public String superposeStructures(AlignmentI[] _alignment,
int[] _refStructure, HiddenColumns[] _hiddenCols)
{
+ // TODO delete method
while (jmolViewer.isScriptExecuting())
{
try
return 1;
}
- @Override
+ /**
+ * Returns a string representation of the given colour suitable for inclusion
+ * in Jmol commands
+ *
+ * @param c
+ * @return
+ */
protected String getColourString(Color c)
{
return c == null ? null
c.getBlue());
}
- /**
- * Returns commands (one per colour key in the map) like
- *
- * <pre>
- * select 2:A/1.1|3-27:B/1.1|9-12:A/2.1;color[173,0,82]
- * </pre>
- */
- @Override
- public String[] colourBySequence(Map<Object, AtomSpecModel> colourMap)
- {
- List<String> colourCommands = buildColourCommands(colourMap);
-
- return colourCommands.toArray(new String[colourCommands.size()]);
- }
public String[] colourBySequence(StructureSelectionManager ssm,
String[] files,
SequenceI[][] sequence, SequenceRenderer sr,
AlignmentViewPanel viewPanel)
{
- // TODO refactor to call buildColoursMap() first...
+ // TODO delete method
FeatureRenderer fr = viewPanel.getFeatureRenderer();
FeatureColourFinder finder = new FeatureColourFinder(fr);
private static final String NO_ALTLOCS = "&~@.B-Z&~@.2-9";
@Override
- public String[] colourBySequence(Map<Object, AtomSpecModel> colourMap)
- {
- List<String> colourCommands = buildColourCommands(colourMap);
-
- return colourCommands.toArray(new String[colourCommands.size()]);
- }
-
- @Override
public String getColourCommand(String atomSpec, Color colour)
{
// https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/color.html
* @param colour
* @return
*/
- @Override
protected String getColourString(Color colour)
{
return ColorUtils.toTkCode(colour);
Map<String, Map<Object, AtomSpecModel>> featureMap = buildFeaturesMap(
ssm, files, seqs, viewPanel);
- List<String> commands = buildSetAttributeCommands(featureMap);
-
- return commands.toArray(new String[commands.size()]);
+ return setAttributes(featureMap);
}
/**
* @param featureMap
* @return
*/
- protected List<String> buildSetAttributeCommands(
+ protected String[] setAttributes(
Map<String, Map<Object, AtomSpecModel>> featureMap)
{
List<String> commands = new ArrayList<>();
AtomSpecModel atomSpecModel = values.get(value);
String featureValue = value.toString();
featureValue = featureValue.replaceAll("\\'", "'");
- String cmd = getSetAttributeCommand(attributeName, featureValue,
+ String cmd = setAttribute(attributeName, featureValue,
atomSpecModel);
commands.add(cmd);
}
}
- return commands;
+ return commands.toArray(new String[commands.size()]);
}
/**
* @param atomSpecModel
* @return
*/
- protected String getSetAttributeCommand(String attributeName,
+ protected String setAttribute(String attributeName,
String attributeValue,
AtomSpecModel atomSpecModel)
{
* @return
*/
@Override
- protected String getSetAttributeCommand(String attributeName,
+ protected String setAttribute(String attributeName,
String attributeValue, AtomSpecModel atomSpecModel)
{
StringBuilder sb = new StringBuilder(128);
for (String chain : atomSpec.getChains(model))
{
boolean firstPositionForChain = true;
- chain = " ".equals(chain) ? chain : chain.trim();
- sb.append("/").append(chain).append(":");
+ sb.append("/").append(chain.trim()).append(":");
List<int[]> rangeList = atomSpec.getRanges(model, chain);
/*
public String superposeStructures(AlignmentI[] _alignment,
int[] _refStructure, HiddenColumns[] _hiddenCols)
{
+ // TODO delete method
StringBuilder allComs = new StringBuilder(128);
String[] files = getStructureFiles();
}
/**
- * <pre>
- * Build a data structure which records contiguous subsequences for each colour.
- * From this we can easily generate the viewer command for colour by sequence.
- * Color
- * Model number
- * Chain
- * list of start/end ranges
- * Ordering is by order of addition (for colours and positions), natural ordering (for models and chains)
- * </pre>
- *
- * @param ssm
- * @param files
- * @param sequence
- * @param sr
- * @param viewPanel
- * @return
- */
- protected Map<Object, AtomSpecModel> buildColoursMap(
- StructureSelectionManager ssm, String[] files,
- SequenceI[][] sequence, SequenceRenderer sr, AlignmentViewPanel viewPanel)
- {
- FeatureRenderer fr = viewPanel.getFeatureRenderer();
- FeatureColourFinder finder = new FeatureColourFinder(fr);
- AlignViewportI viewport = viewPanel.getAlignViewport();
- HiddenColumns cs = viewport.getAlignment().getHiddenColumns();
- AlignmentI al = viewport.getAlignment();
- Map<Object, AtomSpecModel> colourMap = new LinkedHashMap<>();
- Color lastColour = null;
-
- for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
- {
- final int modelNumber = pdbfnum + getModelStartNo();
- StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
-
- if (mapping == null || mapping.length < 1)
- {
- continue;
- }
-
- int startPos = -1, lastPos = -1;
- String lastChain = "";
- for (int s = 0; s < sequence[pdbfnum].length; s++)
- {
- for (int sp, m = 0; m < mapping.length; m++)
- {
- final SequenceI seq = sequence[pdbfnum][s];
- if (mapping[m].getSequence() == seq
- && (sp = al.findIndex(seq)) > -1)
- {
- SequenceI asp = al.getSequenceAt(sp);
- for (int r = 0; r < asp.getLength(); r++)
- {
- // no mapping to gaps in sequence
- if (Comparison.isGap(asp.getCharAt(r)))
- {
- continue;
- }
- int pos = mapping[m].getPDBResNum(asp.findPosition(r));
-
- if (pos < 1 || pos == lastPos)
- {
- continue;
- }
-
- Color colour = sr.getResidueColour(seq, r, finder);
-
- /*
- * darker colour for hidden regions
- */
- if (!cs.isVisible(r))
- {
- colour = Color.GRAY;
- }
-
- final String chain = mapping[m].getChain();
-
- /*
- * Just keep incrementing the end position for this colour range
- * _unless_ colour, PDB model or chain has changed, or there is a
- * gap in the mapped residue sequence
- */
- final boolean newColour = !colour.equals(lastColour);
- final boolean nonContig = lastPos + 1 != pos;
- final boolean newChain = !chain.equals(lastChain);
- if (newColour || nonContig || newChain)
- {
- if (startPos != -1)
- {
- addAtomSpecRange(colourMap, lastColour, modelNumber,
- startPos, lastPos, lastChain);
- }
- startPos = pos;
- }
- lastColour = colour;
- lastPos = pos;
- lastChain = chain;
- }
- // final colour range
- if (lastColour != null)
- {
- addAtomSpecRange(colourMap, lastColour, modelNumber, startPos,
- lastPos, lastChain);
- }
- // break;
- }
- }
- }
- }
- return colourMap;
- }
-
- /**
* Helper method to add one contiguous range to the AtomSpec model for the given
* value (creating the model if necessary). As used by Jalview, {@code value} is
* <ul>
}
/**
- * Returns a colour formatted suitable for use in viewer command syntax
- *
- * @param colour
- * @return
- */
- protected abstract String getColourString(Color colour);
-
- /**
* Traverse the map of colours/models/chains/positions to construct a list of
* 'color' commands (one per distinct colour used). The format of each command
* is specific to the structure viewer.
* @param colourMap
* @return
*/
- public List<String> buildColourCommands(
- Map<Object, AtomSpecModel> colourMap)
+ @Override
+ public String[] colourBySequence(Map<Object, AtomSpecModel> colourMap)
{
/*
* This version concatenates all commands into a single String (semi-colon
sb.append(getColourCommand(colourData, colour));
}
commands.add(sb.toString());
- return commands;
+
+ return commands.toArray(new String[commands.size()]);
}
/**
executeCommand(commandGenerator.showBackbone(), false);
/*
- * superpose each (other) sequence to it in turn
+ * superpose each (other) structure to the reference in turn
*/
for (int i = 0; i < structures.length; i++)
{
}
/**
+ * Builds a data structure which records mapped structure residues for each
+ * colour. From this we can easily generate the viewer commands for colour by
+ * sequence. Constructs and returns a map of {@code Color} to
+ * {@code AtomSpecModel}, where the atomspec model holds
+ *
* <pre>
- * Build a data structure which records residues for each colour.
- * From this we can easily generate the viewer command for colour by sequence.
- * Color
- * Model number
- * Chain
- * Residue positions
- * Ordering is by order of addition (for colours and positions), natural ordering (for models and chains)
+ * Model numbers
+ * Chains
+ * Residue positions
* </pre>
*
+ * Ordering is by order of addition (for colours), natural ordering (for
+ * models and chains)
+ *
* @param ssm
* @param files
* @param sequence
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;
}
@Test(groups = { "Functional" })
- public void testGetColourBySequenceCommand_noFeatures()
- {
- 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!
-
- String[] commands = new JmolCommands().colourBySequence(ssm, files,
- seqs, sr, af.alignPanel);
- assertEquals(commands.length, 0);
- }
-
- @Test(groups = { "Functional" })
public void testGetColourBySequenceCommands_hiddenColumns()
{
/*
}
@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
+ 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);
+ }
+
+ @Test(groups = { "Functional" })
public void testSuperposeStructures()
{
StructureCommandsI testee = new JmolCommands();
toAlignSpec, refSpec, toAlignSpec, refSpec);
assertEquals(command, expected);
}
+
+ @Test(groups = "Functional")
+ public void testGetModelStartNo()
+ {
+ StructureCommandsI testee = new JmolCommands();
+ assertEquals(testee.getModelStartNo(), 1);
+ }
}
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.SequenceRenderer;
-import jalview.schemes.JalviewColourScheme;
import jalview.structure.AtomSpecModel;
import jalview.structure.StructureCommandsI;
-import jalview.structure.StructureMapping;
-import jalview.structure.StructureSelectionManager;
import java.awt.Color;
import java.util.HashMap;
import java.util.LinkedHashMap;
-import java.util.List;
import java.util.Map;
import org.testng.annotations.Test;
{
@Test(groups = { "Functional" })
- public void testBuildColourCommands()
+ public void testColourBySequence()
{
Map<Object, AtomSpecModel> map = new LinkedHashMap<>();
// 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 = new ChimeraCommands().buildColourCommands(map).get(0);
+ String[] commands = new ChimeraCommands().colourBySequence(map);
+ assertEquals(commands.length, 1);
assertEquals(
- command,
+ commands[0],
"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");
}
@Test(groups = { "Functional" })
- public void testBuildSetAttributeCommands()
+ public void testSetAttributes()
{
/*
* make a map of { featureType, {featureValue, {residue range specification } } }
ChimeraCommands.addAtomSpecRange(featureValues, "X", 0, 8, 20, "A");
ChimeraCommands commandGenerator = new ChimeraCommands();
- List<String> commands = commandGenerator
- .buildSetAttributeCommands(featuresMap);
- assertEquals(1, commands.size());
+ String[] commands = commandGenerator.setAttributes(featuresMap);
+ assertEquals(1, commands.length);
/*
* feature name gets a jv_ namespace prefix
* feature value is quoted in case it contains spaces
*/
- assertEquals(commands.get(0), "setattr res jv_chain 'X' #0:8-20.A");
+ assertEquals(commands[0], "setattr res jv_chain 'X' #0:8-20.A");
// add same feature value, overlapping range
ChimeraCommands.addAtomSpecRange(featureValues, "X", 0, 3, 9, "A");
// same feature value, contiguous range
ChimeraCommands.addAtomSpecRange(featureValues, "X", 0, 21, 25, "A");
- commands = commandGenerator.buildSetAttributeCommands(featuresMap);
- assertEquals(1, commands.size());
- assertEquals(commands.get(0), "setattr res jv_chain 'X' #0:3-25.A");
+ commands = commandGenerator.setAttributes(featuresMap);
+ assertEquals(1, commands.length);
+ assertEquals(commands[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");
// same feature value and chain, different model
ChimeraCommands.addAtomSpecRange(featureValues, "X", 1, 26, 30, "A");
- commands = commandGenerator.buildSetAttributeCommands(featuresMap);
- assertEquals(1, commands.size());
- assertEquals(commands.get(0),
- "setattr res jv_chain 'X' #0:3-25.A,21-25.B|#1:26-30.A");
+ commands = commandGenerator.setAttributes(featuresMap);
+ assertEquals(1, commands.length);
+ String expected1 = "setattr res jv_chain 'X' #0:3-25.A,21-25.B|#1:26-30.A";
+ assertEquals(commands[0],
+ expected1);
// same feature, different value
ChimeraCommands.addAtomSpecRange(featureValues, "Y", 0, 40, 50, "A");
- commands = commandGenerator.buildSetAttributeCommands(featuresMap);
- assertEquals(2, commands.size());
+ commands = commandGenerator.setAttributes(featuresMap);
+ assertEquals(2, commands.length);
// commands are ordered by feature type but not by value
- // so use contains to test for the expected command:
- assertTrue(commands
- .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"));
+ // so test for the expected command in either order
+ assertTrue(
+ commands[0].equals(expected1) || commands[1].equals(expected1));
+ String expected2 = "setattr res jv_chain 'Y' #0:40-50.A";
+ assertTrue(
+ commands[0].equals(expected2) || commands[1].equals(expected2));
featuresMap.clear();
featureValues.clear();
"A");
// feature names are sanitised to change non-alphanumeric to underscore
// feature values are sanitised to encode single quote characters
- commands = commandGenerator.buildSetAttributeCommands(featuresMap);
- assertTrue(commands
- .contains(
- "setattr res jv_side_chain_binding_ '<html>metal <a href=\"http:a.b.c/x\"> 'ion!' #0:7-15.A"));
+ commands = commandGenerator.setAttributes(featuresMap);
+ String expected3 = "setattr res jv_side_chain_binding_ '<html>metal <a href=\"http:a.b.c/x\"> 'ion!' #0:7-15.A";
+ assertTrue(
+ commands[0].equals(expected3) || commands[1].equals(expected3));
}
/**
"jv_helixColor_");
}
- @Test(groups = { "Functional" })
- public void testColourBySequence_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<>();
- 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);
-
- String[] commands = new ChimeraCommands()
- .colourBySequence(ssm, files, seqs, sr, af.alignPanel);
- assertEquals(1, commands.length);
- 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
- 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"));
- }
-
@Test(groups = "Functional")
public void testGetAtomSpec()
{
}
+ @Test(groups = { "Functional" })
+ public void testSuperposeStructures()
+ {
+ StructureCommandsI testee = new ChimeraCommands();
+ 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");
+ String command = testee.superposeStructures(ref, toAlign);
+ String refSpec = "#1:12-14.A,18.B,22-23.B@CA|P&~@.B-Z&~@.2-9";
+ String toAlignSpec = "#2:15-17.B,20-21.B,22.C@CA|P&~@.B-Z&~@.2-9";
+ String expected = String.format(
+ "match %s %s;~display all; chain @CA|P; ribbon %s|%s; focus",
+ refSpec, toAlignSpec, refSpec, toAlignSpec);
+ assertEquals(command, expected);
+ }
+
@Test(groups = "Functional")
public void testGetAtomSpec_alphaOnly()
{
AtomSpecModel model = new AtomSpecModel();
assertEquals(testee.getAtomSpec(model, true), "");
model.addRange(1, 2, 4, "A");
- assertEquals(testee.getAtomSpec(model, true), "#1:2-4.A@CA|P");
+ assertEquals(testee.getAtomSpec(model, true),
+ "#1:2-4.A@CA|P&~@.B-Z&~@.2-9");
model.addRange(1, 8, 8, "A");
- assertEquals(testee.getAtomSpec(model, true), "#1:2-4.A,8.A@CA|P");
+ assertEquals(testee.getAtomSpec(model, true),
+ "#1:2-4.A,8.A@CA|P&~@.B-Z&~@.2-9");
model.addRange(1, 5, 7, "B");
assertEquals(testee.getAtomSpec(model, true),
- "#1:2-4.A,8.A,5-7.B@CA|P");
+ "#1:2-4.A,8.A,5-7.B@CA|P&~@.B-Z&~@.2-9");
model.addRange(1, 3, 5, "A");
assertEquals(testee.getAtomSpec(model, true),
- "#1:2-5.A,8.A,5-7.B@CA|P");
+ "#1:2-5.A,8.A,5-7.B@CA|P&~@.B-Z&~@.2-9");
model.addRange(0, 1, 4, "B");
assertEquals(testee.getAtomSpec(model, true),
- "#0:1-4.B@CA|P|#1:2-5.A,8.A,5-7.B@CA|P");
+ "#0:1-4.B@CA|P&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-7.B@CA|P&~@.B-Z&~@.2-9");
model.addRange(0, 5, 9, "C");
assertEquals(testee.getAtomSpec(model, true),
- "#0:1-4.B,5-9.C@CA|P|#1:2-5.A,8.A,5-7.B@CA|P");
+ "#0:1-4.B,5-9.C@CA|P&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-7.B@CA|P&~@.B-Z&~@.2-9");
model.addRange(1, 8, 10, "B");
assertEquals(testee.getAtomSpec(model, true),
- "#0:1-4.B,5-9.C@CA|P|#1:2-5.A,8.A,5-10.B@CA|P");
+ "#0:1-4.B,5-9.C@CA|P&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-10.B@CA|P&~@.B-Z&~@.2-9");
model.addRange(1, 8, 9, "B");
assertEquals(testee.getAtomSpec(model, true),
- "#0:1-4.B,5-9.C@CA|P|#1:2-5.A,8.A,5-10.B@CA|P");
+ "#0:1-4.B,5-9.C@CA|P&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-10.B@CA|P&~@.B-Z&~@.2-9");
model.addRange(0, 3, 10, "C"); // subsumes 5-9
assertEquals(testee.getAtomSpec(model, true),
- "#0:1-4.B,3-10.C@CA|P|#1:2-5.A,8.A,5-10.B@CA|P");
+ "#0:1-4.B,3-10.C@CA|P&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-10.B@CA|P&~@.B-Z&~@.2-9");
model.addRange(5, 25, 35, " "); // empty chain code
assertEquals(testee.getAtomSpec(model, true),
- "#0:1-4.B,3-10.C@CA|P|#1:2-5.A,8.A,5-10.B@CA|P|#5:25-35.@CA|P");
+ "#0:1-4.B,3-10.C@CA|P&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-10.B@CA|P&~@.B-Z&~@.2-9|#5:25-35.@CA|P&~@.B-Z&~@.2-9");
}
- @Test(groups = { "Functional" })
- public void testSuperposeStructures()
+ @Test(groups = "Functional")
+ public void testGetModelStartNo()
{
StructureCommandsI testee = new ChimeraCommands();
- 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");
- String command = testee.superposeStructures(ref, toAlign);
- String refSpec = "#1:12-14.A,18.B,22-23.B@CA|P&~@.B-Z&~@.2-9";
- String toAlignSpec = "#2:15-17.B,20-21.B,22.C@CA|P&~@.B-Z&~@.2-9";
- String expected = String.format(
- "match %s %s;~display all; chain @CA|P; ribbon %s|%s; focus",
- refSpec, toAlignSpec, refSpec, toAlignSpec);
- assertEquals(command, expected);
+ assertEquals(testee.getModelStartNo(), 0);
+ }
+
+ @Test(groups = "Functional")
+ public void testGetResidueSpec()
+ {
+ ChimeraCommands testee = new ChimeraCommands();
+ assertEquals(testee.getResidueSpec("ALA"), "::ALA");
+ }
+
+ @Test(groups = "Functional")
+ public void testShowBackbone()
+ {
+ ChimeraCommands testee = new ChimeraCommands();
+ assertEquals(testee.showBackbone(), "~display all;chain @CA|P");
+ }
+
+ @Test(groups = "Functional")
+ public void testOpenCommandFile()
+ {
+ ChimeraCommands testee = new ChimeraCommands();
+ assertEquals(testee.openCommandFile("nowhere"), "open cmd:nowhere");
+ }
+
+ @Test(groups = "Functional")
+ public void testSaveSession()
+ {
+ ChimeraCommands testee = new ChimeraCommands();
+ assertEquals(testee.saveSession("somewhere"), "save somewhere");
+ }
+
+ @Test(groups = "Functional")
+ public void testGetColourCommand()
+ {
+ ChimeraCommands testee = new ChimeraCommands();
+ assertEquals(testee.getColourCommand("something", Color.MAGENTA),
+ "color #ff00ff something");
+ }
+
+ @Test(groups = "Functional")
+ public void testSetAttribute()
+ {
+ ChimeraCommands testee = new ChimeraCommands();
+ AtomSpecModel model = new AtomSpecModel();
+ model.addRange(1, 89, 92, "A");
+ model.addRange(2, 12, 20, "B");
+ model.addRange(2, 8, 9, "B");
+ assertEquals(testee.setAttribute("phi", "27.3", model),
+ "setattr res phi '27.3' #1:89-92.A|#2:8-9.B,12-20.B");
}
}
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.SequenceRenderer;
-import jalview.schemes.JalviewColourScheme;
import jalview.structure.AtomSpecModel;
import jalview.structure.StructureCommandsI;
-import jalview.structure.StructureMapping;
-import jalview.structure.StructureSelectionManager;
import java.awt.Color;
import java.util.HashMap;
import java.util.LinkedHashMap;
-import java.util.List;
import java.util.Map;
import org.testng.annotations.Test;
public class ChimeraXCommandsTest
{
+ @Test(groups = { "Functional" })
+ public void testColourByCharge()
+ {
+ String cmd = new ChimeraXCommands().colourByCharge();
+ assertEquals(cmd,
+ "color white;color :ASP,GLU red;color :LYS,ARG blue;color :CYS yellow");
+ }
@Test(groups = { "Functional" })
- public void testBuildColourCommands()
+ public void testColourByChain()
{
+ String cmd = new ChimeraXCommands().colourByChain();
+ assertEquals(cmd, "rainbow chain");
+ }
+ @Test(groups = { "Functional" })
+ public void testFocusView()
+ {
+ String cmd = new ChimeraXCommands().focusView();
+ assertEquals(cmd, "view");
+ }
+
+ @Test(groups = { "Functional" })
+ public void testColourBySequence()
+ {
Map<Object, AtomSpecModel> map = new LinkedHashMap<>();
- ChimeraCommands.addAtomSpecRange(map, Color.blue, 0, 2, 5, "A");
- ChimeraCommands.addAtomSpecRange(map, Color.blue, 0, 7, 7, "B");
- ChimeraCommands.addAtomSpecRange(map, Color.blue, 0, 9, 23, "A");
- ChimeraCommands.addAtomSpecRange(map, Color.blue, 1, 1, 1, "A");
- ChimeraCommands.addAtomSpecRange(map, Color.blue, 1, 4, 7, "B");
- ChimeraCommands.addAtomSpecRange(map, Color.yellow, 1, 8, 8, "A");
- ChimeraCommands.addAtomSpecRange(map, Color.yellow, 1, 3, 5, "A");
- ChimeraCommands.addAtomSpecRange(map, Color.red, 0, 3, 5, "A");
- ChimeraCommands.addAtomSpecRange(map, Color.red, 0, 6, 9, "A");
+ ChimeraCommands.addAtomSpecRange(map, Color.blue, 1, 2, 5, "A");
+ ChimeraCommands.addAtomSpecRange(map, Color.blue, 1, 7, 7, "B");
+ ChimeraCommands.addAtomSpecRange(map, Color.blue, 1, 9, 23, "A");
+ ChimeraCommands.addAtomSpecRange(map, Color.blue, 2, 1, 1, "A");
+ ChimeraCommands.addAtomSpecRange(map, Color.blue, 2, 4, 7, "B");
+ ChimeraCommands.addAtomSpecRange(map, Color.yellow, 2, 8, 8, "A");
+ ChimeraCommands.addAtomSpecRange(map, Color.yellow, 2, 3, 5, "A");
+ ChimeraCommands.addAtomSpecRange(map, Color.red, 1, 3, 5, "A");
+ ChimeraCommands.addAtomSpecRange(map, Color.red, 1, 6, 9, "A");
// 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 = new ChimeraXCommands().buildColourCommands(map).get(0);
+ String[] commands = new ChimeraXCommands().colourBySequence(map);
+ assertEquals(commands.length, 1);
assertEquals(
- command,
- "color #0/A:2-5,9-23/B:7|#1/A:1/B:4-7 #0000ff; color #1/A:3-5,8 #ffff00; color #0/A:3-9 #ff0000");
+ commands[0],
+ "color #1/A:2-5,9-23/B:7|#2/A:1/B:4-7 #0000ff; color #2/A:3-5,8 #ffff00; color #1/A:3-9 #ff0000");
}
@Test(groups = { "Functional" })
- public void testBuildSetAttributeCommands()
+ public void testSetAttributes()
{
/*
* make a map of { featureType, {featureValue, {residue range specification } } }
ChimeraCommands.addAtomSpecRange(featureValues, "X", 0, 8, 20, "A");
ChimeraXCommands commandGenerator = new ChimeraXCommands();
- List<String> commands = commandGenerator
- .buildSetAttributeCommands(featuresMap);
- assertEquals(1, commands.size());
+ String[] commands = commandGenerator.setAttributes(featuresMap);
+ assertEquals(commands.length, 1);
/*
* feature name gets a jv_ namespace prefix
* feature value is quoted in case it contains spaces
*/
- assertEquals(commands.get(0),
+ assertEquals(commands[0],
"setattr #0/A:8-20 res jv_chain 'X' create true");
// add same feature value, overlapping range
ChimeraCommands.addAtomSpecRange(featureValues, "X", 0, 3, 9, "A");
// same feature value, contiguous range
ChimeraCommands.addAtomSpecRange(featureValues, "X", 0, 21, 25, "A");
- commands = commandGenerator.buildSetAttributeCommands(featuresMap);
- assertEquals(1, commands.size());
- assertEquals(commands.get(0),
+ commands = commandGenerator.setAttributes(featuresMap);
+ assertEquals(commands.length, 1);
+ assertEquals(commands[0],
"setattr #0/A:3-25 res jv_chain 'X' create true");
// same feature value and model, different chain
ChimeraCommands.addAtomSpecRange(featureValues, "X", 0, 21, 25, "B");
// same feature value and chain, different model
ChimeraCommands.addAtomSpecRange(featureValues, "X", 1, 26, 30, "A");
- commands = commandGenerator.buildSetAttributeCommands(featuresMap);
- assertEquals(1, commands.size());
- assertEquals(commands.get(0),
- "setattr #0/A:3-25/B:21-25|#1/A:26-30 res jv_chain 'X' create true");
+ commands = commandGenerator.setAttributes(featuresMap);
+ assertEquals(commands.length, 1);
+ String expected1 = "setattr #0/A:3-25/B:21-25|#1/A:26-30 res jv_chain 'X' create true";
+ assertEquals(commands[0], expected1);
// same feature, different value
ChimeraCommands.addAtomSpecRange(featureValues, "Y", 0, 40, 50, "A");
- commands = commandGenerator.buildSetAttributeCommands(featuresMap);
- assertEquals(2, commands.size());
+ commands = commandGenerator.setAttributes(featuresMap);
+ assertEquals(2, commands.length);
// commands are ordered by feature type but not by value
- // so use contains to test for the expected command:
- assertTrue(commands
- .contains(
- "setattr #0/A:3-25/B:21-25|#1/A:26-30 res jv_chain 'X' create true"));
- assertTrue(commands
- .contains("setattr #0/A:40-50 res jv_chain 'Y' create true"));
+ // so test for the expected command in either order
+ assertTrue(
+ commands[0].equals(expected1) || commands[1].equals(expected1));
+ String expected2 = "setattr #0/A:40-50 res jv_chain 'Y' create true";
+ assertTrue(
+ commands[0].equals(expected2) || commands[1].equals(expected2));
featuresMap.clear();
featureValues.clear();
"A");
// feature names are sanitised to change non-alphanumeric to underscore
// feature values are sanitised to encode single quote characters
- commands = commandGenerator.buildSetAttributeCommands(featuresMap);
- assertTrue(commands.contains(
- "setattr #0/A:7-15 res jv_side_chain_binding_ '<html>metal <a href=\"http:a.b.c/x\"> 'ion!' create true"));
- }
-
- @Test(groups = { "Functional" })
- public void testColourBySequence_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<>();
- 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);
-
- String[] commands = new ChimeraXCommands()
- .colourBySequence(ssm, files, seqs, sr, af.alignPanel);
- assertEquals(1, commands.length);
- String theCommand = commands[0];
- // M colour is #82827d (see strand.html help page)
- assertTrue(theCommand.contains("color #0/A:21|#1/B:21 #82827d"));// #0:21.A|#1:21.B"));
- // H colour is #60609f
- assertTrue(theCommand.contains("color #0/A:22 #60609f"));
- // V colour is #ffff00
- assertTrue(theCommand.contains("color #1/B:22 #ffff00"));
- // hidden columns are Gray (128, 128, 128)
- assertTrue(theCommand.contains("color #0/A:23-25|#1/B:23-25"));
- // S and G are both coloured #4949b6
- assertTrue(theCommand.contains("color #0/A:26-30|#1/B:26-30"));
+ commands = commandGenerator.setAttributes(featuresMap);
+ String expected3 = "setattr #0/A:7-15 res jv_side_chain_binding_ '<html>metal <a href=\"http:a.b.c/x\"> 'ion!' create true";
+ assertTrue(
+ commands[0].equals(expected3) || commands[1].equals(expected3));
}
@Test(groups = { "Functional" })
String command = testee.superposeStructures(ref, toAlign);
String refSpec = "#1/A:12-14/B:18,22-23";
String toAlignSpec = "#2/B:15-17,20-21/C:22";
+
+ /*
+ * superposition arguments include AlphaCarbon restriction,
+ * ribbon command does not
+ */
String expected = String.format(
- "align %s %s;~display all; chain @CA|P; ribbon %s|%s; focus",
+ "align %s@CA|P toAtoms %s@CA|P; ribbon %s|%s; view",
refSpec, toAlignSpec, refSpec, toAlignSpec);
assertEquals(command, expected);
}
+
+ @Test(groups = "Functional")
+ public void testGetAtomSpec()
+ {
+ StructureCommandsI testee = new ChimeraXCommands();
+ AtomSpecModel model = new AtomSpecModel();
+ assertEquals(testee.getAtomSpec(model, false), "");
+ model.addRange(1, 2, 4, "A");
+ assertEquals(testee.getAtomSpec(model, false), "#1/A:2-4");
+ model.addRange(1, 8, 8, "A");
+ assertEquals(testee.getAtomSpec(model, false), "#1/A:2-4,8");
+ model.addRange(1, 5, 7, "B");
+ assertEquals(testee.getAtomSpec(model, false), "#1/A:2-4,8/B:5-7");
+ model.addRange(1, 3, 5, "A");
+ assertEquals(testee.getAtomSpec(model, false), "#1/A:2-5,8/B:5-7");
+ model.addRange(0, 1, 4, "B");
+ assertEquals(testee.getAtomSpec(model, false),
+ "#0/B:1-4|#1/A:2-5,8/B:5-7");
+ model.addRange(0, 5, 9, "C");
+ assertEquals(testee.getAtomSpec(model, false),
+ "#0/B:1-4/C:5-9|#1/A:2-5,8/B:5-7");
+ model.addRange(1, 8, 10, "B");
+ assertEquals(testee.getAtomSpec(model, false),
+ "#0/B:1-4/C:5-9|#1/A:2-5,8/B:5-10");
+ model.addRange(1, 8, 9, "B");
+ assertEquals(testee.getAtomSpec(model, false),
+ "#0/B:1-4/C:5-9|#1/A:2-5,8/B:5-10");
+ model.addRange(0, 3, 10, "C"); // subsumes 5-9
+ assertEquals(testee.getAtomSpec(model, false),
+ "#0/B:1-4/C:3-10|#1/A:2-5,8/B:5-10");
+ model.addRange(5, 25, 35, " ");
+ assertEquals(testee.getAtomSpec(model, false),
+ "#0/B:1-4/C:3-10|#1/A:2-5,8/B:5-10|#5/:25-35");
+ }
+
+ @Test(groups = "Functional")
+ public void testGetAtomSpec_alphaOnly()
+ {
+ StructureCommandsI testee = new ChimeraXCommands();
+ AtomSpecModel model = new AtomSpecModel();
+ assertEquals(testee.getAtomSpec(model, true), "");
+ model.addRange(1, 2, 4, "A");
+ assertEquals(testee.getAtomSpec(model, true), "#1/A:2-4@CA|P");
+ model.addRange(1, 8, 8, "A");
+ assertEquals(testee.getAtomSpec(model, true), "#1/A:2-4,8@CA|P");
+ model.addRange(1, 5, 7, "B");
+ assertEquals(testee.getAtomSpec(model, true), "#1/A:2-4,8/B:5-7@CA|P");
+ model.addRange(1, 3, 5, "A");
+ assertEquals(testee.getAtomSpec(model, true), "#1/A:2-5,8/B:5-7@CA|P");
+ model.addRange(0, 1, 4, "B");
+ assertEquals(testee.getAtomSpec(model, true),
+ "#0/B:1-4@CA|P|#1/A:2-5,8/B:5-7@CA|P");
+ model.addRange(0, 5, 9, "C");
+ assertEquals(testee.getAtomSpec(model, true),
+ "#0/B:1-4/C:5-9@CA|P|#1/A:2-5,8/B:5-7@CA|P");
+ model.addRange(1, 8, 10, "B");
+ assertEquals(testee.getAtomSpec(model, true),
+ "#0/B:1-4/C:5-9@CA|P|#1/A:2-5,8/B:5-10@CA|P");
+ model.addRange(1, 8, 9, "B");
+ assertEquals(testee.getAtomSpec(model, true),
+ "#0/B:1-4/C:5-9@CA|P|#1/A:2-5,8/B:5-10@CA|P");
+ model.addRange(0, 3, 10, "C"); // subsumes 5-9
+ assertEquals(testee.getAtomSpec(model, true),
+ "#0/B:1-4/C:3-10@CA|P|#1/A:2-5,8/B:5-10@CA|P");
+ model.addRange(5, 25, 35, " "); // empty chain code
+ assertEquals(testee.getAtomSpec(model, true),
+ "#0/B:1-4/C:3-10@CA|P|#1/A:2-5,8/B:5-10@CA|P|#5/:25-35@CA|P");
+ }
+
+ @Test(groups = "Functional")
+ public void testGetModelStartNo()
+ {
+ StructureCommandsI testee = new ChimeraXCommands();
+ assertEquals(testee.getModelStartNo(), 1);
+ }
+
+ @Test(groups = "Functional")
+ public void testGetResidueSpec()
+ {
+ ChimeraCommands testee = new ChimeraXCommands();
+ assertEquals(testee.getResidueSpec("ALA"), ":ALA");
+ }
+
+ @Test(groups = "Functional")
+ public void testShowBackbone()
+ {
+ ChimeraCommands testee = new ChimeraXCommands();
+ assertEquals(testee.showBackbone(), "~display all;show @CA|P pbonds");
+ }
+
+ @Test(groups = "Functional")
+ public void testOpenCommandFile()
+ {
+ ChimeraCommands testee = new ChimeraXCommands();
+ assertEquals(testee.openCommandFile("nowhere"), "open nowhere");
+ }
+
+ @Test(groups = "Functional")
+ public void testSaveSession()
+ {
+ ChimeraCommands testee = new ChimeraXCommands();
+ assertEquals(testee.saveSession("somewhere"), "save session somewhere");
+ }
+
+ @Test(groups = "Functional")
+ public void testGetColourCommand()
+ {
+ ChimeraCommands testee = new ChimeraXCommands();
+ assertEquals(testee.getColourCommand("something", Color.MAGENTA),
+ "color something #ff00ff");
+ }
+
+ @Test(groups = "Functional")
+ public void testSetAttribute()
+ {
+ ChimeraCommands testee = new ChimeraXCommands();
+ AtomSpecModel model = new AtomSpecModel();
+ model.addRange(1, 89, 92, "A");
+ model.addRange(2, 12, 20, "B");
+ model.addRange(2, 8, 9, "B");
+ assertEquals(testee.setAttribute("phi", "27.3", model),
+ "setattr #1/A:89-92|#2/B:8-9,12-20 res phi '27.3' create true");
+ }
}
*/
package jalview.structures.models;
+import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertFalse;
-import static org.testng.AssertJUnit.assertEquals;
-import static org.testng.AssertJUnit.assertTrue;
+import static org.testng.Assert.assertNotNull;
+import static org.testng.Assert.assertTrue;
import jalview.api.AlignmentViewPanel;
import jalview.api.SequenceRenderer;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.PDBEntry.Type;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
+import jalview.ext.rbvi.chimera.ChimeraCommands;
+import jalview.gui.AlignFrame;
import jalview.gui.JvOptionPane;
import jalview.gui.StructureViewer.ViewerType;
import jalview.io.DataSourceType;
import jalview.io.FileFormats;
+import jalview.schemes.JalviewColourScheme;
import jalview.structure.AtomSpec;
+import jalview.structure.AtomSpecModel;
import jalview.structure.StructureCommandsI.SuperposeData;
+import jalview.structure.StructureMapping;
import jalview.structure.StructureSelectionManager;
+import java.awt.Color;
import java.io.IOException;
import java.util.Arrays;
import java.util.BitSet;
+import java.util.HashMap;
import java.util.List;
+import java.util.Map;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
+import junit.extensions.PA;
+
/**
* Unit tests for non-abstract methods of abstract base class
*
String[][] chains = binder.getChains();
assertFalse(chains == null || chains[0] == null,
"No chains discovered by binding");
- assertEquals(2, chains[0].length);
- assertEquals("A", chains[0][0]);
- assertEquals("B", chains[0][1]);
+ assertEquals(chains[0].length, 2);
+ assertEquals(chains[0][0], "A");
+ assertEquals(chains[0][1], "B");
}
AAStructureBindingModel testee;
ssm.setMapping(new SequenceI[] { seq3 }, null, PDB_3,
DataSourceType.PASTE, null);
- testee = new AAStructureBindingModel(ssm, pdbFiles, seqs, null)
+ testee = newBindingModel(pdbFiles, seqs, ssm);
+ }
+
+ /**
+ * A helper method to construct the test target object
+ *
+ * @param pdbFiles
+ * @param seqs
+ * @param ssm
+ */
+ protected AAStructureBindingModel newBindingModel(PDBEntry[] pdbFiles,
+ SequenceI[][] seqs,
+ StructureSelectionManager ssm)
+ {
+ AAStructureBindingModel model = new AAStructureBindingModel(ssm,
+ pdbFiles, seqs, null)
{
@Override
public String[] getStructureFiles()
return null;
}
};
+ PA.setValue(model, "commandGenerator", new ChimeraCommands());
+ return model;
}
/**
int refStructure = testee
.findSuperposableResidues(al, matched, structs);
- assertEquals(0, refStructure);
+ assertEquals(refStructure, 0);
/*
* only ungapped, structure-mapped columns are superposable
assertTrue(matched.get(4));
assertTrue(matched.get(5)); // gap in second sequence
- assertEquals("1YCS", structs[0].pdbId);
- assertEquals("3A6S", structs[1].pdbId);
- assertEquals("1OOT", structs[2].pdbId);
- assertEquals("A", structs[0].chain); // ? struct has chains A _and_ B
- assertEquals("B", structs[1].chain);
- assertEquals("A", structs[2].chain);
+ assertEquals(structs[0].pdbId, "1YCS");
+ assertEquals(structs[1].pdbId, "3A6S");
+ assertEquals(structs[2].pdbId, "1OOT");
+ assertEquals(structs[0].chain, "A"); // ? struct has chains A _and_ B
+ assertEquals(structs[1].chain, "B");
+ assertEquals(structs[2].chain, "A");
// the 0's for unsuperposable positions propagate down the columns:
- assertEquals("[0, 97, 98, 99, 100, 102]",
- Arrays.toString(structs[0].pdbResNo));
- assertEquals("[0, 2, 0, 3, 4, 5]", Arrays.toString(structs[1].pdbResNo));
- assertEquals("[0, 8, 0, 0, 10, 12]",
- Arrays.toString(structs[2].pdbResNo));
+ assertEquals(Arrays.toString(structs[0].pdbResNo),
+ "[0, 97, 98, 99, 100, 102]");
+ assertEquals(Arrays.toString(structs[1].pdbResNo),
+ "[0, 2, 0, 3, 4, 5]");
+ assertEquals(Arrays.toString(structs[2].pdbResNo),
+ "[0, 8, 0, 0, 10, 12]");
}
@Test(groups = { "Functional" })
int refStructure = testee
.findSuperposableResidues(al, matched, structs);
- assertEquals(0, refStructure);
+ assertEquals(refStructure, 0);
// only ungapped, structure-mapped columns are not superposable
assertFalse(matched.get(0));
assertFalse(matched.get(4)); // superposable, but hidden, column
assertTrue(matched.get(5));
}
+
+ @Test(groups = { "Functional" })
+ public void testBuildColoursMap()
+ {
+ /*
+ * 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 jalview.gui.SequenceRenderer(
+ af.getViewport());
+ SequenceI[][] seqs = new SequenceI[][] { { seq1 }, { seq2 } };
+ String[] files = new String[] { "seq1.pdb", "seq2.pdb" };
+ PDBEntry[] pdbFiles = new PDBEntry[2];
+ pdbFiles[0] = new PDBEntry("PDB1", "A", Type.PDB, "INLINEPDB1");
+ pdbFiles[1] = new PDBEntry("PDB2", "B", Type.PDB, "INLINEPDB2");
+ StructureSelectionManager ssm = new StructureSelectionManager();
+
+ /*
+ * 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);
+
+ AAStructureBindingModel binding = newBindingModel(pdbFiles, seqs, ssm);
+
+ /*
+ * method under test builds a map of structures residues by colour
+ * verify the map holds what it should
+ */
+ Map<Object, AtomSpecModel> colours = binding.buildColoursMap(ssm, files,
+ seqs, sr, af.alignPanel);
+ ChimeraCommands helper = new ChimeraCommands();
+
+ /*
+ * M colour is #82827d (see strand.html help page)
+ * sequence residue 1 mapped to structure residue 21
+ */
+ Color mColor = new Color(0x82827d);
+ AtomSpecModel atomSpec = colours.get(mColor);
+ assertNotNull(atomSpec);
+ assertEquals(helper.getAtomSpec(atomSpec, false), "#0:21.A|#1:21.B");
+
+ /*
+ * H colour is #60609f, seq1.2 mapped to structure 0 residue 22
+ */
+ Color hColor = new Color(0x60609f);
+ atomSpec = colours.get(hColor);
+ assertNotNull(atomSpec);
+ assertEquals(helper.getAtomSpec(atomSpec, false), "#0:22.A");
+
+ /*
+ * V colour is #ffff00, seq2.2 mapped to structure 1 residue 22
+ */
+ Color vColor = new Color(0xffff00);
+ atomSpec = colours.get(vColor);
+ assertNotNull(atomSpec);
+ assertEquals(helper.getAtomSpec(atomSpec, false), "#1:22.B");
+
+ /*
+ * hidden columns are Gray (128, 128, 128)
+ * sequence positions 3-5 mapped to structure residues 23-25
+ */
+ Color gray = new Color(128, 128, 128);
+ atomSpec = colours.get(gray);
+ assertNotNull(atomSpec);
+ assertEquals(helper.getAtomSpec(atomSpec, false), "#0:23-25.A|#1:23-25.B");
+
+ /*
+ * S and G are both coloured #4949b6, structure residues 26-30
+ */
+ Color sgColour = new Color(0x4949b6);
+ atomSpec = colours.get(sgColour);
+ assertNotNull(atomSpec);
+ assertEquals(helper.getAtomSpec(atomSpec, false),
+ "#0:26-30.A|#1:26-30.B");
+ }
}
\ No newline at end of file
git://source.jalview.org / jalview.git / commitdiff