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.PDBEntry;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
-import jalview.jbgui.GStructureChooser.FilterOption;
+import jalview.fts.api.FTSData;
+import jalview.gui.structurechooser.PDBStructureChooserQuerySource;
+import jalview.gui.structurechooser.StructureChooserQuerySource;
+import jalview.jbgui.FilterOption;
+import jalview.ws.params.InvalidArgumentException;
+import java.util.Collection;
import java.util.Vector;
import org.testng.annotations.AfterMethod;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
+import junit.extensions.PA;
+
public class StructureChooserTest
{
PDBEntry dbRef = new PDBEntry();
dbRef.setId("1tim");
- Vector<PDBEntry> pdbIds = new Vector<PDBEntry>();
+ Vector<PDBEntry> pdbIds = new Vector<>();
pdbIds.add(dbRef);
seq.setPDBId(pdbIds);
seq = null;
}
+ @SuppressWarnings("deprecation")
@Test(groups = { "Functional" })
public void buildQueryTest()
{
- String query = StructureChooser.buildQuery(seq);
- assertEquals("pdb_id:1tim", query);
System.out.println("seq >>>> " + seq);
+ StructureChooserQuerySource scquery = StructureChooserQuerySource.getPDBfts();
+ String query = scquery.buildQuery(seq);
+ assertEquals("pdb_id:1tim", query);
seq.getAllPDBEntries().clear();
- query = StructureChooser.buildQuery(seq);
+ query = scquery.buildQuery(seq);
assertEquals(
"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);
+ query = scquery.buildQuery(seq);
+ System.out.println(query);
assertEquals("text:4kqy", query);
DBRefEntry uniprotDBRef = new DBRefEntry();
dbRef.setAccessionId("XYZ_" + x);
seq.addDBRef(dbRef);
}
- query = StructureChooser.buildQuery(seq);
+ System.out.println("");
+ System.out.println(seq.getDBRefs());
+ System.out.println(query);
+ query = scquery.buildQuery(seq);
assertEquals(
"uniprot_accession:P12345 OR uniprot_id:P12345 OR pdb_id:1xyz",
query);
assertTrue(sc.getCmbFilterOption().getSelectedItem() != null);
FilterOption filterOpt = (FilterOption) sc.getCmbFilterOption()
.getSelectedItem();
- assertEquals("Cached PDB Entries", filterOpt.getName());
+ assertEquals("Cached Structures", filterOpt.getName());
}
@Test(groups = { "Network" })
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);
}
public void sanitizeSeqNameTest()
{
String name = "ab_cdEF|fwxyz012349";
- assertEquals(name, StructureChooser.sanitizeSeqName(name));
+ assertEquals(name, PDBStructureChooserQuerySource.sanitizeSeqName(name));
// remove a [nn] substring
name = "abcde12[345]fg";
- assertEquals("abcde12fg", StructureChooser.sanitizeSeqName(name));
+ assertEquals("abcde12fg", PDBStructureChooserQuerySource.sanitizeSeqName(name));
// remove characters other than a-zA-Z0-9 | or _
name = "ab[cd],.\t£$*!- \\\"@:e";
- assertEquals("abcde", StructureChooser.sanitizeSeqName(name));
+ assertEquals("abcde", PDBStructureChooserQuerySource.sanitizeSeqName(name));
name = "abcde12[345a]fg";
- assertEquals("abcde12345afg", StructureChooser.sanitizeSeqName(name));
+ assertEquals("abcde12345afg", PDBStructureChooserQuerySource.sanitizeSeqName(name));
}
}