+/*
+ * 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 org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertTrue;
import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
{
Sequence seq;
- @BeforeMethod
+ @BeforeMethod(alwaysRun = true)
public void setUp() throws Exception
{
seq = new Sequence("PDB|4kqy|4KQY|A", "ABCDEFGHIJKLMNOPQRSTUVWXYZ", 1,
seq.setPDBId(pdbIds);
}
- @AfterMethod
+ @AfterMethod(alwaysRun = true)
public void tearDown() throws Exception
{
seq = null;
}
-
-
- @Test
+ @Test(groups = { "Functional" })
public void buildQueryTest()
{
String query = StructureChooser.buildQuery(seq);
- System.out.println(">>>>>>>>>> query : " + query);
+ assertEquals("pdb_id:1tim", query);
+ System.out.println("seq >>>> " + seq);
+ seq.getAllPDBEntries().clear();
+ query = StructureChooser.buildQuery(seq);
assertEquals(
- "4kqy OR text:1tim OR text:XYZ_1 OR text:XYZ_2 OR text:XYZ_3 OR text:XYZ_4",
+ "text:XYZ_1 OR text:XYZ_2 OR text:XYZ_3 OR text:XYZ_4 OR text:4kqy",
+ query);
+ seq.setDBRefs(null);
+ query = StructureChooser.buildQuery(seq);
+ assertEquals("text:4kqy", query);
+
+ DBRefEntry uniprotDBRef = new DBRefEntry();
+ uniprotDBRef.setAccessionId("P12345");
+ uniprotDBRef.setSource(DBRefSource.UNIPROT);
+ seq.addDBRef(uniprotDBRef);
+
+ DBRefEntry pdbDBRef = new DBRefEntry();
+ pdbDBRef.setAccessionId("1XYZ");
+ pdbDBRef.setSource(DBRefSource.PDB);
+ seq.addDBRef(pdbDBRef);
+
+ for (int x = 1; x < 5; x++)
+ {
+ DBRefEntry dbRef = new DBRefEntry();
+ dbRef.setAccessionId("XYZ_" + x);
+ seq.addDBRef(dbRef);
+ }
+ query = StructureChooser.buildQuery(seq);
+ assertEquals(
+ "uniprot_accession:P12345 OR uniprot_id:P12345 OR pdb_id:1xyz",
query);
}
- @Test
+ @Test(groups = { "Functional" })
public void populateFilterComboBoxTest()
{
- SequenceI[] selectedSeqs = new SequenceI[]
- { seq };
- StructureChooser sc = new StructureChooser(selectedSeqs, seq,
- null);
+ SequenceI[] selectedSeqs = new SequenceI[] { seq };
+ StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
sc.populateFilterComboBox();
int optionsSize = sc.getCmbFilterOption().getItemCount();
assertEquals(3, optionsSize); // if structures are not discovered then don't
sc.setStructuresDiscovered(true);
sc.populateFilterComboBox();
+ try
+ {
+ Thread.sleep(2000);
+ } catch (InterruptedException e)
+ {
+ e.printStackTrace();
+ }
optionsSize = sc.getCmbFilterOption().getItemCount();
assertTrue(optionsSize > 3); // if structures are found, filter options
// should be populated
}
- @Test
+ @Test(groups = { "Functional" })
public void fetchStructuresInfoTest()
{
- SequenceI[] selectedSeqs = new SequenceI[]
- { seq };
+ SequenceI[] selectedSeqs = new SequenceI[] { seq };
StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
sc.fetchStructuresMetaData();
assertTrue(sc.getDiscoveredStructuresSet() != null);
assertTrue(sc.getDiscoveredStructuresSet().size() > 0);
}
+
+ @Test(groups = { "Functional" })
+ public void sanitizeSeqNameTest()
+ {
+ String name = "ab_cdEF|fwxyz012349";
+ assertEquals(name, StructureChooser.sanitizeSeqName(name));
+
+ // remove a [nn] substring
+ name = "abcde12[345]fg";
+ assertEquals("abcde12fg", StructureChooser.sanitizeSeqName(name));
+
+ // remove characters other than a-zA-Z0-9 | or _
+ name = "ab[cd],.\t£$*!- \\\"@:e";
+ assertEquals("abcde", StructureChooser.sanitizeSeqName(name));
+
+ name = "abcde12[345a]fg";
+ assertEquals("abcde12345afg", StructureChooser.sanitizeSeqName(name));
+ }
}