import jalview.gui.AlignFrame;
import jalview.io.FileLoader;
import jalview.io.FormatAdapter;
+import jalview.io.StructureFile;
import org.testng.Assert;
import org.testng.AssertJUnit;
import org.testng.annotations.Test;
-import MCview.PDBfile;
-
public class Mapping
{
{ 303, 315 }, sheets[] = new int[] { 267, 268, 269, 270 };
StructureSelectionManager ssm = new jalview.structure.StructureSelectionManager();
- PDBfile pmap = ssm.setMapping(true, new SequenceI[] { uprot },
+ StructureFile pmap = ssm.setMapping(true, new SequenceI[] { uprot },
new String[] { "A" }, "test/jalview/ext/jmol/1QCF.pdb",
jalview.io.FormatAdapter.FILE);
assertTrue(pmap != null);
StructureSelectionManager ssm = new jalview.structure.StructureSelectionManager();
// Associate the 1GAQ pdb file with the subsequence 'imported' from another
// source
- PDBfile pde = ssm.setMapping(true, new SequenceI[] { sq }, new String[]
- { "A" }, inFile = "examples/1gaq.txt", jalview.io.FormatAdapter.FILE);
+ StructureFile pde = ssm.setMapping(true, new SequenceI[] { sq },
+ new String[] { "A" }, inFile = "examples/1gaq.txt",
+ jalview.io.FormatAdapter.FILE);
assertTrue("PDB File couldn't be found", pde != null);
StructureMapping[] mp = ssm.getMapping(inFile);
assertTrue("No mappings made.", mp != null && mp.length > 0);
FormatAdapter.PASTE, "FASTA");
SequenceI newseq = seqf.getViewport().getAlignment().getSequenceAt(0);
StructureSelectionManager ssm = new jalview.structure.StructureSelectionManager();
- PDBfile pmap = ssm.setMapping(true, new SequenceI[] { newseq },
+ StructureFile pmap = ssm.setMapping(true, new SequenceI[] { newseq },
new String[] { null }, "examples/3W5V.pdb",
jalview.io.FormatAdapter.FILE);
if (pmap == null)
@Test(groups = { "Functional" })
public void compareTransferredToRefPDBAnnot() throws Exception
{
+ StructureImportSettings.setShowSeqFeatures(true);
AlignFrame ref = new FileLoader(false)
.LoadFileWaitTillLoaded("test/jalview/ext/jmol/1QCF.pdb",
jalview.io.FormatAdapter.FILE);
StructureSelectionManager ssm = new jalview.structure.StructureSelectionManager();
ssm.setProcessSecondaryStructure(true);
ssm.setAddTempFacAnnot(true);
- PDBfile pmap = ssm.setMapping(true, new SequenceI[] { newseq },
+ StructureFile pmap = ssm.setMapping(true, new SequenceI[] { newseq },
new String[] { null }, "test/jalview/ext/jmol/1QCF.pdb",
jalview.io.FormatAdapter.FILE);
assertTrue(pmap != null);