package jalview.ext.jmol;
import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertNotNull;
import static org.testng.AssertJUnit.assertTrue;
import jalview.bin.Cache;
import jalview.io.AppletFormatAdapter;
import jalview.io.FileLoader;
import jalview.structure.StructureImportSettings;
+import jalview.structure.StructureImportSettings.StructureParser;
+import java.io.IOException;
import java.util.Vector;
import org.jmol.c.STR;
Cache.applicationProperties.setProperty("ADD_SS_ANN",
Boolean.TRUE.toString());
StructureImportSettings.setDefaultStructureFileFormat("PDB");
+ StructureImportSettings
+ .setDefaultPDBFileParser(StructureParser.JALVIEW_PARSER);
}
@Test(groups = { "Functional" })
public void testParse_missingResidues() throws Exception
{
PDBfile mctest = new PDBfile(false, false, false,
- pastePDBDataWithChainBreak,
- AppletFormatAdapter.PASTE);
+ pastePDBDataWithChainBreak, AppletFormatAdapter.PASTE);
JmolParser jtest = new JmolParser(pastePDBDataWithChainBreak,
AppletFormatAdapter.PASTE);
Vector<SequenceI> seqs = jtest.getSeqs();
AppletFormatAdapter.PASTE);
Vector<SequenceI> seqs = jtest.getSeqs();
Vector<SequenceI> mcseqs = mctest.getSeqs();
-
+
assertEquals("Failed to find 1 sequence\n", 1, seqs.size());
assertEquals("Failed to find 1 sequence\n", 1, mcseqs.size());
assertEquals("ALC", seqs.get(0).getSequenceAsString());
assertEquals('H', structCode[4]);
assertEquals('E', structCode[5]);
}
+
+ @Test(groups = "Functional")
+ public void testLocalPDBId()
+ {
+ JmolParser structureData;
+ try
+ {
+ structureData = new JmolParser("examples/DNMT1_MOUSE.pdb",
+ AppletFormatAdapter.FILE);
+ assertNotNull(structureData);
+ assertNotNull(structureData.getId());
+ assertEquals(structureData.getId(), "DNMT1_MOUSE.pdb");
+ assertNotNull(structureData.getSeqs());
+ assertNotNull(structureData.getSeqs().get(0).getSequenceFeatures()[0].featureGroup);
+ assertEquals(
+ structureData.getSeqs().get(0).getSequenceFeatures()[0].featureGroup,
+ "dnmt1_mouse.pdb");
+ } catch (IOException e)
+ {
+ e.printStackTrace();
+ }
+ }
}