X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Frbvi%2Fchimera%2FChimeraCommandsTest.java;h=2c973cac24bd9ea2b1327f432beb9a94c85cc29d;hb=136c0793b90b72b928c4d77dc109dd5c644e00d3;hp=70c6922ee5bbc88240a6aa88b03b8898da882531;hpb=5965127c38ff1a35d10d806c4b4537cdc1e39579;p=jalview.git diff --git a/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java b/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java index 70c6922..2c973ca 100644 --- a/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java +++ b/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java @@ -23,7 +23,18 @@ package jalview.ext.rbvi.chimera; import static org.testng.Assert.assertEquals; import static org.testng.Assert.assertTrue; +import jalview.datamodel.Alignment; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.ColumnSelection; +import jalview.datamodel.Sequence; +import jalview.datamodel.SequenceI; +import jalview.gui.AlignFrame; import jalview.gui.JvOptionPane; +import jalview.gui.SequenceRenderer; +import jalview.schemes.JalviewColourScheme; +import jalview.structure.StructureMapping; +import jalview.structure.StructureMappingcommandSet; +import jalview.structure.StructureSelectionManager; import java.awt.Color; import java.util.HashMap; @@ -49,15 +60,15 @@ public class ChimeraCommandsTest { 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"); + 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 @@ -80,7 +91,7 @@ public class ChimeraCommandsTest * start with just one feature/value... */ featuresMap.put("chain", featureValues); - ChimeraCommands.addRange(featureValues, "X", 0, 8, 20, "A"); + ChimeraCommands.addColourRange(featureValues, "X", 0, 8, 20, "A"); List commands = ChimeraCommands .buildSetAttributeCommands(featuresMap); @@ -90,43 +101,46 @@ public class ChimeraCommandsTest * 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"); + assertEquals(commands.get(0), "setattr r jv_chain 'X' #0:8-20.A"); // add same feature value, overlapping range - ChimeraCommands.addRange(featureValues, "X", 0, 3, 9, "A"); + ChimeraCommands.addColourRange(featureValues, "X", 0, 3, 9, "A"); // same feature value, contiguous range - ChimeraCommands.addRange(featureValues, "X", 0, 21, 25, "A"); + ChimeraCommands.addColourRange(featureValues, "X", 0, 21, 25, "A"); commands = ChimeraCommands.buildSetAttributeCommands(featuresMap); assertEquals(1, commands.size()); - assertEquals(commands.get(0), "setattr r jv_chain \"X\" #0:3-25.A"); + assertEquals(commands.get(0), "setattr r jv_chain 'X' #0:3-25.A"); // same feature value and model, different chain - ChimeraCommands.addRange(featureValues, "X", 0, 21, 25, "B"); + ChimeraCommands.addColourRange(featureValues, "X", 0, 21, 25, "B"); // same feature value and chain, different model - ChimeraCommands.addRange(featureValues, "X", 1, 26, 30, "A"); + ChimeraCommands.addColourRange(featureValues, "X", 1, 26, 30, "A"); commands = ChimeraCommands.buildSetAttributeCommands(featuresMap); assertEquals(1, commands.size()); assertEquals(commands.get(0), - "setattr r jv_chain \"X\" #0:3-25.A,21-25.B|#1:26-30.A"); + "setattr r jv_chain 'X' #0:3-25.A,21-25.B|#1:26-30.A"); // same feature, different value - ChimeraCommands.addRange(featureValues, "Y", 0, 40, 50, "A"); + ChimeraCommands.addColourRange(featureValues, "Y", 0, 40, 50, "A"); commands = ChimeraCommands.buildSetAttributeCommands(featuresMap); 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")); + .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.addRange(featureValues, "metal ion!", 0, 7, 15, "A"); - // feature names are sanitised to change space or hyphen to underscore + 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); assertTrue(commands - .contains("setattr r jv_side_chain_binding_ \"metal ion!\" #0:7-15.A")); + .contains("setattr r jv_side_chain_binding_ 'metal 'ion!' #0:7-15.A")); } /** @@ -148,4 +162,59 @@ public class ChimeraCommandsTest 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); + SequenceRenderer 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); + + StructureMappingcommandSet[] commands = ChimeraCommands + .getColourBySequenceCommand(ssm, files, seqs, sr, af.alignPanel); + 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")); + } }