+
+ /**
+ * If this viewport has a (Protein/cDNA) complement, then scroll the
+ * complementary alignment to match this one.
+ */
+ public void scrollComplementaryAlignment()
+ {
+ /*
+ * Populate a SearchResults object with the mapped location to scroll to. If
+ * there is no complement, or it is not following highlights, or no mapping
+ * is found, the result will be empty.
+ */
+ SearchResultsI sr = new SearchResults();
+ int verticalOffset = findComplementScrollTarget(sr);
+ if (!sr.isEmpty())
+ {
+ // TODO would like next line without cast but needs more refactoring...
+ final AlignmentPanel complementPanel = ((AlignViewport) getCodingComplement())
+ .getAlignPanel();
+ complementPanel.setToScrollComplementPanel(false);
+ complementPanel.scrollToCentre(sr, verticalOffset);
+ complementPanel.setToScrollComplementPanel(true);
+ }
+ }
+
+ /**
+ * Answers true if no alignment holds a reference to the given mapping
+ *
+ * @param acf
+ * @return
+ */
+ protected boolean noReferencesTo(AlignedCodonFrame acf)
+ {
+ AlignFrame[] frames = Desktop.getAlignFrames();
+ if (frames == null)
+ {
+ return true;
+ }
+ for (AlignFrame af : frames)
+ {
+ if (!af.isClosed())
+ {
+ for (AlignmentViewPanel ap : af.getAlignPanels())
+ {
+ AlignmentI al = ap.getAlignment();
+ if (al != null && al.getCodonFrames().contains(acf))
+ {
+ return false;
+ }
+ }
+ }
+ }
+ return true;
+ }
+
+ /**
+ * 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 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<String> origRenderOrder = new ArrayList<>();
+ List<String> 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<String> renderOrder = fr.getRenderOrder();
+ FeaturesDisplayedI displayed = fr.getFeaturesDisplayed();
+ 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
+ */
+ for (String type : renderOrder)
+ {
+ FeatureColourI preferredColour = featureSettings
+ .getFeatureColour(type);
+ FeatureColourI origColour = fr.getFeatureStyle(type);
+ if (!mergeOnly || (!origRenderOrder.contains(type)
+ || origColour == null
+ || (!origColour.isGraduatedColour()
+ && origColour.getColour() != null
+ && origColour.getColour().equals(
+ ColorUtils.createColourFromName(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);
+ }
+ else if (featureSettings.isFeatureHidden(type))
+ {
+ displayed.setHidden(type);
+ }
+ }
+ }
+
+ /*
+ * set visibility of feature groups
+ */
+ for (String group : fr.getFeatureGroups())
+ {
+ 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));
+ }
+ }
+
+ /*
+ * order the features
+ */
+ if (featureSettings.optimiseOrder())
+ {
+ // TODO not supported (yet?)
+ }
+ else
+ {
+ fr.orderFeatures(featureSettings);
+ }
+ fr.setTransparency(featureSettings.getTransparency());
+
+ fr.notifyFeaturesChanged();
+ }
+
+ public String getViewName()
+ {
+ return viewName;
+ }
+
+ public void setViewName(String viewName)
+ {
+ this.viewName = viewName;
+ }