* 115 in PDB Res Numbering secondary structure numbers in jmol seem to be in
* msd numbering, not pdb res numbering.
*/
- @Test(groups =
- { "Functional" }, enabled = false)
+ @Test(groups = { "Functional" }, enabled = false)
public void pdbEntryPositionMap() throws Exception
{
Assert.fail("This test intentionally left to fail");
// original numbers taken from
// http://www.ebi.ac.uk/pdbe-srv/view/entry/1qcf/secondary.html
// these are in numbering relative to the subsequence above
- int coils[] =
- { 266, 275, 278, 287, 289, 298, 302, 316 }, helices[] = new int[]
- { 303, 315 }, sheets[] = new int[]
- { 267, 268, 269, 270 };
+ int coils[] = { 266, 275, 278, 287, 289, 298, 302, 316 }, helices[] = new int[]
+ { 303, 315 }, sheets[] = new int[] { 267, 268, 269, 270 };
StructureSelectionManager ssm = new jalview.structure.StructureSelectionManager();
- PDBfile pmap = ssm.setMapping(true, new SequenceI[]
- { uprot }, new String[]
- { "A" }, "test/jalview/ext/jmol/1QCF.pdb",
+ PDBfile pmap = ssm.setMapping(true, new SequenceI[] { uprot },
+ new String[] { "A" }, "test/jalview/ext/jmol/1QCF.pdb",
jalview.io.FormatAdapter.FILE);
assertTrue(pmap != null);
SequenceI protseq = pmap.getSeqsAsArray()[0];
}
}
- @Test(groups =
- { "Functional" }, enabled = false)
+ @Test(groups = { "Functional" }, enabled = false)
public void testPDBentryMapping() throws Exception
{
Assert.fail("This test intentionally left to fail");
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[]
+ PDBfile 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);
Annotation a = transfer.annotations[tanpos], b = alan.annotations[p];
assertEquals("Non-equivalent annotation element at " + p + "("
+ rseqpos + ")" + " expected at " + fpos + " (alIndex "
- + tanpos + ")",
- a == null ? a : a.toString(),
+ + tanpos + ")", a == null ? a : a.toString(),
b == null ? b : b.toString());
System.out.print("(" + a + "|" + b + ")");
}
* transform
*
*/
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void mapFer1From3W5V() throws Exception
{
AlignFrame seqf = new FileLoader(false)
FormatAdapter.PASTE, "FASTA");
SequenceI newseq = seqf.getViewport().getAlignment().getSequenceAt(0);
StructureSelectionManager ssm = new jalview.structure.StructureSelectionManager();
- PDBfile pmap = ssm.setMapping(true, new SequenceI[]
- { newseq }, new String[]
- { null }, "examples/3W5V.pdb",
+ PDBfile pmap = ssm.setMapping(true, new SequenceI[] { newseq },
+ new String[] { null }, "examples/3W5V.pdb",
jalview.io.FormatAdapter.FILE);
if (pmap == null)
{
* compare reference annotation for imported pdb sequence to identical
* seuqence with transferred annotation from mapped pdb file
*/
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void compareTransferredToRefPDBAnnot() throws Exception
{
AlignFrame ref = new FileLoader(false)
StructureSelectionManager ssm = new jalview.structure.StructureSelectionManager();
ssm.setProcessSecondaryStructure(true);
ssm.setAddTempFacAnnot(true);
- PDBfile pmap = ssm.setMapping(true, new SequenceI[]
- { newseq }, new String[]
- { null }, "test/jalview/ext/jmol/1QCF.pdb",
+ PDBfile pmap = ssm.setMapping(true, new SequenceI[] { newseq },
+ new String[] { null }, "test/jalview/ext/jmol/1QCF.pdb",
jalview.io.FormatAdapter.FILE);
assertTrue(pmap != null);
assertEquals("Original and copied sequence of different lengths.",