X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2Fseqfeatures%2FFeatureRendererModel.java;h=8219c6a7d8e4d018e76fc253c7285e665b52cb25;hb=72f96c9a8773366b67f3766acf1ede5c86c43d01;hp=43b0550e998dc1d7ab50949123be2321f50740ad;hpb=b7cb4c78d9d787e918c9d88f917a41642dd90a7a;p=jalview.git diff --git a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java index 43b0550..8219c6a 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.FeatureMatcherSetI; import jalview.datamodel.features.SequenceFeatures; import jalview.renderer.seqfeatures.FeatureRenderer; import jalview.schemes.FeatureColour; @@ -36,6 +37,7 @@ 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; @@ -48,16 +50,49 @@ 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 */ protected float transparency = 1.0f; + /* + * colour scheme for each feature type + */ protected Map featureColours = 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; Map featureOrder = null; @@ -100,6 +135,7 @@ public abstract class FeatureRendererModel 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()) @@ -284,9 +320,13 @@ 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); } @@ -477,7 +517,8 @@ 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]); } @@ -507,7 +548,8 @@ 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]); } @@ -557,20 +599,11 @@ public abstract class FeatureRendererModel 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. Returns null for a score feature whose score value lies - * outside any colour threshold. - * - * @param feature - * @return - */ + @Override public Color getColour(SequenceFeature feature) { FeatureColourI fc = getFeatureStyle(feature.getType()); - return fc.getColor(feature); + return getColor(feature, fc); } /** @@ -580,9 +613,10 @@ public abstract class FeatureRendererModel * @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 @@ -651,26 +685,27 @@ 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 @@ -709,9 +744,9 @@ 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); } @@ -951,12 +986,12 @@ public abstract class FeatureRendererModel */ 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(); } /** @@ -986,7 +1021,7 @@ public abstract class FeatureRendererModel for (SequenceFeature sf : features) { - if (!featureGroupNotShown(sf)) + if (!featureGroupNotShown(sf) && getColour(sf) != null) { result.add(sf); } @@ -995,25 +1030,28 @@ public abstract class FeatureRendererModel } /** - * 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). + * 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(); @@ -1031,21 +1069,146 @@ public abstract class FeatureRendererModel * 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())) { - 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() + { + 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; + } }