import jalview.datamodel.SearchResultsI;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.datamodel.features.FeatureMatcherSetI;
import jalview.renderer.ResidueShader;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
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 AnnotationColumnChooser annotationColumnSelectionState;
- boolean validCharWidth;
-
- public boolean followSelection = true;
-
- private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<>();
-
/**
* Creates a new AlignViewport object.
*
*/
private void applyViewProperties()
{
- antiAlias = Cache.getDefault("ANTI_ALIAS", false);
+ antiAlias = Cache.getDefault("ANTI_ALIAS", true);
viewStyle.setShowJVSuffix(Cache.getDefault("SHOW_JVSUFFIX", true));
setShowAnnotation(Cache.getDefault("SHOW_ANNOTATIONS", true));
setFont(new Font(fontName, style, Integer.parseInt(fontSize)), true);
- AlignmentI al = getAlignment();
-
- if (Cache.getDefault("NORMALISE_GAPS", true))
- {
- al.setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(0));
- }
+ alignment.setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(0));
// We must set conservation and consensus before setting colour,
// as Blosum and Clustal require this to be done
- if (consensusProfiles == null && !isDataset)
+ if (hconsensus == null && !isDataset)
{
- if (!al.isNucleotide())
+ if (!alignment.isNucleotide())
{
showConservation = Cache.getDefault("SHOW_CONSERVATION", true);
showQuality = Cache.getDefault("SHOW_QUALITY", true);
initAutoAnnotation();
// initInformation();
- String colourProperty = al.isNucleotide()
+ String colourProperty = alignment.isNucleotide()
? Preferences.DEFAULT_COLOUR_NUC
: Preferences.DEFAULT_COLOUR_PROT;
String schemeName = Cache.getProperty(colourProperty);
if (residueShading != null)
{
- residueShading.setConsensus(consensusProfiles);
+ residueShading.setConsensus(hconsensus);
}
setColourAppliesToAllGroups(true);
}
+
+ boolean validCharWidth;
/**
* {@inheritDoc}
/*
* replace mappings on our alignment
*/
- if (getAlignment() != null && align != null)
+ if (alignment != null && align != null)
{
- getAlignment().setCodonFrames(align.getCodonFrames());
+ alignment.setCodonFrames(align.getCodonFrames());
}
}
}
else
{
- end = getAlignment().getWidth();
+ end = alignment.getWidth();
}
- return getAlignment().getHiddenColumns().getVisContigsIterator(start,
- end, false);
+ return (alignment.getHiddenColumns().getVisContigsIterator(start,
+ end, false));
}
/**
return false;
}
+ public boolean followSelection = true;
+
/**
* @return true if view selection should always follow the selections
* broadcast by other selection sources
return StructureSelectionManager
.getStructureSelectionManager(Desktop.instance);
}
+
+ @Override
+ public boolean isNormaliseSequenceLogo()
+ {
+ return normaliseSequenceLogo;
+ }
+
+ @Override
+public void setNormaliseSequenceLogo(boolean state)
+ {
+ normaliseSequenceLogo = state;
+ }
+
/**
*
{
return validCharWidth;
}
+
+ private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<>();
public AutoCalcSetting getCalcIdSettingsFor(String calcId)
{
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();
- 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
{
FeatureColourI preferredColour = featureSettings
.getFeatureColour(type);
- if (preferredColour != null)
- {
- fr.setColour(type, preferredColour);
- }
- if (featureSettings.isFeatureDisplayed(type))
+ FeatureMatcherSetI preferredFilters = featureSettings
+ .getFeatureFilters(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 (preferredFilters != null
+ && (!mergeOnly || fr.getFeatureFilter(type) != null))
+ {
+ fr.setFeatureFilter(type, preferredFilters);
+ }
+ if (featureSettings.isFeatureDisplayed(type))
+ {
+ displayed.setVisible(type);
+ }
}
}
*/
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