X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Fjmol%2FJmolCommandsTest.java;h=968460335741cd431d1d80e941e4d8c4c1163003;hb=cd669a0e8c7b91b379bca8fe6e702cf0fcbd1ce0;hp=3309adf73e6aee1483834ce0bed2499d507dc1d3;hpb=13fd7bc6175d7aa66d8e161d21183e7e33c9150a;p=jalview.git diff --git a/test/jalview/ext/jmol/JmolCommandsTest.java b/test/jalview/ext/jmol/JmolCommandsTest.java index 3309adf..9684603 100644 --- a/test/jalview/ext/jmol/JmolCommandsTest.java +++ b/test/jalview/ext/jmol/JmolCommandsTest.java @@ -23,50 +23,37 @@ package jalview.ext.jmol; import static org.testng.Assert.assertEquals; import static org.testng.Assert.assertTrue; +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 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.AtomSpecModel; +import jalview.structure.StructureCommandI; +import jalview.structure.StructureCommandsI.AtomSpecType; import jalview.structure.StructureMapping; -import jalview.structure.StructureMappingcommandSet; import jalview.structure.StructureSelectionManager; -import java.util.HashMap; - -import org.testng.annotations.BeforeClass; -import org.testng.annotations.Test; - public class JmolCommandsTest { + private JmolCommands testee; @BeforeClass(alwaysRun = true) - public void setUpJvOptionPane() - { - JvOptionPane.setInteractiveMode(false); - JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); - } - - @Test(groups = { "Functional" }) - public void testGetColourBySequenceCommand_noFeatures() + public void setUp() { - SequenceI seq1 = new Sequence("seq1", "MHRSQTRALK"); - SequenceI seq2 = new Sequence("seq2", "MRLEITQSGD"); - AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 }); - AlignFrame af = new AlignFrame(al, 800, 500); - SequenceRenderer sr = new SequenceRenderer(af.getViewport()); - SequenceI[][] seqs = new SequenceI[][] { { seq1 }, { seq2 } }; - String[] files = new String[] { "seq1.pdb", "seq2.pdb" }; - StructureSelectionManager ssm = new StructureSelectionManager(); - - // need some mappings! - - StructureMappingcommandSet[] commands = JmolCommands - .getColourBySequenceCommand(ssm, files, seqs, sr, af.alignPanel); + testee = new JmolCommands(); } @Test(groups = { "Functional" }) @@ -91,11 +78,11 @@ public class JmolCommandsTest 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(); + HashMap map = new HashMap<>(); for (int pos = 1; pos <= seq1.getLength(); pos++) { map.put(pos, new int[] { 20 + pos, 5 * (20 + pos) }); @@ -106,37 +93,197 @@ public class JmolCommandsTest StructureMapping sm2 = new StructureMapping(seq2, "seq2.pdb", "pdb2", "B", map, null); ssm.addStructureMapping(sm2); - - StructureMappingcommandSet[] commands = JmolCommands - .getColourBySequenceCommand(ssm, files, seqs, sr, af.alignPanel); + + String[] commands = testee.colourBySequence(ssm, files, seqs, sr, + af.alignPanel); assertEquals(commands.length, 2); - assertEquals(commands[0].commands.length, 1); - String chainACommand = commands[0].commands[0]; + String chainACommand = commands[0]; // M colour is #82827d == (130, 130, 125) (see strand.html help page) - assertTrue(chainACommand - .contains(";select 21:A/1.1;color[130,130,125]")); + assertTrue( + chainACommand.contains("select 21:A/1.1;color[130,130,125]")); // first + // one // H colour is #60609f == (96, 96, 159) assertTrue(chainACommand.contains(";select 22:A/1.1;color[96,96,159]")); // hidden columns are Gray (128, 128, 128) assertTrue(chainACommand .contains(";select 23-25:A/1.1;color[128,128,128]")); // S and G are both coloured #4949b6 == (73, 73, 182) - assertTrue(chainACommand - .contains(";select 26-30:A/1.1;color[73,73,182]")); + assertTrue( + chainACommand.contains(";select 26-30:A/1.1;color[73,73,182]")); - String chainBCommand = commands[1].commands[0]; + String chainBCommand = commands[1]; // M colour is #82827d == (130, 130, 125) - assertTrue(chainBCommand - .contains(";select 21:B/2.1;color[130,130,125]")); + assertTrue( + chainBCommand.contains("select 21:B/2.1;color[130,130,125]")); // V colour is #ffff00 == (255, 255, 0) - assertTrue(chainBCommand -.contains(";select 22:B/2.1;color[255,255,0]")); + assertTrue(chainBCommand.contains(";select 22:B/2.1;color[255,255,0]")); // hidden columns are Gray (128, 128, 128) assertTrue(chainBCommand .contains(";select 23-25:B/2.1;color[128,128,128]")); // S and G are both coloured #4949b6 == (73, 73, 182) - assertTrue(chainBCommand - .contains(";select 26-30:B/2.1;color[73,73,182]")); + assertTrue( + chainBCommand.contains(";select 26-30:B/2.1;color[73,73,182]")); + } + + @Test(groups = "Functional") + public void testGetAtomSpec() + { + AtomSpecModel model = new AtomSpecModel(); + assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), ""); + model.addRange("1", 2, 4, "A"); + assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), + "2-4:A/1.1"); + model.addRange("1", 8, 8, "A"); + assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), + "2-4:A/1.1|8:A/1.1"); + model.addRange("1", 5, 7, "B"); + assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), + "2-4:A/1.1|8:A/1.1|5-7:B/1.1"); + model.addRange("1", 3, 5, "A"); + assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), + "2-5:A/1.1|8:A/1.1|5-7:B/1.1"); + model.addRange("2", 1, 4, "B"); + assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), + "2-5:A/1.1|8:A/1.1|5-7:B/1.1|1-4:B/2.1"); + model.addRange("2", 5, 9, "C"); + assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), + "2-5:A/1.1|8:A/1.1|5-7:B/1.1|1-4:B/2.1|5-9:C/2.1"); + model.addRange("1", 8, 10, "B"); + assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), + "2-5:A/1.1|8:A/1.1|5-10:B/1.1|1-4:B/2.1|5-9:C/2.1"); + model.addRange("1", 8, 9, "B"); + assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), + "2-5:A/1.1|8:A/1.1|5-10:B/1.1|1-4:B/2.1|5-9:C/2.1"); + model.addRange("2", 3, 10, "C"); // subsumes 5-9 + assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), + "2-5:A/1.1|8:A/1.1|5-10:B/1.1|1-4:B/2.1|3-10:C/2.1"); + model.addRange("5", 25, 35, " "); + assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), + "2-5:A/1.1|8:A/1.1|5-10:B/1.1|1-4:B/2.1|3-10:C/2.1|25-35:/5.1"); + + } + + @Test(groups = { "Functional" }) + public void testColourBySequence() + { + Map map = new LinkedHashMap<>(); + JmolCommands.addAtomSpecRange(map, Color.blue, "1", 2, 5, "A"); + JmolCommands.addAtomSpecRange(map, Color.blue, "1", 7, 7, "B"); + JmolCommands.addAtomSpecRange(map, Color.blue, "1", 9, 23, "A"); + JmolCommands.addAtomSpecRange(map, Color.blue, "2", 1, 1, "A"); + JmolCommands.addAtomSpecRange(map, Color.blue, "2", 4, 7, "B"); + JmolCommands.addAtomSpecRange(map, Color.yellow, "2", 8, 8, "A"); + JmolCommands.addAtomSpecRange(map, Color.yellow, "2", 3, 5, "A"); + JmolCommands.addAtomSpecRange(map, Color.red, "1", 3, 5, "A"); + JmolCommands.addAtomSpecRange(map, Color.red, "1", 6, 9, "A"); + + // Colours should appear in the Jmol command in the order in which + // they were added; within colour, by model, by chain, ranges in start order + List commands = testee.colourBySequence(map); + assertEquals(commands.size(), 1); + String expected1 = "select 2-5:A/1.1|9-23:A/1.1|7:B/1.1|1:A/2.1|4-7:B/2.1;color[0,0,255]"; + String expected2 = "select 3-5:A/2.1|8:A/2.1;color[255,255,0]"; + String expected3 = "select 3-9:A/1.1;color[255,0,0]"; + assertEquals(commands.get(0).getCommand(), + expected1 + ";" + expected2 + ";" + expected3); + } + + @Test(groups = { "Functional" }) + public void testSuperposeStructures() + { + AtomSpecModel ref = new AtomSpecModel(); + ref.addRange("1", 12, 14, "A"); + ref.addRange("1", 18, 18, "B"); + ref.addRange("1", 22, 23, "B"); + AtomSpecModel toAlign = new AtomSpecModel(); + toAlign.addRange("2", 15, 17, "B"); + toAlign.addRange("2", 20, 21, "B"); + toAlign.addRange("2", 22, 22, "C"); + List command = testee.superposeStructures(ref, + toAlign, AtomSpecType.ALPHA); // doesn't matter for Jmol whether nuc + // or protein + assertEquals(command.size(), 1); + String refSpec = "12-14:A/1.1|18:B/1.1|22-23:B/1.1"; + String toAlignSpec = "15-17:B/2.1|20-21:B/2.1|22:C/2.1"; + String expected = String.format( + "compare {2.1} {1.1} SUBSET {(*.CA | *.P) and conformation=1} ATOMS {%s}{%s} ROTATE TRANSLATE ;select %s|%s;cartoons", + toAlignSpec, refSpec, toAlignSpec, refSpec); + assertEquals(command.get(0).getCommand(), expected); + } + + @Test(groups = "Functional") + public void testGetModelStartNo() + { + assertEquals(testee.getModelStartNo(), 1); + } + + @Test(groups = "Functional") + public void testColourByChain() + { + StructureCommandI cmd = testee.colourByChain(); + assertEquals(cmd.getCommand(), "select *;color chain"); + } + + @Test(groups = "Functional") + public void testColourByCharge() + { + List cmds = testee.colourByCharge(); + assertEquals(cmds.size(), 1); + assertEquals(cmds.get(0).getCommand(), + "select *;color white;select ASP,GLU;color red;" + + "select LYS,ARG;color blue;select CYS;color yellow"); + } + + @Test(groups = "Functional") + public void testSetBackgroundColour() + { + StructureCommandI cmd = testee.setBackgroundColour(Color.PINK); + assertEquals(cmd.getCommand(), "background [255,175,175]"); + } + + @Test(groups = "Functional") + public void testFocusView() + { + StructureCommandI cmd = testee.focusView(); + assertEquals(cmd.getCommand(), "zoom 0"); + } + + @Test(groups = "Functional") + public void testSaveSession() + { + StructureCommandI cmd = testee.saveSession("/some/filepath"); + assertEquals(cmd.getCommand(), "write STATE \"/some/filepath\""); + } + + @Test(groups = "Functional") + public void testShowBackbone() + { + List cmds = testee.showBackbone(); + assertEquals(cmds.size(), 1); + assertEquals(cmds.get(0).getCommand(), + "select *; cartoons off; backbone"); + } + + @Test(groups = "Functional") + public void testLoadFile() + { + StructureCommandI cmd = testee.loadFile("/some/filepath"); + assertEquals(cmd.getCommand(), "load FILES \"/some/filepath\""); + + // single backslash gets escaped to double + cmd = testee.loadFile("\\some\\filepath"); + assertEquals(cmd.getCommand(), "load FILES \"\\\\some\\\\filepath\""); + } + + @Test(groups = "Functional") + public void testOpenSession() + { + StructureCommandI cmd = testee.openSession("/some/filepath"); + assertEquals(cmd.getCommand(), "load FILES \"/some/filepath\""); + + // single backslash gets escaped to double + cmd = testee.openSession("\\some\\filepath"); + assertEquals(cmd.getCommand(), "load FILES \"\\\\some\\\\filepath\""); } }