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;
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);
public void sanitizeSeqNameTest()
{
String name = "ab_cdEF|fwxyz012349";
- assertEquals(name, StructureChooser.sanitizeSeqName(name));
+ assertEquals(name, StructureChooserQuerySource.sanitizeSeqName(name));
// remove a [nn] substring
name = "abcde12[345]fg";
- assertEquals("abcde12fg", StructureChooser.sanitizeSeqName(name));
+ assertEquals("abcde12fg", StructureChooserQuerySource.sanitizeSeqName(name));
// remove characters other than a-zA-Z0-9 | or _
name = "ab[cd],.\t£$*!- \\\"@:e";
- assertEquals("abcde", StructureChooser.sanitizeSeqName(name));
+ assertEquals("abcde", StructureChooserQuerySource.sanitizeSeqName(name));
name = "abcde12[345a]fg";
- assertEquals("abcde12345afg", StructureChooser.sanitizeSeqName(name));
+ assertEquals("abcde12345afg", StructureChooserQuerySource.sanitizeSeqName(name));
}
}