X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2Fseqfeatures%2FFeatureRendererModel.java;h=e812ed58c594ad5c3e890ab872344351800f9869;hb=353cb52722490edcba2c13b18836b6d37c5455de;hp=5db8751f58e66d3fbdecfab0a8cc532a85e614fc;hpb=ef7d9bed59341ba8a035dc4578cd9c62b655286b;p=jalview.git diff --git a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java index 5db8751..e812ed5 100644 --- a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java +++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java @@ -20,23 +20,12 @@ */ 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; import java.util.ArrayList; import java.util.Arrays; +import java.util.Comparator; import java.util.HashMap; import java.util.HashSet; import java.util.Hashtable; @@ -46,6 +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.AlignedCodonFrame.SequenceToSequenceMapping; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.MappedFeatures; +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 { @@ -96,11 +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() { @@ -293,14 +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 @@ -320,12 +335,12 @@ 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); } @@ -394,8 +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? @@ -474,6 +489,7 @@ public abstract class FeatureRendererModel } } } + protected Boolean firing = Boolean.FALSE; /** @@ -612,10 +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 @@ -652,7 +669,7 @@ public abstract class FeatureRendererModel { featureOrder = new Hashtable<>(); } - featureOrder.put(type, new Float(position)); + featureOrder.put(type, Float.valueOf(position)); return position; } @@ -693,15 +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) @@ -852,7 +869,7 @@ public abstract class FeatureRendererModel } if (newGroupsVisible) { - featureGroups.put(group, new Boolean(true)); + featureGroups.put(group, Boolean.valueOf(true)); return true; } return false; @@ -888,7 +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 @@ -900,7 +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()); @@ -983,10 +1000,9 @@ 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 + return featureGroups != null && sequenceFeature.featureGroup != null && sequenceFeature.featureGroup.length() != 0 && featureGroups.containsKey(sequenceFeature.featureGroup) && !featureGroups.get(sequenceFeature.featureGroup) @@ -998,7 +1014,7 @@ 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) @@ -1011,13 +1027,12 @@ 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); - + List features = sequence.getFeatures() + .findFeatures(fromResNo, toResNo, visibleTypes); + for (SequenceFeature sf : features) { if (!featureGroupNotShown(sf) && getColour(sf) != null) @@ -1040,6 +1055,14 @@ 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) @@ -1069,8 +1092,7 @@ public abstract class FeatureRendererModel * (checking type and isContactFeature as a fail-safe here, although * currently they are guaranteed to match in this context) */ - if (lastFeature != null - && sf.getBegin() == lastFeature.getBegin() + if (lastFeature != null && sf.getBegin() == lastFeature.getBegin() && sf.getEnd() == lastFeature.getEnd() && sf.isContactFeature() == lastFeature.isContactFeature() && sf.getType().equals(lastFeature.getType())) @@ -1100,7 +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()) { @@ -1115,7 +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 @@ -1138,7 +1161,7 @@ public abstract class FeatureRendererModel { return null; } - + return fc.getColor(sf); } @@ -1156,4 +1179,155 @@ public abstract class FeatureRendererModel return filter == null ? true : filter.matches(sf); } + /** + * Answers true unless the specified group is set to hidden. Defaults to true + * if group visibility is not set. + * + * @param group + * @return + */ + 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 = acf.getCoveringCodonMapping(ds); + if (mapping == null) + { + continue; + } + SearchResultsI sr = new SearchResults(); + mapping.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.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; + } }