import jalview.datamodel.features.FeatureLocationI;
+import java.util.Comparator;
import java.util.HashMap;
import java.util.Map;
import java.util.Map.Entry;
private static final String ATTRIBUTES = "ATTRIBUTES";
/*
- * type, begin, end, featureGroup and contactFeature are final
+ * type, begin, end, featureGroup, score and contactFeature are final
* to ensure that the integrity of SequenceFeatures data store
* can't be broken by direct update of these fields
*/
* A copy constructor that allows the value of final fields to be 'modified'
*
* @param sf
+ * @param newType
* @param newBegin
* @param newEnd
* @param newGroup
* @param newScore
*/
- public SequenceFeature(SequenceFeature sf, int newBegin, int newEnd,
- String newGroup, float newScore)
+ public SequenceFeature(SequenceFeature sf, String newType, int newBegin,
+ int newEnd, String newGroup, float newScore)
{
- this(sf.getType(), sf.getDescription(), newBegin, newEnd, newScore,
+ this(newType, sf.getDescription(), newBegin, newEnd, newScore,
newGroup);
if (sf.otherDetails != null)
{
- otherDetails = new HashMap<String, Object>();
+ otherDetails = new HashMap<>();
for (Entry<String, Object> entry : sf.otherDetails.entrySet())
{
otherDetails.put(entry.getKey(), entry.getValue());
}
if (sf.links != null && sf.links.size() > 0)
{
- links = new Vector<String>();
+ links = new Vector<>();
for (int i = 0, iSize = sf.links.size(); i < iSize; i++)
{
links.addElement(sf.links.elementAt(i));
}
/**
+ * A copy constructor that allows the value of final fields to be 'modified'
+ *
+ * @param sf
+ * @param newBegin
+ * @param newEnd
+ * @param newGroup
+ * @param newScore
+ */
+ public SequenceFeature(SequenceFeature sf, int newBegin, int newEnd,
+ String newGroup, float newScore)
+ {
+ this(sf, sf.getType(), newBegin, newEnd, newGroup, newScore);
+ }
+
+ /**
* Two features are considered equal if they have the same type, group,
* description, start, end, phase, strand, and (if present) 'Name', ID' and
* 'Parent' attributes.
return false;
}
- if (!(type + description + featureGroup + getPhase()).equals(sf.type
- + sf.description + sf.featureGroup + sf.getPhase()))
+ if (!(type + description + featureGroup + getPhase()).equals(
+ sf.type + sf.description + sf.featureGroup + sf.getPhase()))
{
return false;
}
{
if (links == null)
{
- links = new Vector<String>();
+ links = new Vector<>();
}
if (!links.contains(labelLink))
{
if (otherDetails == null)
{
- otherDetails = new HashMap<String, Object>();
+ otherDetails = new HashMap<>();
}
otherDetails.put(key, value);
return begin == 0 && end == 0;
}
}
+
+class SFSortByEnd implements Comparator<SequenceFeature>
+{
+ @Override
+ public int compare(SequenceFeature a, SequenceFeature b)
+ {
+ return a.getEnd() - b.getEnd();
+ }
+}
+
+class SFSortByBegin implements Comparator<SequenceFeature>
+{
+ @Override
+ public int compare(SequenceFeature a, SequenceFeature b)
+ {
+ return a.getBegin() - b.getBegin();
+ }
+}