X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2Fseqfeatures%2FFeatureRendererModel.java;h=eb1030c3640b7d400586d6fa6600d76984aca7a4;hb=27aed96d1aeae689818bd0a0028553186e3c3839;hp=28fceec6b08334bdbf2ed601c999af3f214c06b0;hpb=0ebfeaf22a68a4c2760ef6980d68ede56ad40eb3;p=jalview.git diff --git a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java index 28fceec..eb1030c 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.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; 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; @@ -46,9 +35,50 @@ 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 { + /* + * 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 @@ -68,17 +98,17 @@ public abstract class FeatureRendererModel /* * filters for each feature type */ - protected Map featureFilters = new HashMap<>(); + protected Map featureFilters = new HashMap<>(); protected String[] renderOrder; Map featureOrder = null; - protected PropertyChangeSupport changeSupport = new PropertyChangeSupport( - this); - protected AlignViewportI av; + private PropertyChangeSupport changeSupport = new PropertyChangeSupport( + this); + @Override public AlignViewportI getViewport() { @@ -271,13 +301,19 @@ 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 void notifyFeaturesChanged() + { + changeSupport.firePropertyChange("changeSupport", null, null); + } + + @Override public List findFeaturesAtColumn(SequenceI sequence, int column) { /* @@ -297,9 +333,13 @@ 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); } @@ -586,7 +626,7 @@ 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)); @@ -626,7 +666,7 @@ public abstract class FeatureRendererModel { featureOrder = new Hashtable<>(); } - featureOrder.put(type, new Float(position)); + featureOrder.put(type, Float.valueOf(position)); return position; } @@ -658,26 +698,27 @@ 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 @@ -716,9 +757,9 @@ 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); } @@ -825,7 +866,7 @@ public abstract class FeatureRendererModel } if (newGroupsVisible) { - featureGroups.put(group, new Boolean(true)); + featureGroups.put(group, Boolean.valueOf(true)); return true; } return false; @@ -861,7 +902,7 @@ 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 @@ -873,7 +914,7 @@ 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()); @@ -956,7 +997,7 @@ 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 @@ -971,7 +1012,7 @@ 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) @@ -984,16 +1025,15 @@ 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); } @@ -1002,19 +1042,35 @@ 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. + * 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) { - if (features.isEmpty()) + /* + * 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) + */ + if (features.isEmpty() || transparency != 1f + || !featureFilters.isEmpty()) + { + return; + } + SequenceFeatures.sortFeatures(features, true); SequenceFeature lastFeature = null; @@ -1022,6 +1078,11 @@ 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 @@ -1029,7 +1090,8 @@ 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())) @@ -1041,25 +1103,25 @@ public abstract class FeatureRendererModel } @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()) { @@ -1073,8 +1135,8 @@ 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 type visibility into account. * * @param sf * @param fc @@ -1083,14 +1145,6 @@ 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)) @@ -1119,9 +1173,158 @@ 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); + } + + /** + * 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; + } }