+/*
+ * 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.structure;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
+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.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.JvOptionPane;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
+import jalview.io.FileLoader;
+import jalview.io.StructureFile;
-import org.junit.Test;
-
-import MCview.PDBfile;
+import org.testng.Assert;
+import org.testng.AssertJUnit;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
public class Mapping
{
- @Test
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
+ /*
+ * more test data
+ *
+ * 1QCF|A/101-121 SFQKGDQMVVLEESGEWWKAR Ser 114 jumps to Gly 116 at position
+ * 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)
+ public void pdbEntryPositionMap() throws Exception
+ {
+ 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
+ Sequence uprot = new Sequence("TheProtSeq",
+ "DAWEIPRESLKLEKKLGAGQFGEVWMATYNKHTKVAVKTMKPGSMSVEAFLAEANVMKTL");
+ uprot.setStart(offset + 258); // make it harder - create a fake
+ // relocation problem for jalview to
+ // deal with
+ uprot.setEnd(uprot.getStart() + uprot.getLength() - 1);
+ // 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 };
+
+ StructureSelectionManager ssm = new jalview.structure.StructureSelectionManager();
+ StructureFile pmap = ssm.setMapping(true, new SequenceI[] { uprot },
+ new String[] { "A" }, "test/jalview/ext/jmol/1QCF.pdb",
+ DataSourceType.FILE);
+ assertTrue(pmap != null);
+ SequenceI protseq = pmap.getSeqsAsArray()[0];
+ AlignmentAnnotation pstra = protseq
+ .getAnnotation("Secondary Structure")[0];
+ int pinds, pinde;
+ pstra.restrict((pinds = protseq.findIndex(258) - 1),
+ pinde = (protseq.findIndex(317) - 1));
+ int op;
+ System.out.println("PDB Annot");
+ for (char c : protseq.getSubSequence(pinds, pinde).getSequence())
+ {
+ System.out.print(c + ", ");
+ }
+ System.out.println("\n" + pstra + "\n\nsubsequence\n");
+ for (char c : uprot.getSequence())
+ {
+ System.out.print(c + ", ");
+ }
+ System.out.println("");
+ for (AlignmentAnnotation ss : uprot
+ .getAnnotation("Secondary Structure"))
+ {
+ ss.adjustForAlignment();
+ System.out.println("Uniprot Annot\n" + ss);
+ assertTrue(ss.hasIcons);
+ char expected = 'H';
+ for (int p : helices)
+ {
+ Annotation a = ss.annotations[op = (uprot.findIndex(offset + p) - 1)];
+ assertTrue(
+ "Expected a helix at position " + p + uprot.getCharAt(op)
+ + " but got coil", a != null);
+ assertEquals("Expected a helix at position " + p,
+ a.secondaryStructure, expected);
+ }
+ expected = 'E';
+ for (int p : sheets)
+ {
+ Annotation a = ss.annotations[uprot.findIndex(offset + p) - 1];
+ assertTrue(
+ "Expected a strand at position " + p + " but got coil",
+ a != null);
+ assertEquals("Expected a strand at position " + p,
+ a.secondaryStructure, expected);
+ }
+ expected = ' ';
+ for (int p : coils)
+ {
+ Annotation a = ss.annotations[uprot.findIndex(offset + p) - 1];
+ assertTrue("Expected coil at position " + p + " but got "
+ + a.secondaryStructure, a == null);
+ }
+ }
+ }
+ }
+
+ @Test(groups = { "Functional" }, enabled = false)
public void testPDBentryMapping() throws Exception
{
+ 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[]
- { "A" }, inFile = "examples/1gaq.txt", jalview.io.FormatAdapter.FILE);
+ StructureFile pde = ssm.setMapping(true, new SequenceI[] { sq },
+ new String[]
+ { "A" }, inFile = "examples/1gaq.txt", DataSourceType.FILE);
assertTrue("PDB File couldn't be found", pde != null);
StructureMapping[] mp = ssm.getMapping(inFile);
assertTrue("No mappings made.", mp != null && mp.length > 0);
"Only two line graphs should be transferred to associated sequence.",
2, nsTemp);
// Now test the transfer function and compare annotated positions
- for (StructureMapping origMap:mp)
+ for (StructureMapping origMap : mp)
{
- if (origMap.getSequence()==sq)
+ if (origMap.getSequence() == sq)
{
assertEquals("Mapping was incomplete.", sq.getLength() - 1,
(origMap.getPDBResNum(sq.getEnd()) - origMap
System.out.println("pdb:" + sq.getSequenceAsString());
System.out.println("ann:" + transfer.toString());
- for (int p = 0, pSize = firstChain.getLength() - 1; p < pSize; p++)
+ for (int p = 0, pSize = firstChain.getLength(); p < pSize; p++)
{
// walk along the pdb chain's jalview sequence
int rseqpos;
// p is index into PDB residue entries
// rseqpos is pdb sequence position for position p
// fpos is sequence position for associated position for rseqpos
- int tanpos = sq.findIndex(fpos);
- if (transfer.annotations.length <= tanpos)
+ // tanpos is the column for the mapped sequence position
+ int tanpos = sq.findIndex(fpos) - 1;
+ if (tanpos < 0 || transfer.annotations.length <= tanpos)
{
// gone beyond mapping to the sequence
break;
}
- Annotation a = transfer.annotations[sq.findIndex(fpos)], b = alan.annotations[p];
+
+ Annotation a = transfer.annotations[tanpos], b = alan.annotations[p];
assertEquals("Non-equivalent annotation element at " + p + "("
- + rseqpos + ")"
- + " expected at " + fpos + " (alIndex "
- + sq.findIndex(fpos) + ")",
- a == null ? a : a.toString(),
+ + rseqpos + ")" + " expected at " + fpos + " (alIndex "
+ + tanpos + ")", a == null ? a : a.toString(),
b == null ? b : b.toString());
System.out.print("(" + a + "|" + b + ")");
}
}
}
+ /**
+ * corner case for pdb mapping - revealed a problem with the AlignSeq->Mapping
+ * transform
+ *
+ */
+ @Test(groups = { "Functional" })
+ public void mapFer1From3W5V() throws Exception
+ {
+ AlignFrame seqf = new FileLoader(false)
+ .LoadFileWaitTillLoaded(
+ ">FER1_MAIZE/1-150 Ferredoxin-1, chloroplast precursor\nMATVLGSPRAPAFFFSSSSLRAAPAPTAVALPAAKVGIMGRSASSRRRLRAQATYNVKLITPEGEVELQVPD\nDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSYLDDGQIADGWVLTCHAYPTSDVVIETHKE\nEELTGA",
+ DataSourceType.PASTE, FileFormat.Fasta);
+ SequenceI newseq = seqf.getViewport().getAlignment().getSequenceAt(0);
+ StructureSelectionManager ssm = new jalview.structure.StructureSelectionManager();
+ StructureFile pmap = ssm.setMapping(true, new SequenceI[] { newseq },
+ new String[] { null }, "examples/3W5V.pdb",
+ DataSourceType.FILE);
+ if (pmap == null)
+ {
+ 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(groups = { "Functional" })
+ public void compareTransferredToRefPDBAnnot() throws Exception
+ {
+ // JBPNote this has failed when run on OSX via gradle clean test
+ // possible race condition ?
+ StructureImportSettings.setProcessSecondaryStructure(true);
+ StructureImportSettings.setVisibleChainAnnotation(true);
+ StructureImportSettings.setShowSeqFeatures(true);
+ AlignFrame ref = new FileLoader(false)
+ .LoadFileWaitTillLoaded("test/jalview/ext/jmol/1QCF.pdb",
+ DataSourceType.FILE);
+ SequenceI refseq = ref.getViewport().getAlignment().getSequenceAt(0);
+ SequenceI newseq = new Sequence(refseq.getName() + "Copy",
+ refseq.getSequenceAsString());
+ // make it harder by shifting the copy vs the reference
+ newseq.setStart(refseq.getStart() + 25);
+ newseq.setEnd(refseq.getLength() + 25 + refseq.getStart());
+ StructureSelectionManager ssm = new jalview.structure.StructureSelectionManager();
+ ssm.setProcessSecondaryStructure(true);
+ ssm.setAddTempFacAnnot(true);
+ StructureFile pmap = ssm.setMapping(true, new SequenceI[] { newseq },
+ new String[] { null }, "test/jalview/ext/jmol/1QCF.pdb",
+ DataSourceType.FILE);
+ assertTrue(pmap != null);
+ assertEquals("Original and copied sequence of different lengths.",
+ refseq.getLength(), newseq.getLength());
+ assertTrue(refseq.getAnnotation() != null
+ && refseq.getAnnotation().length > 0);
+ assertTrue(newseq.getAnnotation() != null
+ && newseq.getAnnotation().length > 0);
+ for (AlignmentAnnotation oannot : refseq.getAnnotation())
+ {
+ for (AlignmentAnnotation tannot : newseq.getAnnotation(oannot.label))
+ {
+ for (int p = 0, pSize = refseq.getLength(); p < pSize; p++)
+ {
+ Annotation orig = oannot.annotations[p], tran = tannot.annotations[p];
+ assertTrue("Mismatch: coil and non coil site " + p, orig == tran
+ || orig != null && tran != null);
+ if (tran != null)
+ {
+ assertEquals("Mismatch in secondary structure at site " + p,
+ tran.secondaryStructure, orig.secondaryStructure);
+ }
+ }
+ }
+ }
+ }
}
git://source.jalview.org / jalview.git / blobdiff