X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fstructure%2FStructureSelectionManagerTest.java;h=9b240d3b83763e1f253b974d05e097adb195d4eb;hb=4f30214e8098748469c6a4269ac2ed6c5750e4b0;hp=a7e52ff284bf697f192872cee5d9a34c78a58b01;hpb=483e7163b1fb8d4bcb9393014816c944befce328;p=jalview.git diff --git a/test/jalview/structure/StructureSelectionManagerTest.java b/test/jalview/structure/StructureSelectionManagerTest.java index a7e52ff..9b240d3 100644 --- a/test/jalview/structure/StructureSelectionManagerTest.java +++ b/test/jalview/structure/StructureSelectionManagerTest.java @@ -20,28 +20,53 @@ */ package jalview.structure; +import static org.junit.Assert.assertArrayEquals; +import static org.testng.Assert.assertNotNull; import static org.testng.AssertJUnit.assertEquals; import static org.testng.AssertJUnit.assertTrue; +import jalview.analysis.AlignmentUtils; +import jalview.api.structures.JalviewStructureDisplayI; +import jalview.bin.Cache; import jalview.datamodel.AlignedCodonFrame; +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.Annotation; +import jalview.datamodel.PDBEntry; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; +import jalview.ext.jmol.JmolCommands; +import jalview.gui.AlignFrame; +import jalview.gui.Desktop; import jalview.gui.JvOptionPane; +import jalview.gui.SequenceRenderer; +import jalview.gui.StructureChooser; import jalview.io.DataSourceType; +import jalview.io.FileLoader; +import jalview.io.Jalview2xmlBase; import jalview.io.StructureFile; import jalview.util.MapList; +import jalview.ws.DBRefFetcher; +import jalview.ws.sifts.SiftsSettings; import java.util.ArrayList; +import java.util.LinkedHashMap; import java.util.List; +import java.util.Map; +import java.util.SortedMap; +import java.util.TreeMap; +import org.testng.Assert; import org.testng.annotations.BeforeClass; import org.testng.annotations.BeforeMethod; import org.testng.annotations.Test; -public class StructureSelectionManagerTest +@Test(singleThreaded = true) +public class StructureSelectionManagerTest extends Jalview2xmlBase { + @Override @BeforeClass(alwaysRun = true) public void setUpJvOptionPane() { @@ -99,10 +124,10 @@ public class StructureSelectionManagerTest acf3.addMap(new Sequence("s3", "ttt"), new Sequence("p3", "p"), new MapList(new int[] { 1, 3 }, new int[] { 1, 1 }, 1, 1)); - List set1 = new ArrayList(); + List set1 = new ArrayList<>(); set1.add(acf1); set1.add(acf2); - List set2 = new ArrayList(); + List set2 = new ArrayList<>(); set2.add(acf2); set2.add(acf3); @@ -145,7 +170,7 @@ public class StructureSelectionManagerTest /* * Verify a RESNUM sequence feature in the PDBfile sequence */ - SequenceFeature sf = pmap.getSeqs().get(0).getSequenceFeatures()[0]; + SequenceFeature sf = pmap.getSeqs().get(0).getSequenceFeatures().get(0); assertEquals("RESNUM", sf.getType()); assertEquals("1gaq", sf.getFeatureGroup()); assertEquals("GLU: 19 1gaqA", sf.getDescription()); @@ -155,9 +180,315 @@ public class StructureSelectionManagerTest * sequence */ StructureMapping map = sm.getMapping("examples/1gaq.txt")[0]; - sf = map.sequence.getSequenceFeatures()[0]; + sf = map.sequence.getSequenceFeatures().get(0); assertEquals("RESNUM", sf.getType()); assertEquals("1gaq", sf.getFeatureGroup()); assertEquals("ALA: 1 1gaqB", sf.getDescription()); } + + /** + * Verify that RESNUM sequence features are present after creating a PDB + * mapping from a local file, then that everything stays in the same place + * when the file is viewed. The corner case is that 4IM2 is a fragment of a + * PDB file, which still includes the 'ID' field - a bug in Jalview 2.10.3 + * causes features, annotation and positions to be remapped to the wrong place + * on viewing the structure + */ + @Test(groups = { "Network" }) + public void testMapping_EqualsFeatures() + { + // for some reason 'BeforeMethod' (which should be inherited from + // Jalview2XmlBase isn't always called)... + Desktop.instance.closeAll_actionPerformed(null); + try { + Thread.sleep(200); + } catch (Exception foo) {}; + SequenceI seq = new Sequence("4IM2|A", + "LDFCIRNIEKTVMGEISDIHTKLLRLSSSQGTIE"); + String P4IM2_MISSING = "examples/testdata/4IM2_missing.pdb"; + StructureSelectionManager sm = new StructureSelectionManager(); + sm.setProcessSecondaryStructure(true); + sm.setAddTempFacAnnot(true); + StructureFile pmap = sm.setMapping(true, new SequenceI[] { seq }, + new String[] + { null }, P4IM2_MISSING, + DataSourceType.FILE); + assertTrue(pmap != null); + + assertEquals(1, pmap.getSeqs().size()); + assertEquals("4IM2|A", pmap.getSeqs().get(0).getName()); + + List structuremap1 = new ArrayList<>( + sm.getMapping(P4IM2_MISSING)[0] + .getPDBResNumRanges(seq.getStart(), seq.getEnd())); + + /* + * Verify a RESNUM sequence feature in the PDBfile sequence + * LEU468 - start+0 + * VAL479 - start+11 + * MET486 - start+12 + * GLY496 - start+13 + * GLU516 - start+33 (last) + * + * Expect features and mapping to resolve to same residues. + * Also try creating a view and test again + * + */ + String[] feats = new String[] { "LEU", "468", "VAL", "479", "MET", + "486", "GLY", "496", "GLU", "516" }; + int[] offset = new int[] { 0, 11, 12, 13, 33 }; + + List fdesc = new ArrayList<>(); + for (int f = 0; f < feats.length; f += 2) + { + fdesc.add(feats[f] + ": " + feats[f + 1] + " 4im2A"); + } + SequenceI pdbseq = pmap.getSeqs().get(0); + verifySeqFeats(pdbseq, offset, fdesc); + + /// Now load as a view + + AlignFrame alf = new FileLoader(false).LoadFileWaitTillLoaded( + "examples/testdata/4IM2_missing.pdb", DataSourceType.FILE); + Desktop.addInternalFrame(alf, "examples/testdata/4IM2_missing.pdb", 800, + 400); + AlignmentI pdbal = alf.getViewport().getAlignment(); + SequenceI pdb_viewseq = pdbal.getSequenceAt(0); + assertEquals(pdb_viewseq.getSequenceAsString(), + seq.getSequenceAsString()); + // verify the feature location on the sequence when pdb imported as an + // alignment + verifySeqFeats(pdb_viewseq, offset, fdesc); + + + JalviewStructureDisplayI viewr = openStructureViaChooser(alf, + pdb_viewseq, "4IM2"); + + // and check all is good with feature location still + verifySeqFeats(pdb_viewseq, offset, fdesc); + + // finally check positional mapping for sequence and structure + PDBEntry pdbe = seq.getPDBEntry("4IM2"); + StructureSelectionManager apssm = alf.alignPanel + .getStructureSelectionManager(); + StructureMapping[] smap = apssm + .getMapping(pdbe.getFile()); + assertNotNull(smap); + assertNotNull(smap[0]); + // find the last position in the alignment sequence - this is not + // 'SequenceI.getEnd()' - which gets the last PDBRESNUM rather than + // SequenceI.getStart() + number of residues in file... + int realSeqEnd = pdb_viewseq.findPosition(pdb_viewseq.getLength()); + List ranges = smap[0].getPDBResNumRanges(pdb_viewseq.getStart(), + realSeqEnd); + assertEquals(structuremap1.size(), ranges.size()); + int tot_mapped = 0; + for (int p = 0; p < ranges.size(); p++) + { + assertArrayEquals(structuremap1.get(p), ranges.get(p)); + tot_mapped += 1 + (structuremap1.get(p)[1] - structuremap1.get(p)[0]); + } + + assertEquals(pdb_viewseq.getLength(), tot_mapped); + + int lastmappedp = StructureMapping.UNASSIGNED_VALUE; + for (int rp = pdb_viewseq.getStart(), rpEnd = pdb_viewseq + .findPosition(pdb_viewseq.getLength() - 1); rp <= rpEnd; rp++) + { + int mappedp = smap[0].getPDBResNum(rp); + if (mappedp != StructureMapping.UNASSIGNED_VALUE) + { + tot_mapped--; + if (lastmappedp == mappedp) + { + Assert.fail("Duplicate mapped position at " + rp + " (dupe = " + + mappedp + ")"); + } + } + } + + Assert.assertEquals(tot_mapped, 0, + "Different number of mapped residues compared to ranges of mapped residues"); + + // positional mapping to atoms for color by structure is still wrong, even + // though panel looks correct. + + String[] smcr = new JmolCommands().colourBySequence(apssm, + new String[] + { pdbe.getFile() }, + new SequenceI[][] + { new SequenceI[] { pdb_viewseq } }, + new SequenceRenderer(alf.alignPanel.getAlignViewport()), + alf.alignPanel); + // Expected - all residues are white + for (String c : smcr) + { + assertTrue(c.contains("color[255,255,255]")); + System.out.println(c); + } + } + + private void verifySeqFeats(SequenceI pdbseq, int[] offset, + List fdesc) + { + for (int o = 0; o < offset.length; o++) + { + int res = pdbseq.findPosition(offset[o]); + List sf = pdbseq.getFeatures().findFeatures(res, res, + "RESNUM"); + assertEquals("Expected sequence feature at position " + res + "(" + + offset[o] + ")", 1, sf.size()); + assertEquals("Wrong description at " + res + "(" + offset[o] + ")", + fdesc.get(o), sf.get(0).getDescription()); + } + + } + + @Test(groups = { "Network" }) + public void testAssociatedMappingToSubSeq() throws Exception + { + + // currently this test fails if trimming is enabled + Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, + Boolean.FALSE.toString()); + String TEMP_FACTOR_AA="Temperature Factor"; + String PDBID = "4IM2"; + String FullLengthSeq = ">TBK1_HUMAN Serine/threonine-protein kinase TBK1\n" + + "MQSTSNHLWLLSDILGQGATANVFRGRHKKTGDLFAIKVFNNISFLRPVDVQMREFEVLKKLNHKNIVKLFA\n" + + "IEEETTTRHKVLIMEFCPCGSLYTVLEEPSNAYGLPESEFLIVLRDVVGGMNHLRENGIVHRDIKPGNIMRV\n" + + "IGEDGQSVYKLTDFGAARELEDDEQFVSLYGTEEYLHPDMYERAVLRKDHQKKYGATVDLWSIGVTFYHAAT\n" + + "GSLPFRPFEGPRRNKEVMYKIITGKPSGAISGVQKAENGPIDWSGDMPVSCSLSRGLQVLLTPVLANILEAD\n" + + "QEKCWGFDQFFAETSDILHRMVIHVFSLQQMTAHKIYIHSYNTATIFHELVYKQTKIISSNQELIYEGRRLV\n" + + "LEPGRLAQHFPKTTEENPIFVVSREPLNTIGLIYEKISLPKVHPRYDLDGDASMAKAITGVVCYACRIASTL\n" + + "LLYQELMRKGIRWLIELIKDDYNETVHKKTEVVITLDFCIRNIEKTVKVYEKLMKINLEAAELGEISDIHTK\n" + + "LLRLSSSQGTIETSLQDIDSRLSPGGSLADAWAHQEGTHPKDRNVEKLQVLLNCMTEIYYQFKKDKAERRLA\n" + + "YNEEQIHKFDKQKLYYHATKAMTHFTDECVKKYEAFLNKSEEWIRKMLHLRKQLLSLTNQCFDIEEEVSKYQ\n" + + "EYTNELQETLPQKMFTASSGIKHTMTPIYPSSNTLVEMTLGMKKLKEEMEGVVKELAENNHILERFGSLTMD\n" + + "GGLRNVDCL"; + /* + * annotation exported after importing full length sequence to desktop, opening 4IM2 and selecting 'Add Reference Annotation'. + * + * Note - tabs must be replaced with \t - Eclipse expands them to spaces otherwise. + */ + String FullLengthAnnot = "JALVIEW_ANNOTATION\n" + + "# Created: Mon Feb 05 15:30:20 GMT 2018\n" + + "# Updated: Fri Feb 09 17:05:17 GMT 2018\n" + + "\n" + + "\n" + + "SEQUENCE_REF\tTBK1_HUMAN\n" + + "LINE_GRAPH\tTemperature Factor\tTemperature Factor for 4im2A\t125.22|128.51|120.35|113.12|122.6|114.44|91.49|102.53|98.22|111.41|111.32|116.64|103.55|100.53|95.07|105.55|114.76|128.29|133.55|142.14|121.12|110.36|95.79|95.39|87.14|99.56|93.55|94.21|100.33|110.68|97.85|82.37|75.87|76.53|77.85|82.49|80.92|96.88|122.58|133.31|160.15|180.51|||||242.88|258.97|247.01|227.12|223.24|211.62|184.65|183.51|168.96|160.04|150.88|131.68|130.43|139.87|148.59|136.57|125.7|96.51|74.49|74.08|85.87|70.93|86.47|101.59|97.51|97.39|117.19|114.27|129.5|112.98|147.52|170.26|154.98|168.18|157.51|131.95|105.85|97.78|97.35|76.51|76.31|72.55|71.43|78.82|79.94|75.04|79.54|77.95|83.56|88.5|71.51|71.73|75.96|82.36|81.75|66.51|67.23|69.35|67.92|54.75|71.19|61.85|65.34|67.97|64.51|67.41|62.28|72.85|72.76|70.64|65.23|71.07|67.73|87.72|64.93|75.92|94.02|99.35|93.71|103.59|106.29|115.46|118.69|147.18|130.62|171.64|158.95|164.11||107.42|88.53|83.52|88.06|94.06|80.82|59.01|59.73|78.89|69.21|70.34|81.95|74.53|60.92|64.65|55.79|75.71|68.86|70.95|75.08|87.76|85.43|105.84|||||||||||||||||137.46|151.33|145.17|122.79|111.56|126.72|124.06|161.75|176.84|180.51|198.49|196.75|187.41||195.23|202.27|203.16|226.55|221.75|193.83||||||172.33|177.97|151.47|132.65|99.22|93.7|91.15|88.24|72.35|70.05|70.0|74.92|66.51|68.37|65.76|70.12|74.97|76.89|80.83|70.21|69.48|79.54|82.65|96.54|114.31|140.46|168.51|176.99|205.08|209.27|155.83|139.41|151.3|129.33|111.31|119.62|121.37|102.26|115.39|129.97|128.65|110.38|110.66|116.1|82.53|84.02|82.17|87.63|86.42|77.23|91.23|95.53|102.21|120.73|133.26|109.67|108.49|93.25|92.85|86.39|95.66|94.92|85.82|80.13|76.17|86.61|78.9|77.97|105.6|70.66|69.35|78.94|66.68|63.03|69.91|79.05|75.43|70.73|70.02|80.57|81.74|77.99|84.1|91.66|92.42|94.03|116.47|132.01|154.55|163.99|161.37|155.23|132.78|109.3|90.38|101.83|99.61|91.68|82.77|86.12|82.73|90.13|85.14|79.54|74.27|74.06|72.88|86.34|72.0|69.32|60.9|68.15|52.99|63.53|61.3|66.01|68.28|77.41|71.52|67.18|66.17|71.51|65.47|52.63|65.08|66.37|73.76|77.79|67.58|79.53|84.75|87.42|78.9|79.19|85.57|73.67|80.56|86.19|72.17|66.27|72.8|86.28|78.89|74.5|90.6|80.42|92.5|92.84|96.18|92.08|88.5|87.25|64.6|68.95|65.56|67.55|71.62|78.24|84.95|71.35|86.41|84.73|94.41|95.09|84.74|87.64|88.85|75.1|86.42|79.28|73.14|78.54|80.81|60.66|67.93|71.64|59.85|64.7|61.22|63.84|65.9|62.18|74.95|72.92|93.37|90.47|96.0|93.8|88.46|79.78|83.4|66.55|68.7|73.2|78.76|85.67|84.8|89.59|96.52|79.53|103.51|134.72|126.7|145.31|156.17|149.35|128.48|117.29|118.98|131.59|109.36|90.39|87.68|91.81|78.77|80.11|91.39|75.57|78.98|71.53|76.85|70.9|64.71|73.55|73.45|60.0|69.92|57.89|69.07|66.45|62.85|57.83|57.89|66.4|61.61|60.85|66.47|63.53|63.84|65.96|73.06|70.82|64.51|63.66|73.37|73.59|68.09|78.93|76.99|75.05|71.32|88.4|78.88|93.08|110.61|94.32|99.24|128.99|129.49|132.74|124.21|120.32|142.06|166.41|149.87|153.29|172.19|165.89|181.6|223.11|237.73|176.41|171.09|189.65|188.61|154.84|142.72|154.25|170.99|175.65|||||||110.61||||||||||158.07|170.73|167.93|198.47|212.36|181.71|157.69|163.31|138.96|120.29|131.63|152.26|125.06|136.66|148.97|129.68|120.52|135.31|136.05|119.39|124.18|128.94|123.02|103.37|128.44|134.12|118.88|120.94|130.38|124.67|112.21|113.69|123.65|132.06|114.97|110.75|92.38|101.2|103.25|94.84|85.3|82.19|89.81|98.81|83.03|68.91|65.24|70.31|63.49|86.38|71.07|62.65|63.95|66.98|58.06|68.28|62.11|63.86|67.4|68.69|69.57|68.03|74.23|75.66|70.67|81.08|81.31|82.49|88.15|95.99|92.97|100.01|113.18|122.37|110.99|122.19|159.27|147.74|133.96|111.2|115.64|126.55|107.15|102.85|117.06|116.56|109.55|96.82|98.92|96.53|86.0|88.11|92.76|85.77|79.41|93.06|86.96|76.35|72.37|74.19|68.6|67.46|74.47|76.25|66.73|73.18|75.2|88.21|84.93|75.04|71.09|82.6|80.03|76.22|75.76|83.72|75.85|79.36|90.35|86.9|78.24|95.64|97.38|86.41|85.02|91.87|87.36|77.56|81.25|91.66|83.65|77.67|85.07|89.21|92.66|92.46|89.0|100.83|96.71|94.81|101.37|111.28|124.48|119.73|127.81|134.41|132.4|140.32|140.86|166.52|160.16|168.39|176.74|174.63|172.86|168.55|155.9|132.71|113.44|113.49|123.9|151.11|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n" + + + "\n" + + ""; + AlignFrame alf_full=new + FileLoader(false).LoadFileWaitTillLoaded(FullLengthSeq,DataSourceType.PASTE); + alf_full.loadJalviewDataFile(FullLengthAnnot, DataSourceType.PASTE, null, null); + AlignmentI al_full = alf_full.getViewport().getAlignment(); + AlignmentAnnotation fullseq_tf = al_full.findAnnotations(al_full.getSequences().get(0), null, TEMP_FACTOR_AA).iterator() + .next(); + assertNotNull(fullseq_tf); + + // getMappingFor + // AlignmentI al_full=alf_full.getViewport().getAlignment(); + // + // // load 4IM2 (full length, SIFTS onto full alingnment) + // SiftsSettings.setMapWithSifts(true); + // StructureChooser schoose = new StructureChooser(selectedSeqs_full, + // seq_full, + // alf_full.getViewport().getAlignPanel()); + // schoose.selectStructure(PDBID); + // schoose.ok_ActionPerformed(); + + AlignFrame alf = new FileLoader(false).LoadFileWaitTillLoaded( + ">TBK1_HUMAN/470-502 Serine/threonine-protein kinase TBK1\nFCIRNIEKTVKVYEKLMKINLEAAELGEISDIH", + DataSourceType.PASTE); + Desktop.addInternalFrame(alf, "Foo", 800, 600); + ; + AlignmentI al = alf.getViewport().getAlignment(); + SequenceI seq = al.getSequenceAt(0); + assertEquals(470, seq.getStart()); + // load 4IM2 (full length, SIFTS) + SiftsSettings.setMapWithSifts(true); + StructureImportSettings.setProcessSecondaryStructure(true); + StructureImportSettings.setVisibleChainAnnotation(true); + JalviewStructureDisplayI sview = openStructureViaChooser(alf, seq, + PDBID); + + AlignmentAnnotation subseq_tf=null; + assertTrue(seq.getDBRefs() != null && seq.getDBRefs().size() > 0); + + if (!al.findAnnotations(seq, null, TEMP_FACTOR_AA).iterator().hasNext()) + { + // FIXME JAL-2321 - don't see reference annotation on alignment the first + // time + // around + SortedMap tipEntries = new TreeMap<>(); + final Map> candidates = new LinkedHashMap<>(); + + AlignmentUtils.findAddableReferenceAnnotations(al.getSequences(), + tipEntries, candidates, al); + AlignmentUtils.addReferenceAnnotations(candidates, al, null); + + if (!al.findAnnotations(seq, null, TEMP_FACTOR_AA).iterator() + .hasNext()) + { + Assert.fail( + "JAL-2321 or worse has occured. No secondary structure added to alignment."); + } + } + subseq_tf = al.findAnnotations(seq, null, TEMP_FACTOR_AA).iterator() + .next(); + // verify against annotation after loading 4IM2 to full length TBK1_HUMAN + // verify location of mapped residues + // verify location of secondary structure annotation + // Specific positions: LYS477 (h),THR478 (no helix), ... GLY496(no helix), + // GLU497 (helix), + + // check there is or is not a tempfactor for each mapped position, and that + // values are equal for those positions. + for (int p=seq.getStart();p<=seq.getEnd();p++) + { + Annotation orig,subseq; + orig = fullseq_tf.getAnnotationForPosition(p); + subseq = subseq_tf.getAnnotationForPosition(p); + if (orig == null) + { + Assert.assertNull(subseq, + "Expected no annotation transferred at position " + p); + } + ; + if (orig != null) + { + Assert.assertNotNull(subseq, + "Expected annotation transfer at position " + p); + assertEquals(orig.value, subseq.value); + } + ; + + } + } + + private JalviewStructureDisplayI openStructureViaChooser(AlignFrame alf, + SequenceI seq, + String pDBID) + { + + SequenceI[] selectedSeqs = new SequenceI[] { seq }; + + StructureChooser schoose = new StructureChooser(selectedSeqs, seq, + alf.getViewport().getAlignPanel()); + + try + { + Thread.sleep(5000); + } catch (InterruptedException q) + { + } + ; + Assert.assertTrue(schoose.selectStructure(pDBID), + "Couldn't select structure via structure chooser: " + pDBID); + schoose.showStructures(true); + return schoose.getOpenedStructureViewer(); + } + }