X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2Fseqfeatures%2FFeatureRendererModel.java;h=5ca3ac5b8fd02ad9768c6b9494c62c62f13b0eed;hb=6200addf078b7f7ace90597dc056dafc7fc602c1;hp=8219c6a7d8e4d018e76fc253c7285e665b52cb25;hpb=4b1c969e87feaefd4fb9c49ba3d6b828b3ce1a9c;p=jalview.git diff --git a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java index 8219c6a..5ca3ac5 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 { @@ -324,6 +331,8 @@ public abstract class FeatureRendererModel * include features unless their feature group is not displayed, or * they are hidden (have no colour) based on a filter or colour threshold */ + + // BH! check -- !featureGroupNotShown(sf) is from applet branch. for (SequenceFeature sf : features) { if (!featureGroupNotShown(sf) && getColour(sf) != null) @@ -653,7 +662,7 @@ public abstract class FeatureRendererModel { featureOrder = new Hashtable<>(); } - featureOrder.put(type, new Float(position)); + featureOrder.put(type, Float.valueOf(position)); return position; } @@ -853,7 +862,7 @@ public abstract class FeatureRendererModel } if (newGroupsVisible) { - featureGroups.put(group, new Boolean(true)); + featureGroups.put(group, Boolean.valueOf(true)); return true; } return false; @@ -889,7 +898,7 @@ 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 +910,7 @@ 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()); @@ -984,14 +993,14 @@ public abstract class FeatureRendererModel * @param sequenceFeature * @return */ - protected boolean featureGroupNotShown(final SequenceFeature sequenceFeature) + public boolean featureGroupNotShown(final SequenceFeature sequenceFeature) { - Boolean b; return featureGroups != null && sequenceFeature.featureGroup != null - && sequenceFeature.featureGroup.length() > 0 - && (b = featureGroups.get(sequenceFeature.featureGroup)) != null - && !b.booleanValue(); + && sequenceFeature.featureGroup.length() != 0 + && featureGroups.containsKey(sequenceFeature.featureGroup) + && !featureGroups.get(sequenceFeature.featureGroup) + .booleanValue(); } /** @@ -999,7 +1008,7 @@ 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 +1021,11 @@ 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) { @@ -1040,6 +1048,16 @@ public abstract class FeatureRendererModel */ public void filterFeaturesForDisplay(List features) { +// BH! check -- what was the problem here? How is JalviewJS's IntervalStore different from + // other IntervalStore? + /* + * 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) @@ -1185,6 +1203,99 @@ public abstract class FeatureRendererModel } @Override + 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 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 + */ + List 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); + } + + @Override public boolean isVisible(SequenceFeature feature) { if (feature == null)