+/*
+ * 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.junit.Assert.fail;
-
-import org.junit.Assert;
-import org.junit.Ignore;
-import org.junit.Test;
-
-import MCview.PDBfile;
+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.FormatAdapter;
+import jalview.io.StructureFile;
+
+import org.testng.Assert;
+import org.testng.AssertJUnit;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
public class Mapping
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
/*
* more test data
*
* 115 in PDB Res Numbering secondary structure numbers in jmol seem to be in
* msd numbering, not pdb res numbering.
*/
- @Test
- @Ignore
+ @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",
- jalview.io.FormatAdapter.FILE);
+ 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
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);
+ 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);
}
for (int p : sheets)
{
Annotation a = ss.annotations[uprot.findIndex(offset + p) - 1];
- assertTrue(
- "Expected a strand at position " + p + " but got coil",
+ assertTrue("Expected a strand at position " + p + " but got coil",
a != null);
assertEquals("Expected a strand at position " + p,
a.secondaryStructure, expected);
}
}
- @Test
- @Ignore
+ @Test(groups = { "Functional" }, enabled = false)
public void testPDBentryMapping() throws Exception
{
- fail("This test intentionally left to fail");
- Sequence sq = new Sequence(
- "1GAQ A subseq 126 to 219",
+ Assert.fail("This test intentionally left to fail");
+ Sequence sq = new Sequence("1GAQ A subseq 126 to 219",
"EIVKGVCSNFLCDLQPGDNVQITGPVGKEMLMPKDPNATIIMLATGTGIAPFRSFLWKMFFEKHDDYKFNGLGWLFLGVPTSSSLLYKEEFGKM");
Sequence sq1 = new Sequence(sq);
String inFile;
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);
if (origMap.getSequence() == sq)
{
assertEquals("Mapping was incomplete.", sq.getLength() - 1,
- (origMap.getPDBResNum(sq.getEnd()) - origMap
- .getPDBResNum(sq.getStart())));
+ (origMap.getPDBResNum(sq.getEnd())
+ - origMap.getPDBResNum(sq.getStart())));
// sanity check - if this fails, mapping from first position in sequence
// we want to transfer to is not where we expect
assertEquals(1, origMap.getSeqPos(126));
{
// walk along the pdb chain's jalview sequence
int rseqpos;
- int fpos = origMap.getSeqPos(rseqpos = firstChain
- .findPosition(p));
+ int fpos = origMap
+ .getSeqPos(rseqpos = firstChain.findPosition(p));
// only look at positions where there is a corresponding position in
// mapping
if (fpos < 1)
break;
}
- Annotation a = transfer.annotations[tanpos], b = alan.annotations[p];
- assertEquals("Non-equivalent annotation element at " + p + "("
- + rseqpos + ")" + " expected at " + fpos + " (alIndex "
- + tanpos + ")",
+ 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(),
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)
- .LoadFileWaitTillLoaded(
- ">FER1_MAIZE/1-150 Ferredoxin-1, chloroplast precursor\nMATVLGSPRAPAFFFSSSSLRAAPAPTAVALPAAKVGIMGRSASSRRRLRAQATYNVKLITPEGEVELQVPD\nDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSYLDDGQIADGWVLTCHAYPTSDVVIETHKE\nEELTGA",
- FormatAdapter.PASTE, "FASTA");
+ 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();
- PDBfile pmap = ssm.setMapping(true, new SequenceI[]
- { newseq }, new String[]
- { null }, "examples/3W5V.pdb",
- jalview.io.FormatAdapter.FILE);
+ StructureFile pmap = ssm.setMapping(true, new SequenceI[] { newseq },
+ new String[]
+ { null }, "examples/3W5V.pdb", DataSourceType.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)
- .LoadFileWaitTillLoaded("test/jalview/ext/jmol/1QCF.pdb",
- jalview.io.FormatAdapter.FILE);
+ 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());
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",
- jalview.io.FormatAdapter.FILE);
+ 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());
{
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);
+ 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,
git://source.jalview.org / jalview.git / blobdiff