X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2Fseqfeatures%2FFeatureRendererModel.java;h=43b0550e998dc1d7ab50949123be2321f50740ad;hb=b7cb4c78d9d787e918c9d88f917a41642dd90a7a;hp=de1ee5ebb37a15332c5b800ac7a2780bc2710d43;hpb=f0115a38526bc70b87ee919b3c0f1ba0f7e53989;p=jalview.git diff --git a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java index de1ee5e..43b0550 100644 --- a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java +++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java @@ -45,8 +45,8 @@ 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 { /** @@ -54,9 +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; @@ -156,7 +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)) @@ -192,7 +192,7 @@ public abstract class FeatureRendererModel implements renderOrder = neworder; } - protected Map minmax = new Hashtable(); + protected Map minmax = new Hashtable<>(); public Map getMinMax() { @@ -215,7 +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 { @@ -270,7 +271,7 @@ public abstract class FeatureRendererModel implements * 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; @@ -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++) @@ -332,7 +333,7 @@ public abstract class FeatureRendererModel implements } AlignmentI alignment = av.getAlignment(); - List allfeatures = new ArrayList(); + List allfeatures = new ArrayList<>(); for (int i = 0; i < alignment.getHeight(); i++) { @@ -412,7 +413,7 @@ public abstract class FeatureRendererModel implements */ if (minmax == null) { - minmax = new Hashtable(); + minmax = new Hashtable<>(); } synchronized (minmax) { @@ -449,7 +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); @@ -462,7 +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])) { @@ -559,7 +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 @@ -571,19 +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 * @@ -627,7 +617,7 @@ public abstract class FeatureRendererModel implements { if (featureOrder == null) { - featureOrder = new Hashtable(); + featureOrder = new Hashtable<>(); } featureOrder.put(type, new Float(position)); return position; @@ -686,7 +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; @@ -698,7 +688,8 @@ public abstract class FeatureRendererModel implements } else { - av.setFeaturesDisplayed(av_featuresdisplayed = new FeaturesDisplayed()); + av.setFeaturesDisplayed( + av_featuresdisplayed = new FeaturesDisplayed()); } } else @@ -810,11 +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) { @@ -844,7 +836,7 @@ public abstract class FeatureRendererModel implements { if (featureGroups != null) { - List gp = new ArrayList(); + List gp = new ArrayList<>(); for (String grp : featureGroups.keySet()) { @@ -890,7 +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; @@ -918,7 +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) { @@ -939,7 +931,7 @@ 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)) @@ -974,7 +966,7 @@ public abstract class FeatureRendererModel implements public List findFeaturesAtResidue(SequenceI sequence, int resNo) { - List result = new ArrayList(); + List result = new ArrayList<>(); if (!av.areFeaturesDisplayed() || getFeaturesDisplayed() == null) { return result; @@ -1005,7 +997,9 @@ public abstract class FeatureRendererModel implements /** * 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 is applied) + * 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 @@ -1017,8 +1011,9 @@ public abstract class FeatureRendererModel implements { return; } + SequenceFeatures.sortFeatures(features, true); - boolean graduated = fc != null && fc.isGraduatedColour(); + boolean simpleColour = fc == null || fc.isSimpleColour(); SequenceFeature lastFeature = null; Iterator it = features.iterator(); @@ -1036,8 +1031,10 @@ public abstract class FeatureRendererModel implements * 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 (!graduated) + if (simpleColour && transparency == 1f) { if (lastFeature != null && sf.getBegin() == lastFeature.getBegin() && sf.getEnd() == lastFeature.getEnd()