X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2Fseqfeatures%2FFeatureRendererModel.java;h=4af6fde9b5b06282edd98ad524a9b6d4d286e028;hb=09d3b755d9b00f5c3acb44049aedd49361dc0690;hp=6461748ac607a1813f6f8dfbb9ec6be9cc8571e3;hpb=baa077bd19420018433d78927aad3ad139e47351;p=jalview.git diff --git a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java index 6461748..4af6fde 100644 --- a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java +++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java @@ -26,11 +26,11 @@ 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 jalview.util.matcher.KeyedMatcherSetI; import java.awt.Color; import java.beans.PropertyChangeListener; @@ -49,6 +49,28 @@ 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 +90,7 @@ public abstract class FeatureRendererModel /* * filters for each feature type */ - protected Map featureFilters = new HashMap<>(); + protected Map featureFilters = new HashMap<>(); protected String[] renderOrder; @@ -169,7 +191,7 @@ 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 +227,7 @@ public abstract class FeatureRendererModel renderOrder = neworder; } - protected Map minmax = new Hashtable(); + protected Map minmax = new Hashtable<>(); public Map getMinMax() { @@ -284,7 +306,7 @@ 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 +319,13 @@ public abstract class FeatureRendererModel List features = sequence.findFeatures(column, column, visibleTypes); + /* + * include features unless their feature group is not displayed, or + * they are hidden (have no colour) based on a filter or colour threshold + */ for (SequenceFeature sf : features) { - if (!featureGroupNotShown(sf)) + if (!featureGroupNotShown(sf) && getColour(sf) != null) { result.add(sf); } @@ -333,7 +359,7 @@ 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 +372,7 @@ 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 +452,7 @@ public abstract class FeatureRendererModel */ if (minmax == null) { - minmax = new Hashtable(); + minmax = new Hashtable<>(); } synchronized (minmax) { @@ -463,7 +489,7 @@ 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 +516,8 @@ 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 +547,8 @@ 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 +614,8 @@ 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 @@ -621,7 +650,7 @@ public abstract class FeatureRendererModel { if (featureOrder == null) { - featureOrder = new Hashtable(); + featureOrder = new Hashtable<>(); } featureOrder.put(type, new Float(position)); return position; @@ -655,32 +684,33 @@ 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 +743,9 @@ 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); } @@ -840,7 +870,7 @@ public abstract class FeatureRendererModel { if (featureGroups != null) { - List gp = new ArrayList(); + List gp = new ArrayList<>(); for (String grp : featureGroups.keySet()) { @@ -886,7 +916,7 @@ public abstract class FeatureRendererModel @Override public Map getDisplayedFeatureCols() { - Map fcols = new Hashtable(); + Map fcols = new Hashtable<>(); if (getViewport().getFeaturesDisplayed() == null) { return fcols; @@ -914,7 +944,7 @@ 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 +965,7 @@ public abstract class FeatureRendererModel @Override public List getDisplayedFeatureGroups() { - List _gps = new ArrayList(); + List _gps = new ArrayList<>(); for (String gp : getFeatureGroups()) { if (checkGroupVisibility(gp, false)) @@ -970,7 +1000,7 @@ public abstract class FeatureRendererModel public List findFeaturesAtResidue(SequenceI sequence, int resNo) { - List result = new ArrayList(); + List result = new ArrayList<>(); if (!av.areFeaturesDisplayed() || getFeaturesDisplayed() == null) { return result; @@ -990,7 +1020,7 @@ public abstract class FeatureRendererModel for (SequenceFeature sf : features) { - if (!featureGroupNotShown(sf)) + if (!featureGroupNotShown(sf) && getColour(sf) != null) { result.add(sf); } @@ -999,30 +1029,39 @@ 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 +1069,38 @@ 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 +1114,8 @@ 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 +1124,6 @@ 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 +1152,36 @@ 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 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; } }