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;
* 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.addColourRange(featureValues, "X", 0, 3, 9, "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.addColourRange(featureValues, "X", 0, 21, 25, "B");
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.addColourRange(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 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.addColourRange(featureValues, "metal ion!", 0, 7, 15,
+ ChimeraCommands.addColourRange(featureValues,
+ "<html>metal <a href=\"http:a.b.c/x\"> 'ion!", 0, 7, 15,
"A");
- // feature names are sanitised to change space or hyphen to underscore
+ // 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_ '<html>metal <a href=\"http:a.b.c/x\"> 'ion!' #0:7-15.A"));
}
/**
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<Integer, int[]> map = new HashMap<Integer, int[]>();
+ 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, null,
+ af.getViewport());
+ 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"));
+ }
}
git://source.jalview.org / jalview.git / blobdiff