import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertTrue;
-import jalview.api.AlignmentViewPanel;
-import jalview.api.FeatureRenderer;
+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.HiddenColumns;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
-import jalview.ext.rbvi.chimera.AtomSpecModel;
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.AtomSpecModel;
+import jalview.structure.StructureCommandI;
import jalview.structure.StructureMapping;
-import jalview.structure.StructureMappingcommandSet;
import jalview.structure.StructureSelectionManager;
-import jalview.structures.models.AAStructureBindingModel;
-import jalview.util.StructureCommands;
-
-import java.awt.Color;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.Test;
-
-import junit.extensions.PA;
public class JmolCommandsTest
{
- private SequenceRenderer sr;
-
- private String[] files;
-
- private AAStructureBindingModel mockBinding = new AAStructureBindingModel(
- null, null)
- {
- @Override
- public void releaseReferences(Object svl)
- {
- }
-
- @Override
- public void highlightAtoms(List<AtomSpec> atoms)
- {
- }
-
- @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
- public jalview.api.SequenceRenderer getSequenceRenderer(
- AlignmentViewPanel alignment)
- {
- return sr;
- }
-
- @Override
- protected void colourBySequence(AlignmentViewPanel avp)
- {
- }
-
- @Override
- public void colourByChain()
- {
- }
-
- @Override
- public void colourByCharge()
- {
- }
-
- @Override
- public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
- {
- return null;
- }
-
- @Override
- public String[] getStructureFiles()
- {
- return files;
- }
-
- @Override
- public String getModelSpec(int model)
- {
- return "#" + String.valueOf(model);
- }
- };
+ private JmolCommands testee;
@BeforeClass(alwaysRun = true)
- public void setUpJvOptionPane()
+ public void setUp()
{
- JvOptionPane.setInteractiveMode(false);
- JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ testee = new JmolCommands();
}
/**
"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]")); // first one
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]"));
public void testGetAtomSpec()
{
AtomSpecModel model = new AtomSpecModel();
- assertEquals(JmolCommands.getAtomSpec(model), "");
+ assertEquals(testee.getAtomSpec(model, false), "");
/*
* Jalview numbers models from 0, Jmol from 1
*/
- model.addRange(1, 2, 4, "A");
- assertEquals(JmolCommands.getAtomSpec(model), "2-4:A/2.1");
+ model.addRange("2", 2, 4, "A");
+ assertEquals(testee.getAtomSpec(model, false), "2-4:A/2.1");
- model.addRange(1, 8, 8, "A");
- assertEquals(JmolCommands.getAtomSpec(model), "(2-4,8)&:A/2.1");
+ model.addRange("2", 8, 8, "A");
+ assertEquals(testee.getAtomSpec(model, false), "(2-4,8)&:A/2.1");
- model.addRange(1, 5, 7, "B");
- assertEquals(JmolCommands.getAtomSpec(model),
+ model.addRange("2", 5, 7, "B");
+ assertEquals(testee.getAtomSpec(model,
+ false),
"(2-4,8)&:A/2.1,5-7:B/2.1");
- model.addRange(1, 3, 5, "A");
+ model.addRange("2", 3, 5, "A");
// 3-5 merges with 2-4 to make 2-5:
- assertEquals(JmolCommands.getAtomSpec(model),
+ assertEquals(testee.getAtomSpec(model,
+ false),
"(2-5,8)&:A/2.1,5-7:B/2.1");
- model.addRange(0, 1, 4, "B");
- assertEquals(JmolCommands.getAtomSpec(model),
+ model.addRange("1", 1, 4, "B");
+ assertEquals(testee.getAtomSpec(model,
+ false),
"1-4:B/1.1,(2-5,8)&:A/2.1,5-7:B/2.1");
- model.addRange(0, 5, 9, "C");
- assertEquals(JmolCommands.getAtomSpec(model),
+ model.addRange("1", 5, 9, "C");
+ assertEquals(testee.getAtomSpec(model,
+ false),
"1-4:B/1.1,5-9:C/1.1,(2-5,8)&:A/2.1,5-7:B/2.1");
- model.addRange(1, 8, 10, "B");
+ model.addRange("2", 8, 10, "B");
// 8-10 extends 5-7 to make 5-10
- // note code generates (5-10)&:B which is equivalent to 5-10:B
- assertEquals(JmolCommands.getAtomSpec(model),
- "1-4:B/1.1,5-9:C/1.1,(2-5,8)&:A/2.1,(5-10)&:B/2.1");
+ assertEquals(testee.getAtomSpec(model,
+ false),
+ "1-4:B/1.1,5-9:C/1.1,(2-5,8)&:A/2.1,5-10:B/2.1");
- model.addRange(1, 8, 9, "B");
+ model.addRange("2", 8, 9, "B");
// subsumed by 5-10 so makes no difference
- assertEquals(JmolCommands.getAtomSpec(model),
- "1-4:B/1.1,5-9:C/1.1,(2-5,8)&:A/2.1,(5-10)&:B/2.1");
+ assertEquals(testee.getAtomSpec(model,
+ false),
+ "1-4:B/1.1,5-9:C/1.1,(2-5,8)&:A/2.1,5-10:B/2.1");
- model.addRange(0, 3, 10, "C");
+ model.addRange("1", 3, 10, "C");
// subsumes 5-9 so replaces it
- assertEquals(JmolCommands.getAtomSpec(model),
- "1-4:B/1.1,(3-10)&:C/1.1,(2-5,8)&:A/2.1,(5-10)&:B/2.1");
+ assertEquals(testee.getAtomSpec(model,
+ false),
+ "1-4:B/1.1,3-10:C/1.1,(2-5,8)&:A/2.1,5-10:B/2.1");
// empty chain code - e.g. from homology modelling
- model.addRange(5, 25, 35, " ");
- assertEquals(JmolCommands.getAtomSpec(model),
- "1-4:B/1.1,(3-10)&:C/1.1,(2-5,8)&:A/2.1,(5-10)&:B/2.1,25-35:/6.1");
+ model.addRange("6", 25, 35, " ");
+ assertEquals(testee.getAtomSpec(model,
+ false),
+ "1-4:B/1.1,3-10:C/1.1,(2-5,8)&:A/2.1,5-10:B/2.1,25-35:/6.1");
+ }
+
+ @Test(groups = { "Functional" })
+ public void testColourBySequence()
+ {
+ Map<Object, AtomSpecModel> 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<StructureCommandI> commands = testee.colourBySequence(map);
+ assertEquals(commands.size(), 1);
+ String expected1 = "select (2-5,9-23)&:A/1.1,7:B/1.1,1:A/2.1,4-7:B/2.1;color[0,0,255]";
+ String expected2 = "select (3-5,8)&: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<StructureCommandI> command = testee.superposeStructures(ref,
+ toAlign);
+ assertEquals(command.size(), 1);
+ String refSpec = "12-14:A/1.1,(18,22-23)&:B/1.1";
+ String toAlignSpec = "(15-17,20-21)&: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 testGetColourBySequenceCommand()
+ public void testGetModelStartNo()
{
- /*
- * load these sequences, coloured by Strand propensity,
- * with columns 2-4 hidden (counting from 0)
- */
- SequenceI seq1 = new Sequence("seq1", "MHRSQSSSGG");
- SequenceI seq2 = new Sequence("seq2", "MVRSNGGMSS");
- 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 } };
- files = new String[] { "seq1.pdb", "seq2.pdb" };
- StructureSelectionManager ssm = new StructureSelectionManager();
+ assertEquals(testee.getModelStartNo(), 1);
+ }
- /*
- * map residues 1-10 to residues 21-30 (atoms 105-150) in structures
- */
- HashMap<Integer, int[]> 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);
+ @Test(groups = "Functional")
+ public void testColourByChain()
+ {
+ StructureCommandI cmd = testee.colourByChain();
+ assertEquals(cmd.getCommand(), "select *;color chain");
+ }
- /*
- * put data into the mock binding object
- */
- PA.setValue(mockBinding, "ssm", ssm);
- PA.setValue(mockBinding, "sequence", seqs);
+ @Test(groups = "Functional")
+ public void testColourByCharge()
+ {
+ List<StructureCommandI> 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");
+ }
- Map<Object, AtomSpecModel> colourMap = StructureCommands
- .buildColoursMap(mockBinding, af.alignPanel);
+ @Test(groups = "Functional")
+ public void testSetBackgroundColour()
+ {
+ StructureCommandI cmd = testee.setBackgroundColour(Color.PINK);
+ assertEquals(cmd.getCommand(), "background [255,175,175]");
+ }
- String[] commands = JmolCommands.getColourBySequenceCommand(colourMap);
+ @Test(groups = "Functional")
+ public void testFocusView()
+ {
+ StructureCommandI cmd = testee.focusView();
+ assertEquals(cmd.getCommand(), "zoom 0");
+ }
- assertEquals(commands.length, 5);
+ @Test(groups = "Functional")
+ public void testSaveSession()
+ {
+ StructureCommandI cmd = testee.saveSession("/some/filepath");
+ assertEquals(cmd.getCommand(), "write STATE \"/some/filepath\"");
+ }
- /*
- * verify selections and colours match Strand Propensity colour scheme
- * (see strand.html help page for colours)
- *
- * M is #82827d == (130, 130, 125) at model 1 pos 21A, model 2 21B
- */
- assertEquals(commands[0],
- "color (21:A/1.1,(21,28)&:B/2.1) [130,130,125];");
+ @Test(groups = "Functional")
+ public void testShowBackbone()
+ {
+ List<StructureCommandI> cmds = testee.showBackbone();
+ assertEquals(cmds.size(), 1);
+ assertEquals(cmds.get(0).getCommand(),
+ "select *; cartoons off; backbone");
+ }
- /*
- * H is #60609f == (96, 96, 159)
- */
- assertEquals(commands[1], "color (22:A/1.1) [96,96,159];");
+ @Test(groups = "Functional")
+ public void testLoadFile()
+ {
+ StructureCommandI cmd = testee.loadFile("/some/filepath");
+ assertEquals(cmd.getCommand(), "load FILES \"/some/filepath\"");
- /*
- * hidden columns are Gray (128, 128, 128)
- */
- assertEquals(commands[2],
- "color (23-25:A/1.1,23-25:B/2.1) [128,128,128];");
+ // single backslash gets escaped to double
+ cmd = testee.loadFile("\\some\\filepath");
+ assertEquals(cmd.getCommand(), "load FILES \"\\\\some\\\\filepath\"");
+ }
- /*
- * S and G are both coloured #4949b6 == (73, 73, 182)
- */
- assertEquals(commands[3],
- "color (26-30:A/1.1,(26-27,29-30)&:B/2.1) [73,73,182];");
+ @Test(groups = "Functional")
+ public void testOpenSession()
+ {
+ StructureCommandI cmd = testee.openSession("/some/filepath");
+ assertEquals(cmd.getCommand(), "load FILES \"/some/filepath\"");
- /*
- * V is ffff00 == (255, 255, 0)
- */
- assertEquals(commands[4], "color (22:B/2.1) [255,255,0];");
+ // single backslash gets escaped to double
+ cmd = testee.openSession("\\some\\filepath");
+ assertEquals(cmd.getCommand(), "load FILES \"\\\\some\\\\filepath\"");
}
}
git://source.jalview.org / jalview.git / blobdiff