X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2Fseqfeatures%2FFeatureRendererModel.java;h=43b0550e998dc1d7ab50949123be2321f50740ad;hb=b7cb4c78d9d787e918c9d88f917a41642dd90a7a;hp=5bbdbec383f822af464c1174220c7d8a7edf8eb7;hpb=f5c1419b96dc540087bcf565140e6bbcdc2096aa;p=jalview.git diff --git a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java index 5bbdbec..43b0550 100644 --- a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java +++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java @@ -26,6 +26,7 @@ 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; @@ -35,17 +36,17 @@ import java.beans.PropertyChangeListener; import java.beans.PropertyChangeSupport; import java.util.ArrayList; import java.util.Arrays; -import java.util.Collections; 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 { /** @@ -53,9 +54,9 @@ public abstract class FeatureRendererModel implements */ protected float transparency = 1.0f; - protected Map featureColours = new ConcurrentHashMap(); + protected Map featureColours = new ConcurrentHashMap<>(); - protected Map featureGroups = new ConcurrentHashMap(); + protected Map featureGroups = new ConcurrentHashMap<>(); protected String[] renderOrder; @@ -155,7 +156,7 @@ 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 +192,7 @@ public abstract class FeatureRendererModel implements renderOrder = neworder; } - protected Map minmax = new Hashtable(); + protected Map minmax = new Hashtable<>(); public Map getMinMax() { @@ -214,7 +215,8 @@ 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 +265,14 @@ 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; } @@ -275,13 +281,8 @@ public abstract class FeatureRendererModel implements .getVisibleFeatures(); String[] visibleTypes = visibleFeatures .toArray(new String[visibleFeatures.size()]); - - /* - * include features at the position provided their feature type is - * displayed, and feature group is null or marked for display - */ - List features = sequence.getFeatures().findFeatures( - res, res, visibleTypes); + List features = sequence.findFeatures(column, column, + visibleTypes); for (SequenceFeature sf : features) { @@ -319,7 +320,7 @@ 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++) @@ -332,17 +333,13 @@ public abstract class FeatureRendererModel implements } 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)) { - /* - * features in null group are always displayed; other groups - * keep their current visibility; new groups as 'newMadeVisible' - */ boolean groupDisplayed = true; if (group != null) { @@ -372,10 +369,8 @@ public abstract class FeatureRendererModel implements } } - /* - * 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) @@ -418,7 +413,7 @@ public abstract class FeatureRendererModel implements */ if (minmax == null) { - minmax = new Hashtable(); + minmax = new Hashtable<>(); } synchronized (minmax) { @@ -455,7 +450,7 @@ 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); @@ -468,7 +463,8 @@ 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])) { @@ -565,7 +561,8 @@ public abstract class FeatureRendererModel implements * 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. + * transparency. Returns null for a score feature whose score value lies + * outside any colour threshold. * * @param feature * @return @@ -577,19 +574,6 @@ public abstract class FeatureRendererModel implements } /** - * 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); - } - - /** * Answers true if the feature type is currently selected to be displayed, * else false * @@ -633,7 +617,7 @@ public abstract class FeatureRendererModel implements { if (featureOrder == null) { - featureOrder = new Hashtable(); + featureOrder = new Hashtable<>(); } featureOrder.put(type, new Float(position)); return position; @@ -692,7 +676,7 @@ public abstract class FeatureRendererModel implements * note visible feature ordering and colours before update */ List visibleFeatures = getDisplayedFeatureTypes(); - Map visibleColours = new HashMap( + Map visibleColours = new HashMap<>( getFeatureColours()); FeaturesDisplayedI av_featuresdisplayed = null; @@ -704,7 +688,8 @@ public abstract class FeatureRendererModel implements } else { - av.setFeaturesDisplayed(av_featuresdisplayed = new FeaturesDisplayed()); + av.setFeaturesDisplayed( + av_featuresdisplayed = new FeaturesDisplayed()); } } else @@ -816,11 +801,12 @@ 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) { @@ -850,7 +836,7 @@ public abstract class FeatureRendererModel implements { if (featureGroups != null) { - List gp = new ArrayList(); + List gp = new ArrayList<>(); for (String grp : featureGroups.keySet()) { @@ -896,7 +882,7 @@ public abstract class FeatureRendererModel implements @Override public Map getDisplayedFeatureCols() { - Map fcols = new Hashtable(); + Map fcols = new Hashtable<>(); if (getViewport().getFeaturesDisplayed() == null) { return fcols; @@ -924,7 +910,7 @@ 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) { @@ -945,24 +931,13 @@ public abstract class FeatureRendererModel implements @Override public List getDisplayedFeatureGroups() { - List _gps = new ArrayList(); - boolean valid = false; + List _gps = new ArrayList<>(); for (String gp : getFeatureGroups()) { if (checkGroupVisibility(gp, false)) { - valid = true; _gps.add(gp); } - if (!valid) - { - return null; - } - else - { - // gps = new String[_gps.size()]; - // _gps.toArray(gps); - } } return _gps; } @@ -984,4 +959,93 @@ public abstract class FeatureRendererModel implements .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)) + { + result.add(sf); + } + } + return result; + } + + /** + * Removes from the list of features any that have a feature group that is not + * displayed, or duplicate the location of a feature of the same type (unless + * 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). + * + * @param features + * @param fc + */ + public void filterFeaturesForDisplay(List features, + FeatureColourI fc) + { + if (features.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 + * 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) + * don't remove 'redundant' features if transparency is applied + * (as feature count affects depth of feature colour) + */ + if (simpleColour && transparency == 1f) + { + if (lastFeature != null && sf.getBegin() == lastFeature.getBegin() + && sf.getEnd() == lastFeature.getEnd() + && sf.isContactFeature() == lastFeature.isContactFeature() + && sf.getType().equals(lastFeature.getType())) + { + it.remove(); + } + } + lastFeature = sf; + } + } + }