();
linkMenu = (JMenu) seqItems[6];
linkItems = linkMenu.getMenuComponents();
// 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])
+ String msg = seq.getName() + " link[" + i + "]";
+ assertEquals(msg, refs.get(i + 3).getSource(),
+ ((JMenuItem) linkItems[i])
.getText().split("\\|")[0].toUpperCase());
- assertEquals(refs.get(i + 3).getAccessionId(),
+ 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<String>();
+ 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());
}
}
git://source.jalview.org / jalview.git / blobdiff