X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2Fseqfeatures%2FFeatureRendererModel.java;h=9a8a0861fb5e21c084c4ee46f6dd3a389b967ac8;hb=335026a8f716032fcd79f576ba8c61ee57671baa;hp=6461748ac607a1813f6f8dfbb9ec6be9cc8571e3;hpb=9bcdd1d38988de350482acfd1a21628f73cdbd6d;p=jalview.git diff --git a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java index 6461748..9a8a086 100644 --- a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java +++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java @@ -23,14 +23,20 @@ package jalview.viewmodel.seqfeatures; 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; @@ -49,6 +55,28 @@ import java.util.concurrent.ConcurrentHashMap; public abstract class FeatureRendererModel implements jalview.api.FeatureRenderer { + /* + * a data bean to hold one row of feature settings from the gui + */ + public static class FeatureSettingsBean + { + public final String featureType; + + public final FeatureColourI featureColour; + + public final FeatureMatcherSetI filter; + + public final Boolean show; + + public FeatureSettingsBean(String type, FeatureColourI colour, + FeatureMatcherSetI theFilter, Boolean isShown) + { + featureType = type; + featureColour = colour; + filter = theFilter; + show = isShown; + } + } /* * global transparency for feature @@ -68,7 +96,7 @@ public abstract class FeatureRendererModel /* * filters for each feature type */ - protected Map featureFilters = new HashMap<>(); + protected Map featureFilters = new HashMap<>(); protected String[] renderOrder; @@ -169,7 +197,7 @@ public abstract class FeatureRendererModel { av.setFeaturesDisplayed(fdi = new FeaturesDisplayed()); } - List nft = new ArrayList(); + List nft = new ArrayList<>(); for (String featureType : featureTypes) { if (!fdi.isRegistered(featureType)) @@ -205,7 +233,7 @@ public abstract class FeatureRendererModel renderOrder = neworder; } - protected Map minmax = new Hashtable(); + protected Map minmax = new Hashtable<>(); public Map getMinMax() { @@ -284,7 +312,7 @@ public abstract class FeatureRendererModel * include features at the position provided their feature type is * displayed, and feature group is null or marked for display */ - List result = new ArrayList(); + List result = new ArrayList<>(); if (!av.areFeaturesDisplayed() || getFeaturesDisplayed() == null) { return result; @@ -297,9 +325,13 @@ public abstract class FeatureRendererModel List features = sequence.findFeatures(column, column, visibleTypes); + /* + * 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)) + if (getColour(sf) != null) { result.add(sf); } @@ -333,7 +365,7 @@ public abstract class FeatureRendererModel } FeaturesDisplayedI featuresDisplayed = av.getFeaturesDisplayed(); - Set oldfeatures = new HashSet(); + Set oldfeatures = new HashSet<>(); if (renderOrder != null) { for (int i = 0; i < renderOrder.length; i++) @@ -346,7 +378,7 @@ public abstract class FeatureRendererModel } AlignmentI alignment = av.getAlignment(); - List allfeatures = new ArrayList(); + List allfeatures = new ArrayList<>(); for (int i = 0; i < alignment.getHeight(); i++) { @@ -426,7 +458,7 @@ public abstract class FeatureRendererModel */ if (minmax == null) { - minmax = new Hashtable(); + minmax = new Hashtable<>(); } synchronized (minmax) { @@ -463,7 +495,7 @@ public abstract class FeatureRendererModel */ private void updateRenderOrder(List allFeatures) { - List allfeatures = new ArrayList(allFeatures); + List allfeatures = new ArrayList<>(allFeatures); String[] oldRender = renderOrder; renderOrder = new String[allfeatures.size()]; boolean initOrders = (featureOrder == null); @@ -490,7 +522,8 @@ public abstract class FeatureRendererModel if (mmrange != null) { FeatureColourI fc = featureColours.get(oldRender[j]); - if (fc != null && !fc.isSimpleColour() && fc.isAutoScaled()) + if (fc != null && !fc.isSimpleColour() && fc.isAutoScaled() + && !fc.isColourByAttribute()) { fc.updateBounds(mmrange[0][0], mmrange[0][1]); } @@ -520,7 +553,8 @@ public abstract class FeatureRendererModel if (mmrange != null) { FeatureColourI fc = featureColours.get(newf[i]); - if (fc != null && !fc.isSimpleColour() && fc.isAutoScaled()) + if (fc != null && !fc.isSimpleColour() && fc.isAutoScaled() + && !fc.isColourByAttribute()) { fc.updateBounds(mmrange[0][0], mmrange[0][1]); } @@ -586,7 +620,8 @@ public abstract class FeatureRendererModel */ protected boolean showFeatureOfType(String type) { - return type == null ? false : av.getFeaturesDisplayed().isVisible(type); + return type == null ? false : (av.getFeaturesDisplayed() == null ? true + : av.getFeaturesDisplayed().isVisible(type)); } @Override @@ -621,9 +656,9 @@ public abstract class FeatureRendererModel { if (featureOrder == null) { - featureOrder = new Hashtable(); + featureOrder = new Hashtable<>(); } - featureOrder.put(type, new Float(position)); + featureOrder.put(type, Float.valueOf(position)); return position; } @@ -655,32 +690,33 @@ public abstract class FeatureRendererModel * Replace current ordering with new ordering * * @param data - * { String(Type), Colour(Type), Boolean(Displayed) } + * an array of { Type, Colour, Filter, Boolean } * @return true if any visible features have been reordered, else false */ - public boolean setFeaturePriority(Object[][] data) + public boolean setFeaturePriority(FeatureSettingsBean[] data) { return setFeaturePriority(data, true); } /** - * 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 - * { String(Type), Colour(Type), Boolean(Displayed) } + * 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(Object[][] data, boolean visibleNew) + public boolean setFeaturePriority(FeatureSettingsBean[] data, + boolean visibleNew) { /* * note visible feature ordering and colours before update */ List visibleFeatures = getDisplayedFeatureTypes(); - Map visibleColours = new HashMap( + Map visibleColours = new HashMap<>( getFeatureColours()); FeaturesDisplayedI av_featuresdisplayed = null; @@ -713,9 +749,9 @@ public abstract class FeatureRendererModel { for (int i = 0; i < data.length; i++) { - String type = data[i][0].toString(); - setColour(type, (FeatureColourI) data[i][1]); - if (((Boolean) data[i][2]).booleanValue()) + String type = data[i].featureType; + setColour(type, data[i].featureColour); + if (data[i].show) { av_featuresdisplayed.setVisible(type); } @@ -822,7 +858,7 @@ public abstract class FeatureRendererModel } if (newGroupsVisible) { - featureGroups.put(group, new Boolean(true)); + featureGroups.put(group, Boolean.valueOf(true)); return true; } return false; @@ -840,7 +876,7 @@ public abstract class FeatureRendererModel { if (featureGroups != null) { - List gp = new ArrayList(); + List gp = new ArrayList<>(); for (String grp : featureGroups.keySet()) { @@ -858,7 +894,7 @@ 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 @@ -870,7 +906,7 @@ 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()); @@ -886,7 +922,7 @@ public abstract class FeatureRendererModel @Override public Map getDisplayedFeatureCols() { - Map fcols = new Hashtable(); + Map fcols = new Hashtable<>(); if (getViewport().getFeaturesDisplayed() == null) { return fcols; @@ -914,7 +950,7 @@ public abstract class FeatureRendererModel public List getDisplayedFeatureTypes() { List typ = getRenderOrder(); - List displayed = new ArrayList(); + List displayed = new ArrayList<>(); FeaturesDisplayedI feature_disp = av.getFeaturesDisplayed(); if (feature_disp != null) { @@ -935,7 +971,7 @@ public abstract class FeatureRendererModel @Override public List getDisplayedFeatureGroups() { - List _gps = new ArrayList(); + List _gps = new ArrayList<>(); for (String gp : getFeatureGroups()) { if (checkGroupVisibility(gp, false)) @@ -953,7 +989,7 @@ 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 @@ -968,9 +1004,9 @@ public abstract class FeatureRendererModel */ @Override public List findFeaturesAtResidue(SequenceI sequence, - int resNo) + int fromResNo, int toResNo) { - List result = new ArrayList(); + List result = new ArrayList<>(); if (!av.areFeaturesDisplayed() || getFeaturesDisplayed() == null) { return result; @@ -981,16 +1017,15 @@ 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) { - if (!featureGroupNotShown(sf)) + if (!featureGroupNotShown(sf) && getColour(sf) != null) { result.add(sf); } @@ -999,30 +1034,39 @@ public abstract class FeatureRendererModel } /** - * Removes from the list of features any that duplicate the location of a - * feature of the same type (unless feature is filtered out, or a graduated - * colour scheme or colour by label is applied). Should be used only for - * features of the same feature colour (which normally implies the same - * feature type). + * 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 - * @param fc */ - public void filterFeaturesForDisplay(List features, - FeatureColourI fc) + public void filterFeaturesForDisplay(List 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); - boolean simpleColour = fc == null || fc.isSimpleColour(); SequenceFeature lastFeature = null; Iterator it = features.iterator(); while (it.hasNext()) { SequenceFeature sf = it.next(); + if (featureGroupNotShown(sf)) + { + it.remove(); + continue; + } /* * a feature is redundant for rendering purposes if it has the @@ -1030,40 +1074,38 @@ public abstract class FeatureRendererModel * (checking type and isContactFeature as a fail-safe here, although * currently they are guaranteed to match in this context) */ - if (simpleColour) + if (lastFeature != null + && sf.getBegin() == lastFeature.getBegin() + && sf.getEnd() == lastFeature.getEnd() + && sf.isContactFeature() == lastFeature.isContactFeature() + && sf.getType().equals(lastFeature.getType())) { - if (lastFeature != null && sf.getBegin() == lastFeature.getBegin() - && sf.getEnd() == lastFeature.getEnd() - && sf.isContactFeature() == lastFeature.isContactFeature() - && sf.getType().equals(lastFeature.getType())) - { - it.remove(); - } + it.remove(); } lastFeature = sf; } } @Override - public Map getFeatureFilters() + public Map getFeatureFilters() { - return new HashMap<>(featureFilters); + return featureFilters; } @Override - public void setFeatureFilters(Map filters) + public void setFeatureFilters(Map 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()) { @@ -1077,8 +1119,8 @@ public abstract class FeatureRendererModel /** * 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 @@ -1087,14 +1129,6 @@ public abstract class FeatureRendererModel 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)) @@ -1123,9 +1157,129 @@ public abstract class FeatureRendererModel */ protected boolean featureMatchesFilters(SequenceFeature sf) { - KeyedMatcherSetI filter = featureFilters.get(sf.getType()); - return filter == null ? true : filter.matches(key -> sf - .getValueAsString(key)); + FeatureMatcherSetI filter = featureFilters.get(sf.getType()); + return filter == null ? true : filter.matches(sf); + } + + @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) + { + 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; } }