X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fgui%2FPopupMenuTest.java;h=6d0422d16ddec2fa53f94affce5e4ae0705e36e7;hb=75f946e709e456513093575f9ae1145480ccd914;hp=8f60021831eba332bd7c4e0ebad701cdce63b938;hpb=b3cd7fa160c1323a80af9dd69d13e1a45e7c189c;p=jalview.git
diff --git a/test/jalview/gui/PopupMenuTest.java b/test/jalview/gui/PopupMenuTest.java
index 8f60021..6d0422d 100644
--- a/test/jalview/gui/PopupMenuTest.java
+++ b/test/jalview/gui/PopupMenuTest.java
@@ -26,6 +26,7 @@ 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;
@@ -34,16 +35,21 @@ 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.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.Iterator;
import java.util.List;
@@ -84,6 +90,25 @@ public class PopupMenuTest
@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,
DataSourceType.PASTE, FileFormat.Fasta);
AlignFrame af = new AlignFrame(alignment, 700, 500);
@@ -171,8 +196,12 @@ public class PopupMenuTest
testee.configureReferenceAnnotationsMenu(menu, seqs);
assertTrue(menu.isEnabled());
String s = MessageManager.getString("label.add_annotations_for");
- String expected = ""
- + s + "
Jmol/secondary structure
PDB/Temp
";
+ // String expected = ""
+ // + s + "
Jmol/secondary structure
PDB/Temp
";
+ String expected = ""
+ + "" + s
+ + "
Jmol/secondary structure
PDB/Temp
";
assertEquals(expected, menu.getToolTipText());
}
@@ -194,8 +223,11 @@ public class PopupMenuTest
testee.configureReferenceAnnotationsMenu(menu, seqs);
assertTrue(menu.isEnabled());
String s = MessageManager.getString("label.add_annotations_for");
- String expected = ""
- + s + "
Jmol/secondary structure
PDB/Temp
";
+ // String expected = ""
+ // + s + "
Jmol/secondary structure
PDB/Temp
";
+ String expected = ""
+ + "Add annotations for
Jmol/secondary structure
PDB/Temp
";
assertEquals(expected, menu.getToolTipText());
}
@@ -499,17 +531,19 @@ public class PopupMenuTest
// 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 noFeatures = Collections. emptyList();
+ testee = new PopupMenu(parentPanel, seq, noFeatures);
Component[] seqItems = testee.sequenceMenu.getMenuComponents();
JMenu linkMenu = (JMenu) seqItems[6];
Component[] linkItems = linkMenu.getMenuComponents();
@@ -523,15 +557,18 @@ public class PopupMenuTest
// 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();
@@ -545,9 +582,11 @@ public class PopupMenuTest
// 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]);
}
@@ -556,8 +595,7 @@ public class PopupMenuTest
nomatchlinks.add("NOMATCH | http://www.uniprot.org/uniprot/$"
+ DB_ACCESSION + "$");
- testee = new PopupMenu(parentPanel, (Sequence) seqs.get(0),
- nomatchlinks);
+ testee = new PopupMenu(parentPanel, seq, noFeatures);
seqItems = testee.sequenceMenu.getMenuComponents();
linkMenu = (JMenu) seqItems[6];
assertFalse(linkMenu.isEnabled());
@@ -597,7 +635,7 @@ public class PopupMenuTest
.revealAllHiddenColumns(sel);
// get the Popup Menu for 7th sequence - no insertions
- testee = new PopupMenu(parentPanel, (Sequence) seqs.get(7), null);
+ testee = new PopupMenu(parentPanel, seqs.get(7), null);
testee.hideInsertions_actionPerformed(null);
HiddenColumns hidden = parentPanel.av.getAlignment().getHiddenColumns();
@@ -605,7 +643,7 @@ public class PopupMenuTest
assertFalse(it.hasNext());
// get the Popup Menu for GappySeq - this time we have insertions
- testee = new PopupMenu(parentPanel, (Sequence) seqs.get(4), null);
+ testee = new PopupMenu(parentPanel, seqs.get(4), null);
testee.hideInsertions_actionPerformed(null);
hidden = parentPanel.av.getAlignment().getHiddenColumns();
it = hidden.iterator();
@@ -655,7 +693,7 @@ public class PopupMenuTest
hidden.hideColumns(31, 40);
// get the Popup Menu for LessGappySeq in the sequence group
- testee = new PopupMenu(parentPanel, (Sequence) seqs.get(5), null);
+ testee = new PopupMenu(parentPanel, seqs.get(5), null);
testee.hideInsertions_actionPerformed(null);
hidden = parentPanel.av.getAlignment().getHiddenColumns();
it = hidden.iterator();