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;
* @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));
}
/**
- * Answers a bean containing a mapping, and a list of features in this
- * alignment at a position (or range) which is mappable from the given
- * sequence residue position in a mapped alignment. Features are returned in
- * render order of feature type (on top last), with order within feature type
- * undefined. If no features or mapping are found, answers null.
+ * Answers true unless the specified group is set to hidden. Defaults to true
+ * if group visibility is not set.
*
- * @param sequence
- * @param pos
+ * @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(SequenceI sequence,
int pos)
{
.getCodonFrame(sequence);
/*
+ * fudge: if no mapping found, check the complementary alignment
+ * todo: only store in one place? StructureSelectionManager?
+ */
+ if (mappings.isEmpty())
+ {
+ mappings = this.av.getCodingComplement().getAlignment()
+ .getCodonFrame(sequence);
+ }
+
+ /*
* todo: direct lookup of CDS for peptide and vice-versa; for now,
* have to search through an unordered list of mappings for a candidate
*/
for (AlignedCodonFrame acf : mappings)
{
- mapping = acf.getMappingForSequence(sequence, true);
- if (mapping == null || mapping.getMap().getFromRatio() == mapping
- .getMap().getToRatio())
+ mapping = acf.getMappingForSequence(sequence);
+ if (mapping == null || !mapping.getMap().isTripletMap())
{
continue; // we are only looking for 3:1 or 1:3 mappings
}
}
return true;
}
-
}