import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import jalview.datamodel.features.SequenceFeatures;
import jalview.gui.AlignFrame;
+import jalview.gui.JvOptionPane;
import jalview.structure.StructureImportSettings;
+import jalview.structure.StructureImportSettings.StructureParser;
import java.io.File;
+import java.util.List;
+import org.junit.Assert;
import org.testng.annotations.AfterClass;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.BeforeMethod;
public class AnnotatedPDBFileInputTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
AlignmentI al;
String pdbId;
al = af.getViewport().getAlignment();
pdbId = al.getSequenceAt(0).getDatasetSequence().getAllPDBEntries()
.get(0).getId();
- StructureImportSettings.setCurrentDefaultFormat("PDB");
+ StructureImportSettings.setDefaultStructureFileFormat("PDB");
+ // StructureImportSettings
+ // .setDefaultPDBFileParser(StructureParser.JALVIEW_PARSER);
}
@Test(groups = { "Functional" })
{
for (int q = p + 1; q < avec.length; q++)
{
- assertTrue("Found a duplicate annotation row "
- + avec[p].label, avec[p] != avec[q]);
+ assertTrue("Found a duplicate annotation row " + avec[p].label,
+ avec[p] != avec[q]);
}
}
}
- @Test(groups = { "Functional" })
+ @Test(groups = { "Functional" }, enabled = false)
public void checkPDBannotationSource()
{
-
+ Assert.fail(
+ "This test is incorrect - does not verify that JmolParser's annotation rows can be recognised as generated by the Jmol parser.");
for (SequenceI asq : al.getSequences())
{
for (AlignmentAnnotation aa : asq.getAnnotation())
{
System.out.println("CalcId: " + aa.getCalcId());
- assertTrue(MCview.PDBfile.isCalcIdForFile(aa, pdbId));
+ if (StructureImportSettings.getDefaultPDBFileParser()
+ .equals(StructureParser.JALVIEW_PARSER))
+ {
+ assertTrue(MCview.PDBfile.isCalcIdForFile(aa, pdbId));
+ }
}
}
}
/*
* 1GAQ/A
*/
- SequenceFeature[] sf = al.getSequenceAt(0).getSequenceFeatures();
- assertEquals(296, sf.length);
- assertEquals("RESNUM", sf[0].getType());
- assertEquals("GLU: 19 1gaqA", sf[0].getDescription());
- assertEquals("RESNUM", sf[295].getType());
- assertEquals("TYR: 314 1gaqA", sf[295].getDescription());
+ List<SequenceFeature> sf = al.getSequenceAt(0).getSequenceFeatures();
+ SequenceFeatures.sortFeatures(sf, true);
+ assertEquals(296, sf.size());
+ assertEquals("RESNUM", sf.get(0).getType());
+ assertEquals("GLU: 19 1gaqA", sf.get(0).getDescription());
+ assertEquals("RESNUM", sf.get(295).getType());
+ assertEquals("TYR: 314 1gaqA", sf.get(295).getDescription());
/*
* 1GAQ/B
*/
sf = al.getSequenceAt(1).getSequenceFeatures();
- assertEquals(98, sf.length);
- assertEquals("RESNUM", sf[0].getType());
- assertEquals("ALA: 1 1gaqB", sf[0].getDescription());
- assertEquals("RESNUM", sf[97].getType());
- assertEquals("ALA: 98 1gaqB", sf[97].getDescription());
+ SequenceFeatures.sortFeatures(sf, true);
+ assertEquals(98, sf.size());
+ assertEquals("RESNUM", sf.get(0).getType());
+ assertEquals("ALA: 1 1gaqB", sf.get(0).getDescription());
+ assertEquals("RESNUM", sf.get(97).getType());
+ assertEquals("ALA: 98 1gaqB", sf.get(97).getDescription());
/*
* 1GAQ/C
*/
sf = al.getSequenceAt(2).getSequenceFeatures();
- assertEquals(296, sf.length);
- assertEquals("RESNUM", sf[0].getType());
- assertEquals("GLU: 19 1gaqC", sf[0].getDescription());
- assertEquals("RESNUM", sf[295].getType());
- assertEquals("TYR: 314 1gaqC", sf[295].getDescription());
+ SequenceFeatures.sortFeatures(sf, true);
+ assertEquals(296, sf.size());
+ assertEquals("RESNUM", sf.get(0).getType());
+ assertEquals("GLU: 19 1gaqC", sf.get(0).getDescription());
+ assertEquals("RESNUM", sf.get(295).getType());
+ assertEquals("TYR: 314 1gaqC", sf.get(295).getDescription());
}
@Test(groups = { "Functional" })
sq = sq.getDatasetSequence();
}
assertNotNull(sq.getAllPDBEntries());
- assertEquals("Expected only one PDB ID",
- sq.getAllPDBEntries().size(), 1);
+ assertEquals("Expected only one PDB ID", 1, sq.getAllPDBEntries()
+ .size());
for (PDBEntry pdbentry : sq.getAllPDBEntries())
{
System.err.println("PDB Entry " + pdbentry.getId() + " "