From 2a71f039ec3e1fdf9d9b13e4cef388b9c090c29c Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Mon, 24 Jun 2019 17:43:33 +0100 Subject: [PATCH] JAL-3330 mergeFeatureStyles - needs test coverage --- src/jalview/api/AlignViewportI.java | 10 ++++ src/jalview/appletgui/AlignViewport.java | 22 +++++++-- src/jalview/gui/AlignViewport.java | 79 ++++++++++++++++++++++++++---- 3 files changed, 97 insertions(+), 14 deletions(-) diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java index 389d9cf..785dd14 100644 --- a/src/jalview/api/AlignViewportI.java +++ b/src/jalview/api/AlignViewportI.java @@ -431,9 +431,19 @@ public interface AlignViewportI extends ViewStyleI */ void setFollowHighlight(boolean b); + /** + * configure the feature renderer with predefined feature settings + * + * @param featureSettings + */ public void applyFeaturesStyle(FeatureSettingsModelI featureSettings); /** + * Apply the given feature settings on top of existing feature settings. + */ + public void mergeFeaturesStyle(FeatureSettingsModelI featureSettings); + + /** * check if current selection group is defined on the view, or is simply a * temporary group. * diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java index 45180db..66bb7a5 100644 --- a/src/jalview/appletgui/AlignViewport.java +++ b/src/jalview/appletgui/AlignViewport.java @@ -396,10 +396,10 @@ public class AlignViewport extends AlignmentViewport } /** - * Applies the supplied feature settings descriptor to currently known - * features. This supports an 'initial configuration' of feature colouring - * based on a preset or user favourite. This may then be modified in the usual - * way using the Feature Settings dialogue. + * Applies the supplied feature settings descriptor to currently known features. + * This supports an 'initial configuration' of feature colouring based on a + * preset or user favourite. This may then be modified in the usual way using + * the Feature Settings dialogue. NOT IMPLEMENTED FOR APPLET * * @param featureSettings */ @@ -409,4 +409,18 @@ public class AlignViewport extends AlignmentViewport // TODO implement for applet } + /** + * Merges the supplied feature settings descriptor with existing feature styles. + * This supports an 'initial configuration' of feature colouring based on a + * preset or user favourite. This may then be modified in the usual way using + * the Feature Settings dialogue. NOT IMPLEMENTED FOR APPLET + * + * @param featureSettings + */ + @Override + public void mergeFeaturesStyle(FeatureSettingsModelI featureSettings) + { + // TODO Auto-generated method stub + + } } diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java index bc668fd..61b0d1b 100644 --- a/src/jalview/gui/AlignViewport.java +++ b/src/jalview/gui/AlignViewport.java @@ -47,6 +47,7 @@ import jalview.schemes.UserColourScheme; import jalview.structure.SelectionSource; import jalview.structure.StructureSelectionManager; import jalview.structure.VamsasSource; +import jalview.util.ColorUtils; import jalview.util.MessageManager; import jalview.viewmodel.AlignmentViewport; import jalview.ws.params.AutoCalcSetting; @@ -56,6 +57,7 @@ import java.awt.Dimension; import java.awt.Font; import java.awt.FontMetrics; import java.awt.Rectangle; +import java.util.ArrayList; import java.util.Hashtable; import java.util.Iterator; import java.util.List; @@ -981,19 +983,60 @@ public class AlignViewport extends AlignmentViewport @Override public void applyFeaturesStyle(FeatureSettingsModelI featureSettings) { + transferFeaturesStyles(featureSettings, false); + } + + /** + * Applies the supplied feature settings descriptor to currently known features. + * This supports an 'initial configuration' of feature colouring based on a + * preset or user favourite. This may then be modified in the usual way using + * the Feature Settings dialogue. + * + * @param featureSettings + */ + @Override + public void mergeFeaturesStyle(FeatureSettingsModelI featureSettings) + { + transferFeaturesStyles(featureSettings, true); + } + + /** + * when mergeOnly is set, then group and feature visibility or feature colours + * are not modified for features and groups already known to the feature + * renderer. Feature ordering is always adjusted, and transparency is always set + * regardless. + * + * @param featureSettings + * @param mergeOnly + */ + private void transferFeaturesStyles(FeatureSettingsModelI featureSettings, + boolean mergeOnly) + { if (featureSettings == null) { return; } - + FeatureRenderer fr = getAlignPanel().getSeqPanel().seqCanvas .getFeatureRenderer(); + List origRenderOrder = new ArrayList(), + origGroups = new ArrayList(); + // preserve original render order - allows differentiation between user configured colours and autogenerated ones + origRenderOrder.addAll(fr.getRenderOrder()); + origGroups.addAll(fr.getFeatureGroups()); + fr.findAllFeatures(true); List renderOrder = fr.getRenderOrder(); FeaturesDisplayedI displayed = fr.getFeaturesDisplayed(); - displayed.clear(); + if (!mergeOnly) + { + // only clear displayed features if we are mergeing + displayed.clear(); + } // TODO this clears displayed.featuresRegistered - do we care? - + // + // JAL-3330 - JBP - yes we do - calling applyFeatureStyle to a view where + // feature visibility has already been configured is not very friendly /* * set feature colour if specified by feature settings * set visibility of all features @@ -1002,13 +1045,24 @@ public class AlignViewport extends AlignmentViewport { FeatureColourI preferredColour = featureSettings .getFeatureColour(type); - if (preferredColour != null) - { - fr.setColour(type, preferredColour); - } - if (featureSettings.isFeatureDisplayed(type)) + FeatureColourI origColour = fr.getFeatureStyle(type); + if (!mergeOnly || (!origRenderOrder.contains(type) + || origColour == null + || (!origColour.isGraduatedColour() + && origColour.getColour() != null + && origColour.getColour().equals( + ColorUtils.createColourFromName(type))))) { - displayed.setVisible(type); + // if we are merging, only update if there wasn't already a colour defined for + // this type + if (preferredColour != null) + { + fr.setColour(type, preferredColour); + } + if (featureSettings.isFeatureDisplayed(type)) + { + displayed.setVisible(type); + } } } @@ -1017,7 +1071,12 @@ public class AlignViewport extends AlignmentViewport */ for (String group : fr.getFeatureGroups()) { - fr.setGroupVisibility(group, featureSettings.isGroupDisplayed(group)); + if (!mergeOnly || !origGroups.contains(group)) + { + // when merging, display groups only if the aren't already marked as not visible + fr.setGroupVisibility(group, + featureSettings.isGroupDisplayed(group)); + } } /* -- 1.7.10.2