*/
package jalview.ext.rbvi.chimera;
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureRenderer;
import jalview.api.SequenceRenderer;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import jalview.renderer.seqfeatures.FeatureColourFinder;
import jalview.structure.StructureMapping;
import jalview.structure.StructureMappingcommandSet;
import jalview.structure.StructureSelectionManager;
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.SortedMap;
-import java.util.TreeMap;
/**
* Routines for generating Chimera commands for Jalview/Chimera binding
public class ChimeraCommands
{
+ public static final String NAMESPACE_PREFIX = "jv_";
+
/**
- * utility to construct the commands to colour chains by the given alignment
- * for passing to Chimera
- *
- * @returns Object[] { Object[] { <model being coloured>,
+ * Constructs Chimera commands to colour residues as per the Jalview alignment
*
+ * @param ssm
+ * @param files
+ * @param sequence
+ * @param sr
+ * @param fr
+ * @param viewPanel
+ * @return
*/
public static StructureMappingcommandSet[] getColourBySequenceCommand(
StructureSelectionManager ssm, String[] files,
- SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr,
- AlignmentI alignment)
+ SequenceI[][] sequence, SequenceRenderer sr,
+ AlignmentViewPanel viewPanel)
{
- Map<Color, SortedMap<Integer, Map<String, List<int[]>>>> colourMap = buildColoursMap(
- ssm, files, sequence, sr, fr, alignment);
+ Map<Object, AtomSpecModel> colourMap = buildColoursMap(ssm, files,
+ sequence, sr, viewPanel);
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 };
}
* 'color' commands (one per distinct colour used). The format of each command
* is
*
- * <blockquote> color colorname #modelnumber:range.chain e.g. color #00ff00
- * #0:2.B,4.B,9-12.B|#1:1.A,2-6.A,...
- *
- * @see http
- * ://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/frameatom_spec
- * .html </pre>
+ * <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>
+ * </pre>
*
* @param colourMap
* @return
*/
protected static List<String> buildColourCommands(
- Map<Color, SortedMap<Integer, Map<String, List<int[]>>>> colourMap)
+ Map<Object, AtomSpecModel> colourMap)
{
/*
* This version concatenates all commands into a single String (semi-colon
List<String> commands = new ArrayList<String>();
StringBuilder sb = new StringBuilder(256);
boolean firstColour = true;
- for (Color colour : colourMap.keySet())
+ for (Object key : colourMap.keySet())
{
+ Color colour = (Color) key;
String colourCode = ColorUtils.toTkCode(colour);
if (!firstColour)
{
}
sb.append("color ").append(colourCode).append(" ");
firstColour = false;
- boolean firstModelForColour = true;
- final Map<Integer, Map<String, List<int[]>>> colourData = colourMap
- .get(colour);
- for (Integer model : colourData.keySet())
+ final AtomSpecModel colourData = colourMap.get(colour);
+ 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();
}
/**
* <pre>
- * Build a data structure which maps contiguous subsequences for each colour.
- * This generates a data structure from which we can easily generate the
- * Chimera command for colour by sequence.
+ * Build a data structure which records contiguous subsequences for each colour.
+ * From this we can easily generate the Chimera command for colour by sequence.
* Color
* Model number
* Chain
* Ordering is by order of addition (for colours and positions), natural ordering (for models and chains)
* </pre>
*/
- protected static Map<Color, SortedMap<Integer, Map<String, List<int[]>>>> buildColoursMap(
+ protected static Map<Object, AtomSpecModel> buildColoursMap(
StructureSelectionManager ssm, String[] files,
- SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr,
- AlignmentI alignment)
+ SequenceI[][] sequence, SequenceRenderer sr,
+ AlignmentViewPanel viewPanel)
{
- Map<Color, SortedMap<Integer, Map<String, List<int[]>>>> colourMap = new LinkedHashMap<Color, SortedMap<Integer, Map<String, List<int[]>>>>();
+ FeatureRenderer fr = viewPanel.getFeatureRenderer();
+ FeatureColourFinder finder = new FeatureColourFinder(fr);
+ AlignViewportI viewport = viewPanel.getAlignViewport();
+ ColumnSelection cs = viewport.getColumnSelection();
+ AlignmentI al = viewport.getAlignment();
+ Map<Object, AtomSpecModel> colourMap = new LinkedHashMap<Object, AtomSpecModel>();
Color lastColour = null;
+
for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
{
StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
{
final SequenceI seq = sequence[pdbfnum][s];
if (mapping[m].getSequence() == seq
- && (sp = alignment.findIndex(seq)) > -1)
+ && (sp = al.findIndex(seq)) > -1)
{
- SequenceI asp = alignment.getSequenceAt(sp);
+ SequenceI asp = al.getSequenceAt(sp);
for (int r = 0; r < asp.getLength(); r++)
{
// no mapping to gaps in sequence
continue;
}
- Color colour = sr.getResidueColour(seq, r, fr);
+ Color colour = sr.getResidueColour(seq, r, finder);
+
+ /*
+ * darker colour for hidden regions
+ */
+ if (!cs.isVisible(r))
+ {
+ // colour = ColorUtils.darkerThan(colour);
+ colour = Color.GRAY;
+ }
+
final String chain = mapping[m].getChain();
/*
// final colour range
if (lastColour != null)
{
- addColourRange(colourMap, lastColour, pdbfnum, startPos,
- lastPos, lastChain);
+ addColourRange(colourMap, lastColour, pdbfnum, startPos, lastPos,
+ lastChain);
}
// break;
}
/**
* Helper method to add one contiguous colour range to the colour map.
*
- * @param colourMap
- * @param colour
+ * @param map
+ * @param key
* @param model
* @param startPos
* @param endPos
* @param chain
*/
- protected static void addColourRange(
- Map<Color, SortedMap<Integer, Map<String, List<int[]>>>> colourMap,
- Color colour, int model, int startPos, int endPos, String chain)
+ protected static void addColourRange(Map<Object, AtomSpecModel> map,
+ Object key, int model, int startPos, int endPos, String chain)
{
/*
* Get/initialize map of data for the colour
*/
- SortedMap<Integer, Map<String, List<int[]>>> colourData = colourMap
- .get(colour);
- if (colourData == null)
+ AtomSpecModel atomSpec = map.get(key);
+ if (atomSpec == null)
{
- colourMap
- .put(colour,
- colourData = new TreeMap<Integer, Map<String, List<int[]>>>());
+ atomSpec = new AtomSpecModel();
+ map.put(key, atomSpec);
}
- /*
- * Get/initialize map of data for the colour and model
- */
- Map<String, List<int[]>> modelData = colourData.get(model);
- if (modelData == null)
+ atomSpec.addRange(model, startPos, endPos, chain);
+ }
+
+ /**
+ * Constructs and returns Chimera commands to set attributes on residues
+ * corresponding to features in Jalview. Attribute names are the Jalview
+ * feature type, with a "jv_" prefix.
+ *
+ * @param ssm
+ * @param files
+ * @param seqs
+ * @param viewPanel
+ * @return
+ */
+ public static StructureMappingcommandSet getSetAttributeCommandsForFeatures(
+ StructureSelectionManager ssm, String[] files,
+ SequenceI[][] seqs, AlignmentViewPanel viewPanel)
+ {
+ Map<String, Map<Object, AtomSpecModel>> featureMap = buildFeaturesMap(
+ ssm, files, seqs, viewPanel);
+
+ List<String> commands = buildSetAttributeCommands(featureMap);
+
+ StructureMappingcommandSet cs = new StructureMappingcommandSet(
+ ChimeraCommands.class, null,
+ commands.toArray(new String[commands.size()]));
+
+ return cs;
+ }
+
+ /**
+ * <pre>
+ * Helper method to build a map of
+ * { featureType, { feature value, AtomSpecModel } }
+ * </pre>
+ *
+ * @param ssm
+ * @param files
+ * @param seqs
+ * @param viewPanel
+ * @return
+ */
+ protected static Map<String, Map<Object, AtomSpecModel>> buildFeaturesMap(
+ StructureSelectionManager ssm, String[] files,
+ SequenceI[][] seqs, AlignmentViewPanel viewPanel)
+ {
+ Map<String, Map<Object, AtomSpecModel>> theMap = new LinkedHashMap<String, Map<Object, AtomSpecModel>>();
+
+ FeatureRenderer fr = viewPanel.getFeatureRenderer();
+ if (fr == null)
{
- colourData.put(model, modelData = new TreeMap<String, List<int[]>>());
+ return theMap;
}
- /*
- * Get/initialize map of data for colour, model and chain
- */
- List<int[]> chainData = modelData.get(chain);
- if (chainData == null)
+ List<String> visibleFeatures = fr.getDisplayedFeatureTypes();
+ if (visibleFeatures.isEmpty())
{
- modelData.put(chain, chainData = new ArrayList<int[]>());
+ return theMap;
}
+ AlignmentI alignment = viewPanel.getAlignment();
+ for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
+ {
+ StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
+
+ if (mapping == null || mapping.length < 1)
+ {
+ continue;
+ }
+
+ 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)
+ {
+ /*
+ * found a sequence with a mapping to a structure;
+ * now scan its features
+ */
+ SequenceI asp = alignment.getSequenceAt(sp);
+
+ scanSequenceFeatures(visibleFeatures, mapping[m], asp, theMap,
+ pdbfnum);
+ }
+ }
+ }
+ }
+ return theMap;
+ }
+
+ /**
+ * Inspect features on the sequence; for each feature that is visible,
+ * determine its mapped ranges in the structure (if any) according to the
+ * given mapping, and add them to the map
+ *
+ * @param visibleFeatures
+ * @param mapping
+ * @param seq
+ * @param theMap
+ * @param modelNumber
+ */
+ protected static void scanSequenceFeatures(List<String> visibleFeatures,
+ StructureMapping mapping, SequenceI seq,
+ Map<String, Map<Object, AtomSpecModel>> theMap, int modelNumber)
+ {
+ SequenceFeature[] sfs = seq.getSequenceFeatures();
+ if (sfs == null)
+ {
+ return;
+ }
+
+ for (SequenceFeature sf : sfs)
+ {
+ String type = sf.getType();
+
+ /*
+ * Only copy visible features, don't copy any which originated
+ * from Chimera, and suppress uninteresting ones (e.g. RESNUM)
+ */
+ boolean isFromViewer = JalviewChimeraBinding.CHIMERA_FEATURE_GROUP
+ .equals(sf.getFeatureGroup());
+ if (isFromViewer || !visibleFeatures.contains(type))
+ {
+ continue;
+ }
+ List<int[]> mappedRanges = mapping.getPDBResNumRanges(sf.getBegin(),
+ sf.getEnd());
+
+ if (!mappedRanges.isEmpty())
+ {
+ String value = sf.getDescription();
+ if (value == null || value.length() == 0)
+ {
+ value = type;
+ }
+ float score = sf.getScore();
+ if (score != 0f && !Float.isNaN(score))
+ {
+ value = Float.toString(score);
+ }
+ Map<Object, AtomSpecModel> featureValues = theMap.get(type);
+ if (featureValues == null)
+ {
+ featureValues = new HashMap<Object, AtomSpecModel>();
+ theMap.put(type, featureValues);
+ }
+ for (int[] range : mappedRanges)
+ {
+ addColourRange(featureValues, value, modelNumber, range[0], range[1],
+ mapping.getChain());
+ }
+ }
+ }
+ }
+
+ /**
+ * Traverse the map of features/values/models/chains/positions to construct a
+ * list of 'setattr' commands (one per distinct feature type and value).
+ * <p>
+ * The format of each command is
+ *
+ * <pre>
+ * <blockquote> setattr r <featureName> " " #modelnumber:range.chain
+ * e.g. setattr r jv:chain <value> #0:2.B,4.B,9-12.B|#1:1.A,2-6.A,...
+ * </blockquote>
+ * </pre>
+ *
+ * @param featureMap
+ * @return
+ */
+ protected static List<String> buildSetAttributeCommands(
+ Map<String, Map<Object, AtomSpecModel>> featureMap)
+ {
+ List<String> commands = new ArrayList<String>();
+ for (String featureType : featureMap.keySet())
+ {
+ String attributeName = makeAttributeName(featureType);
+
+ /*
+ * clear down existing attributes for this feature
+ */
+ // 'problem' - sets attribute to None on all residues - overkill?
+ // commands.add("~setattr r " + attributeName + " :*");
+
+ Map<Object, AtomSpecModel> values = featureMap.get(featureType);
+ for (Object value : values.keySet())
+ {
+ /*
+ * for each distinct value recorded for this feature type,
+ * add a command to set the attribute on the mapped residues
+ * Put values in single quotes, encoding any embedded single quotes
+ */
+ StringBuilder sb = new StringBuilder(128);
+ String featureValue = value.toString();
+ featureValue = featureValue.replaceAll("\\'", "'");
+ sb.append("setattr r ").append(attributeName).append(" '")
+ .append(featureValue).append("' ");
+ sb.append(values.get(value).getAtomSpec());
+ commands.add(sb.toString());
+ }
+ }
+
+ return commands;
+ }
+
+ /**
+ * Makes a prefixed and valid Chimera attribute name. A jv_ prefix is applied
+ * for a 'Jalview' namespace, and any non-alphanumeric character is converted
+ * to an underscore.
+ *
+ * @param featureType
+ * @return <pre>
+ * @see https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/setattr.html
+ * </pre>
+ */
+ protected static String makeAttributeName(String featureType)
+ {
+ StringBuilder sb = new StringBuilder();
+ if (featureType != null)
+ {
+ for (char c : featureType.toCharArray())
+ {
+ sb.append(Character.isLetterOrDigit(c) ? c : '_');
+ }
+ }
+ String attName = NAMESPACE_PREFIX + sb.toString();
+
/*
- * Add the start/end positions
+ * Chimera treats an attribute name ending in 'color' as colour-valued;
+ * Jalview doesn't, so prevent this by appending an underscore
*/
- chainData.add(new int[] { startPos, endPos });
+ if (attName.toUpperCase().endsWith("COLOR"))
+ {
+ attName += "_";
+ }
+
+ return attName;
}
}
git://source.jalview.org / jalview.git / blobdiff