import java.beans.PropertyChangeSupport;
import java.util.ArrayList;
import java.util.Arrays;
+import java.util.Comparator;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Hashtable;
import java.util.concurrent.ConcurrentHashMap;
import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureColourI;
import jalview.api.FeaturesDisplayedI;
import jalview.datamodel.AlignedCodonFrame;
import jalview.renderer.seqfeatures.FeatureRenderer;
import jalview.schemes.FeatureColour;
import jalview.util.ColorUtils;
+import jalview.util.Platform;
public abstract class FeatureRendererModel
implements jalview.api.FeatureRenderer
}
@Override
- public List<SequenceFeature> findFeaturesAtColumn(SequenceI sequence, int column)
+ public List<SequenceFeature> findFeaturesAtColumn(SequenceI sequence,
+ int column)
{
/*
* include features at the position provided their feature type is
}
if (groupDisplayed)
{
- Set<String> types = asq.getFeatures().getFeatureTypesForGroups(
- true, group);
+ Set<String> types = asq.getFeatures()
+ .getFeatureTypesForGroups(true, group);
for (String type : types)
{
if (!allfeatures.contains(type)) // or use HashSet and no test?
}
}
}
+
protected Boolean firing = Boolean.FALSE;
/**
* @param type
* @return
*/
- protected boolean showFeatureOfType(String type)
+ public boolean showFeatureOfType(String type)
{
- return type == null ? false : (av.getFeaturesDisplayed() == null ? true
- : av.getFeaturesDisplayed().isVisible(type));
+ return type == null ? false
+ : (av.getFeaturesDisplayed() == null ? true
+ : av.getFeaturesDisplayed().isVisible(type));
}
@Override
}
/**
- * 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
* 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(FeatureSettingsBean[] data,
boolean visibleNew)
* @param listener
* @see java.beans.PropertyChangeSupport#addPropertyChangeListener(java.beans.PropertyChangeListener)
*/
+ @Override
public void addPropertyChangeListener(PropertyChangeListener listener)
{
changeSupport.addPropertyChangeListener(listener);
* @param listener
* @see java.beans.PropertyChangeSupport#removePropertyChangeListener(java.beans.PropertyChangeListener)
*/
+ @Override
public void removePropertyChangeListener(PropertyChangeListener listener)
{
changeSupport.removePropertyChangeListener(listener);
*/
public boolean featureGroupNotShown(final SequenceFeature sequenceFeature)
{
- return featureGroups != null
- && sequenceFeature.featureGroup != null
+ return featureGroups != null && sequenceFeature.featureGroup != null
&& sequenceFeature.featureGroup.length() != 0
&& featureGroups.containsKey(sequenceFeature.featureGroup)
&& !featureGroups.get(sequenceFeature.featureGroup)
List<String> visibleFeatures = getDisplayedFeatureTypes();
String[] visibleTypes = visibleFeatures
.toArray(new String[visibleFeatures.size()]);
- List<SequenceFeature> features = sequence.getFeatures().findFeatures(
- fromResNo, toResNo, visibleTypes);
-
+ List<SequenceFeature> features = sequence.getFeatures()
+ .findFeatures(fromResNo, toResNo, visibleTypes);
+
for (SequenceFeature sf : features)
{
if (!featureGroupNotShown(sf) && getColour(sf) != null)
public void filterFeaturesForDisplay(List<SequenceFeature> features)
{
/*
+ * fudge: JalviewJS's IntervalStore lacks the sort method called :-(
+ */
+ if (Platform.isJS())
+ {
+ return;
+ }
+
+ /*
* 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)
* (checking type and isContactFeature as a fail-safe here, although
* currently they are guaranteed to match in this context)
*/
- if (lastFeature != null
- && sf.getBegin() == lastFeature.getBegin()
+ if (lastFeature != null && sf.getBegin() == lastFeature.getBegin()
&& sf.getEnd() == lastFeature.getEnd()
&& sf.isContactFeature() == lastFeature.isContactFeature()
&& sf.getType().equals(lastFeature.getType()))
}
@Override
- public void setFeatureFilter(String featureType, FeatureMatcherSetI 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 group visibility, by filters, or by colour threshold settings. This
- * method does not take feature visibility into account.
+ * method does not take feature type visibility into account.
*
* @param sf
* @param fc
{
return null;
}
-
+
return fc.getColor(sf);
}
return filter == null ? true : filter.matches(sf);
}
+ /**
+ * Answers true unless the specified group is set to hidden. Defaults to true
+ * if group visibility is not set.
+ *
+ * @param group
+ * @return
+ */
+ public boolean isGroupVisible(String group)
+ {
+ if (!featureGroups.containsKey(group))
+ {
+ return true;
+ }
+ return featureGroups.get(group);
+ }
+
+ /**
+ * Orders features in render precedence (last in order is last to render, so
+ * displayed on top of other features)
+ *
+ * @param order
+ */
+ public void orderFeatures(Comparator<String> order)
+ {
+ Arrays.sort(renderOrder, order);
+ }
+
@Override
public MappedFeatures findComplementFeaturesAtResidue(
final SequenceI sequence, final int pos)
int fromRes = match.getStart();
int toRes = match.getEnd();
mapFrom = match.getSequence();
- List<SequenceFeature> fs = findFeaturesAtResidue(
- mapFrom, fromRes, toRes);
+ List<SequenceFeature> fs = findFeaturesAtResidue(mapFrom, fromRes,
+ toRes);
for (SequenceFeature sf : fs)
{
if (!found.contains(sf))
}
}
}
-
- return new MappedFeatures(mapping.getMapping(), mapFrom, pos, residue, result);
+
+ return new MappedFeatures(mapping.getMapping(), mapFrom, pos, residue,
+ result);
}
@Override
return true;
}
+ @Override
+ public AlignmentViewPanel getAlignPanel()
+ {
+ return null;
+ }
}
git://source.jalview.org / jalview.git / blobdiff