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.List;
import java.util.Map;
-import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class ChimeraCommandsTest
{
- @BeforeClass(alwaysRun = true)
- public void setUpJvOptionPane()
- {
- JvOptionPane.setInteractiveMode(false);
- JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
- }
-
@Test(groups = { "Functional" })
public void testBuildColourCommands()
{
// 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, false).get(0);
+ String command = new ChimeraCommands().buildColourCommands(map).get(0);
assertEquals(
command,
"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");
* 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 res jv_chain 'X' #0:8-20.A");
// add same feature value, overlapping range
ChimeraCommands.addAtomSpecRange(featureValues, "X", 0, 3, 9, "A");
commands = ChimeraCommands.buildSetAttributeCommands(featuresMap,
false);
assertEquals(1, commands.size());
- assertEquals(commands.get(0), "setattr r jv_chain 'X' #0:3-25.A");
+ assertEquals(commands.get(0), "setattr res jv_chain 'X' #0:3-25.A");
// same feature value and model, different chain
ChimeraCommands.addAtomSpecRange(featureValues, "X", 0, 21, 25, "B");
false);
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 res jv_chain 'X' #0:3-25.A,21-25.B|#1:26-30.A");
// same feature, different value
ChimeraCommands.addAtomSpecRange(featureValues, "Y", 0, 40, 50, "A");
// 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 res jv_chain 'X' #0:3-25.A,21-25.B|#1:26-30.A"));
+ assertTrue(commands.contains("setattr res jv_chain 'Y' #0:40-50.A"));
featuresMap.clear();
featureValues.clear();
commands = ChimeraCommands.buildSetAttributeCommands(featuresMap,
false);
assertTrue(commands
- .contains("setattr r jv_side_chain_binding_ '<html>metal <a href=\"http:a.b.c/x\"> 'ion!' #0:7-15.A"));
+ .contains(
+ "setattr res jv_side_chain_binding_ '<html>metal <a href=\"http:a.b.c/x\"> 'ion!' #0:7-15.A"));
}
/**
"B", map, null);
ssm.addStructureMapping(sm2);
- StructureMappingcommandSet[] commands = ChimeraCommands
- .getColourBySequenceCommand(ssm, files, seqs, sr, af.alignPanel,
- false);
+ String[] commands = new ChimeraCommands()
+ .colourBySequence(ssm, files, seqs, sr, af.alignPanel);
assertEquals(1, commands.length);
- assertEquals(1, commands[0].commands.length);
- String theCommand = commands[0].commands[0];
+ String theCommand = 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