import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.structure.StructureMapping;
+import jalview.structure.StructureSelectionManager;
import java.io.File;
import java.util.Vector;
AlignmentI al;
- String pdbStr = "examples/2GIS.pdb";
+ String pdbStr = "examples/1gaq.txt";
String pdbId;
{
System.out.println("CalcId: " + aa.getCalcId());
- assertTrue(MCview.PDBfile.isCalcIdForFile(aa.getCalcId(), pdbId));
+ assertTrue(MCview.PDBfile.isCalcIdForFile(aa, pdbId));
}
}
}
+ /**
+ * Check sequence features have been added
+ */
+ @Test
+ public void checkPDBSequenceFeatures()
+ {
+ StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
+ StructureMapping[] mappings = ssm.getMapping("1gaq");
+ // suspect we really want to make assertions on sequence features
+ // in these mappings' sequencess
+ /*
+ * 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());
+
+ /*
+ * 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());
+
+ /*
+ * 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());
+ }
+
@Test
public void checkAnnotationWiring()
{
public void testJalviewProjectRelocationAnnotation() throws Exception
{
- String inFile = "examples/2GIS.pdb";
+ String inFile = "examples/1gaq.txt";
String tfile = File.createTempFile("JalviewTest", ".jvp")
.getAbsolutePath();
AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
&& MCview.PDBfile.isCalcIdHandled(ana.getCalcId()))
{
exists = true;
- if (MCview.PDBfile.isCalcIdForFile(ana.getCalcId(),
+ if (MCview.PDBfile.isCalcIdForFile(ana,
pdbentry.getId()))
{
found = true;