X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2Fseqfeatures%2FFeatureRendererModel.java;h=e812ed58c594ad5c3e890ab872344351800f9869;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=2324a646e3c616caf8fb930de7d481779109c2f8;hpb=442ca8fed9a8cd9a65388c5537ebbbc078b02961;p=jalview.git diff --git a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java index 2324a64..e812ed5 100644 --- a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java +++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java @@ -20,12 +20,28 @@ */ package jalview.viewmodel.seqfeatures; +import java.awt.Color; +import java.beans.PropertyChangeListener; +import java.beans.PropertyChangeSupport; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.Comparator; +import java.util.HashMap; +import java.util.HashSet; +import java.util.Hashtable; +import java.util.Iterator; +import java.util.List; +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.AlignedCodonFrame.SequenceToSequenceMapping; import jalview.datamodel.AlignmentI; -import jalview.datamodel.Mapping; +import jalview.datamodel.MappedFeatures; import jalview.datamodel.SearchResultMatchI; import jalview.datamodel.SearchResults; import jalview.datamodel.SearchResultsI; @@ -36,20 +52,7 @@ 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; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.HashMap; -import java.util.HashSet; -import java.util.Hashtable; -import java.util.Iterator; -import java.util.List; -import java.util.Map; -import java.util.Set; -import java.util.concurrent.ConcurrentHashMap; +import jalview.util.Platform; public abstract class FeatureRendererModel implements jalview.api.FeatureRenderer @@ -101,11 +104,11 @@ public abstract class FeatureRendererModel Map featureOrder = null; - protected PropertyChangeSupport changeSupport = new PropertyChangeSupport( - this); - protected AlignViewportI av; + private PropertyChangeSupport changeSupport = new PropertyChangeSupport( + this); + @Override public AlignViewportI getViewport() { @@ -298,14 +301,21 @@ public abstract class FeatureRendererModel { firing = Boolean.TRUE; findAllFeatures(true); // add all new features as visible - changeSupport.firePropertyChange("changeSupport", null, null); + notifyFeaturesChanged(); firing = Boolean.FALSE; } } } @Override - public List findFeaturesAtColumn(SequenceI sequence, int column) + public void notifyFeaturesChanged() + { + changeSupport.firePropertyChange("changeSupport", null, null); + } + + @Override + public List findFeaturesAtColumn(SequenceI sequence, + int column) { /* * include features at the position provided their feature type is @@ -399,8 +409,8 @@ public abstract class FeatureRendererModel } if (groupDisplayed) { - Set types = asq.getFeatures().getFeatureTypesForGroups( - true, group); + Set types = asq.getFeatures() + .getFeatureTypesForGroups(true, group); for (String type : types) { if (!allfeatures.contains(type)) // or use HashSet and no test? @@ -479,6 +489,7 @@ public abstract class FeatureRendererModel } } } + protected Boolean firing = Boolean.FALSE; /** @@ -617,10 +628,11 @@ public abstract class FeatureRendererModel * @param type * @return */ - protected boolean showFeatureOfType(String type) + public boolean showFeatureOfType(String type) { - return type == null ? false : (av.getFeaturesDisplayed() == null ? true - : av.getFeaturesDisplayed().isVisible(type)); + return type == null ? false + : (av.getFeaturesDisplayed() == null ? true + : av.getFeaturesDisplayed().isVisible(type)); } @Override @@ -657,7 +669,7 @@ public abstract class FeatureRendererModel { featureOrder = new Hashtable<>(); } - featureOrder.put(type, new Float(position)); + featureOrder.put(type, Float.valueOf(position)); return position; } @@ -698,15 +710,15 @@ public abstract class FeatureRendererModel } /** - * Sets the priority order for features, with the highest priority (displayed on - * top) at the start of the data array + * Sets the priority order for features, with the highest priority (displayed + * on top) at the start of the data array * * @param data * an array of { Type, Colour, Filter, Boolean } * @param visibleNew * when true current featureDisplay list will be cleared - * @return true if any visible features have been reordered or recoloured, else - * false (i.e. no need to repaint) + * @return true if any visible features have been reordered or recoloured, + * else false (i.e. no need to repaint) */ public boolean setFeaturePriority(FeatureSettingsBean[] data, boolean visibleNew) @@ -857,7 +869,7 @@ public abstract class FeatureRendererModel } if (newGroupsVisible) { - featureGroups.put(group, new Boolean(true)); + featureGroups.put(group, Boolean.valueOf(true)); return true; } return false; @@ -893,7 +905,7 @@ 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 @@ -905,7 +917,7 @@ 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()); @@ -990,8 +1002,7 @@ public abstract class FeatureRendererModel */ public boolean featureGroupNotShown(final SequenceFeature sequenceFeature) { - return featureGroups != null - && sequenceFeature.featureGroup != null + return featureGroups != null && sequenceFeature.featureGroup != null && sequenceFeature.featureGroup.length() != 0 && featureGroups.containsKey(sequenceFeature.featureGroup) && !featureGroups.get(sequenceFeature.featureGroup) @@ -1019,9 +1030,9 @@ public abstract class FeatureRendererModel List visibleFeatures = getDisplayedFeatureTypes(); String[] visibleTypes = visibleFeatures .toArray(new String[visibleFeatures.size()]); - List features = sequence.getFeatures().findFeatures( - fromResNo, toResNo, visibleTypes); - + List features = sequence.getFeatures() + .findFeatures(fromResNo, toResNo, visibleTypes); + for (SequenceFeature sf : features) { if (!featureGroupNotShown(sf) && getColour(sf) != null) @@ -1033,17 +1044,25 @@ public abstract class FeatureRendererModel } /** - * 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. No - * filtering is done if transparency, or any feature filters, are in force. + * Removes from the list of features any whose group is not shown, or that are + * visible and duplicate the location of a visible feature of the same type. + * Should be used only for features of the same, simple, feature colour (which + * normally implies the same feature type). No filtering is done if + * transparency, or any feature filters, are in force. * * @param features */ 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) @@ -1061,6 +1080,11 @@ public abstract class FeatureRendererModel while (it.hasNext()) { SequenceFeature sf = it.next(); + if (featureGroupNotShown(sf)) + { + it.remove(); + continue; + } /* * a feature is redundant for rendering purposes if it has the @@ -1098,7 +1122,8 @@ public abstract class FeatureRendererModel } @Override - public void setFeatureFilter(String featureType, FeatureMatcherSetI filter) + public void setFeatureFilter(String featureType, + FeatureMatcherSetI filter) { if (filter == null || filter.isEmpty()) { @@ -1113,7 +1138,7 @@ 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 @@ -1136,7 +1161,7 @@ public abstract class FeatureRendererModel { return null; } - + return fc.getColor(sf); } @@ -1155,42 +1180,80 @@ public abstract class FeatureRendererModel } /** - * Answers a (possibly empty) 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. + * Answers true unless the specified group is set to hidden. Defaults to true + * if group visibility is not set. * - * @param sequence - * @param pos + * @param group * @return */ - public List findComplementFeaturesAtResidue(SequenceI sequence, int pos) + public boolean isGroupVisible(String group) + { + if (!featureGroups.containsKey(group)) + { + return true; + } + return featureGroups.get(group); + } + + /** + * Orders features in render precedence (last in order is last to render, so + * displayed on top of other features) + * + * @param order + */ + public void orderFeatures(Comparator order) + { + Arrays.sort(renderOrder, order); + } + + @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 */ + SequenceToSequenceMapping mapping = null; + SequenceI mapFrom = null; + for (AlignedCodonFrame acf : mappings) { - Mapping mapping = acf.getMappingForSequence(sequence, true); - if (mapping == null || mapping.getMap().getFromRatio() == mapping - .getMap().getToRatio()) + mapping = acf.getCoveringCodonMapping(ds); + if (mapping == null) { - continue; // we are only looking for 3:1 or 1:3 mappings + continue; } SearchResultsI sr = new SearchResults(); - acf.markMappedRegion(ds, pos, sr); + mapping.markMappedRegion(ds, pos, sr); for (SearchResultMatchI match : sr.getResults()) { int fromRes = match.getStart(); int toRes = match.getEnd(); - List fs = findFeaturesAtResidue( - match.getSequence(), fromRes, toRes); + mapFrom = match.getSequence(); + List fs = findFeaturesAtResidue(mapFrom, fromRes, + toRes); for (SequenceFeature sf : fs) { if (!found.contains(sf)) @@ -1199,11 +1262,27 @@ public abstract class FeatureRendererModel } } } + + /* + * just take the first mapped features we find + */ + if (!found.isEmpty()) + { + break; + } + } + if (found.isEmpty()) + { + return null; } + /* - * sort by renderorder, inefficiently + * 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) @@ -1211,15 +1290,44 @@ public abstract class FeatureRendererModel if (type.equals(sf.getType())) { result.add(sf); - if (result.size() == found.size()) - { - return result; - } + added++; + } + if (added == toAdd) + { + break; } } } - - return result; + + return new MappedFeatures(mapping.getMapping(), mapFrom, pos, residue, + result); } + @Override + public boolean isVisible(SequenceFeature feature) + { + if (feature == null) + { + return false; + } + if (getFeaturesDisplayed() == null + || !getFeaturesDisplayed().isVisible(feature.getType())) + { + return false; + } + if (featureGroupNotShown(feature)) + { + return false; + } + FeatureColourI fc = featureColours.get(feature.getType()); + if (fc != null && fc.isOutwithThreshold(feature)) + { + return false; + } + if (!featureMatchesFilters(feature)) + { + return false; + } + return true; + } }