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package jalview.structure; |
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import static org.junit.Assert.assertArrayEquals; |
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import static org.testng.Assert.assertNotNull; |
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import static org.testng.AssertJUnit.assertEquals; |
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import static org.testng.AssertJUnit.assertTrue; |
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import jalview.analysis.AlignmentUtils; |
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import jalview.api.structures.JalviewStructureDisplayI; |
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import jalview.bin.Cache; |
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import jalview.datamodel.AlignedCodonFrame; |
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import jalview.datamodel.AlignmentAnnotation; |
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import jalview.datamodel.AlignmentI; |
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import jalview.datamodel.Annotation; |
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import jalview.datamodel.PDBEntry; |
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import jalview.datamodel.Sequence; |
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import jalview.datamodel.SequenceFeature; |
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import jalview.datamodel.SequenceI; |
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import jalview.ext.jmol.JmolCommands; |
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import jalview.gui.AlignFrame; |
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import jalview.gui.Desktop; |
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import jalview.gui.JvOptionPane; |
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import jalview.gui.SequenceRenderer; |
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import jalview.gui.StructureChooser; |
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import jalview.io.DataSourceType; |
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import jalview.io.FileLoader; |
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import jalview.io.Jalview2xmlBase; |
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import jalview.io.StructureFile; |
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import jalview.util.MapList; |
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import jalview.ws.DBRefFetcher; |
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import jalview.ws.sifts.SiftsSettings; |
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import java.util.ArrayList; |
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import java.util.LinkedHashMap; |
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import java.util.List; |
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import java.util.Map; |
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import java.util.SortedMap; |
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import java.util.TreeMap; |
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import org.testng.Assert; |
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import org.testng.annotations.BeforeClass; |
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import org.testng.annotations.BeforeMethod; |
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import org.testng.annotations.Test; |
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@Test(singleThreaded = true) |
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| 32% |
Uncovered Elements: 134 (197) |
Complexity: 22 |
Complexity Density: 0.13 |
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public class StructureSelectionManagerTest extends Jalview2xmlBase |
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{ |
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| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
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@Override... |
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@BeforeClass(alwaysRun = true) |
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public void setUpJvOptionPane() |
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{ |
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JvOptionPane.setInteractiveMode(false); |
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JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); |
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} |
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private StructureSelectionManager ssm; |
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| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
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@BeforeMethod(alwaysRun = true)... |
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public void setUp() |
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{ |
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StructureImportSettings.setShowSeqFeatures(true); |
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ssm = new StructureSelectionManager(); |
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} |
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| 100% |
Uncovered Elements: 0 (15) |
Complexity: 1 |
Complexity Density: 0.07 |
1PASS
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@Test(groups = { "Functional" })... |
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public void testRegisterMapping() |
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{ |
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AlignedCodonFrame acf1 = new AlignedCodonFrame(); |
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acf1.addMap(new Sequence("s1", "ttt"), new Sequence("p1", "p"), |
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new MapList(new int[] { 1, 3 }, new int[] { 1, 1 }, 1, 1)); |
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AlignedCodonFrame acf2 = new AlignedCodonFrame(); |
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acf2.addMap(new Sequence("s2", "ttt"), new Sequence("p2", "p"), |
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new MapList(new int[] { 1, 3 }, new int[] { 1, 1 }, 1, 1)); |
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ssm.registerMapping(acf1); |
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assertEquals(1, ssm.getSequenceMappings().size()); |
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assertTrue(ssm.getSequenceMappings().contains(acf1)); |
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ssm.registerMapping(acf2); |
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assertEquals(2, ssm.getSequenceMappings().size()); |
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assertTrue(ssm.getSequenceMappings().contains(acf1)); |
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assertTrue(ssm.getSequenceMappings().contains(acf2)); |
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ssm.registerMapping(acf1); |
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assertEquals(2, ssm.getSequenceMappings().size()); |
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assertTrue(ssm.getSequenceMappings().contains(acf1)); |
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assertTrue(ssm.getSequenceMappings().contains(acf2)); |
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} |
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| 100% |
Uncovered Elements: 0 (20) |
Complexity: 1 |
Complexity Density: 0.05 |
1PASS
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@Test(groups = { "Functional" })... |
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public void testRegisterMappings() |
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{ |
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AlignedCodonFrame acf1 = new AlignedCodonFrame(); |
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acf1.addMap(new Sequence("s1", "ttt"), new Sequence("p1", "p"), |
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new MapList(new int[] { 1, 3 }, new int[] { 1, 1 }, 1, 1)); |
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AlignedCodonFrame acf2 = new AlignedCodonFrame(); |
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acf2.addMap(new Sequence("s2", "ttt"), new Sequence("p2", "p"), |
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new MapList(new int[] { 1, 3 }, new int[] { 1, 1 }, 1, 1)); |
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AlignedCodonFrame acf3 = new AlignedCodonFrame(); |
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acf3.addMap(new Sequence("s3", "ttt"), new Sequence("p3", "p"), |
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new MapList(new int[] { 1, 3 }, new int[] { 1, 1 }, 1, 1)); |
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List<AlignedCodonFrame> set1 = new ArrayList<AlignedCodonFrame>(); |
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set1.add(acf1); |
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set1.add(acf2); |
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List<AlignedCodonFrame> set2 = new ArrayList<AlignedCodonFrame>(); |
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set2.add(acf2); |
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set2.add(acf3); |
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ssm.registerMappings(set1); |
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ssm.registerMappings(set1); |
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ssm.registerMappings(set2); |
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ssm.registerMappings(set2); |
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assertEquals(3, ssm.getSequenceMappings().size()); |
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assertTrue(ssm.getSequenceMappings().contains(acf1)); |
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assertTrue(ssm.getSequenceMappings().contains(acf2)); |
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assertTrue(ssm.getSequenceMappings().contains(acf3)); |
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} |
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| 100% |
Uncovered Elements: 0 (19) |
Complexity: 1 |
Complexity Density: 0.05 |
1PASS
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@Test(groups = { "Functional" })... |
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public void testSetMapping_seqFeatures() |
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{ |
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SequenceI seq = new Sequence( |
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"1GAQ|B", |
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"ATYNVKLITPEGEVELQVPDDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSYLDDGQIADGWVLTCHAYPTSDVVIETHKEEELTGA"); |
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StructureSelectionManager sm = new StructureSelectionManager(); |
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sm.setProcessSecondaryStructure(true); |
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sm.setAddTempFacAnnot(true); |
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StructureFile pmap = sm.setMapping(true, new SequenceI[] { seq }, |
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new String[] { null }, "examples/1gaq.txt", DataSourceType.FILE); |
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assertTrue(pmap != null); |
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assertEquals(3, pmap.getSeqs().size()); |
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assertEquals("1GAQ|A", pmap.getSeqs().get(0).getName()); |
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assertEquals("1GAQ|B", pmap.getSeqs().get(1).getName()); |
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assertEquals("1GAQ|C", pmap.getSeqs().get(2).getName()); |
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SequenceFeature sf = pmap.getSeqs().get(0).getSequenceFeatures().get(0); |
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assertEquals("RESNUM", sf.getType()); |
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assertEquals("1gaq", sf.getFeatureGroup()); |
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assertEquals("GLU: 19 1gaqA", sf.getDescription()); |
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StructureMapping map = sm.getMapping("examples/1gaq.txt")[0]; |
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sf = map.sequence.getSequenceFeatures().get(0); |
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assertEquals("RESNUM", sf.getType()); |
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assertEquals("1gaq", sf.getFeatureGroup()); |
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assertEquals("ALA: 1 1gaqB", sf.getDescription()); |
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} |
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196 |
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| 0% |
Uncovered Elements: 64 (64) |
Complexity: 7 |
Complexity Density: 0.13 |
1PASS
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197 |
0 |
@Test(groups = { "Network" })... |
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public void testMapping_EqualsFeatures() |
199 |
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{ |
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201 |
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202 |
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Desktop.instance.closeAll_actionPerformed(null); |
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try { |
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Thread.sleep(200); |
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} catch (Exception foo) {}; |
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SequenceI seq = new Sequence("4IM2|A", |
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"LDFCIRNIEKTVMGEISDIHTKLLRLSSSQGTIE"); |
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String P4IM2_MISSING = "examples/testdata/4IM2_missing.pdb"; |
209 |
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StructureSelectionManager sm = new StructureSelectionManager(); |
210 |
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sm.setProcessSecondaryStructure(true); |
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sm.setAddTempFacAnnot(true); |
212 |
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StructureFile pmap = sm.setMapping(true, new SequenceI[] { seq }, |
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new String[] |
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{ null }, P4IM2_MISSING, |
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DataSourceType.FILE); |
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assertTrue(pmap != null); |
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assertEquals(1, pmap.getSeqs().size()); |
219 |
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assertEquals("4IM2|A", pmap.getSeqs().get(0).getName()); |
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List<int[]> structuremap1 = new ArrayList( |
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sm.getMapping(P4IM2_MISSING)[0] |
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.getPDBResNumRanges(seq.getStart(), seq.getEnd())); |
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236 |
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237 |
0 |
String[] feats = new String[] { "LEU", "468", "VAL", "479", "MET", |
238 |
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"486", "GLY", "496", "GLU", "516" }; |
239 |
0 |
int[] offset = new int[] { 0, 11, 12, 13, 33 }; |
240 |
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|
241 |
0 |
List<String> fdesc = new ArrayList<>(); |
242 |
0 |
for (int f = 0; f < feats.length; f += 2) |
243 |
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{ |
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fdesc.add(feats[f] + ": " + feats[f + 1] + " 4im2A"); |
245 |
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} |
246 |
0 |
SequenceI pdbseq = pmap.getSeqs().get(0); |
247 |
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verifySeqFeats(pdbseq, offset, fdesc); |
248 |
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249 |
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250 |
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251 |
0 |
AlignFrame alf = new FileLoader(false).LoadFileWaitTillLoaded( |
252 |
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"examples/testdata/4IM2_missing.pdb", DataSourceType.FILE); |
253 |
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Desktop.addInternalFrame(alf, "examples/testdata/4IM2_missing.pdb", 800, |
254 |
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400); |
255 |
0 |
AlignmentI pdbal = alf.getViewport().getAlignment(); |
256 |
0 |
SequenceI pdb_viewseq = pdbal.getSequenceAt(0); |
257 |
0 |
assertEquals(pdb_viewseq.getSequenceAsString(), |
258 |
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seq.getSequenceAsString()); |
259 |
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260 |
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261 |
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verifySeqFeats(pdb_viewseq, offset, fdesc); |
262 |
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263 |
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264 |
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JalviewStructureDisplayI viewr = openStructureViaChooser(alf, |
265 |
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pdb_viewseq, "4IM2"); |
266 |
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267 |
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268 |
0 |
verifySeqFeats(pdb_viewseq, offset, fdesc); |
269 |
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|
270 |
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271 |
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PDBEntry pdbe = seq.getPDBEntry("4IM2"); |
272 |
0 |
StructureSelectionManager apssm = alf.alignPanel |
273 |
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.getStructureSelectionManager(); |
274 |
0 |
StructureMapping[] smap = apssm |
275 |
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.getMapping(pdbe.getFile()); |
276 |
0 |
assertNotNull(smap); |
277 |
0 |
assertNotNull(smap[0]); |
278 |
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279 |
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280 |
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281 |
0 |
int realSeqEnd = pdb_viewseq.findPosition(pdb_viewseq.getLength()); |
282 |
0 |
List<int[]> ranges = smap[0].getPDBResNumRanges(pdb_viewseq.getStart(), |
283 |
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realSeqEnd); |
284 |
0 |
assertEquals(structuremap1.size(), ranges.size()); |
285 |
0 |
int tot_mapped = 0; |
286 |
0 |
for (int p = 0; p < ranges.size(); p++) |
287 |
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{ |
288 |
0 |
assertArrayEquals(structuremap1.get(p), ranges.get(p)); |
289 |
0 |
tot_mapped += 1 + (structuremap1.get(p)[1] - structuremap1.get(p)[0]); |
290 |
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} |
291 |
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292 |
0 |
assertEquals(pdb_viewseq.getLength(), tot_mapped); |
293 |
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|
294 |
0 |
int lastmappedp = StructureMapping.UNASSIGNED_VALUE; |
295 |
0 |
for (int rp = pdb_viewseq.getStart(), rpEnd = pdb_viewseq |
296 |
0 |
.findPosition(pdb_viewseq.getLength() - 1); rp <= rpEnd; rp++) |
297 |
|
{ |
298 |
0 |
int mappedp = smap[0].getPDBResNum(rp); |
299 |
0 |
if (mappedp != StructureMapping.UNASSIGNED_VALUE) |
300 |
|
{ |
301 |
0 |
tot_mapped--; |
302 |
0 |
if (lastmappedp == mappedp) |
303 |
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{ |
304 |
0 |
Assert.fail("Duplicate mapped position at " + rp + " (dupe = " |
305 |
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+ mappedp + ")"); |
306 |
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} |
307 |
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} |
308 |
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} |
309 |
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|
310 |
0 |
Assert.assertEquals(tot_mapped, 0, |
311 |
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"Different number of mapped residues compared to ranges of mapped residues"); |
312 |
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|
313 |
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|
314 |
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|
315 |
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|
316 |
0 |
StructureMappingcommandSet smcr[] = JmolCommands |
317 |
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.getColourBySequenceCommand(apssm, |
318 |
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new String[] |
319 |
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{ pdbe.getFile() }, |
320 |
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new SequenceI[][] |
321 |
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{ new SequenceI[] { pdb_viewseq } }, |
322 |
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new SequenceRenderer(alf.alignPanel.getAlignViewport()), |
323 |
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alf.alignPanel); |
324 |
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|
325 |
0 |
for (StructureMappingcommandSet smm : smcr) |
326 |
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{ |
327 |
0 |
for (String c : smm.commands) |
328 |
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{ |
329 |
0 |
System.out.println(c); |
330 |
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} |
331 |
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} |
332 |
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} |
333 |
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|
|
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| 0% |
Uncovered Elements: 7 (7) |
Complexity: 2 |
Complexity Density: 0.4 |
|
334 |
0 |
private void verifySeqFeats(SequenceI pdbseq, int[] offset,... |
335 |
|
List<String> fdesc) |
336 |
|
{ |
337 |
0 |
for (int o = 0; o < offset.length; o++) |
338 |
|
{ |
339 |
0 |
int res = pdbseq.findPosition(offset[o]); |
340 |
0 |
List<SequenceFeature> sf = pdbseq.getFeatures().findFeatures(res, res, |
341 |
|
"RESNUM"); |
342 |
0 |
assertEquals("Expected sequence feature at position " + res + "(" |
343 |
|
+ offset[o] + ")", 1, sf.size()); |
344 |
0 |
assertEquals("Wrong description at " + res + "(" + offset[o] + ")", |
345 |
|
fdesc.get(o), sf.get(0).getDescription()); |
346 |
|
} |
347 |
|
|
348 |
|
} |
349 |
|
|
|
|
| 0% |
Uncovered Elements: 51 (51) |
Complexity: 6 |
Complexity Density: 0.15 |
1PASS
|
|
350 |
0 |
@Test(groups = { "Network" })... |
351 |
|
public void testAssociatedMappingToSubSeq() throws Exception |
352 |
|
{ |
353 |
|
|
354 |
|
|
355 |
0 |
Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, |
356 |
|
Boolean.FALSE.toString()); |
357 |
0 |
String TEMP_FACTOR_AA="Temperature Factor"; |
358 |
0 |
String PDBID = "4IM2"; |
359 |
0 |
String FullLengthSeq = ">TBK1_HUMAN Serine/threonine-protein kinase TBK1\n" + |
360 |
|
"MQSTSNHLWLLSDILGQGATANVFRGRHKKTGDLFAIKVFNNISFLRPVDVQMREFEVLKKLNHKNIVKLFA\n" + |
361 |
|
"IEEETTTRHKVLIMEFCPCGSLYTVLEEPSNAYGLPESEFLIVLRDVVGGMNHLRENGIVHRDIKPGNIMRV\n" + |
362 |
|
"IGEDGQSVYKLTDFGAARELEDDEQFVSLYGTEEYLHPDMYERAVLRKDHQKKYGATVDLWSIGVTFYHAAT\n" + |
363 |
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"GSLPFRPFEGPRRNKEVMYKIITGKPSGAISGVQKAENGPIDWSGDMPVSCSLSRGLQVLLTPVLANILEAD\n" + |
364 |
|
"QEKCWGFDQFFAETSDILHRMVIHVFSLQQMTAHKIYIHSYNTATIFHELVYKQTKIISSNQELIYEGRRLV\n" + |
365 |
|
"LEPGRLAQHFPKTTEENPIFVVSREPLNTIGLIYEKISLPKVHPRYDLDGDASMAKAITGVVCYACRIASTL\n" + |
366 |
|
"LLYQELMRKGIRWLIELIKDDYNETVHKKTEVVITLDFCIRNIEKTVKVYEKLMKINLEAAELGEISDIHTK\n" + |
367 |
|
"LLRLSSSQGTIETSLQDIDSRLSPGGSLADAWAHQEGTHPKDRNVEKLQVLLNCMTEIYYQFKKDKAERRLA\n" + |
368 |
|
"YNEEQIHKFDKQKLYYHATKAMTHFTDECVKKYEAFLNKSEEWIRKMLHLRKQLLSLTNQCFDIEEEVSKYQ\n" + |
369 |
|
"EYTNELQETLPQKMFTASSGIKHTMTPIYPSSNTLVEMTLGMKKLKEEMEGVVKELAENNHILERFGSLTMD\n" + |
370 |
|
"GGLRNVDCL"; |
371 |
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|
372 |
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|
373 |
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|
374 |
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|
375 |
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|
376 |
0 |
String FullLengthAnnot = "JALVIEW_ANNOTATION\n" + |
377 |
|
"# Created: Mon Feb 05 15:30:20 GMT 2018\n" + |
378 |
|
"# Updated: Fri Feb 09 17:05:17 GMT 2018\n" + |
379 |
|
"\n" + |
380 |
|
"\n" + |
381 |
|
"SEQUENCE_REF\tTBK1_HUMAN\n" |
382 |
|
+ "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" |
383 |
|
+ |
384 |
|
"\n" + |
385 |
|
""; |
386 |
0 |
AlignFrame alf_full=new |
387 |
|
FileLoader(false).LoadFileWaitTillLoaded(FullLengthSeq,DataSourceType.PASTE); |
388 |
0 |
alf_full.loadJalviewDataFile(FullLengthAnnot, DataSourceType.PASTE, null, null); |
389 |
0 |
AlignmentI al_full = alf_full.getViewport().getAlignment(); |
390 |
0 |
AlignmentAnnotation fullseq_tf = al_full.findAnnotations(al_full.getSequences().get(0), null, TEMP_FACTOR_AA).iterator() |
391 |
|
.next(); |
392 |
0 |
assertNotNull(fullseq_tf); |
393 |
|
|
394 |
|
|
395 |
|
|
396 |
|
|
397 |
|
|
398 |
|
|
399 |
|
|
400 |
|
|
401 |
|
|
402 |
|
|
403 |
|
|
404 |
|
|
405 |
0 |
AlignFrame alf = new FileLoader(false).LoadFileWaitTillLoaded( |
406 |
|
">TBK1_HUMAN/470-502 Serine/threonine-protein kinase TBK1\nFCIRNIEKTVKVYEKLMKINLEAAELGEISDIH", |
407 |
|
DataSourceType.PASTE); |
408 |
0 |
Desktop.addInternalFrame(alf, "Foo", 800, 600); |
409 |
0 |
; |
410 |
0 |
AlignmentI al = alf.getViewport().getAlignment(); |
411 |
0 |
SequenceI seq = al.getSequenceAt(0); |
412 |
0 |
assertEquals(470, seq.getStart()); |
413 |
|
|
414 |
0 |
SiftsSettings.setMapWithSifts(true); |
415 |
0 |
StructureImportSettings.setProcessSecondaryStructure(true); |
416 |
0 |
StructureImportSettings.setVisibleChainAnnotation(true); |
417 |
0 |
JalviewStructureDisplayI sview = openStructureViaChooser(alf, seq, |
418 |
|
PDBID); |
419 |
|
|
420 |
0 |
AlignmentAnnotation subseq_tf=null; |
421 |
0 |
assertTrue(seq.getDBRefs() != null && seq.getDBRefs().length > 0); |
422 |
|
|
423 |
0 |
if (!al.findAnnotations(seq, null, TEMP_FACTOR_AA).iterator().hasNext()) |
424 |
|
{ |
425 |
|
|
426 |
|
|
427 |
|
|
428 |
0 |
SortedMap<String, String> tipEntries = new TreeMap<>(); |
429 |
0 |
final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<>(); |
430 |
|
|
431 |
0 |
AlignmentUtils.findAddableReferenceAnnotations(al.getSequences(), |
432 |
|
tipEntries, candidates, al); |
433 |
0 |
AlignmentUtils.addReferenceAnnotations(candidates, al, null); |
434 |
|
|
435 |
0 |
if (!al.findAnnotations(seq, null, TEMP_FACTOR_AA).iterator() |
436 |
|
.hasNext()) |
437 |
|
{ |
438 |
0 |
Assert.fail( |
439 |
|
"JAL-2321 or worse has occured. No secondary structure added to alignment."); |
440 |
|
} |
441 |
|
} |
442 |
0 |
subseq_tf = al.findAnnotations(seq, null, TEMP_FACTOR_AA).iterator() |
443 |
|
.next(); |
444 |
|
|
445 |
|
|
446 |
|
|
447 |
|
|
448 |
|
|
449 |
|
|
450 |
|
|
451 |
|
|
452 |
0 |
for (int p=seq.getStart();p<=seq.getEnd();p++) |
453 |
|
{ |
454 |
0 |
Annotation orig,subseq; |
455 |
0 |
orig = fullseq_tf.getAnnotationForPosition(p); |
456 |
0 |
subseq = subseq_tf.getAnnotationForPosition(p); |
457 |
0 |
if (orig == null) |
458 |
|
{ |
459 |
0 |
Assert.assertNull(subseq, |
460 |
|
"Expected no annotation transferred at position " + p); |
461 |
|
} |
462 |
0 |
; |
463 |
0 |
if (orig != null) |
464 |
|
{ |
465 |
0 |
Assert.assertNotNull(subseq, |
466 |
|
"Expected annotation transfer at position " + p); |
467 |
0 |
assertEquals(orig.value, subseq.value); |
468 |
|
} |
469 |
0 |
; |
470 |
|
|
471 |
|
} |
472 |
|
} |
473 |
|
|
|
|
| 0% |
Uncovered Elements: 8 (8) |
Complexity: 2 |
Complexity Density: 0.25 |
|
474 |
0 |
private JalviewStructureDisplayI openStructureViaChooser(AlignFrame alf,... |
475 |
|
SequenceI seq, |
476 |
|
String pDBID) |
477 |
|
{ |
478 |
|
|
479 |
0 |
SequenceI[] selectedSeqs = new SequenceI[] { seq }; |
480 |
|
|
481 |
0 |
StructureChooser schoose = new StructureChooser(selectedSeqs, seq, |
482 |
|
alf.getViewport().getAlignPanel()); |
483 |
|
|
484 |
0 |
try |
485 |
|
{ |
486 |
0 |
Thread.sleep(5000); |
487 |
|
} catch (InterruptedException q) |
488 |
|
{ |
489 |
|
} |
490 |
0 |
; |
491 |
0 |
Assert.assertTrue(schoose.selectStructure(pDBID), |
492 |
|
"Couldn't select structure via structure chooser: " + pDBID); |
493 |
0 |
schoose.showStructures(true); |
494 |
0 |
return schoose.getOpenedStructureViewer(); |
495 |
|
} |
496 |
|
|
497 |
|
} |