X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2Fseqfeatures%2FFeatureRendererModel.java;h=3608626798ac273c475ffad0469b0b7056c564de;hb=ec8f3cedf60fb1feed6d34de6b49f6bfa78b9dd8;hp=6bf1f4501bd58319bb38f03b37e1364d5ab81fff;hpb=3da878124135ff033f42d19d8733891b09e953cd;p=jalview.git diff --git a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java index 6bf1f45..3608626 100644 --- a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java +++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java @@ -20,18 +20,6 @@ */ package jalview.viewmodel.seqfeatures; -import jalview.api.AlignViewportI; -import jalview.api.FeatureColourI; -import jalview.api.FeaturesDisplayedI; -import jalview.datamodel.AlignmentI; -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 java.awt.Color; import java.beans.PropertyChangeListener; import java.beans.PropertyChangeSupport; @@ -47,6 +35,25 @@ import java.util.Map; import java.util.Set; import java.util.concurrent.ConcurrentHashMap; +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.Platform; + public abstract class FeatureRendererModel implements jalview.api.FeatureRenderer { @@ -321,12 +328,12 @@ public abstract class FeatureRendererModel 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); } @@ -653,7 +660,7 @@ public abstract class FeatureRendererModel { featureOrder = new Hashtable<>(); } - featureOrder.put(type, new Float(position)); + featureOrder.put(type, Float.valueOf(position)); return position; } @@ -853,7 +860,7 @@ public abstract class FeatureRendererModel } if (newGroupsVisible) { - featureGroups.put(group, new Boolean(true)); + featureGroups.put(group, Boolean.valueOf(true)); return true; } return false; @@ -889,7 +896,7 @@ public abstract class FeatureRendererModel @Override public void setGroupVisibility(String group, boolean visible) { - featureGroups.put(group, new Boolean(visible)); + featureGroups.put(group, Boolean.valueOf(visible)); } @Override @@ -901,7 +908,7 @@ public abstract class FeatureRendererModel for (String gst : toset) { Boolean st = featureGroups.get(gst); - featureGroups.put(gst, new Boolean(visible)); + featureGroups.put(gst, Boolean.valueOf(visible)); if (st != null) { rdrw = rdrw || (visible != st.booleanValue()); @@ -984,7 +991,7 @@ public abstract class FeatureRendererModel * @param sequenceFeature * @return */ - protected boolean featureGroupNotShown(final SequenceFeature sequenceFeature) + public boolean featureGroupNotShown(final SequenceFeature sequenceFeature) { return featureGroups != null && sequenceFeature.featureGroup != null @@ -999,7 +1006,7 @@ public abstract class FeatureRendererModel */ @Override public List findFeaturesAtResidue(SequenceI sequence, - int resNo) + int fromResNo, int toResNo) { List result = new ArrayList<>(); if (!av.areFeaturesDisplayed() || getFeaturesDisplayed() == null) @@ -1012,12 +1019,11 @@ public abstract class FeatureRendererModel * displayed, and feature group is null or the empty string * or marked for display */ - Set visibleFeatures = getFeaturesDisplayed() - .getVisibleFeatures(); + List visibleFeatures = getDisplayedFeatureTypes(); String[] visibleTypes = visibleFeatures .toArray(new String[visibleFeatures.size()]); List features = sequence.getFeatures().findFeatures( - resNo, resNo, visibleTypes); + fromResNo, toResNo, visibleTypes); for (SequenceFeature sf : features) { @@ -1041,6 +1047,14 @@ public abstract class FeatureRendererModel public void filterFeaturesForDisplay(List features) { /* + * fudge: JalviewJS's IntervalStore lacks the sort method called :-( + */ + if (Platform.isJS()) + { + return; + } + + /* * 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) @@ -1116,7 +1130,7 @@ public abstract class FeatureRendererModel /** * Answers the colour for the feature, or null if the feature is excluded by * feature group visibility, by filters, or by colour threshold settings. This - * method does not take feature visibility into account. + * method does not take feature type visibility into account. * * @param sf * @param fc @@ -1185,6 +1199,102 @@ public abstract class FeatureRendererModel } @Override + public MappedFeatures findComplementFeaturesAtResidue( + final SequenceI sequence, final int pos) + { + SequenceI ds = sequence.getDatasetSequence(); + if (ds == null) + { + ds = sequence; + } + final char residue = ds.getCharAt(pos - ds.getStart()); + + List found = new ArrayList<>(); + List mappings = this.av.getAlignment() + .getCodonFrame(sequence); + + /* + * fudge: if no mapping found, check the complementary alignment + * todo: only store in one place? StructureSelectionManager? + */ + if (mappings.isEmpty()) + { + mappings = this.av.getCodingComplement().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); + if (mapping == null || !mapping.getMap().isTripletMap()) + { + 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 fs = findFeaturesAtResidue( + mapFrom, 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 but ok for small scale); + * NB this sorts 'on top' feature to end, for rendering + */ + List result = new ArrayList<>(); + final int toAdd = found.size(); + int added = 0; + for (String type : renderOrder) + { + for (SequenceFeature sf : found) + { + if (type.equals(sf.getType())) + { + result.add(sf); + added++; + } + if (added == toAdd) + { + break; + } + } + } + + return new MappedFeatures(mapping, mapFrom, pos, residue, result); + } + + @Override public boolean isVisible(SequenceFeature feature) { if (feature == null)