import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
import jalview.structure.StructureImportSettings;
+import jalview.structure.StructureImportSettings.StructureParser;
import jalview.ws.seqfetcher.DbSourceProxy;
import java.util.List;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
public class PDBSequenceFetcherTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
SequenceFetcher sf;
@BeforeMethod(alwaysRun = true)
public void setUp() throws Exception
{
+ Cache.loadProperties("test/jalview/io/testProps.jvprops");
// ensure 'add annotation from structure' is selected
Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
Boolean.TRUE.toString());
@Test(groups = { "Network" }, enabled = true)
public void testRnaSeqRetrieve() throws Exception
{
- Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
- Boolean.TRUE.toString());
- Cache.applicationProperties.setProperty("DEFAULT_STRUCTURE_FORMAT",
- "PDB");
+ Cache.applicationProperties.setProperty("PDB_DOWNLOAD_FORMAT", "PDB");
List<DbSourceProxy> sps = sf.getSourceProxy("PDB");
AlignmentI response = sps.get(0).getSequenceRecords("2GIS");
assertTrue(response != null);
@Test(groups = { "Network" }, enabled = true)
public void testPdbSeqRetrieve() throws Exception
{
- Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
- Boolean.TRUE.toString());
StructureImportSettings.setDefaultStructureFileFormat("PDB");
StructureImportSettings
- .setDefaultPDBFileParser(StructureImportSettings.JALVIEW_PARSER);
+ .setDefaultPDBFileParser(StructureParser.JALVIEW_PARSER);
testRetrieveProteinSeqFromPDB();
}
@Test(groups = { "Network" }, enabled = true)
public void testmmCifSeqRetrieve() throws Exception
{
- Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
- Boolean.TRUE.toString());
StructureImportSettings.setDefaultStructureFileFormat("mmCIF");
testRetrieveProteinSeqFromPDB();
}