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;
public abstract class FeatureRendererModel
implements jalview.api.FeatureRenderer
{
+ /*
+ * a data bean to hold one row of feature settings from the gui
+ */
+ public static class FeatureSettingsBean
+ {
+ public final String featureType;
+
+ public final FeatureColourI featureColour;
+
+ public final FeatureMatcherSetI filter;
+
+ public final Boolean show;
+
+ public FeatureSettingsBean(String type, FeatureColourI colour,
+ FeatureMatcherSetI theFilter, Boolean isShown)
+ {
+ featureType = type;
+ featureColour = colour;
+ filter = theFilter;
+ show = isShown;
+ }
+ }
/*
* global transparency for feature
/*
* filters for each feature type
*/
- protected Map<String, KeyedMatcherSetI> featureFilters = new HashMap<>();
+ protected Map<String, FeatureMatcherSetI> featureFilters = new HashMap<>();
protected String[] renderOrder;
{
av.setFeaturesDisplayed(fdi = new FeaturesDisplayed());
}
- List<String> nft = new ArrayList<String>();
+ List<String> nft = new ArrayList<>();
for (String featureType : featureTypes)
{
if (!fdi.isRegistered(featureType))
renderOrder = neworder;
}
- protected Map<String, float[][]> minmax = new Hashtable<String, float[][]>();
+ protected Map<String, float[][]> minmax = new Hashtable<>();
public Map<String, float[][]> getMinMax()
{
* include features at the position provided their feature type is
* displayed, and feature group is null or marked for display
*/
- List<SequenceFeature> result = new ArrayList<SequenceFeature>();
+ List<SequenceFeature> result = new ArrayList<>();
if (!av.areFeaturesDisplayed() || getFeaturesDisplayed() == null)
{
return result;
List<SequenceFeature> features = sequence.findFeatures(column, column,
visibleTypes);
+ /*
+ * include features unless their feature group is not displayed, or
+ * they are hidden (have no colour) based on a filter or colour threshold
+ */
for (SequenceFeature sf : features)
{
- if (!featureGroupNotShown(sf))
+ if (!featureGroupNotShown(sf) && getColour(sf) != null)
{
result.add(sf);
}
}
FeaturesDisplayedI featuresDisplayed = av.getFeaturesDisplayed();
- Set<String> oldfeatures = new HashSet<String>();
+ Set<String> oldfeatures = new HashSet<>();
if (renderOrder != null)
{
for (int i = 0; i < renderOrder.length; i++)
}
AlignmentI alignment = av.getAlignment();
- List<String> allfeatures = new ArrayList<String>();
+ List<String> allfeatures = new ArrayList<>();
for (int i = 0; i < alignment.getHeight(); i++)
{
*/
if (minmax == null)
{
- minmax = new Hashtable<String, float[][]>();
+ minmax = new Hashtable<>();
}
synchronized (minmax)
{
*/
private void updateRenderOrder(List<String> allFeatures)
{
- List<String> allfeatures = new ArrayList<String>(allFeatures);
+ List<String> allfeatures = new ArrayList<>(allFeatures);
String[] oldRender = renderOrder;
renderOrder = new String[allfeatures.size()];
boolean initOrders = (featureOrder == null);
if (mmrange != null)
{
FeatureColourI fc = featureColours.get(oldRender[j]);
- if (fc != null && !fc.isSimpleColour() && fc.isAutoScaled())
+ if (fc != null && !fc.isSimpleColour() && fc.isAutoScaled()
+ && !fc.isColourByAttribute())
{
fc.updateBounds(mmrange[0][0], mmrange[0][1]);
}
if (mmrange != null)
{
FeatureColourI fc = featureColours.get(newf[i]);
- if (fc != null && !fc.isSimpleColour() && fc.isAutoScaled())
+ if (fc != null && !fc.isSimpleColour() && fc.isAutoScaled()
+ && !fc.isColourByAttribute())
{
fc.updateBounds(mmrange[0][0], mmrange[0][1]);
}
*/
protected boolean showFeatureOfType(String type)
{
- return type == null ? false : av.getFeaturesDisplayed().isVisible(type);
+ return type == null ? false : (av.getFeaturesDisplayed() == null ? true
+ : av.getFeaturesDisplayed().isVisible(type));
}
@Override
{
if (featureOrder == null)
{
- featureOrder = new Hashtable<String, Float>();
+ featureOrder = new Hashtable<>();
}
featureOrder.put(type, new Float(position));
return position;
* 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
*/
List<String> visibleFeatures = getDisplayedFeatureTypes();
- Map<String, FeatureColourI> visibleColours = new HashMap<String, FeatureColourI>(
+ Map<String, FeatureColourI> visibleColours = new HashMap<>(
getFeatureColours());
FeaturesDisplayedI av_featuresdisplayed = null;
{
for (int i = 0; i < data.length; i++)
{
- String type = data[i][0].toString();
- setColour(type, (FeatureColourI) data[i][1]);
- if (((Boolean) data[i][2]).booleanValue())
+ String type = data[i].featureType;
+ setColour(type, data[i].featureColour);
+ if (data[i].show)
{
av_featuresdisplayed.setVisible(type);
}
{
if (featureGroups != null)
{
- List<String> gp = new ArrayList<String>();
+ List<String> gp = new ArrayList<>();
for (String grp : featureGroups.keySet())
{
@Override
public Map<String, FeatureColourI> getDisplayedFeatureCols()
{
- Map<String, FeatureColourI> fcols = new Hashtable<String, FeatureColourI>();
+ Map<String, FeatureColourI> fcols = new Hashtable<>();
if (getViewport().getFeaturesDisplayed() == null)
{
return fcols;
public List<String> getDisplayedFeatureTypes()
{
List<String> typ = getRenderOrder();
- List<String> displayed = new ArrayList<String>();
+ List<String> displayed = new ArrayList<>();
FeaturesDisplayedI feature_disp = av.getFeaturesDisplayed();
if (feature_disp != null)
{
@Override
public List<String> getDisplayedFeatureGroups()
{
- List<String> _gps = new ArrayList<String>();
+ List<String> _gps = new ArrayList<>();
for (String gp : getFeatureGroups())
{
if (checkGroupVisibility(gp, false))
public List<SequenceFeature> findFeaturesAtResidue(SequenceI sequence,
int resNo)
{
- List<SequenceFeature> result = new ArrayList<SequenceFeature>();
+ List<SequenceFeature> result = new ArrayList<>();
if (!av.areFeaturesDisplayed() || getFeaturesDisplayed() == null)
{
return result;
for (SequenceFeature sf : features)
{
- if (!featureGroupNotShown(sf))
+ if (!featureGroupNotShown(sf) && getColour(sf) != null)
{
result.add(sf);
}
}
/**
- * Removes from the list of features any that duplicate the location of a
- * feature of the same type (unless feature is filtered out, or a graduated
- * colour scheme or colour by label is applied). Should be used only for
- * features of the same feature colour (which normally implies the same
- * feature type).
+ * 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
- * @param fc
*/
- public void filterFeaturesForDisplay(List<SequenceFeature> features,
- FeatureColourI fc)
+ public void filterFeaturesForDisplay(List<SequenceFeature> 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);
- boolean simpleColour = fc == null || fc.isSimpleColour();
SequenceFeature lastFeature = null;
Iterator<SequenceFeature> it = features.iterator();
while (it.hasNext())
{
SequenceFeature sf = it.next();
+ if (featureGroupNotShown(sf))
+ {
+ it.remove();
+ continue;
+ }
/*
* a feature is redundant for rendering purposes if it has the
* (checking type and isContactFeature as a fail-safe here, although
* currently they are guaranteed to match in this context)
*/
- if (simpleColour)
+ if (lastFeature != null
+ && sf.getBegin() == lastFeature.getBegin()
+ && sf.getEnd() == lastFeature.getEnd()
+ && sf.isContactFeature() == lastFeature.isContactFeature()
+ && sf.getType().equals(lastFeature.getType()))
{
- if (lastFeature != null && sf.getBegin() == lastFeature.getBegin()
- && sf.getEnd() == lastFeature.getEnd()
- && sf.isContactFeature() == lastFeature.isContactFeature()
- && sf.getType().equals(lastFeature.getType()))
- {
- it.remove();
- }
+ it.remove();
}
lastFeature = sf;
}
}
@Override
- public Map<String, KeyedMatcherSetI> getFeatureFilters()
+ public Map<String, FeatureMatcherSetI> getFeatureFilters()
{
- return new HashMap<>(featureFilters);
+ return featureFilters;
}
@Override
- public void setFeatureFilters(Map<String, KeyedMatcherSetI> filters)
+ public void setFeatureFilters(Map<String, FeatureMatcherSetI> 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())
{
/**
* 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
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))
*/
protected boolean featureMatchesFilters(SequenceFeature sf)
{
- KeyedMatcherSetI filter = featureFilters.get(sf.getType());
- return filter == null ? true : filter.matches(key -> 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;
}
}
git://source.jalview.org / jalview.git / blobdiff