-/**
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.ext.jmol;
-import static org.junit.Assert.*;
-
-import java.util.Vector;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertTrue;
+import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.io.AppletFormatAdapter;
+import jalview.io.FileLoader;
-import org.junit.Test;
+import java.util.Vector;
+
+import org.jmol.c.STR;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+import MCview.PDBfile;
/**
* @author jimp
- *
+ *
*/
public class PDBFileWithJmolTest
{
+ /*
+ * 1GAQ has been reduced to alpha carbons only
+ * 1QCF is the full PDB file including headers, HETATM etc
+ */
+ String[] testFile = new String[] { "./examples/1GAQ.txt",
+ "./test/jalview/ext/jmol/1QCF.pdb" }; // ,
+
+ //@formatter:off
+ // a modified and very cut-down extract of 4UJ4
+ String pdbWithChainBreak =
+ "HEADER TRANSPORT PROTEIN 08-APR-15 4UJ4\n" +
+ // chain B has missing residues; these should all go in the same sequence:
+ "ATOM 1909 CA VAL B 358 21.329 -19.739 -67.740 1.00201.05 C\n" +
+ "ATOM 1916 CA GLY B 359 21.694 -23.563 -67.661 1.00198.09 C\n" +
+ "ATOM 1920 CA LYS B 367 32.471 -12.135 -77.100 1.00257.97 C\n" +
+ "ATOM 1925 CA ALA B 368 31.032 -9.324 -74.946 1.00276.01 C\n" +
+ // switch to chain C; should be a separate sequence
+ "ATOM 1930 CA SER C 369 32.589 -7.517 -71.978 1.00265.44 C\n" +
+ "ATOM 1936 CA ALA C 370 31.650 -6.849 -68.346 1.00249.48 C\n";
+ //@formatter:on
+
+ //@formatter:off
+ // a very cut-down extract of 1ejg
+ String pdbWithAltLoc =
+ "HEADER TRANSPORT PROTEIN 08-APR-15 1EJG\n" +
+ "ATOM 448 CA ALA A 24 6.619 16.195 1.970 1.00 1.65 C\n" +
+ "ATOM 458 CA ALEU A 25 3.048 14.822 1.781 0.57 1.48 C\n" +
+ // alternative residue 25 entries (with ILE instead of LEU) should be ignored:
+ "ATOM 478 CA BILE A 25 3.048 14.822 1.781 0.21 1.48 C\n" +
+ // including the next altloc causes the unit test to fail but it works with the full file
+ // not sure why!
+ // "ATOM 479 CA CILE A 25 3.048 14.822 1.781 0.22 1.48 C\n" +
+ "ATOM 512 CA CYS A 26 4.137 11.461 3.154 1.00 1.52 C\n";
+ //@formatter:on
+
+ @BeforeMethod(alwaysRun = true)
+ public void setUp()
+ {
+ Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
+ Boolean.TRUE.toString());
+ Cache.applicationProperties.setProperty("ADD_SS_ANN",
+ Boolean.TRUE.toString());
+ }
+
+ @Test(groups = { "Functional" })
+ public void testAlignmentLoader() throws Exception
+ {
+ for (String f : testFile)
+ {
+ FileLoader fl = new jalview.io.FileLoader(false);
+ AlignFrame af = fl
+ .LoadFileWaitTillLoaded(f, AppletFormatAdapter.FILE);
+ validateSecStrRows(af.getViewport().getAlignment());
+ }
+ }
+
+ @Test(groups = { "Functional" })
+ public void testFileParser() throws Exception
+ {
+ for (String pdbStr : testFile)
+ {
+ PDBfile mctest = new PDBfile(false, false, false, pdbStr,
+ AppletFormatAdapter.FILE);
+ PDBFileWithJmol jtest = new PDBFileWithJmol(pdbStr,
+ jalview.io.AppletFormatAdapter.FILE);
+ Vector<SequenceI> seqs = jtest.getSeqs(), mcseqs = mctest.getSeqs();
+
+ assertTrue(
+ "No sequences extracted from testfile\n"
+ + (jtest.hasWarningMessage() ? jtest.getWarningMessage()
+ : "(No warnings raised)"), seqs != null
+ && seqs.size() > 0);
+ for (SequenceI sq : seqs)
+ {
+ assertEquals("JMol didn't process " + pdbStr
+ + " to the same sequence as MCView",
+ sq.getSequenceAsString(), mcseqs.remove(0)
+ .getSequenceAsString());
+ AlignmentI al = new Alignment(new SequenceI[] { sq });
+ validateSecStrRows(al);
+ }
+ }
+ }
- @Test
- public void test() throws Exception
+ private void validateSecStrRows(AlignmentI al)
{
- PDBFileWithJmol jtest=new PDBFileWithJmol("./examples/1GAQ.txt", jalview.io.AppletFormatAdapter.FILE);
- Vector<SequenceI> seqs=jtest.getSeqs();
-
- assertTrue("No sequences extracted from testfile\n"+(jtest.hasWarningMessage() ? jtest.getWarningMessage(): "(No warnings raised)"), seqs!=null && seqs.size()>0);
- for (SequenceI sq:seqs)
+ if (!al.isNucleotide())
{
- AlignmentI al = new Alignment(new SequenceI[] { sq});
- if (!al.isNucleotide())
+ for (SequenceI asq : al.getSequences())
{
- assertTrue("No secondary structure assigned for protein sequence.",sq.getAnnotation()!=null && sq.getAnnotation().length>=1 && sq.getAnnotation()[0].hasIcons);
+ SequenceI sq = asq;
+ boolean hasDs = false;
+ while (sq.getDatasetSequence() != null
+ && sq.getAnnotation() == null)
+ {
+ sq = sq.getDatasetSequence();
+ hasDs = true;
+ }
+ checkFirstAAIsAssoc(sq);
+ if (hasDs)
+ {
+ // also verify if alignment sequence has annotation on it
+ // that is correctly mapped
+ checkFirstAAIsAssoc(asq);
+ }
}
}
}
+ private void checkFirstAAIsAssoc(SequenceI sq)
+ {
+ assertTrue("No secondary structure assigned for protein sequence.",
+ sq.getAnnotation() != null && sq.getAnnotation().length >= 1
+ && sq.getAnnotation()[0].hasIcons);
+ assertTrue(
+ "Secondary structure not associated for sequence "
+ + sq.getName(), sq.getAnnotation()[0].sequenceRef == sq);
+ }
+
+ /**
+ * Test parsing a chain with missing residues
+ *
+ * @throws Exception
+ */
+ @Test(groups = { "Functional" })
+ public void testParse_missingResidues() throws Exception
+ {
+ PDBfile mctest = new PDBfile(false, false, false, pdbWithChainBreak,
+ AppletFormatAdapter.PASTE);
+ PDBFileWithJmol jtest = new PDBFileWithJmol(pdbWithChainBreak,
+ jalview.io.AppletFormatAdapter.PASTE);
+ Vector<SequenceI> seqs = jtest.getSeqs();
+ Vector<SequenceI> mcseqs = mctest.getSeqs();
+
+ assertEquals("Failed to find 2 sequences\n", 2, seqs.size());
+ assertEquals("Failed to find 2 sequences\n", 2, mcseqs.size());
+ assertEquals("VGKA", seqs.get(0).getSequenceAsString());
+ assertEquals("VGKA", mcseqs.get(0).getSequenceAsString());
+ assertEquals("SA", seqs.get(1).getSequenceAsString());
+ assertEquals("SA", mcseqs.get(1).getSequenceAsString());
+ }
+
+ /**
+ * Test parsing a chain with 'altloc' residues
+ *
+ * @throws Exception
+ */
+ @Test(groups = { "Functional" })
+ public void testParse_alternativeResidues() throws Exception
+ {
+ PDBfile mctest = new PDBfile(false, false, false, pdbWithAltLoc,
+ AppletFormatAdapter.PASTE);
+ PDBFileWithJmol jtest = new PDBFileWithJmol(pdbWithAltLoc,
+ jalview.io.AppletFormatAdapter.PASTE);
+ Vector<SequenceI> seqs = jtest.getSeqs();
+ Vector<SequenceI> mcseqs = mctest.getSeqs();
+
+ assertEquals("Failed to find 1 sequence\n", 1, seqs.size());
+ assertEquals("Failed to find 1 sequence\n", 1, mcseqs.size());
+ assertEquals("ALC", seqs.get(0).getSequenceAsString());
+ assertEquals("ALC", mcseqs.get(0).getSequenceAsString());
+ }
+
+ @Test(groups = "Functional")
+ public void testSetSecondaryStructure()
+ {
+ PDBFileWithJmol testee = new PDBFileWithJmol();
+ char[] struct = new char[10];
+ char[] structCode = new char[10];
+ struct[0] = '1';
+ structCode[0] = '1';
+
+ testee.setSecondaryStructure(STR.NONE, 0, struct, structCode);
+ testee.setSecondaryStructure(STR.HELIX, 1, struct, structCode);
+ testee.setSecondaryStructure(STR.HELIX310, 2, struct, structCode);
+ testee.setSecondaryStructure(STR.HELIXALPHA, 3, struct, structCode);
+ testee.setSecondaryStructure(STR.HELIXPI, 4, struct, structCode);
+ testee.setSecondaryStructure(STR.SHEET, 5, struct, structCode);
+
+ assertEquals(0, struct[0]);
+ assertEquals('H', struct[1]);
+ assertEquals('3', struct[2]);
+ assertEquals('H', struct[3]);
+ assertEquals('P', struct[4]);
+ assertEquals('E', struct[5]);
+
+ assertEquals(0, structCode[0]);
+ assertEquals('H', structCode[1]);
+ assertEquals('H', structCode[2]);
+ assertEquals('H', structCode[3]);
+ assertEquals('H', structCode[4]);
+ assertEquals('E', structCode[5]);
+ }
}
git://source.jalview.org / jalview.git / blobdiff