X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Frbvi%2Fchimera%2FJalviewChimeraView.java;h=734f7ebd19fc54adfd3ff54487a51db49286d937;hb=136c0793b90b72b928c4d77dc109dd5c644e00d3;hp=870ed99fb9e78d0f67727a2733096206553a2bd0;hpb=b6d59133dc27bd71385d525ca49c7b31f378cb17;p=jalview.git diff --git a/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java b/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java index 870ed99..734f7eb 100644 --- a/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java +++ b/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java @@ -35,15 +35,20 @@ import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; import jalview.gui.AlignFrame; import jalview.gui.Desktop; +import jalview.gui.JvOptionPane; import jalview.gui.Preferences; import jalview.gui.StructureViewer; import jalview.gui.StructureViewer.ViewerType; +import jalview.io.DataSourceType; import jalview.io.FileLoader; -import jalview.io.FormatAdapter; import jalview.structure.StructureMapping; import jalview.structure.StructureSelectionManager; -import jalview.structures.models.AAStructureBindingModel; +import jalview.ws.sifts.SiftsClient; +import jalview.ws.sifts.SiftsException; +import jalview.ws.sifts.SiftsSettings; +import java.io.File; +import java.io.IOException; import java.util.List; import java.util.Vector; @@ -56,6 +61,13 @@ import org.testng.annotations.Test; public class JalviewChimeraView { + @BeforeClass(alwaysRun = true) + public void setUpJvOptionPane() + { + JvOptionPane.setInteractiveMode(false); + JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); + } + private JalviewStructureDisplayI chimeraViewer; /** @@ -64,8 +76,7 @@ public class JalviewChimeraView @BeforeClass(alwaysRun = true) public static void setUpBeforeClass() throws Exception { - Jalview.main(new String[] { - "-noquestionnaire -nonews -props", + Jalview.main(new String[] { "-noquestionnaire", "-nonews", "-props", "test/jalview/ext/rbvi/chimera/testProps.jvprops" }); Cache.setProperty(Preferences.STRUCTURE_DISPLAY, ViewerType.CHIMERA.name()); @@ -74,6 +85,8 @@ public class JalviewChimeraView Cache.setProperty(Preferences.STRUCTURE_DISPLAY, ViewerType.CHIMERA.name()); Cache.setProperty("MAP_WITH_SIFTS", "true"); + // TODO this should not be necessary! + SiftsSettings.setMapWithSifts(true); } /** @@ -88,6 +101,7 @@ public class JalviewChimeraView @AfterMethod(alwaysRun = true) public void tearDownAfterTest() throws Exception { + SiftsClient.setMockSiftsFile(null); if (chimeraViewer != null) { chimeraViewer.closeViewer(true); @@ -95,14 +109,17 @@ public class JalviewChimeraView } /** - * Load 1GAQ and view the first structure for which a PDB id is found + * Load 1GAQ and view the first structure for which a PDB id is found. Note no + * network connection is needed - PDB file is read locally, SIFTS fetch fails + * so mapping falls back to Needleman-Wunsch - ok for this test. */ - @Test(groups = { "External", "Network" }) + // External as local install of Chimera required + @Test(groups = { "External" }) public void testSingleSeqViewChimera() { String inFile = "examples/1gaq.txt"; AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile, - FormatAdapter.FILE); + DataSourceType.FILE); assertNotNull(af, "Failed to create AlignFrame"); SequenceI sq = af.getViewport().getAlignment().getSequenceAt(0); assertEquals(sq.getName(), "1GAQ|A"); @@ -115,10 +132,13 @@ public class JalviewChimeraView .getStructureSelectionManager()); chimeraViewer = structureViewer.viewStructures(pdbEntry, new SequenceI[] { sq }, af.getCurrentView().getAlignPanel()); + JalviewChimeraBinding binding = (JalviewChimeraBinding) chimeraViewer + .getBinding(); + /* * Wait for viewer load thread to complete */ - while (!chimeraViewer.getBinding().isFinishedInit()) + while (!binding.isFinishedInit()) { try { @@ -127,6 +147,9 @@ public class JalviewChimeraView { } } + + assertTrue(binding.isChimeraRunning(), "Failed to start Chimera"); + assertEquals(chimeraViewer.getBinding().getPdbCount(), 1); chimeraViewer.closeViewer(true); chimeraViewer = null; @@ -135,16 +158,19 @@ public class JalviewChimeraView /** * Test for writing Jalview features as attributes on mapped residues in - * Chimera + * Chimera. Note this uses local copies of PDB and SIFTS file, no network + * connection required. + * + * @throws IOException + * @throws SiftsException */ // External as this requires a local install of Chimera - // Network as fetch from PDB/SIFTS is involved TODO mock this - @Test(groups = { "External", "Network" }) - public void testTransferFeatures() + @Test(groups = { "External" }) + public void testTransferFeatures() throws IOException, SiftsException { String inFile = "examples/uniref50.fa"; AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile, - FormatAdapter.FILE); + DataSourceType.FILE); assertNotNull(af, "Failed to create AlignFrame"); SequenceI sq = af.getViewport().getAlignment().findName("FER2_ARATH"); assertNotNull(sq, "Didn't find FER2_ARATH"); @@ -153,25 +179,37 @@ public class JalviewChimeraView * need a Uniprot dbref for SIFTS mapping to work!! */ sq.addDBRef(new DBRefEntry("UNIPROT", "0", "P16972", null)); - PDBEntry pdbEntry = new PDBEntry("4ZHO", null, null, null); - // addPDBId() doesn't (yet) delegate to dataset sequence if there is one! - sq.getDatasetSequence().addPDBId(pdbEntry); + + /* + * use local test PDB and SIFTS files + */ + String pdbFilePath = new File( + "test/jalview/ext/rbvi/chimera/4zho.pdb").getPath(); + PDBEntry pdbEntry = new PDBEntry("4ZHO", null, null, pdbFilePath); + String siftsFilePath = new File( + "test/jalview/ext/rbvi/chimera/4zho.xml.gz") + .getPath(); + SiftsClient.setMockSiftsFile(new File(siftsFilePath)); + StructureViewer structureViewer = new StructureViewer(af.getViewport() .getStructureSelectionManager()); chimeraViewer = structureViewer.viewStructures(pdbEntry, new SequenceI[] { sq }, af.getCurrentView().getAlignPanel()); - AAStructureBindingModel binding = chimeraViewer.getBinding(); + JalviewChimeraBinding binding = (JalviewChimeraBinding) chimeraViewer + .getBinding(); do { try { Thread.sleep(500); } catch (InterruptedException e) - { - } + { + } } while (!binding.isFinishedInit()); + assertTrue(binding.isChimeraRunning(), "Failed to launch Chimera"); + assertEquals(binding.getPdbCount(), 1); /* @@ -179,8 +217,10 @@ public class JalviewChimeraView * (or possibly 52-145 to 1-94 - see JAL-2319) */ StructureSelectionManager ssm = binding.getSsm(); - String pdbFile = binding.getPdbFile()[0]; + String pdbFile = binding.getStructureFiles()[0]; StructureMapping[] mappings = ssm.getMapping(pdbFile); + assertTrue(mappings[0].getMappingDetailsOutput().contains("SIFTS"), + "Failed to perform SIFTS mapping"); assertEquals(mappings.length, 2); assertEquals(mappings[0].getChain(), "A"); assertEquals(mappings[0].getPDBResNum(53), 2); @@ -214,6 +254,8 @@ public class JalviewChimeraView 62, -2.1f, null)); sq.addSequenceFeature(new SequenceFeature("kd", "hydrophobicity", 65, 65, 3.6f, null)); + sq.addSequenceFeature(new SequenceFeature("RESNUM", "ALA: 2 4zhoA", + 53, 53, Float.NaN, null)); /* * set all features visible except for chain @@ -225,6 +267,7 @@ public class JalviewChimeraView fr.setVisible("metal ion-binding site"); fr.setVisible("helix"); fr.setVisible("kd"); + fr.setVisible("RESNUM"); /* * 'perform' menu action to copy visible features to @@ -232,8 +275,7 @@ public class JalviewChimeraView */ // TODO rename and pull up method to binding interface // once functionality is added for Jmol as well - ((JalviewChimeraBinding) binding).sendFeaturesToChimera(af - .getViewport().getAlignPanel()); + binding.sendFeaturesToViewer(af.getViewport().getAlignPanel()); /* * give Chimera time to open the commands file and execute it @@ -248,13 +290,13 @@ public class JalviewChimeraView /* * ask Chimera for its residue attribute names */ - List reply = ((JalviewChimeraBinding) binding) - .sendChimeraCommand("list resattr", true); + List reply = binding.sendChimeraCommand("list resattr", true); // prefixed and sanitised attribute names for Jalview features: assertTrue(reply.contains("resattr jv_domain")); assertTrue(reply.contains("resattr jv_metal_ion_binding_site")); assertTrue(reply.contains("resattr jv_helix")); assertTrue(reply.contains("resattr jv_kd")); + assertTrue(reply.contains("resattr jv_RESNUM")); // feature is not on a mapped region - no attribute created assertFalse(reply.contains("resattr jv_transit_peptide")); // feature is not visible - no attribute created @@ -264,7 +306,7 @@ public class JalviewChimeraView * ask Chimera for residues with an attribute * 91 and 96 on sequence --> residues 40 and 45 on chains A and B */ - reply = ((JalviewChimeraBinding) binding).sendChimeraCommand( + reply = binding.sendChimeraCommand( "list resi att jv_metal_ion_binding_site", true); assertEquals(reply.size(), 4); assertTrue(reply @@ -280,8 +322,7 @@ public class JalviewChimeraView * check attributes with score values * sequence positions 62 and 65 --> residues 11 and 14 on chains A and B */ - reply = ((JalviewChimeraBinding) binding).sendChimeraCommand( - "list resi att jv_kd", true); + reply = binding.sendChimeraCommand("list resi att jv_kd", true); assertEquals(reply.size(), 4); assertTrue(reply.contains("residue id #0:11.A jv_kd -2.1 index 11")); assertTrue(reply.contains("residue id #0:14.A jv_kd 3.6 index 14")); @@ -291,13 +332,155 @@ public class JalviewChimeraView /* * list residues with positive kd score */ - reply = ((JalviewChimeraBinding) binding).sendChimeraCommand( + reply = binding.sendChimeraCommand( "list resi spec :*/jv_kd>0 attr jv_kd", true); assertEquals(reply.size(), 2); assertTrue(reply.contains("residue id #0:14.A jv_kd 3.6 index 14")); assertTrue(reply.contains("residue id #0:14.B jv_kd 3.6 index 14")); + SiftsClient.setMockSiftsFile(null); + chimeraViewer.closeViewer(true); + chimeraViewer = null; + } + + /** + * Test for creating Jalview features from attributes on mapped residues in + * Chimera. Note this uses local copies of PDB and SIFTS file, no network + * connection required. + * + * @throws IOException + * @throws SiftsException + */ + // External as this requires a local install of Chimera + @Test(groups = { "External" }) + public void testGetAttributes() throws IOException, SiftsException + { + String inFile = "examples/uniref50.fa"; + AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile, + DataSourceType.FILE); + assertNotNull(af, "Failed to create AlignFrame"); + SequenceI fer2Arath = af.getViewport().getAlignment() + .findName("FER2_ARATH"); + assertNotNull(fer2Arath, "Didn't find FER2_ARATH"); + + /* + * need a Uniprot dbref for SIFTS mapping to work!! + */ + fer2Arath.addDBRef(new DBRefEntry("UNIPROT", "0", "P16972", null)); + + /* + * use local test PDB and SIFTS files + */ + String pdbFilePath = new File( + "test/jalview/ext/rbvi/chimera/4zho.pdb").getPath(); + PDBEntry pdbEntry = new PDBEntry("4ZHO", null, null, pdbFilePath); + String siftsFilePath = new File( + "test/jalview/ext/rbvi/chimera/4zho.xml.gz") + .getPath(); + SiftsClient.setMockSiftsFile(new File(siftsFilePath)); + + StructureViewer structureViewer = new StructureViewer(af.getViewport() + .getStructureSelectionManager()); + chimeraViewer = structureViewer.viewStructures(pdbEntry, + new SequenceI[] { fer2Arath }, af.getCurrentView() + .getAlignPanel()); + + JalviewChimeraBinding binding = (JalviewChimeraBinding) chimeraViewer + .getBinding(); + do + { + try + { + Thread.sleep(500); + } catch (InterruptedException e) + { + } + } while (!binding.isFinishedInit()); + + assertTrue(binding.isChimeraRunning(), "Failed to launch Chimera"); + + assertEquals(binding.getPdbCount(), 1); + + /* + * 'perform' menu action to copy visible features to + * attributes in Chimera + */ + // TODO rename and pull up method to binding interface + // once functionality is added for Jmol as well + binding.copyStructureAttributesToFeatures("isHelix", af.getViewport() + .getAlignPanel()); + + /* + * verify 22 residues have isHelix feature + * (may merge into ranges in future) + */ + af.setShowSeqFeatures(true); + FeatureRenderer fr = af.getFeatureRenderer(); + fr.setVisible("isHelix"); + for (int res = 75; res <= 83; res++) + { + checkFeaturesAtRes(fer2Arath, fr, res, "isHelix"); + } + for (int res = 117; res <= 123; res++) + { + checkFeaturesAtRes(fer2Arath, fr, res, "isHelix"); + } + for (int res = 129; res <= 131; res++) + { + checkFeaturesAtRes(fer2Arath, fr, res, "isHelix"); + } + for (int res = 143; res <= 145; res++) + { + checkFeaturesAtRes(fer2Arath, fr, res, "isHelix"); + } + + /* + * fetch a numeric valued attribute + */ + binding.copyStructureAttributesToFeatures("phi", af.getViewport() + .getAlignPanel()); + fr.setVisible("phi"); + List fs = fer2Arath.getFeatures().findFeatures(54, 54); + assertEquals(fs.size(), 3); + /* + * order of returned features is not guaranteed + */ + assertTrue("RESNUM".equals(fs.get(0).getType()) + || "RESNUM".equals(fs.get(1).getType()) + || "RESNUM".equals(fs.get(2).getType())); + assertTrue(fs.contains(new SequenceFeature("phi", "A", 54, 54, + -131.0713f, "Chimera"))); + assertTrue(fs.contains(new SequenceFeature("phi", "B", 54, 54, + -127.39512f, "Chimera"))); + + /* + * tear down - also in AfterMethod + */ + SiftsClient.setMockSiftsFile(null); chimeraViewer.closeViewer(true); chimeraViewer = null; } + + /** + * Helper method to verify new feature at a sequence position + * + * @param seq + * @param fr + * @param res + * @param featureType + */ + protected void checkFeaturesAtRes(SequenceI seq, FeatureRenderer fr, + int res, String featureType) + { + String where = "at position " + res; + List fs = seq.getFeatures().findFeatures(res, res); + + assertEquals(fs.size(), 2, where); + assertEquals(fs.get(0).getType(), "RESNUM", where); + SequenceFeature sf = fs.get(1); + assertEquals(sf.getType(), featureType, where); + assertEquals(sf.getFeatureGroup(), "Chimera", where); + assertEquals(sf.getDescription(), "True", where); + assertEquals(sf.getScore(), Float.NaN, where); + } }