import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import jalview.datamodel.features.SequenceFeatures;
import jalview.renderer.seqfeatures.FeatureRenderer;
import jalview.schemes.FeatureColour;
import jalview.util.ColorUtils;
import java.beans.PropertyChangeSupport;
import java.util.ArrayList;
import java.util.Arrays;
-import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Hashtable;
+import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Set;
}
@Override
- public List<SequenceFeature> findFeaturesAtRes(SequenceI sequence, int res)
+ public List<SequenceFeature> findFeaturesAtColumn(SequenceI sequence, int column)
{
+ /*
+ * 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>();
- if (!av.areFeaturesDisplayed())
+ if (!av.areFeaturesDisplayed() || getFeaturesDisplayed() == null)
{
return result;
}
.getVisibleFeatures();
String[] visibleTypes = visibleFeatures
.toArray(new String[visibleFeatures.size()]);
-
- /*
- * include features at the position provided their feature type is
- * displayed, and feature group is null or marked for display
- */
- List<SequenceFeature> features = sequence.getFeatures().findFeatures(
- res, res, visibleTypes);
+ List<SequenceFeature> features = sequence.findFeatures(column, column,
+ visibleTypes);
for (SequenceFeature sf : features)
{
}
AlignmentI alignment = av.getAlignment();
- List<String> allfeatures = new ArrayList<String>(); // or HashSet?
+ List<String> allfeatures = new ArrayList<String>();
for (int i = 0; i < alignment.getHeight(); i++)
{
SequenceI asq = alignment.getSequenceAt(i);
for (String group : asq.getFeatures().getFeatureGroups(true))
{
- /*
- * features in null group are always displayed; other groups
- * keep their current visibility; new groups as 'newMadeVisible'
- */
boolean groupDisplayed = true;
if (group != null)
{
}
}
- /*
- * mark any new feature types as visible
- */
- Collections.sort(allfeatures, String.CASE_INSENSITIVE_ORDER);
+ // uncomment to add new features in alphebetical order (but JAL-2575)
+ // Collections.sort(allfeatures, String.CASE_INSENSITIVE_ORDER);
if (newMadeVisible)
{
for (String type : allfeatures)
* Returns the configured colour for a particular feature instance. This
* includes calculation of 'colour by label', or of a graduated score colour,
* if applicable. It does not take into account feature visibility or colour
- * transparency.
+ * transparency. Returns null for a score feature whose score value lies
+ * outside any colour threshold.
*
* @param feature
* @return
}
/**
- * Answers true unless the feature has a graduated colour scheme and the
- * feature value lies outside the current threshold for display
- *
- * @param sequenceFeature
- * @return
- */
- protected boolean showFeature(SequenceFeature sequenceFeature)
- {
- FeatureColourI fc = getFeatureStyle(sequenceFeature.type);
- return fc.isColored(sequenceFeature);
- }
-
- /**
* Answers true if the feature type is currently selected to be displayed,
* else false
*
public List<String> getDisplayedFeatureGroups()
{
List<String> _gps = new ArrayList<String>();
- boolean valid = false;
for (String gp : getFeatureGroups())
{
if (checkGroupVisibility(gp, false))
{
- valid = true;
_gps.add(gp);
}
- if (!valid)
- {
- return null;
- }
- else
- {
- // gps = new String[_gps.size()];
- // _gps.toArray(gps);
- }
}
return _gps;
}
.booleanValue();
}
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ public List<SequenceFeature> findFeaturesAtResidue(SequenceI sequence,
+ int resNo)
+ {
+ List<SequenceFeature> result = new ArrayList<SequenceFeature>();
+ if (!av.areFeaturesDisplayed() || getFeaturesDisplayed() == null)
+ {
+ return result;
+ }
+
+ /*
+ * include features at the position provided their feature type is
+ * displayed, and feature group is null or the empty string
+ * or marked for display
+ */
+ Set<String> visibleFeatures = getFeaturesDisplayed()
+ .getVisibleFeatures();
+ String[] visibleTypes = visibleFeatures
+ .toArray(new String[visibleFeatures.size()]);
+ List<SequenceFeature> features = sequence.getFeatures().findFeatures(
+ resNo, resNo, visibleTypes);
+
+ for (SequenceFeature sf : features)
+ {
+ if (!featureGroupNotShown(sf))
+ {
+ result.add(sf);
+ }
+ }
+ return result;
+ }
+
+ /**
+ * Removes from the list of features any that have a feature group that is not
+ * displayed, or duplicate the location of a feature of the same type (unless
+ * 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).
+ *
+ * @param features
+ * @param fc
+ */
+ public void filterFeaturesForDisplay(List<SequenceFeature> features,
+ FeatureColourI fc)
+ {
+ if (features.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
+ * same extent as another (so would just redraw the same colour);
+ * (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()))
+ {
+ it.remove();
+ }
+ }
+ lastFeature = sf;
+ }
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff