import jalview.api.FeatureColourI;
import jalview.api.FeaturesDisplayedI;
import jalview.datamodel.AlignedCodonFrame;
import jalview.api.FeatureColourI;
import jalview.api.FeaturesDisplayedI;
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.SearchResultMatchI;
import jalview.datamodel.SearchResults;
import jalview.datamodel.SearchResultsI;
import jalview.datamodel.SearchResultMatchI;
import jalview.datamodel.SearchResults;
import jalview.datamodel.SearchResultsI;
- return type == null ? false : (av.getFeaturesDisplayed() == null ? true
- : av.getFeaturesDisplayed().isVisible(type));
+ return type == null ? false
+ : (av.getFeaturesDisplayed() == null ? true
+ : av.getFeaturesDisplayed().isVisible(type));
- * 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
*
* @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)
&& sequenceFeature.featureGroup.length() != 0
&& featureGroups.containsKey(sequenceFeature.featureGroup)
&& !featureGroups.get(sequenceFeature.featureGroup)
&& 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<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);
+
* (checking type and isContactFeature as a fail-safe here, although
* currently they are guaranteed to match in this context)
*/
* (checking type and isContactFeature as a fail-safe here, although
* currently they are guaranteed to match in this context)
*/
&& sf.getEnd() == lastFeature.getEnd()
&& sf.isContactFeature() == lastFeature.isContactFeature()
&& sf.getType().equals(lastFeature.getType()))
&& sf.getEnd() == lastFeature.getEnd()
&& sf.isContactFeature() == lastFeature.isContactFeature()
&& sf.getType().equals(lastFeature.getType()))
* todo: direct lookup of CDS for peptide and vice-versa; for now,
* have to search through an unordered list of mappings for a candidate
*/
* 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 (SearchResultMatchI match : sr.getResults())
{
int fromRes = match.getStart();
int toRes = match.getEnd();
mapFrom = match.getSequence();
for (SearchResultMatchI match : sr.getResults())
{
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);
-
- return new MappedFeatures(mapping, mapFrom, pos, residue, result);
+
+ return new MappedFeatures(mapping.getMapping(), mapFrom, pos, residue,
+ result);