X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2Fseqfeatures%2FFeatureRendererModel.java;h=4af6fde9b5b06282edd98ad524a9b6d4d286e028;hb=09d3b755d9b00f5c3acb44049aedd49361dc0690;hp=479767593428bf88bc81141a1c942c92e3bb0bf4;hpb=9e926ac4305fd9dff38b6e079e55b4f50664d544;p=jalview.git diff --git a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java index 4797675..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; @@ -50,16 +50,27 @@ public abstract class FeatureRendererModel implements jalview.api.FeatureRenderer { /* - * column indices of fields in Feature Settings table - * todo: transfer valuers as data beans instead of Object[][] + * a data bean to hold one row of feature settings from the gui */ - public static final int TYPE_COLUMN = 0; + public static class FeatureSettingsBean + { + public final String featureType; + + public final FeatureColourI featureColour; - public static final int COLOUR_COLUMN = 1; + public final FeatureMatcherSetI filter; - public static final int FILTER_COLUMN = 2; + public final Boolean show; - public static final int SHOW_COLUMN = 3; + public FeatureSettingsBean(String type, FeatureColourI colour, + FeatureMatcherSetI theFilter, Boolean isShown) + { + featureType = type; + featureColour = colour; + filter = theFilter; + show = isShown; + } + } /* * global transparency for feature @@ -79,7 +90,7 @@ public abstract class FeatureRendererModel /* * filters for each feature type */ - protected Map featureFilters = new HashMap<>(); + protected Map featureFilters = new HashMap<>(); protected String[] renderOrder; @@ -673,26 +684,27 @@ 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 @@ -731,9 +743,9 @@ public abstract class FeatureRendererModel { for (int i = 0; i < data.length; i++) { - String type = data[i][TYPE_COLUMN].toString(); - setColour(type, (FeatureColourI) data[i][COLOUR_COLUMN]); - if (((Boolean) data[i][SHOW_COLUMN]).booleanValue()) + String type = data[i].featureType; + setColour(type, data[i].featureColour); + if (data[i].show) { av_featuresdisplayed.setVisible(type); } @@ -1017,19 +1029,27 @@ public abstract class FeatureRendererModel } /** - * Removes from the list of features any that duplicate the location of a - * feature of the same type. Should be used only for features of the same, - * simple, feature colour (which normally implies the same feature type). Does - * not check visibility settings for feature type or feature group. + * 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) { - 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); SequenceFeature lastFeature = null; @@ -1037,6 +1057,11 @@ public abstract class FeatureRendererModel while (it.hasNext()) { SequenceFeature sf = it.next(); + if (featureGroupNotShown(sf)) + { + it.remove(); + continue; + } /* * a feature is redundant for rendering purposes if it has the @@ -1044,7 +1069,8 @@ public abstract class FeatureRendererModel * (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() + if (lastFeature != null + && sf.getBegin() == lastFeature.getBegin() && sf.getEnd() == lastFeature.getEnd() && sf.isContactFeature() == lastFeature.isContactFeature() && sf.getType().equals(lastFeature.getType())) @@ -1056,25 +1082,25 @@ public abstract class FeatureRendererModel } @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()) { @@ -1088,8 +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 @@ -1098,14 +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)) @@ -1134,14 +1152,36 @@ public abstract class FeatureRendererModel */ protected boolean featureMatchesFilters(SequenceFeature sf) { - KeyedMatcherSetI filter = featureFilters.get(sf.getType()); - // TODO temporary fudge for Score and Label - return filter == null ? true - : filter.matches( - key -> "Label".equals(key[0]) ? sf.getDescription() - : ("Score".equals(key[0]) - ? String.valueOf(sf.getScore()) - : 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; } }