+/*
+ * 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.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.HashSet;
-import java.util.Set;
+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()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
private StructureSelectionManager ssm;
- @BeforeMethod
+ @BeforeMethod(alwaysRun = true)
public void setUp()
{
+ StructureImportSettings.setShowSeqFeatures(true);
ssm = new StructureSelectionManager();
}
- @Test
- public void testAddMapping()
+ @Test(groups = { "Functional" })
+ public void testRegisterMapping()
{
AlignedCodonFrame acf1 = new AlignedCodonFrame();
+ acf1.addMap(new Sequence("s1", "ttt"), new Sequence("p1", "p"),
+ new MapList(new int[] { 1, 3 }, new int[] { 1, 1 }, 1, 1));
AlignedCodonFrame acf2 = new AlignedCodonFrame();
+ acf2.addMap(new Sequence("s2", "ttt"), new Sequence("p2", "p"),
+ new MapList(new int[] { 1, 3 }, new int[] { 1, 1 }, 1, 1));
- /*
- * One mapping only.
- */
- ssm.addMapping(acf1);
- assertEquals(1, ssm.seqmappings.size());
- assertTrue(ssm.seqmappings.contains(acf1));
- assertEquals(1, ssm.seqMappingRefCounts.size());
- assertEquals(1, ssm.seqMappingRefCounts.get(acf1).intValue());
+ ssm.registerMapping(acf1);
+ assertEquals(1, ssm.getSequenceMappings().size());
+ assertTrue(ssm.getSequenceMappings().contains(acf1));
- /*
- * A second mapping.
- */
- ssm.addMapping(acf2);
- assertEquals(2, ssm.seqmappings.size());
- assertTrue(ssm.seqmappings.contains(acf1));
- assertTrue(ssm.seqmappings.contains(acf2));
- assertEquals(2, ssm.seqMappingRefCounts.size());
- assertEquals(1, ssm.seqMappingRefCounts.get(acf1).intValue());
- assertEquals(1, ssm.seqMappingRefCounts.get(acf2).intValue());
+ ssm.registerMapping(acf2);
+ assertEquals(2, ssm.getSequenceMappings().size());
+ assertTrue(ssm.getSequenceMappings().contains(acf1));
+ assertTrue(ssm.getSequenceMappings().contains(acf2));
/*
- * A second reference to the first mapping.
+ * Re-adding the first mapping does nothing
*/
- ssm.addMapping(acf1);
- assertEquals(2, ssm.seqmappings.size());
- assertTrue(ssm.seqmappings.contains(acf1));
- assertTrue(ssm.seqmappings.contains(acf2));
- assertEquals(2, ssm.seqMappingRefCounts.size());
- assertEquals(2, ssm.seqMappingRefCounts.get(acf1).intValue());
- assertEquals(1, ssm.seqMappingRefCounts.get(acf2).intValue());
+ ssm.registerMapping(acf1);
+ assertEquals(2, ssm.getSequenceMappings().size());
+ assertTrue(ssm.getSequenceMappings().contains(acf1));
+ assertTrue(ssm.getSequenceMappings().contains(acf2));
}
- @Test
- public void testAddMappings()
+ @Test(groups = { "Functional" })
+ public void testRegisterMappings()
{
AlignedCodonFrame acf1 = new AlignedCodonFrame();
+ acf1.addMap(new Sequence("s1", "ttt"), new Sequence("p1", "p"),
+ new MapList(new int[] { 1, 3 }, new int[] { 1, 1 }, 1, 1));
AlignedCodonFrame acf2 = new AlignedCodonFrame();
+ acf2.addMap(new Sequence("s2", "ttt"), new Sequence("p2", "p"),
+ new MapList(new int[] { 1, 3 }, new int[] { 1, 1 }, 1, 1));
AlignedCodonFrame acf3 = new AlignedCodonFrame();
+ acf3.addMap(new Sequence("s3", "ttt"), new Sequence("p3", "p"),
+ new MapList(new int[] { 1, 3 }, new int[] { 1, 1 }, 1, 1));
- Set<AlignedCodonFrame> set1 = new HashSet<AlignedCodonFrame>();
+ List<AlignedCodonFrame> set1 = new ArrayList<>();
set1.add(acf1);
set1.add(acf2);
- Set<AlignedCodonFrame> set2 = new HashSet<AlignedCodonFrame>();
+ List<AlignedCodonFrame> set2 = new ArrayList<>();
set2.add(acf2);
set2.add(acf3);
/*
- * Adding both sets adds acf2 twice and acf1 and acf3 once each.
+ * Add both sets twice; each mapping should be added once only
*/
- ssm.addMappings(set1);
- ssm.addMappings(set2);
-
- assertEquals(3, ssm.seqmappings.size());
- assertTrue(ssm.seqmappings.contains(acf1));
- assertTrue(ssm.seqmappings.contains(acf2));
- assertTrue(ssm.seqmappings.contains(acf3));
- assertEquals(3, ssm.seqMappingRefCounts.size());
- assertEquals(1, ssm.seqMappingRefCounts.get(acf1).intValue());
- assertEquals(2, ssm.seqMappingRefCounts.get(acf2).intValue());
- assertEquals(1, ssm.seqMappingRefCounts.get(acf3).intValue());
+ ssm.registerMappings(set1);
+ ssm.registerMappings(set1);
+ ssm.registerMappings(set2);
+ ssm.registerMappings(set2);
+
+ assertEquals(3, ssm.getSequenceMappings().size());
+ assertTrue(ssm.getSequenceMappings().contains(acf1));
+ assertTrue(ssm.getSequenceMappings().contains(acf2));
+ assertTrue(ssm.getSequenceMappings().contains(acf3));
}
- @Test
- public void testRemoveMapping()
+ /**
+ * Verify that RESNUM sequence features are present after creating a PDB
+ * mapping
+ */
+ @Test(groups = { "Functional" })
+ public void testSetMapping_seqFeatures()
{
- AlignedCodonFrame acf1 = new AlignedCodonFrame();
- AlignedCodonFrame acf2 = new AlignedCodonFrame();
- ssm.addMapping(acf1);
+ SequenceI seq = new Sequence(
+ "1GAQ|B",
+ "ATYNVKLITPEGEVELQVPDDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSYLDDGQIADGWVLTCHAYPTSDVVIETHKEEELTGA");
+ StructureSelectionManager sm = new StructureSelectionManager();
+ sm.setProcessSecondaryStructure(true);
+ sm.setAddTempFacAnnot(true);
+ StructureFile pmap = sm.setMapping(true, new SequenceI[] { seq },
+ new String[] { null }, "examples/1gaq.txt", DataSourceType.FILE);
+ assertTrue(pmap != null);
- /*
- * Add one and remove it.
- */
- ssm.removeMapping(acf1);
- ssm.removeMapping(acf2);
- assertEquals(0, ssm.seqmappings.size());
- assertEquals(0, ssm.seqMappingRefCounts.size());
+ assertEquals(3, pmap.getSeqs().size());
+ assertEquals("1GAQ|A", pmap.getSeqs().get(0).getName());
+ assertEquals("1GAQ|B", pmap.getSeqs().get(1).getName());
+ assertEquals("1GAQ|C", pmap.getSeqs().get(2).getName());
/*
- * Add one twice and remove it once.
+ * Verify a RESNUM sequence feature in the PDBfile sequence
*/
- ssm.addMapping(acf1);
- ssm.addMapping(acf2);
- ssm.addMapping(acf1);
- ssm.removeMapping(acf1);
- assertEquals(2, ssm.seqmappings.size());
- assertTrue(ssm.seqmappings.contains(acf1));
- assertTrue(ssm.seqmappings.contains(acf2));
- assertEquals(2, ssm.seqMappingRefCounts.size());
- assertEquals(1, ssm.seqMappingRefCounts.get(acf1).intValue());
- assertEquals(1, ssm.seqMappingRefCounts.get(acf2).intValue());
+ SequenceFeature sf = pmap.getSeqs().get(0).getSequenceFeatures().get(0);
+ assertEquals("RESNUM", sf.getType());
+ assertEquals("1gaq", sf.getFeatureGroup());
+ assertEquals("GLU: 19 1gaqA", sf.getDescription());
/*
- * Remove both once more to clear the set.
+ * Verify a RESNUM sequence feature in the StructureSelectionManager mapped
+ * sequence
*/
- ssm.removeMapping(acf1);
- ssm.removeMapping(acf2);
- assertEquals(0, ssm.seqmappings.size());
- assertEquals(0, ssm.seqMappingRefCounts.size());
+ StructureMapping map = sm.getMapping("examples/1gaq.txt")[0];
+ sf = map.sequence.getSequenceFeatures().get(0);
+ assertEquals("RESNUM", sf.getType());
+ assertEquals("1gaq", sf.getFeatureGroup());
+ assertEquals("ALA: 1 1gaqB", sf.getDescription());
}
- @Test
- public void testRemoveMappings()
+ /**
+ * 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()
{
- AlignedCodonFrame acf1 = new AlignedCodonFrame();
- AlignedCodonFrame acf2 = new AlignedCodonFrame();
- AlignedCodonFrame acf3 = new AlignedCodonFrame();
+ // 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);
- /*
- * Initial ref counts are 3/2/1:
- */
- ssm.addMapping(acf1);
- ssm.addMapping(acf1);
- ssm.addMapping(acf1);
- ssm.addMapping(acf2);
- ssm.addMapping(acf2);
- ssm.addMapping(acf3);
-
- Set<AlignedCodonFrame> set1 = new HashSet<AlignedCodonFrame>();
- set1.add(acf1);
- set1.add(acf2);
- Set<AlignedCodonFrame> set2 = new HashSet<AlignedCodonFrame>();
- set2.add(acf2);
- set2.add(acf3);
+ assertEquals(1, pmap.getSeqs().size());
+ assertEquals("4IM2|A", pmap.getSeqs().get(0).getName());
+
+ List<int[]> structuremap1 = new ArrayList<>(
+ sm.getMapping(P4IM2_MISSING)[0]
+ .getPDBResNumRanges(seq.getStart(), seq.getEnd()));
/*
- * Remove one ref each to acf1, acf2, counts are now 2/1/1:
+ * 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
+ *
*/
- ssm.removeMappings(set1);
- assertEquals(3, ssm.seqmappings.size());
- assertTrue(ssm.seqmappings.contains(acf1));
- assertTrue(ssm.seqmappings.contains(acf2));
- assertTrue(ssm.seqmappings.contains(acf3));
- assertEquals(3, ssm.seqMappingRefCounts.size());
- assertEquals(2, ssm.seqMappingRefCounts.get(acf1).intValue());
- assertEquals(1, ssm.seqMappingRefCounts.get(acf2).intValue());
- assertEquals(1, ssm.seqMappingRefCounts.get(acf3).intValue());
+ String[] feats = new String[] { "LEU", "468", "VAL", "479", "MET",
+ "486", "GLY", "496", "GLU", "516" };
+ int[] offset = new int[] { 0, 11, 12, 13, 33 };
+
+ List<String> 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<int[]> 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<String> fdesc)
+ {
+ for (int o = 0; o < offset.length; o++)
+ {
+ int res = pdbseq.findPosition(offset[o]);
+ List<SequenceFeature> 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";
/*
- * Remove one ref each to acf2, acf3 - they are removed
+ * 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.
*/
- ssm.removeMappings(set2);
- assertEquals(1, ssm.seqmappings.size());
- assertTrue(ssm.seqmappings.contains(acf1));
- assertEquals(1, ssm.seqMappingRefCounts.size());
- assertEquals(2, ssm.seqMappingRefCounts.get(acf1).intValue());
+ 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<String, String> tipEntries = new TreeMap<>();
+ final Map<SequenceI, List<AlignmentAnnotation>> 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();
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff