--- /dev/null
+package jalview.ext.rbvi.chimera;
+
+import jalview.util.RangeComparator;
+
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.TreeMap;
+
+/**
+ * A class to model a Chimera atomspec pattern, for example
+ *
+ * <pre>
+ * #0:15.A,28.A,54.A,63.A,70-72.A,83-84.A,97-98.A|#1:2.A,6.A,11.A,13-14.A,70.A,82.A,96-97.A
+ * </pre>
+ *
+ * where
+ * <ul>
+ * <li>#0 is a model number</li>
+ * <li>15 or 70-72 is a residue number, or range of residue numbers</li>
+ * <li>.A is a chain identifier</li>
+ * <li>residue ranges are separated by comma</li>
+ * <li>atomspecs for distinct models are separated by | (or)</li>
+ * </ul>
+ *
+ * <pre>
+ * @see http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/frameatom_spec.html
+ * </pre>
+ */
+public class AtomSpecModel
+{
+ private Map<Integer, Map<String, List<int[]>>> atomSpec;
+
+ /**
+ * Constructor
+ */
+ public AtomSpecModel()
+ {
+ atomSpec = new TreeMap<Integer, Map<String, List<int[]>>>();
+ }
+
+ /**
+ * Adds one contiguous range to this atom spec
+ *
+ * @param model
+ * @param startPos
+ * @param endPos
+ * @param chain
+ */
+ public void addRange(int model, int startPos, int endPos, String chain)
+ {
+ /*
+ * Get/initialize map of data for the colour and model
+ */
+ Map<String, List<int[]>> modelData = atomSpec.get(model);
+ if (modelData == null)
+ {
+ atomSpec.put(model, modelData = new TreeMap<String, List<int[]>>());
+ }
+
+ /*
+ * Get/initialize map of data for colour, model and chain
+ */
+ List<int[]> chainData = modelData.get(chain);
+ if (chainData == null)
+ {
+ chainData = new ArrayList<int[]>();
+ modelData.put(chain, chainData);
+ }
+
+ /*
+ * Add the start/end positions
+ */
+ chainData.add(new int[] { startPos, endPos });
+ // TODO add intelligently, using a RangeList class
+ }
+
+ /**
+ * Returns the range(s) formatted as a Chimera atomspec
+ *
+ * @return
+ */
+ public String getAtomSpec()
+ {
+ StringBuilder sb = new StringBuilder(128);
+ boolean firstModel = true;
+ for (Integer model : atomSpec.keySet())
+ {
+ if (!firstModel)
+ {
+ sb.append("|");
+ }
+ firstModel = false;
+ sb.append("#").append(model).append(":");
+
+ boolean firstPositionForModel = true;
+ final Map<String, List<int[]>> modelData = atomSpec.get(model);
+
+ for (String chain : modelData.keySet())
+ {
+ chain = chain.trim();
+
+ List<int[]> rangeList = modelData.get(chain);
+
+ /*
+ * sort ranges into ascending start position order
+ */
+ Collections.sort(rangeList, new RangeComparator(true));
+
+ int start = rangeList.isEmpty() ? 0 : rangeList.get(0)[0];
+ int end = rangeList.isEmpty() ? 0 : rangeList.get(0)[1];
+
+ Iterator<int[]> iterator = rangeList.iterator();
+ while (iterator.hasNext())
+ {
+ int[] range = iterator.next();
+ if (range[0] <= end + 1)
+ {
+ /*
+ * range overlaps or is contiguous with the last one
+ * - so just extend the end position, and carry on
+ * (unless this is the last in the list)
+ */
+ end = Math.max(end, range[1]);
+ }
+ else
+ {
+ /*
+ * we have a break so append the last range
+ */
+ appendRange(sb, start, end, chain, firstPositionForModel);
+ firstPositionForModel = false;
+ start = range[0];
+ end = range[1];
+ }
+ }
+
+ /*
+ * and append the last range
+ */
+ if (!rangeList.isEmpty())
+ {
+ appendRange(sb, start, end, chain, firstPositionForModel);
+ firstPositionForModel = false;
+ }
+ }
+ }
+ return sb.toString();
+ }
+
+ /**
+ * @param sb
+ * @param start
+ * @param end
+ * @param chain
+ * @param firstPositionForModel
+ */
+ protected void appendRange(StringBuilder sb, int start, int end,
+ String chain, boolean firstPositionForModel)
+ {
+ if (!firstPositionForModel)
+ {
+ sb.append(",");
+ }
+ if (end == start)
+ {
+ sb.append(start);
+ }
+ else
+ {
+ sb.append(start).append("-").append(end);
+ }
+ if (chain.length() > 0)
+ {
+ sb.append(".").append(chain);
+ }
+ }
+}
import jalview.api.FeatureRenderer;
import jalview.api.SequenceRenderer;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.structure.StructureMapping;
import jalview.structure.StructureMappingcommandSet;
import java.awt.Color;
import java.util.ArrayList;
+import java.util.HashMap;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
-import java.util.TreeMap;
/**
* Routines for generating Chimera commands for Jalview/Chimera binding
* @returns Object[] { Object[] { <model being coloured>,
*
*/
- public static StructureMappingcommandSet[] getColourBySequenceCommand(
+ public static StructureMappingcommandSet getColourBySequenceCommand(
StructureSelectionManager ssm, String[] files,
SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr,
AlignmentI alignment)
{
- Map<Color, Map<Integer, Map<String, List<int[]>>>> colourMap = buildColoursMap(
+ Map<Color, AtomSpecModel> colourMap = buildColoursMap(
ssm, files, sequence, sr, fr, alignment);
List<String> colourCommands = buildColourCommands(colourMap);
StructureMappingcommandSet cs = new StructureMappingcommandSet(
ChimeraCommands.class, null,
- colourCommands.toArray(new String[0]));
+ colourCommands.toArray(new String[colourCommands.size()]));
- return new StructureMappingcommandSet[] { cs };
+ return cs;
}
/**
* is
*
* <pre>
- * <blockquote> color colorname #modelnumber:range.chain e.g. color #00ff00
- * #0:2.B,4.B,9-12.B|#1:1.A,2-6.A,...
+ * <blockquote>
+ * color colorname #modelnumber:range.chain
+ * e.g. color #00ff00 #0:2.B,4.B,9-12.B|#1:1.A,2-6.A,...
* </blockquote>
* </pre>
*
* @param colourMap
* @return
- * @see http
- * ://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/frameatom_spec
- * .html
*/
protected static List<String> buildColourCommands(
- Map<Color, Map<Integer, Map<String, List<int[]>>>> colourMap)
+ Map<Color, AtomSpecModel> colourMap)
{
/*
* This version concatenates all commands into a single String (semi-colon
}
sb.append("color ").append(colourCode).append(" ");
firstColour = false;
- boolean firstModelForColour = true;
- final Map<Integer, Map<String, List<int[]>>> colourData = colourMap
+ final AtomSpecModel colourData = colourMap
.get(colour);
- for (Integer model : colourData.keySet())
+ sb.append(colourData.getAtomSpec());
+ }
+ commands.add(sb.toString());
+ return commands;
+ }
+
+ /**
+ * Traverses a map of { modelNumber, {chain, {list of from-to ranges} } } and
+ * builds a Chimera format atom spec
+ *
+ * @param modelAndChainRanges
+ */
+ protected static String getAtomSpec(
+ Map<Integer, Map<String, List<int[]>>> modelAndChainRanges)
+ {
+ StringBuilder sb = new StringBuilder(128);
+ boolean firstModelForColour = true;
+ for (Integer model : modelAndChainRanges.keySet())
+ {
+ boolean firstPositionForModel = true;
+ if (!firstModelForColour)
{
- boolean firstPositionForModel = true;
- if (!firstModelForColour)
- {
- sb.append("|");
- }
- firstModelForColour = false;
- sb.append("#").append(model).append(":");
+ sb.append("|");
+ }
+ firstModelForColour = false;
+ sb.append("#").append(model).append(":");
- final Map<String, List<int[]>> modelData = colourData.get(model);
- for (String chain : modelData.keySet())
+ final Map<String, List<int[]>> modelData = modelAndChainRanges
+ .get(model);
+ for (String chain : modelData.keySet())
+ {
+ boolean hasChain = !"".equals(chain.trim());
+ for (int[] range : modelData.get(chain))
{
- boolean hasChain = !"".equals(chain.trim());
- for (int[] range : modelData.get(chain))
+ if (!firstPositionForModel)
{
- if (!firstPositionForModel)
- {
- sb.append(",");
- }
- if (range[0] == range[1])
- {
- sb.append(range[0]);
- }
- else
- {
- sb.append(range[0]).append("-").append(range[1]);
- }
- if (hasChain)
- {
- sb.append(".").append(chain);
- }
- firstPositionForModel = false;
+ sb.append(",");
+ }
+ if (range[0] == range[1])
+ {
+ sb.append(range[0]);
+ }
+ else
+ {
+ sb.append(range[0]).append("-").append(range[1]);
+ }
+ if (hasChain)
+ {
+ sb.append(".").append(chain);
}
+ firstPositionForModel = false;
}
}
}
- commands.add(sb.toString());
- return commands;
+ return sb.toString();
}
/**
* Ordering is by order of addition (for colours and positions), natural ordering (for models and chains)
* </pre>
*/
- protected static Map<Color, Map<Integer, Map<String, List<int[]>>>> buildColoursMap(
+ protected static Map<Color, AtomSpecModel> buildColoursMap(
StructureSelectionManager ssm, String[] files,
SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr,
AlignmentI alignment)
{
- Map<Color, Map<Integer, Map<String, List<int[]>>>> colourMap = new LinkedHashMap<Color, Map<Integer, Map<String, List<int[]>>>>();
+ Map<Color, AtomSpecModel> colourMap = new LinkedHashMap<Color, AtomSpecModel>();
Color lastColour = null;
for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
{
* @param chain
*/
protected static void addColourRange(
- Map<Color, Map<Integer, Map<String, List<int[]>>>> colourMap,
+Map<Color, AtomSpecModel> colourMap,
Color colour, int model, int startPos, int endPos, String chain)
{
+ // refactor for reuse as addRange
/*
* Get/initialize map of data for the colour
*/
- Map<Integer, Map<String, List<int[]>>> colourData = colourMap
- .get(colour);
+ AtomSpecModel colourData = colourMap.get(colour);
if (colourData == null)
{
- colourMap
- .put(colour,
- colourData = new TreeMap<Integer, Map<String, List<int[]>>>());
+ colourData = new AtomSpecModel();
+ colourMap.put(colour, colourData);
}
- /*
- * Get/initialize map of data for the colour and model
- */
- Map<String, List<int[]>> modelData = colourData.get(model);
- if (modelData == null)
+ colourData.addRange(model, startPos, endPos, chain);
+ }
+
+ /**
+ * Constructs and returns a set of Chimera commands to set attributes on
+ * residues corresponding to features in Jalview.
+ *
+ * @param ssm
+ * @param files
+ * @param seqs
+ * @param fr
+ * @param alignment
+ * @return
+ */
+ public static StructureMappingcommandSet getSetAttributeCommandsForFeatures(
+ StructureSelectionManager ssm, String[] files,
+ SequenceI[][] seqs, FeatureRenderer fr, AlignmentI alignment)
+ {
+ Map<String, Map<Integer, Map<String, List<int[]>>>> featureMap = buildFeaturesMap(
+ ssm, files, seqs, fr, alignment);
+
+ List<String> colourCommands = buildSetAttributeCommands(featureMap);
+
+ StructureMappingcommandSet cs = new StructureMappingcommandSet(
+ ChimeraCommands.class, null,
+ colourCommands.toArray(new String[colourCommands.size()]));
+
+ return cs;
+ }
+
+ /**
+ * <pre>
+ * Helper method to build a map of
+ * { featureType, {modelNumber, {chain, {list of from-to ranges} } } }
+ * </pre>
+ *
+ * @param ssm
+ * @param files
+ * @param seqs
+ * @param fr
+ * @param alignment
+ * @return
+ */
+ protected static Map<String, Map<Integer, Map<String, List<int[]>>>> buildFeaturesMap(
+ StructureSelectionManager ssm, String[] files,
+ SequenceI[][] seqs, FeatureRenderer fr, AlignmentI alignment)
+ {
+ Map<String, Map<Integer, Map<String, List<int[]>>>> theMap = new HashMap<String, Map<Integer, Map<String, List<int[]>>>>();
+
+ List<String> visibleFeatures = fr.getDisplayedFeatureTypes();
+ if (visibleFeatures.isEmpty())
{
- colourData.put(model, modelData = new TreeMap<String, List<int[]>>());
+ return theMap;
}
-
+
/*
- * Get/initialize map of data for colour, model and chain
+ * traverse mappings to structures
*/
- List<int[]> chainData = modelData.get(chain);
- if (chainData == null)
+ for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
{
- modelData.put(chain, chainData = new ArrayList<int[]>());
+ StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
+
+ if (mapping == null || mapping.length < 1)
+ {
+ continue;
+ }
+
+ int lastPos = -1;
+ for (int seqNo = 0; seqNo < seqs[pdbfnum].length; seqNo++)
+ {
+ for (int m = 0; m < mapping.length; m++)
+ {
+ final SequenceI seq = seqs[pdbfnum][seqNo];
+ int sp = alignment.findIndex(seq);
+ if (mapping[m].getSequence() == seq && sp > -1)
+ {
+ SequenceI asp = alignment.getSequenceAt(sp);
+
+ /*
+ * traverse each sequence for its mapped positions
+ */
+ for (int r = 0; r < asp.getLength(); r++)
+ {
+ // no mapping to gaps in sequence
+ if (Comparison.isGap(asp.getCharAt(r)))
+ {
+ continue;
+ }
+ int residuePos = asp.findPosition(r);
+ int pos = mapping[m].getPDBResNum(residuePos);
+
+ if (pos < 1 || pos == lastPos)
+ {
+ continue;
+ }
+ final String chain = mapping[m].getChain();
+
+ /*
+ * record any features at this position, with the model, chain
+ * and residue number they map to
+ */
+ List<SequenceFeature> features = fr.findFeaturesAtRes(asp,
+ residuePos);
+ for (SequenceFeature feature : features)
+ {
+ if (!visibleFeatures.contains(feature))
+ {
+ continue;
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+ return theMap;
+ }
+
+ /**
+ * Traverse the map of features/models/chains/positions to construct a list of
+ * 'setattr' commands (one per feature type). The format of each command is
+ *
+ * <pre>
+ * <blockquote> setattr r <featureName> " " #modelnumber:range.chain
+ * e.g. setattr r jv:chain " " #0:2.B,4.B,9-12.B|#1:1.A,2-6.A,...
+ * </blockquote>
+ * </pre>
+ * <p>
+ * Note we are not (currently) setting attribute values, only the type
+ * (presence) of each attribute. This is to avoid overloading the Chimera REST
+ * interface by sending too many distinct commands. Analysis by feature values
+ * may still be performed in Jalview, on selections created in Chimera.
+ *
+ * @param featureMap
+ * @return
+ * @see http
+ * ://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/frameatom_spec
+ * .html
+ */
+ protected static List<String> buildSetAttributeCommands(
+ Map<String, Map<Integer, Map<String, List<int[]>>>> featureMap)
+ {
+ List<String> commands = new ArrayList<String>();
+ for (String featureType : featureMap.keySet())
+ {
+ StringBuilder sb = new StringBuilder(128);
+ featureType = featureType.replace(" ", "_");
+ sb.append("setattr r jv:").append(featureType).append(" \" \" ");
+ final Map<Integer, Map<String, List<int[]>>> featureData = featureMap
+ .get(featureType);
+ sb.append(getAtomSpec(featureData));
+ commands.add(sb.toString());
}
- /*
- * Add the start/end positions
- */
- chainData.add(new int[] { startPos, endPos });
+ return commands;
}
}
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.httpserver.AbstractRequestHandler;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ResidueProperties;
import jalview.structure.AtomSpec;
-import jalview.structure.StructureMapping;
import jalview.structure.StructureMappingcommandSet;
import jalview.structure.StructureSelectionManager;
import jalview.structures.models.AAStructureBindingModel;
-import jalview.util.Comparison;
import jalview.util.MessageManager;
import java.awt.Color;
}
AlignmentI alignment = alignmentv.getAlignment();
- for (jalview.structure.StructureMappingcommandSet cpdbbyseq : getColourBySequenceCommands(
- files, sr, fr, alignment))
+ StructureMappingcommandSet colourBySequenceCommands = ChimeraCommands
+ .getColourBySequenceCommand(getSsm(), files, getSequence(), sr,
+ fr, alignment);
+ for (String command : colourBySequenceCommands.commands)
{
- for (String command : cpdbbyseq.commands)
- {
- sendAsynchronousCommand(command, COLOURING_CHIMERA);
- }
+ sendAsynchronousCommand(command, COLOURING_CHIMERA);
}
}
/**
- * @param files
- * @param sr
- * @param fr
- * @param alignment
- * @return
- */
- protected StructureMappingcommandSet[] getColourBySequenceCommands(
- String[] files, SequenceRenderer sr, FeatureRenderer fr,
- AlignmentI alignment)
- {
- return ChimeraCommands.getColourBySequenceCommand(getSsm(), files,
- getSequence(), sr, fr, alignment);
- }
-
- /**
* @param command
*/
protected void executeWhenReady(String command)
{
return;
}
- for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
- {
- StructureMapping[] mapping = getSsm().getMapping(files[pdbfnum]);
-
- if (mapping == null || mapping.length < 1)
- {
- continue;
- }
-
- int lastPos = -1;
- for (int seqNo = 0; seqNo < getSequence()[pdbfnum].length; seqNo++)
- {
- for (int m = 0; m < mapping.length; m++)
- {
- final SequenceI seq = getSequence()[pdbfnum][seqNo];
- int sp = alignment.findIndex(seq);
- if (mapping[m].getSequence() == seq && sp > -1)
- {
- SequenceI asp = alignment.getSequenceAt(sp);
- for (int r = 0; r < asp.getLength(); r++)
- {
- // no mapping to gaps in sequence
- if (Comparison.isGap(asp.getCharAt(r)))
- {
- continue;
- }
- int residuePos = asp.findPosition(r);
- int pos = mapping[m].getPDBResNum(residuePos);
- if (pos < 1 || pos == lastPos)
- {
- continue;
- }
- final String chain = mapping[m].getChain();
- List<SequenceFeature> features = fr.findFeaturesAtRes(asp,
- residuePos);
- for (SequenceFeature feature : features)
- {
- String desc = feature.getDescription();
- float score = feature.getScore();
- if (score != 0 && score != Float.NaN)
- {
- desc = Float.toString(score);
- }
- String attName = "jv:"
- + feature.getType().replace(" ", "_");
- String cmd = "setattr r " + attName + " \""
- + desc + "\" #" + pdbfnum + ":" + pos + "." + chain;
- System.out.println(cmd);
- sendAsynchronousCommand(cmd, null);
- }
- }
- }
- }
- }
+ StructureMappingcommandSet commandSet = ChimeraCommands
+ .getSetAttributeCommandsForFeatures(getSsm(), files,
+ getSequence(), fr, alignment);
+ for (String command : commandSet.commands)
+ {
+ sendAsynchronousCommand(command, null);
}
+
}
}
--- /dev/null
+package jalview.ext.rbvi.chimera;
+
+import static org.testng.Assert.assertEquals;
+
+import org.testng.annotations.Test;
+
+public class AtomSpecModelTest
+{
+ @Test(groups = "Functional")
+ public void testGetAtomSpec()
+ {
+ AtomSpecModel model = new AtomSpecModel();
+ assertEquals(model.getAtomSpec(), "");
+ model.addRange(1, 2, 4, "A");
+ assertEquals(model.getAtomSpec(), "#1:2-4.A");
+ model.addRange(1, 8, 8, "A");
+ assertEquals(model.getAtomSpec(), "#1:2-4.A,8.A");
+ model.addRange(1, 5, 7, "B");
+ assertEquals(model.getAtomSpec(), "#1:2-4.A,8.A,5-7.B");
+ model.addRange(1, 3, 5, "A");
+ assertEquals(model.getAtomSpec(), "#1:2-5.A,8.A,5-7.B");
+ model.addRange(0, 1, 4, "B");
+ assertEquals(model.getAtomSpec(), "#0:1-4.B|#1:2-5.A,8.A,5-7.B");
+ model.addRange(0, 5, 9, "C");
+ assertEquals(model.getAtomSpec(), "#0:1-4.B,5-9.C|#1:2-5.A,8.A,5-7.B");
+ model.addRange(1, 8, 10, "B");
+ assertEquals(model.getAtomSpec(), "#0:1-4.B,5-9.C|#1:2-5.A,8.A,5-10.B");
+ model.addRange(1, 8, 9, "B");
+ assertEquals(model.getAtomSpec(), "#0:1-4.B,5-9.C|#1:2-5.A,8.A,5-10.B");
+ model.addRange(0, 3, 10, "C"); // subsumes 5-9
+ assertEquals(model.getAtomSpec(), "#0:1-4.B,3-10.C|#1:2-5.A,8.A,5-10.B");
+ }
+
+}
package jalview.ext.rbvi.chimera;
import static org.testng.AssertJUnit.assertEquals;
-import static org.testng.AssertJUnit.assertTrue;
import java.awt.Color;
-import java.util.Arrays;
import java.util.LinkedHashMap;
-import java.util.List;
import java.util.Map;
import org.testng.annotations.Test;
public class ChimeraCommandsTest
{
@Test(groups = { "Functional" })
- public void testAddColourRange()
- {
- Map<Color, Map<Integer, Map<String, List<int[]>>>> map = new LinkedHashMap<Color, Map<Integer, Map<String, List<int[]>>>>();
- ChimeraCommands.addColourRange(map, Color.pink, 1, 2, 4, "A");
- ChimeraCommands.addColourRange(map, Color.pink, 1, 8, 8, "A");
- ChimeraCommands.addColourRange(map, Color.pink, 1, 5, 7, "B");
- ChimeraCommands.addColourRange(map, Color.red, 1, 3, 5, "A");
- ChimeraCommands.addColourRange(map, Color.red, 0, 1, 4, "B");
- ChimeraCommands.addColourRange(map, Color.orange, 0, 5, 9, "C");
-
- // three colours mapped
- assertEquals(3, map.keySet().size());
-
- // Red has two models, Pink and Orange one each
- assertEquals(2, map.get(Color.red).keySet().size());
- assertEquals(1, map.get(Color.orange).keySet().size());
- assertEquals(1, map.get(Color.pink).keySet().size());
-
- // pink model 1 has two chains, red.0 / red.1 / orange.0 one each
- assertEquals(2, map.get(Color.pink).get(1).keySet().size());
- assertEquals(1, map.get(Color.red).get(0).keySet().size());
- assertEquals(1, map.get(Color.red).get(1).keySet().size());
- assertEquals(1, map.get(Color.orange).get(0).keySet().size());
-
- // inspect positions
- List<int[]> posList = map.get(Color.pink).get(1).get("A");
- assertEquals(2, posList.size());
- assertTrue(Arrays.equals(new int[] { 2, 4 }, posList.get(0)));
- assertTrue(Arrays.equals(new int[] { 8, 8 }, posList.get(1)));
-
- posList = map.get(Color.pink).get(1).get("B");
- assertEquals(1, posList.size());
- assertTrue(Arrays.equals(new int[] { 5, 7 }, posList.get(0)));
-
- posList = map.get(Color.red).get(0).get("B");
- assertEquals(1, posList.size());
- assertTrue(Arrays.equals(new int[] { 1, 4 }, posList.get(0)));
-
- posList = map.get(Color.red).get(1).get("A");
- assertEquals(1, posList.size());
- assertTrue(Arrays.equals(new int[] { 3, 5 }, posList.get(0)));
-
- posList = map.get(Color.orange).get(0).get("C");
- assertEquals(1, posList.size());
- assertTrue(Arrays.equals(new int[] { 5, 9 }, posList.get(0)));
- }
-
- @Test(groups = { "Functional" })
public void testBuildColourCommands()
{
- Map<Color, Map<Integer, Map<String, List<int[]>>>> map = new LinkedHashMap<Color, Map<Integer, Map<String, List<int[]>>>>();
+ Map<Color, AtomSpecModel> map = new LinkedHashMap<Color, AtomSpecModel>();
ChimeraCommands.addColourRange(map, Color.blue, 0, 2, 5, "A");
ChimeraCommands.addColourRange(map, Color.blue, 0, 7, 7, "B");
ChimeraCommands.addColourRange(map, Color.blue, 0, 9, 23, "A");
ChimeraCommands.addColourRange(map, Color.yellow, 1, 8, 8, "A");
ChimeraCommands.addColourRange(map, Color.yellow, 1, 3, 5, "A");
ChimeraCommands.addColourRange(map, Color.red, 0, 3, 5, "A");
+ ChimeraCommands.addColourRange(map, Color.red, 0, 6, 9, "A");
// Colours should appear in the Chimera command in the order in which
- // they were added; within colour, by model, by chain, and positions as
- // added
+ // they were added; within colour, by model, by chain, ranges in start order
String command = ChimeraCommands.buildColourCommands(map).get(0);
assertEquals(
- "color #0000ff #0:2-5.A,9-23.A,7.B|#1:1.A,4-7.B; color #ffff00 #1:8.A,3-5.A; color #ff0000 #0:3-5.A",
+ "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",
command);
}
}
git://source.jalview.org / jalview.git / commitdiff