X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2Fseqfeatures%2FFeatureRendererModel.java;h=8219c6a7d8e4d018e76fc253c7285e665b52cb25;hb=c1b4720c07631ff280cdc7b3396a4a4e251c03e6;hp=a8e89893982632483e04501bc09682ce7b9e0b81;hpb=60e252f7e0084336b0a85620842ce3db8f63e5b0;p=jalview.git diff --git a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java index a8e8989..8219c6a 100644 --- a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java +++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java @@ -26,6 +26,8 @@ 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; @@ -35,27 +37,61 @@ import java.beans.PropertyChangeListener; import java.beans.PropertyChangeSupport; import java.util.ArrayList; import java.util.Arrays; -import java.util.Collections; +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; -public abstract class FeatureRendererModel implements - jalview.api.FeatureRenderer +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 */ protected float transparency = 1.0f; - protected Map featureColours = new ConcurrentHashMap(); + /* + * colour scheme for each feature type + */ + protected Map featureColours = new ConcurrentHashMap<>(); - protected Map featureGroups = new ConcurrentHashMap(); + /* + * visibility flag for each feature group + */ + protected Map featureGroups = new ConcurrentHashMap<>(); + + /* + * filters for each feature type + */ + protected Map featureFilters = new HashMap<>(); protected String[] renderOrder; @@ -99,6 +135,7 @@ public abstract class FeatureRendererModel implements this.renderOrder = frs.renderOrder; this.featureGroups = frs.featureGroups; this.featureColours = frs.featureColours; + this.featureFilters = frs.featureFilters; this.transparency = frs.transparency; this.featureOrder = frs.featureOrder; if (av != null && av != fr.getViewport()) @@ -155,7 +192,7 @@ public abstract class FeatureRendererModel implements { av.setFeaturesDisplayed(fdi = new FeaturesDisplayed()); } - List nft = new ArrayList(); + List nft = new ArrayList<>(); for (String featureType : featureTypes) { if (!fdi.isRegistered(featureType)) @@ -191,7 +228,7 @@ public abstract class FeatureRendererModel implements renderOrder = neworder; } - protected Map minmax = new Hashtable(); + protected Map minmax = new Hashtable<>(); public Map getMinMax() { @@ -214,7 +251,8 @@ public abstract class FeatureRendererModel implements if (r[0] != 0 || mm[0] < 0.0) { r[0] = 1; - r[1] = (byte) ((int) 128.0 + 127.0 * (sequenceFeature.score / mm[1])); + r[1] = (byte) ((int) 128.0 + + 127.0 * (sequenceFeature.score / mm[1])); } else { @@ -263,10 +301,14 @@ public abstract class FeatureRendererModel implements } @Override - public List findFeaturesAtRes(SequenceI sequence, int res) + public List findFeaturesAtColumn(SequenceI sequence, int column) { - List result = new ArrayList(); - if (!av.areFeaturesDisplayed()) + /* + * include features at the position provided their feature type is + * displayed, and feature group is null or marked for display + */ + List result = new ArrayList<>(); + if (!av.areFeaturesDisplayed() || getFeaturesDisplayed() == null) { return result; } @@ -275,17 +317,16 @@ public abstract class FeatureRendererModel implements .getVisibleFeatures(); String[] visibleTypes = visibleFeatures .toArray(new String[visibleFeatures.size()]); + List features = sequence.findFeatures(column, column, + visibleTypes); /* - * include features at the position provided their feature type is - * displayed, and feature group is null or marked for display + * include features unless their feature group is not displayed, or + * they are hidden (have no colour) based on a filter or colour threshold */ - List features = sequence.getFeatures().findFeatures( - res, res, visibleTypes); - for (SequenceFeature sf : features) { - if (!featureGroupNotShown(sf)) + if (!featureGroupNotShown(sf) && getColour(sf) != null) { result.add(sf); } @@ -319,7 +360,7 @@ public abstract class FeatureRendererModel implements } FeaturesDisplayedI featuresDisplayed = av.getFeaturesDisplayed(); - Set oldfeatures = new HashSet(); + Set oldfeatures = new HashSet<>(); if (renderOrder != null) { for (int i = 0; i < renderOrder.length; i++) @@ -330,48 +371,19 @@ public abstract class FeatureRendererModel implements } } } - // <<<<<<< HEAD - // - // ======= - // if (minmax == null) - // { - // minmax = new Hashtable(); - // } - // - // Set oldGroups = new HashSet(featureGroups.keySet()); - // >>>>>>> refs/heads/develop + AlignmentI alignment = av.getAlignment(); - List allfeatures = new ArrayList(); // or HashSet? + List allfeatures = new ArrayList<>(); for (int i = 0; i < alignment.getHeight(); i++) { SequenceI asq = alignment.getSequenceAt(i); for (String group : asq.getFeatures().getFeatureGroups(true)) { - // <<<<<<< HEAD - /* - * features in null group are always displayed; other groups - * keep their current visibility; new groups as 'newMadeVisible' - */ boolean groupDisplayed = true; if (group != null) - // ======= - // continue; - // } - // - // int index = 0; - // while (index < features.length) - // { - // String fgrp = features[index].getFeatureGroup(); - // oldGroups.remove(fgrp); - // if (!featuresDisplayed.isRegistered(features[index].getType())) - // >>>>>>> refs/heads/develop { - // <<<<<<< HEAD if (featureGroups.containsKey(group)) - // ======= - // if (fgrp != null) - // >>>>>>> refs/heads/develop { groupDisplayed = featureGroups.get(group); } @@ -397,11 +409,8 @@ public abstract class FeatureRendererModel implements } } - /* - //<<<<<<< HEAD - * mark any new feature types as visible - */ - Collections.sort(allfeatures, String.CASE_INSENSITIVE_ORDER); + // uncomment to add new features in alphebetical order (but JAL-2575) + // Collections.sort(allfeatures, String.CASE_INSENSITIVE_ORDER); if (newMadeVisible) { for (String type : allfeatures) @@ -412,14 +421,6 @@ public abstract class FeatureRendererModel implements setOrder(type, 0); } } - // ======= - // * oldGroups now consists of groups that no longer - // * have any feature in them - remove these - // */ - // for (String grp : oldGroups) - // { - // featureGroups.remove(grp); - // >>>>>>> refs/heads/develop } updateRenderOrder(allfeatures); @@ -452,7 +453,7 @@ public abstract class FeatureRendererModel implements */ if (minmax == null) { - minmax = new Hashtable(); + minmax = new Hashtable<>(); } synchronized (minmax) { @@ -489,7 +490,7 @@ public abstract class FeatureRendererModel implements */ 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); @@ -502,7 +503,8 @@ public abstract class FeatureRendererModel implements { if (initOrders) { - setOrder(oldRender[j], (1 - (1 + (float) j) / oldRender.length)); + setOrder(oldRender[j], + (1 - (1 + (float) j) / oldRender.length)); } if (allfeatures.contains(oldRender[j])) { @@ -515,7 +517,8 @@ public abstract class FeatureRendererModel implements 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]); } @@ -545,7 +548,8 @@ public abstract class FeatureRendererModel implements 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]); } @@ -595,32 +599,11 @@ public abstract class FeatureRendererModel implements return fc; } - /** - * Returns the configured colour for a particular feature instance. This - * includes calculation of 'colour by label', or of a graduated score colour, - * if applicable. It does not take into account feature visibility or colour - * transparency. - * - * @param feature - * @return - */ + @Override public Color getColour(SequenceFeature feature) { FeatureColourI fc = getFeatureStyle(feature.getType()); - return fc.getColor(feature); - } - - /** - * Answers true unless the feature has a graduated colour scheme and the - * feature value lies outside the current threshold for display - * - * @param sequenceFeature - * @return - */ - protected boolean showFeature(SequenceFeature sequenceFeature) - { - FeatureColourI fc = getFeatureStyle(sequenceFeature.type); - return fc.isColored(sequenceFeature); + return getColor(feature, fc); } /** @@ -630,9 +613,10 @@ public abstract class FeatureRendererModel implements * @param type * @return */ - protected boolean showFeatureOfType(String type) + public 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 @@ -667,7 +651,7 @@ public abstract class FeatureRendererModel implements { if (featureOrder == null) { - featureOrder = new Hashtable(); + featureOrder = new Hashtable<>(); } featureOrder.put(type, new Float(position)); return position; @@ -701,32 +685,33 @@ public abstract class FeatureRendererModel implements * 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; @@ -738,7 +723,8 @@ public abstract class FeatureRendererModel implements } else { - av.setFeaturesDisplayed(av_featuresdisplayed = new FeaturesDisplayed()); + av.setFeaturesDisplayed( + av_featuresdisplayed = new FeaturesDisplayed()); } } else @@ -758,9 +744,9 @@ public abstract class FeatureRendererModel implements { 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); } @@ -850,11 +836,12 @@ public abstract class FeatureRendererModel implements { // conflict between applet and desktop - featureGroups returns the map in // the desktop featureRenderer - return (featureGroups == null) ? Arrays.asList(new String[0]) : Arrays - .asList(featureGroups.keySet().toArray(new String[0])); + return (featureGroups == null) ? Arrays.asList(new String[0]) + : Arrays.asList(featureGroups.keySet().toArray(new String[0])); } - public boolean checkGroupVisibility(String group, boolean newGroupsVisible) + public boolean checkGroupVisibility(String group, + boolean newGroupsVisible) { if (featureGroups == null) { @@ -884,7 +871,7 @@ public abstract class FeatureRendererModel implements { if (featureGroups != null) { - List gp = new ArrayList(); + List gp = new ArrayList<>(); for (String grp : featureGroups.keySet()) { @@ -930,7 +917,7 @@ public abstract class FeatureRendererModel implements @Override public Map getDisplayedFeatureCols() { - Map fcols = new Hashtable(); + Map fcols = new Hashtable<>(); if (getViewport().getFeaturesDisplayed() == null) { return fcols; @@ -958,7 +945,7 @@ public abstract class FeatureRendererModel implements public List getDisplayedFeatureTypes() { List typ = getRenderOrder(); - List displayed = new ArrayList(); + List displayed = new ArrayList<>(); FeaturesDisplayedI feature_disp = av.getFeaturesDisplayed(); if (feature_disp != null) { @@ -979,7 +966,7 @@ public abstract class FeatureRendererModel implements @Override public List getDisplayedFeatureGroups() { - List _gps = new ArrayList(); + List _gps = new ArrayList<>(); for (String gp : getFeatureGroups()) { if (checkGroupVisibility(gp, false)) @@ -999,12 +986,229 @@ public abstract class FeatureRendererModel implements */ protected boolean featureGroupNotShown(final SequenceFeature sequenceFeature) { + Boolean b; return featureGroups != null && sequenceFeature.featureGroup != null - && sequenceFeature.featureGroup.length() != 0 - && featureGroups.containsKey(sequenceFeature.featureGroup) - && !featureGroups.get(sequenceFeature.featureGroup) - .booleanValue(); + && sequenceFeature.featureGroup.length() > 0 + && (b = featureGroups.get(sequenceFeature.featureGroup)) != null + && !b.booleanValue(); + } + + /** + * {@inheritDoc} + */ + @Override + public List findFeaturesAtResidue(SequenceI sequence, + int resNo) + { + List result = new ArrayList<>(); + if (!av.areFeaturesDisplayed() || getFeaturesDisplayed() == null) + { + return result; + } + + /* + * include features at the position provided their feature type is + * displayed, and feature group is null or the empty string + * or marked for display + */ + Set visibleFeatures = getFeaturesDisplayed() + .getVisibleFeatures(); + String[] visibleTypes = visibleFeatures + .toArray(new String[visibleFeatures.size()]); + List features = sequence.getFeatures().findFeatures( + resNo, resNo, visibleTypes); + + for (SequenceFeature sf : features) + { + if (!featureGroupNotShown(sf) && getColour(sf) != null) + { + result.add(sf); + } + } + return result; + } + + /** + * 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) + { + /* + * 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; + + 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 + * same extent as another (so would just redraw the same colour); + * (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() + && sf.getEnd() == lastFeature.getEnd() + && sf.isContactFeature() == lastFeature.isContactFeature() + && sf.getType().equals(lastFeature.getType())) + { + it.remove(); + } + lastFeature = sf; + } + } + + @Override + public Map getFeatureFilters() + { + return featureFilters; + } + + @Override + public void setFeatureFilters(Map filters) + { + featureFilters = filters; + } + + @Override + public FeatureMatcherSetI getFeatureFilter(String featureType) + { + return featureFilters.get(featureType); + } + + @Override + public void setFeatureFilter(String featureType, FeatureMatcherSetI filter) + { + if (filter == null || filter.isEmpty()) + { + featureFilters.remove(featureType); + } + else + { + featureFilters.put(featureType, filter); + } + } + + /** + * 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. + * + * @param sf + * @param fc + * @return + */ + public Color getColor(SequenceFeature sf, FeatureColourI fc) + { + /* + * is the feature group displayed? + */ + if (featureGroupNotShown(sf)) + { + return null; + } + + /* + * does the feature pass filters? + */ + if (!featureMatchesFilters(sf)) + { + return null; + } + + return fc.getColor(sf); + } + + /** + * Answers true if there no are filters defined for the feature type, or this + * feature matches the filters. Answers false if the feature fails to match + * filters. + * + * @param sf + * @return + */ + protected boolean featureMatchesFilters(SequenceFeature sf) + { + 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 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; + } }