+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.structure;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertTrue;
+
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
import jalview.datamodel.Sequence;
import jalview.io.FileLoader;
import jalview.io.FormatAdapter;
-import org.junit.Assert;
-import org.junit.Test;
+import org.testng.Assert;
+import org.testng.AssertJUnit;
+import org.testng.annotations.Test;
import MCview.PDBfile;
* 115 in PDB Res Numbering secondary structure numbers in jmol seem to be in
* msd numbering, not pdb res numbering.
*/
- @Test
+ @Test(groups = { "Functional" }, enabled = false)
public void pdbEntryPositionMap() throws Exception
{
- fail("This test intentionally left to fail");
+ Assert.fail("This test intentionally left to fail");
for (int offset = 0; offset < 20; offset += 6)
{
// check we put the secondary structure in the right position
// 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
+ @Test(groups = { "Functional" }, enabled = false)
public void testPDBentryMapping() throws Exception
{
- fail("This test intentionally left to fail");
+ Assert.fail("This test intentionally left to fail");
Sequence sq = new Sequence(
"1GAQ A subseq 126 to 219",
"EIVKGVCSNFLCDLQPGDNVQITGPVGKEMLMPKDPNATIIMLATGTGIAPFRSFLWKMFFEKHDDYKFNGLGWLFLGVPTSSSLLYKEEFGKM");
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
+ @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)
{
- Assert.fail("Couldn't make a mapping for 3W5V to FER1_MAIZE");
+ AssertJUnit.fail("Couldn't make a mapping for 3W5V to FER1_MAIZE");
}
}
* compare reference annotation for imported pdb sequence to identical
* seuqence with transferred annotation from mapped pdb file
*/
- @Test
+ @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.",
git://source.jalview.org / jalview.git / blobdiff