X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Fjmol%2FJmolCommandsTest.java;h=88e5833ec972eb3537e1874f463cee74a0449590;hb=refs%2Fheads%2Fbug%2FJAL-4313-make-visible-annot-fix;hp=d1a9df6ce5bb089c44411628084069bb6db8d9e5;hpb=fea6f8ed76719fd78b600adfea8891dafb8c9d12;p=jalview.git diff --git a/test/jalview/ext/jmol/JmolCommandsTest.java b/test/jalview/ext/jmol/JmolCommandsTest.java index d1a9df6..88e5833 100644 --- a/test/jalview/ext/jmol/JmolCommandsTest.java +++ b/test/jalview/ext/jmol/JmolCommandsTest.java @@ -23,36 +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.StructureCommandsI; +import jalview.structure.StructureCommandI; +import jalview.structure.StructureCommandsI.AtomSpecType; import jalview.structure.StructureMapping; import jalview.structure.StructureSelectionManager; -import java.awt.Color; -import java.util.HashMap; -import java.util.LinkedHashMap; -import java.util.Map; - -import org.testng.annotations.BeforeClass; -import org.testng.annotations.Test; - public class JmolCommandsTest { + private JmolCommands testee; @BeforeClass(alwaysRun = true) - public void setUpJvOptionPane() + public void setUp() { - JvOptionPane.setInteractiveMode(false); - JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); + testee = new JmolCommands(); } @Test(groups = { "Functional" }) @@ -76,7 +77,7 @@ public class JmolCommandsTest SequenceRenderer sr = new SequenceRenderer(af.getViewport()); SequenceI[][] seqs = new SequenceI[][] { { seq1 }, { seq2 } }; String[] files = new String[] { "seq1.pdb", "seq2.pdb" }; - StructureSelectionManager ssm = new StructureSelectionManager(); + StructureSelectionManager ssm = StructureSelectionManager.getStructureSelectionManager(null); /* * map residues 1-10 to residues 21-30 (atoms 105-150) in structures @@ -93,8 +94,9 @@ public class JmolCommandsTest "B", map, null); ssm.addStructureMapping(sm2); - String[] commands = new JmolCommands().colourBySequence(ssm, files, - seqs, sr, af.alignPanel); + // TODO - comments in testee suggest this tests an obsolete method! + String[] commands = testee.colourBySequence(ssm, files, seqs, sr, + af.alignPanel); assertEquals(commands.length, 2); String chainACommand = commands[0]; @@ -128,89 +130,161 @@ public class JmolCommandsTest @Test(groups = "Functional") public void testGetAtomSpec() { - StructureCommandsI testee = new JmolCommands(); AtomSpecModel model = new AtomSpecModel(); - assertEquals(testee.getAtomSpec(model, false), ""); - model.addRange(1, 2, 4, "A"); - assertEquals(testee.getAtomSpec(model, false), "2-4:A/1.1"); - model.addRange(1, 8, 8, "A"); - assertEquals(testee.getAtomSpec(model, false), "2-4:A/1.1|8:A/1.1"); - model.addRange(1, 5, 7, "B"); - assertEquals(testee.getAtomSpec(model, false), + 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, false), + 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, false), + 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, false), + 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, false), + 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, false), + 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, false), + 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, false), + 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"); + 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 - String[] commands = new JmolCommands().colourBySequence(map); - assertEquals(commands.length, 1); - String expected = "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]; " - + "select 3-5:A/2.1|8:A/2.1;color[255,255,0]; " - + "select 3-9:A/1.1;color[255,0,0]"; - assertEquals(commands[0], expected); + 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() { - StructureCommandsI testee = new JmolCommands(); AtomSpecModel ref = new AtomSpecModel(); - ref.addRange(1, 12, 14, "A"); - ref.addRange(1, 18, 18, "B"); - ref.addRange(1, 22, 23, "B"); + 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"); - String command = testee.superposeStructures(ref, toAlign); + 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, expected); + assertEquals(command.get(0).getCommand(), expected); } @Test(groups = "Functional") public void testGetModelStartNo() { - StructureCommandsI testee = new JmolCommands(); 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\""); + } }