Console.initLogger();
String inMenuString = ("EMBL-EBI Search | http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$"
- + SEQUENCE_ID
- + "$"
- + "|"
- + "UNIPROT | http://www.uniprot.org/uniprot/$" + DB_ACCESSION + "$")
- + "|"
+ + 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");
seq0.addDBRef(new DBRefEntry("INTERPRO", "1", "IPR006058"));
seq1.addDBRef(new DBRefEntry(DBRefSource.UNIPROT, "1", "Q9ZTS2"));
seq1.addDBRef(new DBRefEntry("GENE3D", "1", "3.10.20.30"));
-
+
/*
* check the Link Menu for the first sequence
*/
JMenu linkMenu = PopupMenu.buildLinkMenu(seq0, noFeatures);
assertEquals(linkText, linkMenu.getText());
Component[] linkItems = linkMenu.getMenuComponents();
-
+
/*
* menu items are ordered: SEQUENCE_ID search first, then dbrefs in order
* of database name (and within that by order of dbref addition)
{
// 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",
// 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());
/*
* long feature descriptions are truncated to 40 characters
*/
- sf1.setDescription(
- "this is a quite extraordinarily long description");
+ 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);