import static jalview.util.UrlConstants.SEQUENCE_ID;
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.assertNull;
import static org.testng.AssertJUnit.assertTrue;
+import java.awt.Component;
+import java.awt.Container;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.Iterator;
+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;
+
import jalview.bin.Cache;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
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.Iterator;
-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
{
public void setUp() throws IOException
{
Cache.loadProperties("test/jalview/io/testProps.jvprops");
+ Cache.initLogger();
+
String inMenuString = ("EMBL-EBI Search | http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$"
+ SEQUENCE_ID
+ "$"
DataSourceType.PASTE, FileFormat.Fasta);
AlignFrame af = new AlignFrame(alignment, 700, 500);
parentPanel = new AlignmentPanel(af, af.getViewport());
- testee = new PopupMenu(parentPanel, null, null);
+ testee = new PopupMenu(parentPanel, alignment.getSequenceAt(0), null);
int i = 0;
for (SequenceI seq : alignment.getSequences())
{
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>";
- String expected = "<html><style> div.ttip {width:350px;white-space:pre-wrap;padding:2px;overflow-wrap:break-word;}</style>"
- + "<div class=\"ttip\">" + s
- + "<br/>Jmol/secondary structure<br/>PDB/Temp </div></html>";
+// String expected = "<html><style> div.ttip {width:350px;white-space:pre-wrap;padding:2px;overflow-wrap:break-word;}</style>"
+// + "<div class=\"ttip\">" + s
+// + "<br/>Jmol/secondary structure<br/>PDB/Temp </div></html>";
+ String expected = "<html>" + s + "<br>Jmol/secondary structure<br>PDB/Temp</html>";
assertEquals(expected, menu.getToolTipText());
}
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>";
- String expected = "<html><style> div.ttip {width:350px;white-space:pre-wrap;padding:2px;overflow-wrap:break-word;}</style>"
- + "<div class=\"ttip\">Add annotations for<br/>Jmol/secondary structure<br/>PDB/Temp </div></html>";
- assertEquals(expected, menu.getToolTipText());
+// String expected = "<html><style> div.ttip {width:350px;white-space:pre-wrap;padding:2px;overflow-wrap:break-word;}</style>"
+// + "<div class=\"ttip\">" + s
+// + "<br/>Jmol/secondary structure<br/>PDB/Temp</html>";
+ String expected = "<html>" + s
+ + "<br>Jmol/secondary structure<br>PDB/Temp</html>";
+ s = menu.getToolTipText();
+ assertEquals(expected, s);
}
/**
// PDB.secondary structure on Sequence0
AlignmentAnnotation annotation = new AlignmentAnnotation(
"secondary structure", "", 0);
+ annotation.annotations = new Annotation[] { new Annotation(2f) };
annotation.setCalcId("PDB");
seqs.get(0).getDatasetSequence().addAlignmentAnnotation(annotation);
if (addToSequence)
// PDB.Temp on Sequence1
annotation = new AlignmentAnnotation("Temp", "", 0);
annotation.setCalcId("PDB");
+ annotation.annotations = new Annotation[] { new Annotation(2f) };
seqs.get(1).getDatasetSequence().addAlignmentAnnotation(annotation);
if (addToSequence)
{
// JMOL.secondary structure on Sequence0
annotation = new AlignmentAnnotation("secondary structure", "", 0);
annotation.setCalcId("Jmol");
+ annotation.annotations = new Annotation[] { new Annotation(2f) };
seqs.get(0).getDatasetSequence().addAlignmentAnnotation(annotation);
if (addToSequence)
{
* note dbref GENE3D is matched to link Gene3D, the latter is displayed
*/
linkMenu = PopupMenu.buildLinkMenu(seq1, noFeatures);
- assertEquals(linkText, linkMenu.getText());
linkItems = linkMenu.getMenuComponents();
assertEquals(3, linkItems.length);
assertEquals("EMBL-EBI Search", ((JMenuItem) linkItems[0]).getText());
Preferences.sequenceUrlLinks = factory.createUrlProvider();
linkMenu = PopupMenu.buildLinkMenu(seq1, noFeatures);
- assertEquals(linkText, linkMenu.getText());
linkItems = linkMenu.getMenuComponents();
assertEquals(1, linkItems.length);
assertEquals("EMBL-EBI Search", ((JMenuItem) linkItems[0]).getText());
+
+ /*
+ * if sequence is null, only feature links are shown (alignment popup submenu)
+ */
+ linkMenu = PopupMenu.buildLinkMenu(null, noFeatures);
+ linkItems = linkMenu.getMenuComponents();
+ assertEquals(0, linkItems.length);
+
+ List<SequenceFeature> features = new ArrayList<>();
+ SequenceFeature sf = new SequenceFeature("type", "desc", 1, 20, null);
+ features.add(sf);
+ linkMenu = PopupMenu.buildLinkMenu(null, features);
+ linkItems = linkMenu.getMenuComponents();
+ assertEquals(0, linkItems.length); // feature has no links
+
+ sf.addLink("Pfam family|http://pfam.xfam.org/family/PF00111");
+ linkMenu = PopupMenu.buildLinkMenu(null, features);
+ linkItems = linkMenu.getMenuComponents();
+ assertEquals(1, linkItems.length);
+ JMenuItem item = (JMenuItem) linkItems[0];
+ assertEquals("Pfam family", item.getText());
+ // ? no way to verify URL, compiled into link's actionListener
}
@Test(groups = { "Functional" })
assertEquals(region[1], 34);
}
+ @Test(groups = { "Functional" })
+ public void testAddFeatureDetails()
+ {
+ String menuText = MessageManager.getString("label.feature_details");
+
+ /*
+ * with no features, sub-menu should not be created
+ */
+ List<SequenceFeature> features = new ArrayList<>();
+ SequenceI seq = this.alignment.getSequenceAt(0); // FER_CAPAA/1-12
+ testee.addFeatureDetails(features, seq, 10);
+ JMenu menu = findMenu(testee, menuText);
+ assertNull(menu);
+
+ /*
+ * add some features; the menu item text is wrapped in html, and includes
+ * feature type, position, description, group (if not null)
+ */
+ SequenceFeature sf1 = new SequenceFeature("helix", "curly", 2, 6, null);
+ SequenceFeature sf2 = new SequenceFeature("chain", "straight", 1, 1,
+ "uniprot");
+ features.add(sf1);
+ features.add(sf2);
+ testee.addFeatureDetails(features, seq, 10);
+ menu = findMenu(testee, menuText);
+ assertNotNull(menu);
+ assertEquals(2, menu.getItemCount());
+ JMenuItem item = menu.getItem(0);
+ assertEquals("<html>helix 2-6 curly</html>", item.getText());
+ item = menu.getItem(1);
+ assertEquals("<html>chain 1 straight (uniprot)</html>", item.getText());
+
+ /*
+ * long feature descriptions are truncated to 40 characters
+ */
+ sf1.setDescription(
+ "this is a quite extraordinarily long description");
+ testee.remove(menu); // don't create the sub-menu twice
+ testee.addFeatureDetails(features, seq, 10);
+ menu = findMenu(testee, menuText);
+ item = menu.getItem(0);
+ assertEquals(
+ "<html>helix 2-6 this is a quite extraordinarily long des...</html>",
+ item.getText());
+ }
+
+ /**
+ * Returns the first component which is a JMenu with the given text
+ *
+ * @param c
+ * @param text
+ * @return
+ */
+ private JMenu findMenu(Container c, String text)
+ {
+ for (int i = 0; i < c.getComponentCount(); i++)
+ {
+ Component comp = c.getComponent(i);
+ if ((comp instanceof JMenu) && ((JMenu) comp).getText().equals(text))
+ {
+ return (JMenu) comp;
+ }
+ }
+ return null;
+ }
+
+ @Test(groups = { "Functional" })
+ public void testAddFeatureDetails_linkedFeatures()
+ {
+ // todo tests that verify menu items for complement features
+ }
}
git://source.jalview.org / jalview.git / blobdiff