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;
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;
boolean antiAlias = false;
- private Rectangle explodedGeometry;
+ private Rectangle explodedGeometry = null;
- private String viewName;
+ private String viewName = null;
/*
* Flag set true on the view that should 'gather' multiple views of the same
*/
private void applyViewProperties()
{
- antiAlias = Cache.getDefault(Preferences.ANTI_ALIAS, false);
+ // BH! using final static strings here because we also use these in
+ // JS version startup api
+ // BH was false
+ antiAlias = Cache.getDefault(Preferences.ANTI_ALIAS, true);
viewStyle.setShowJVSuffix(
Cache.getDefault(Preferences.SHOW_JVSUFFIX, true));
schemeName = Cache.getDefault(Preferences.DEFAULT_COLOUR,
ResidueColourScheme.NONE);
}
- ColourSchemeI colourScheme = ColourSchemeProperty.getColourScheme(this,
- alignment, schemeName);
+ ColourSchemeI colourScheme = ColourSchemeProperty
+ .getColourScheme(this, alignment, schemeName);
residueShading = new ResidueShader(colourScheme);
if (colourScheme instanceof UserColourScheme)
public static void openLinkedAlignmentAs(AlignFrame thisFrame,
AlignmentI thisAlignment, AlignmentI al, String title, int mode)
{
- /*
- * Identify protein and dna alignments. Make a copy of this one if opening
- * in a new split pane.
- */
+ // BH: thisAlignment is already a copy if mode == SPLIT_FRAME
+ // Identify protein and dna alignments. Make a copy of this one if opening
+ // in a new split pane.
+
AlignmentI protein = al.isNucleotide() ? thisAlignment : al;
AlignmentI cdna = al.isNucleotide() ? al : thisAlignment;
try
{
- newAlignFrame.setMaximum(jalview.bin.Cache
- .getDefault(Preferences.SHOW_FULLSCREEN, false));
+ newAlignFrame.setMaximum(Cache.getDefault(Preferences.SHOW_FULLSCREEN, false));
} catch (java.beans.PropertyVetoException ex)
{
}
if (ap != null)
{
// modify GUI elements to reflect geometry change
- Dimension idw = getAlignPanel().getIdPanel().getIdCanvas()
- .getPreferredSize();
+ Dimension idw = ap.getIdPanel().getIdCanvas().getPreferredSize();
idw.width = i;
- getAlignPanel().getIdPanel().getIdCanvas().setPreferredSize(idw);
+ ap.getIdPanel().getIdCanvas().setPreferredSize(idw);
}
}
@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<>(),
+ 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 merging
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
{
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);
displayed.setVisible(type);
}
}
+ }
/*
* set visibility of feature groups
*/
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));
+ }
}
/*
git://source.jalview.org / jalview.git / blobdiff