/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
package jalview.gui;
import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertNotNull;
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;
+import jalview.fts.api.FTSData;
+import jalview.jbgui.GStructureChooser.FilterOption;
+import jalview.ws.params.InvalidArgumentException;
+import java.util.Collection;
import java.util.Vector;
import org.testng.annotations.AfterMethod;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
+import junit.extensions.PA;
+
public class StructureChooserTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
Sequence seq;
@BeforeMethod(alwaysRun = true)
{
seq = new Sequence("PDB|4kqy|4KQY|A", "ABCDEFGHIJKLMNOPQRSTUVWXYZ", 1,
26);
- seq.setDatasetSequence(seq);
+ seq.createDatasetSequence();
for (int x = 1; x < 5; x++)
{
DBRefEntry dbRef = new DBRefEntry();
PDBEntry dbRef = new PDBEntry();
dbRef.setId("1tim");
- Vector<PDBEntry> pdbIds = new Vector<PDBEntry>();
+ Vector<PDBEntry> pdbIds = new Vector<>();
pdbIds.add(dbRef);
seq.setPDBId(pdbIds);
}
- @AfterMethod
+ @AfterMethod(alwaysRun = true)
public void tearDown() throws Exception
{
seq = null;
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);
+ try {
+ seq.setDBRefs(null);
+ } catch (InvalidArgumentException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ 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(groups = { "Functional" })
- public void populateFilterComboBoxTest()
+ public void populateFilterComboBoxTest() throws InterruptedException
{
SequenceI[] selectedSeqs = new SequenceI[] { seq };
StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
- sc.populateFilterComboBox();
+ sc.populateFilterComboBox(false, false);
int optionsSize = sc.getCmbFilterOption().getItemCount();
- assertEquals(3, optionsSize); // if structures are not discovered then don't
+ assertEquals(2, optionsSize); // if structures are not discovered then don't
// populate filter options
- sc.setStructuresDiscovered(true);
- sc.populateFilterComboBox();
+ sc.populateFilterComboBox(true, false);
optionsSize = sc.getCmbFilterOption().getItemCount();
assertTrue(optionsSize > 3); // if structures are found, filter options
// should be populated
+
+ sc.populateFilterComboBox(true, true);
+ assertTrue(sc.getCmbFilterOption().getSelectedItem() != null);
+ FilterOption filterOpt = (FilterOption) sc.getCmbFilterOption()
+ .getSelectedItem();
+ assertEquals("Cached Structures", filterOpt.getName());
}
- @Test(groups = { "Functional" })
+ @Test(groups = { "Network" })
public void fetchStructuresInfoTest()
{
SequenceI[] selectedSeqs = new SequenceI[] { seq };
StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
sc.fetchStructuresMetaData();
- assertTrue(sc.getDiscoveredStructuresSet() != null);
- assertTrue(sc.getDiscoveredStructuresSet().size() > 0);
+ Collection<FTSData> ss = (Collection<FTSData>) PA.getValue(sc,
+ "discoveredStructuresSet");
+ assertNotNull(ss);
+ assertTrue(ss.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));
}
}