X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Frbvi%2Fchimera%2FChimeraCommandsTest.java;h=24ca6e95c37106a9214cb636aecdd2a38eb0b2bb;hb=2d62933ef95beb94c1ec2444bcced4a3a7ec42c0;hp=b534b4ff26a54b4fdb6703d929a7e52d3ac475c0;hpb=8c0955545a1a10062467e2d6dc7feb1e855655c0;p=jalview.git diff --git a/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java b/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java index b534b4f..24ca6e9 100644 --- a/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java +++ b/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java @@ -20,36 +20,347 @@ */ package jalview.ext.rbvi.chimera; -import static org.testng.AssertJUnit.assertEquals; +import static org.testng.Assert.assertEquals; +import static org.testng.Assert.assertTrue; + +import jalview.api.AlignmentViewPanel; +import jalview.api.FeatureRenderer; +import jalview.datamodel.Alignment; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.ColumnSelection; +import jalview.datamodel.HiddenColumns; +import jalview.datamodel.Sequence; +import jalview.datamodel.SequenceI; +import jalview.gui.AlignFrame; +import jalview.gui.JvOptionPane; +import jalview.gui.SequenceRenderer; +import jalview.schemes.ColourSchemeI; +import jalview.schemes.JalviewColourScheme; +import jalview.structure.AtomSpec; +import jalview.structure.StructureMapping; +import jalview.structure.StructureMappingcommandSet; +import jalview.structure.StructureSelectionManager; +import jalview.structures.models.AAStructureBindingModel; import java.awt.Color; +import java.util.HashMap; import java.util.LinkedHashMap; +import java.util.List; import java.util.Map; +import org.testng.annotations.BeforeClass; import org.testng.annotations.Test; +import junit.extensions.PA; + public class ChimeraCommandsTest { + + private SequenceRenderer sr; + + private AAStructureBindingModel mockBinding = new AAStructureBindingModel( + null, null) + { + @Override + public void releaseReferences(Object svl) + { + } + + @Override + public void highlightAtoms(List atoms) + { + } + + @Override + public List getChainNames() + { + return null; + } + + @Override + public void setJalviewColourScheme(ColourSchemeI cs) + { + } + + @Override + public String superposeStructures(AlignmentI[] alignments, + int[] structureIndices, HiddenColumns[] hiddenCols) + { + return null; + } + + @Override + public void setBackgroundColour(Color col) + { + } + + @Override + protected StructureMappingcommandSet[] getColourBySequenceCommands( + String[] files, AlignmentViewPanel avp) + { + return null; + } + + @Override + public jalview.api.SequenceRenderer getSequenceRenderer( + AlignmentViewPanel alignment) + { + return sr; + } + + @Override + protected void colourBySequence( + StructureMappingcommandSet[] colourBySequenceCommands) + { + } + + @Override + public void colourByChain() + { + } + + @Override + public void colourByCharge() + { + } + + @Override + public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment) + { + return null; + } + + @Override + public String[] getStructureFiles() + { + return null; + } + + @Override + public String getModelSpec(int model) + { + return "#" + String.valueOf(model); + } + }; + + @BeforeClass(alwaysRun = true) + public void setUpJvOptionPane() + { + JvOptionPane.setInteractiveMode(false); + JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); + } + @Test(groups = { "Functional" }) public void testBuildColourCommands() { - Map map = new LinkedHashMap(); - ChimeraCommands.addRange(map, Color.blue, 0, 2, 5, "A"); - ChimeraCommands.addRange(map, Color.blue, 0, 7, 7, "B"); - ChimeraCommands.addRange(map, Color.blue, 0, 9, 23, "A"); - ChimeraCommands.addRange(map, Color.blue, 1, 1, 1, "A"); - ChimeraCommands.addRange(map, Color.blue, 1, 4, 7, "B"); - ChimeraCommands.addRange(map, Color.yellow, 1, 8, 8, "A"); - ChimeraCommands.addRange(map, Color.yellow, 1, 3, 5, "A"); - ChimeraCommands.addRange(map, Color.red, 0, 3, 5, "A"); - ChimeraCommands.addRange(map, Color.red, 0, 6, 9, "A"); + Map map = new LinkedHashMap<>(); + ChimeraCommands.addColourRange(map, Color.blue, 0, 2, 5, "A"); + ChimeraCommands.addColourRange(map, Color.blue, 0, 7, 7, "B"); + ChimeraCommands.addColourRange(map, Color.blue, 0, 9, 23, "A"); + ChimeraCommands.addColourRange(map, Color.blue, 1, 1, 1, "A"); + ChimeraCommands.addColourRange(map, Color.blue, 1, 4, 7, "B"); + ChimeraCommands.addColourRange(map, Color.yellow, 1, 8, 8, "A"); + ChimeraCommands.addColourRange(map, Color.yellow, 1, 3, 5, "A"); + ChimeraCommands.addColourRange(map, Color.red, 0, 3, 5, "A"); + ChimeraCommands.addColourRange(map, Color.red, 0, 6, 9, "A"); // Colours should appear in the Chimera command in the order in which // they were added; within colour, by model, by chain, ranges in start order - String command = ChimeraCommands.buildColourCommands(map).get(0); + // all prefixed with #808080 to colour hidden regions (if shown) gray + String command = ChimeraCommands.buildColourCommands(map, mockBinding) + .get(0); assertEquals( - "color #0000ff #0:2-5.A,9-23.A,7.B|#1:1.A,4-7.B; color #ffff00 #1:3-5.A,8.A; color #ff0000 #0:3-9.A", - command); + command, + "color #808080; color #0000ff #0:2-5.A,9-23.A,7.B|#1:1.A,4-7.B; color #ffff00 #1:3-5.A,8.A; color #ff0000 #0:3-9.A"); + } + + @Test(groups = { "Functional" }) + public void testBuildSetAttributeCommands() + { + /* + * make a map of { featureType, {featureValue, {residue range specification } } } + */ + Map> featuresMap = new LinkedHashMap<>(); + Map featureValues = new HashMap<>(); + + /* + * start with just one feature/value... + */ + featuresMap.put("chain", featureValues); + ChimeraCommands.addColourRange(featureValues, "X", 0, 8, 20, "A"); + + List commands = ChimeraCommands + .buildSetAttributeCommands(featuresMap, mockBinding); + assertEquals(1, commands.size()); + + /* + * feature name gets a jv_ namespace prefix + * feature value is quoted in case it contains spaces + */ + assertEquals(commands.get(0), "setattr r jv_chain 'X' #0:8-20.A"); + + // add same feature value, overlapping range + ChimeraCommands.addColourRange(featureValues, "X", 0, 3, 9, "A"); + // same feature value, contiguous range + ChimeraCommands.addColourRange(featureValues, "X", 0, 21, 25, "A"); + commands = ChimeraCommands.buildSetAttributeCommands(featuresMap, + mockBinding); + assertEquals(1, commands.size()); + assertEquals(commands.get(0), "setattr r jv_chain 'X' #0:3-25.A"); + + // same feature value and model, different chain + ChimeraCommands.addColourRange(featureValues, "X", 0, 21, 25, "B"); + // same feature value and chain, different model + ChimeraCommands.addColourRange(featureValues, "X", 1, 26, 30, "A"); + commands = ChimeraCommands.buildSetAttributeCommands(featuresMap, + mockBinding); + assertEquals(1, commands.size()); + assertEquals(commands.get(0), + "setattr r jv_chain 'X' #0:3-25.A,21-25.B|#1:26-30.A"); + + // same feature, different value + ChimeraCommands.addColourRange(featureValues, "Y", 0, 40, 50, "A"); + commands = ChimeraCommands.buildSetAttributeCommands(featuresMap, + mockBinding); + assertEquals(2, commands.size()); + // commands are ordered by feature type but not by value + // so use contains to test for the expected command: + assertTrue(commands + .contains("setattr r jv_chain 'X' #0:3-25.A,21-25.B|#1:26-30.A")); + assertTrue(commands.contains("setattr r jv_chain 'Y' #0:40-50.A")); + + featuresMap.clear(); + featureValues.clear(); + featuresMap.put("side-chain binding!", featureValues); + ChimeraCommands.addColourRange(featureValues, + "metal 'ion!", 0, 7, 15, + "A"); + // feature names are sanitised to change non-alphanumeric to underscore + // feature values are sanitised to encode single quote characters + commands = ChimeraCommands.buildSetAttributeCommands(featuresMap, + mockBinding); + assertTrue(commands + .contains("setattr r jv_side_chain_binding_ 'metal 'ion!' #0:7-15.A")); + } + + /** + * Tests for the method that prefixes and sanitises a feature name so it can + * be used as a valid, namespaced attribute name in Chimera + */ + @Test(groups = { "Functional" }) + public void testMakeAttributeName() + { + assertEquals(ChimeraCommands.makeAttributeName(null), "jv_"); + assertEquals(ChimeraCommands.makeAttributeName(""), "jv_"); + assertEquals(ChimeraCommands.makeAttributeName("helix"), "jv_helix"); + assertEquals(ChimeraCommands.makeAttributeName("Hello World 24"), + "jv_Hello_World_24"); + assertEquals( + ChimeraCommands.makeAttributeName("!this is-a_very*{odd(name"), + "jv__this_is_a_very__odd_name"); + // name ending in color gets underscore appended + assertEquals(ChimeraCommands.makeAttributeName("helixColor"), + "jv_helixColor_"); + } + + @Test(groups = { "Functional" }) + public void testGetColourBySequenceCommands_hiddenColumns() + { + /* + * load these sequences, coloured by Strand propensity, + * with columns 2-4 hidden + */ + SequenceI seq1 = new Sequence("seq1", "MHRSQSSSGG"); + SequenceI seq2 = new Sequence("seq2", "MVRSNGGSSS"); + AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 }); + AlignFrame af = new AlignFrame(al, 800, 500); + af.changeColour_actionPerformed(JalviewColourScheme.Strand.toString()); + ColumnSelection cs = new ColumnSelection(); + cs.addElement(2); + cs.addElement(3); + cs.addElement(4); + af.getViewport().setColumnSelection(cs); + af.hideSelColumns_actionPerformed(null); + sr = new SequenceRenderer(af.getViewport()); + SequenceI[][] seqs = new SequenceI[][] { { seq1 }, { seq2 } }; + String[] files = new String[] { "seq1.pdb", "seq2.pdb" }; + StructureSelectionManager ssm = new StructureSelectionManager(); + + /* + * map residues 1-10 to residues 21-30 (atoms 105-150) in structures + */ + HashMap map = new HashMap<>(); + for (int pos = 1; pos <= seq1.getLength(); pos++) + { + map.put(pos, new int[] { 20 + pos, 5 * (20 + pos) }); + } + StructureMapping sm1 = new StructureMapping(seq1, "seq1.pdb", "pdb1", + "A", map, null); + ssm.addStructureMapping(sm1); + StructureMapping sm2 = new StructureMapping(seq2, "seq2.pdb", "pdb2", + "B", map, null); + ssm.addStructureMapping(sm2); + + /* + * put data into the mock binding object + */ + PA.setValue(mockBinding, "ssm", ssm); + PA.setValue(mockBinding, "sequence", seqs); + + StructureMappingcommandSet[] commands = ChimeraCommands + .getColourBySequenceCommand(files, af.alignPanel, mockBinding); + assertEquals(1, commands.length); + assertEquals(1, commands[0].commands.length); + String theCommand = commands[0].commands[0]; + // M colour is #82827d (see strand.html help page) + assertTrue(theCommand.contains("color #82827d #0:21.A|#1:21.B")); + // H colour is #60609f + assertTrue(theCommand.contains("color #60609f #0:22.A")); + // V colour is #ffff00 + assertTrue(theCommand.contains("color #ffff00 #1:22.B")); + // hidden columns are Gray (128, 128, 128) + assertTrue(theCommand.contains("color #808080 #0:23-25.A|#1:23-25.B")); + // S and G are both coloured #4949b6 + assertTrue(theCommand.contains("color #4949b6 #0:26-30.A|#1:26-30.B")); + } + + @Test(groups = "Functional") + public void testGetAtomSpec() + { + AtomSpecModel model = new AtomSpecModel(); + assertEquals(ChimeraCommands.getAtomSpec(model, mockBinding), ""); + model.addRange(1, 2, 4, "A"); + assertEquals(ChimeraCommands.getAtomSpec(model, mockBinding), + "#1:2-4.A"); + model.addRange(1, 8, 8, "A"); + assertEquals(ChimeraCommands.getAtomSpec(model, mockBinding), + "#1:2-4.A,8.A"); + model.addRange(1, 5, 7, "B"); + assertEquals(ChimeraCommands.getAtomSpec(model, mockBinding), + "#1:2-4.A,8.A,5-7.B"); + model.addRange(1, 3, 5, "A"); + assertEquals(ChimeraCommands.getAtomSpec(model, mockBinding), + "#1:2-5.A,8.A,5-7.B"); + model.addRange(0, 1, 4, "B"); + assertEquals(ChimeraCommands.getAtomSpec(model, mockBinding), + "#0:1-4.B|#1:2-5.A,8.A,5-7.B"); + model.addRange(0, 5, 9, "C"); + assertEquals(ChimeraCommands.getAtomSpec(model, mockBinding), + "#0:1-4.B,5-9.C|#1:2-5.A,8.A,5-7.B"); + model.addRange(1, 8, 10, "B"); + assertEquals(ChimeraCommands.getAtomSpec(model, mockBinding), + "#0:1-4.B,5-9.C|#1:2-5.A,8.A,5-10.B"); + model.addRange(1, 8, 9, "B"); + assertEquals(ChimeraCommands.getAtomSpec(model, mockBinding), + "#0:1-4.B,5-9.C|#1:2-5.A,8.A,5-10.B"); + model.addRange(0, 3, 10, "C"); // subsumes 5-9 + assertEquals(ChimeraCommands.getAtomSpec(model, mockBinding), + "#0:1-4.B,3-10.C|#1:2-5.A,8.A,5-10.B"); + model.addRange(5, 25, 35, " "); // empty chain code - e.g. from homology + // modelling + assertEquals(ChimeraCommands.getAtomSpec(model, mockBinding), + "#0:1-4.B,3-10.C|#1:2-5.A,8.A,5-10.B|#5:25-35."); + } }