import jalview.api.AlignViewportI;
import jalview.api.FeatureColourI;
import jalview.api.FeaturesDisplayedI;
+import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.MappedFeatures;
+import jalview.datamodel.Mapping;
+import jalview.datamodel.SearchResultMatchI;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SearchResultsI;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import jalview.datamodel.features.FeatureMatcherSetI;
import jalview.datamodel.features.SequenceFeatures;
import jalview.renderer.seqfeatures.FeatureRenderer;
import jalview.schemes.FeatureColour;
import jalview.util.ColorUtils;
-import jalview.util.matcher.KeyedMatcherSetI;
import java.awt.Color;
import java.beans.PropertyChangeListener;
public final FeatureColourI featureColour;
- public final KeyedMatcherSetI filter;
+ public final FeatureMatcherSetI filter;
public final Boolean show;
public FeatureSettingsBean(String type, FeatureColourI colour,
- KeyedMatcherSetI theFilter, Boolean isShown)
+ FeatureMatcherSetI theFilter, Boolean isShown)
{
featureType = type;
featureColour = colour;
/*
* filters for each feature type
*/
- protected Map<String, KeyedMatcherSetI> featureFilters = new HashMap<>();
+ protected Map<String, FeatureMatcherSetI> featureFilters = new HashMap<>();
protected String[] renderOrder;
visibleTypes);
/*
- * include features unless their feature group is not displayed, or
- * they are hidden (have no colour) based on a filter or colour threshold
+ * include features unless they are hidden (have no colour), based on
+ * feature group visibility, or a filter or colour threshold
*/
for (SequenceFeature sf : features)
{
- if (!featureGroupNotShown(sf) && getColour(sf) != null)
+ if (getColour(sf) != null)
{
result.add(sf);
}
* @param sequenceFeature
* @return
*/
- protected boolean featureGroupNotShown(final SequenceFeature sequenceFeature)
+ public boolean featureGroupNotShown(final SequenceFeature sequenceFeature)
{
return featureGroups != null
&& sequenceFeature.featureGroup != null
*/
@Override
public List<SequenceFeature> findFeaturesAtResidue(SequenceI sequence,
- int resNo)
+ int fromResNo, int toResNo)
{
List<SequenceFeature> result = new ArrayList<>();
if (!av.areFeaturesDisplayed() || getFeaturesDisplayed() == null)
* displayed, and feature group is null or the empty string
* or marked for display
*/
- Set<String> visibleFeatures = getFeaturesDisplayed()
- .getVisibleFeatures();
+ List<String> visibleFeatures = getDisplayedFeatureTypes();
String[] visibleTypes = visibleFeatures
.toArray(new String[visibleFeatures.size()]);
List<SequenceFeature> features = sequence.getFeatures().findFeatures(
- resNo, resNo, visibleTypes);
+ fromResNo, toResNo, visibleTypes);
for (SequenceFeature sf : features)
{
* Removes from the list of features any that duplicate the location of a
* feature of the same type. Should be used only for features of the same,
* simple, feature colour (which normally implies the same feature type). Does
- * not check visibility settings for feature type or feature group.
+ * not check visibility settings for feature type or feature group. No
+ * filtering is done if transparency, or any feature filters, are in force.
*
* @param features
*/
public void filterFeaturesForDisplay(List<SequenceFeature> features)
{
- if (features.isEmpty())
+ /*
+ * don't remove 'redundant' features if
+ * - transparency is applied (feature count affects depth of feature colour)
+ * - filters are applied (not all features may be displayable)
+ */
+ if (features.isEmpty() || transparency != 1f
+ || !featureFilters.isEmpty())
{
return;
}
+
SequenceFeatures.sortFeatures(features, true);
SequenceFeature lastFeature = null;
}
@Override
- public Map<String, KeyedMatcherSetI> getFeatureFilters()
+ public Map<String, FeatureMatcherSetI> getFeatureFilters()
{
- return new HashMap<>(featureFilters);
+ return featureFilters;
}
@Override
- public void setFeatureFilters(Map<String, KeyedMatcherSetI> filters)
+ public void setFeatureFilters(Map<String, FeatureMatcherSetI> filters)
{
featureFilters = filters;
}
@Override
- public KeyedMatcherSetI getFeatureFilter(String featureType)
+ public FeatureMatcherSetI getFeatureFilter(String featureType)
{
return featureFilters.get(featureType);
}
@Override
- public void setFeatureFilter(String featureType, KeyedMatcherSetI filter)
+ public void setFeatureFilter(String featureType, FeatureMatcherSetI filter)
{
if (filter == null || filter.isEmpty())
{
/**
* Answers the colour for the feature, or null if the feature is excluded by
- * feature type or group visibility, by filters, or by colour threshold
- * settings
+ * feature group visibility, by filters, or by colour threshold settings. This
+ * method does not take feature visibility into account.
*
* @param sf
* @param fc
public Color getColor(SequenceFeature sf, FeatureColourI fc)
{
/*
- * is the feature type displayed?
- */
- if (!showFeatureOfType(sf.getType()))
- {
- return null;
- }
-
- /*
* is the feature group displayed?
*/
if (featureGroupNotShown(sf))
*/
protected boolean featureMatchesFilters(SequenceFeature sf)
{
- KeyedMatcherSetI filter = featureFilters.get(sf.getType());
- // TODO temporary fudge for Score and Label
- return filter == null ? true
- : filter.matches(
- key -> "Label".equals(key[0]) ? sf.getDescription()
- : ("Score".equals(key[0])
- ? String.valueOf(sf.getScore())
- : sf.getValueAsString(key)));
+ FeatureMatcherSetI filter = featureFilters.get(sf.getType());
+ return filter == null ? true : filter.matches(sf);
+ }
+
+ /**
+ * Answers a bean containing a mapping, and a list of features in this
+ * alignment at a position (or range) which is mappable from the given
+ * sequence residue position in a mapped alignment. Features are returned in
+ * render order of feature type (on top last), with order within feature type
+ * undefined. If no features or mapping are found, answers null.
+ *
+ * @param sequence
+ * @param pos
+ * @return
+ */
+ public MappedFeatures findComplementFeaturesAtResidue(SequenceI sequence,
+ int pos)
+ {
+ SequenceI ds = sequence.getDatasetSequence();
+ if (ds == null)
+ {
+ ds = sequence;
+ }
+ final char residue = ds.getCharAt(pos - ds.getStart());
+
+ List<SequenceFeature> found = new ArrayList<>();
+ List<AlignedCodonFrame> mappings = this.av.getAlignment()
+ .getCodonFrame(sequence);
+
+ /*
+ * todo: direct lookup of CDS for peptide and vice-versa; for now,
+ * have to search through an unordered list of mappings for a candidate
+ */
+ Mapping mapping = null;
+ SequenceI mapFrom = null;
+
+ for (AlignedCodonFrame acf : mappings)
+ {
+ mapping = acf.getMappingForSequence(sequence, true);
+ if (mapping == null || mapping.getMap().getFromRatio() == mapping
+ .getMap().getToRatio())
+ {
+ continue; // we are only looking for 3:1 or 1:3 mappings
+ }
+ SearchResultsI sr = new SearchResults();
+ acf.markMappedRegion(ds, pos, sr);
+ for (SearchResultMatchI match : sr.getResults())
+ {
+ int fromRes = match.getStart();
+ int toRes = match.getEnd();
+ mapFrom = match.getSequence();
+ List<SequenceFeature> fs = findFeaturesAtResidue(
+ match.getSequence(), fromRes, toRes);
+ for (SequenceFeature sf : fs)
+ {
+ if (!found.contains(sf))
+ {
+ found.add(sf);
+ }
+ }
+ }
+
+ /*
+ * just take the first mapped features we find
+ */
+ if (!found.isEmpty())
+ {
+ break;
+ }
+ }
+ if (found.isEmpty())
+ {
+ return null;
+ }
+
+ /*
+ * sort by renderorder, inefficiently
+ */
+ List<SequenceFeature> result = new ArrayList<>();
+ for (String type : renderOrder)
+ {
+ for (SequenceFeature sf : found)
+ {
+ if (type.equals(sf.getType()))
+ {
+ result.add(sf);
+ if (result.size() == found.size())
+ {
+ return new MappedFeatures(mapping, mapFrom, pos, residue,
+ result);
+ }
+ }
+ }
+ }
+
+ return new MappedFeatures(mapping, mapFrom, pos, residue, result);
}
}