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;
}
}
git://source.jalview.org / jalview.git / blobdiff