*/
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.HiddenColumns;
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;
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(
+ public static StructureMappingcommandSet[] getColourBySequenceCommand(
StructureSelectionManager ssm, String[] files,
- SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr,
- AlignmentI alignment)
+ SequenceI[][] sequence, SequenceRenderer sr,
+ AlignmentViewPanel viewPanel)
{
- Map<Object, AtomSpecModel> colourMap = buildColoursMap(
- ssm, files, sequence, sr, fr, alignment);
+ Map<Object, AtomSpecModel> colourMap = buildColoursMap(ssm, files,
+ sequence, sr, viewPanel);
List<String> colourCommands = buildColourCommands(colourMap);
ChimeraCommands.class, null,
colourCommands.toArray(new String[colourCommands.size()]));
- return cs;
+ return new StructureMappingcommandSet[] { cs };
}
/**
}
sb.append("color ").append(colourCode).append(" ");
firstColour = false;
- final AtomSpecModel colourData = colourMap
- .get(colour);
+ final AtomSpecModel colourData = colourMap.get(colour);
sb.append(colourData.getAtomSpec());
}
commands.add(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
*/
protected static Map<Object, AtomSpecModel> buildColoursMap(
StructureSelectionManager ssm, String[] files,
- SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr,
- AlignmentI alignment)
+ 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<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 = Color.GRAY;
+ }
+
final String chain = mapping[m].getChain();
/*
{
if (startPos != -1)
{
- addRange(colourMap, lastColour, pdbfnum, startPos,
+ addColourRange(colourMap, lastColour, pdbfnum, startPos,
lastPos, lastChain);
}
startPos = pos;
// final colour range
if (lastColour != null)
{
- addRange(colourMap, lastColour, pdbfnum, startPos,
+ addColourRange(colourMap, lastColour, pdbfnum, startPos,
lastPos, lastChain);
}
// break;
* @param endPos
* @param chain
*/
- protected static void addRange(Map<Object, AtomSpecModel> map,
+ protected static void addColourRange(Map<Object, AtomSpecModel> map,
Object key, int model, int startPos, int endPos, String chain)
{
/*
}
/**
- * Constructs and returns a set of Chimera commands to set attributes on
- * residues corresponding to features in Jalview
+ * 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 fr
- * @param alignment
+ * @param viewPanel
* @return
*/
public static StructureMappingcommandSet getSetAttributeCommandsForFeatures(
- StructureSelectionManager ssm, String[] files,
- SequenceI[][] seqs, FeatureRenderer fr, AlignmentI alignment)
+ StructureSelectionManager ssm, String[] files, SequenceI[][] seqs,
+ AlignmentViewPanel viewPanel)
{
- Map<String, AtomSpecModel> featureMap = buildFeaturesMap(
- ssm, files, seqs, fr, alignment);
+ Map<String, Map<Object, AtomSpecModel>> featureMap = buildFeaturesMap(
+ ssm, files, seqs, viewPanel);
List<String> commands = buildSetAttributeCommands(featureMap);
}
/**
- * Helper method to build a map of { featureType, AtomSpecModel }
+ * <pre>
+ * Helper method to build a map of
+ * { featureType, { feature value, AtomSpecModel } }
+ * </pre>
*
* @param ssm
* @param files
* @param seqs
- * @param fr
- * @param alignment
+ * @param viewPanel
* @return
*/
- protected static Map<String, AtomSpecModel> buildFeaturesMap(
- StructureSelectionManager ssm, String[] files,
- SequenceI[][] seqs, FeatureRenderer fr, AlignmentI alignment)
+ protected static Map<String, Map<Object, AtomSpecModel>> buildFeaturesMap(
+ StructureSelectionManager ssm, String[] files, SequenceI[][] seqs,
+ AlignmentViewPanel viewPanel)
{
- Map<String, AtomSpecModel> theMap = new LinkedHashMap<String, AtomSpecModel>();
+ Map<String, Map<Object, AtomSpecModel>> theMap = new LinkedHashMap<String, Map<Object, AtomSpecModel>>();
+
+ FeatureRenderer fr = viewPanel.getFeatureRenderer();
+ if (fr == null)
+ {
+ return theMap;
+ }
List<String> visibleFeatures = fr.getDisplayedFeatureTypes();
if (visibleFeatures.isEmpty())
{
return theMap;
}
-
+
+ AlignmentI alignment = viewPanel.getAlignment();
for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
{
StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
*/
protected static void scanSequenceFeatures(List<String> visibleFeatures,
StructureMapping mapping, SequenceI seq,
- Map<String, AtomSpecModel> theMap, int modelNumber)
+ Map<String, Map<Object, AtomSpecModel>> theMap, int modelNumber)
{
- SequenceFeature[] sfs = seq.getSequenceFeatures();
- if (sfs == null)
- {
- return;
- }
-
+ List<SequenceFeature> sfs = seq.getFeatures().getPositionalFeatures(
+ visibleFeatures.toArray(new String[visibleFeatures.size()]));
for (SequenceFeature sf : sfs)
{
String type = sf.getType();
- if (!visibleFeatures.contains(type))
+
+ /*
+ * 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)
{
continue;
}
if (!mappedRanges.isEmpty())
{
- AtomSpecModel atomSpec = theMap.get(type);
- if (atomSpec == null)
+ 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)
{
- atomSpec = new AtomSpecModel();
- theMap.put(type, atomSpec);
+ featureValues = new HashMap<Object, AtomSpecModel>();
+ theMap.put(type, featureValues);
}
for (int[] range : mappedRanges)
{
- atomSpec.addRange(modelNumber, range[0], range[1],
- mapping.getChain());
+ addColourRange(featureValues, value, modelNumber, range[0],
+ range[1], mapping.getChain());
}
}
}
}
/**
- * 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
+ * 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 " " #0:2.B,4.B,9-12.B|#1:1.A,2-6.A,...
+ * e.g. setattr r jv:chain <value> #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
*/
protected static List<String> buildSetAttributeCommands(
- Map<String, AtomSpecModel> featureMap)
+ Map<String, Map<Object, AtomSpecModel>> featureMap)
{
List<String> commands = new ArrayList<String>();
for (String featureType : featureMap.keySet())
{
- StringBuilder sb = new StringBuilder(128);
- String sanitised = featureType.replace(" ", "_").replace("-", "_");
- sb.append("setattr r jv_").append(sanitised).append(" \" \" ");
- sb.append(featureMap.get(featureType).getAtomSpec());
- commands.add(sb.toString());
+ 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();
+
+ /*
+ * Chimera treats an attribute name ending in 'color' as colour-valued;
+ * Jalview doesn't, so prevent this by appending an underscore
+ */
+ if (attName.toUpperCase().endsWith("COLOR"))
+ {
+ attName += "_";
+ }
+
+ return attName;
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff