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 are final to ensure that
- * the integrity of SequenceFeatures data store can't be
- * broken by direct update of these fields
+ * 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
*/
public final String type;
public final String featureGroup;
- public float score;
+ public final float score;
+
+ private final boolean contactFeature;
public String description;
*/
public SequenceFeature(SequenceFeature cpy)
{
- this(cpy, cpy.getBegin(), cpy.getEnd(), cpy.getFeatureGroup());
+ this(cpy, cpy.getBegin(), cpy.getEnd(), cpy.getFeatureGroup(), cpy
+ .getScore());
}
/**
public SequenceFeature(String theType, String theDesc, int theBegin,
int theEnd, String group)
{
- this.type = theType;
- this.description = theDesc;
- this.begin = theBegin;
- this.end = theEnd;
- this.featureGroup = group;
- this.score = NO_SCORE;
+ this(theType, theDesc, theBegin, theEnd, NO_SCORE, group);
}
/**
public SequenceFeature(String theType, String theDesc, int theBegin,
int theEnd, float theScore, String group)
{
- this(theType, theDesc, theBegin, theEnd, group);
+ this.type = theType;
+ this.description = theDesc;
+ this.begin = theBegin;
+ this.end = theEnd;
+ this.featureGroup = group;
this.score = theScore;
+
+ /*
+ * for now, only "Disulfide/disulphide bond" is treated as a contact feature
+ */
+ this.contactFeature = "disulfide bond".equalsIgnoreCase(type)
+ || "disulphide bond".equalsIgnoreCase(type);
}
/**
- * A copy constructor that allows the begin and end positions and group to be
- * modified
+ * 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)
+ public SequenceFeature(SequenceFeature sf, String newType, int newBegin,
+ int newEnd, String newGroup, float newScore)
{
- this(sf.getType(), newBegin, newEnd, newGroup);
- score = sf.score;
- description = sf.description;
+ 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));
}
/**
- * Constructor that sets the final fields type, begin, end, group
+ * A copy constructor that allows the value of final fields to be 'modified'
*
- * @param theType
- * @param theBegin
- * @param theEnd
- * @param theGroup
+ * @param sf
+ * @param newBegin
+ * @param newEnd
+ * @param newGroup
+ * @param newScore
*/
- private SequenceFeature(String theType, int theBegin, int theEnd,
- String theGroup)
+ public SequenceFeature(SequenceFeature sf, int newBegin, int newEnd,
+ String newGroup, float newScore)
{
- type = theType;
- begin = theBegin;
- end = theEnd;
- featureGroup = theGroup;
+ this(sf, sf.getType(), newBegin, newEnd, newGroup, newScore);
}
/**
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))
return score;
}
- public void setScore(float value)
- {
- score = value;
- }
-
/**
* Used for getting values which are not in the basic set. eg STRAND, PHASE
* for GFF file
{
if (otherDetails == null)
{
- otherDetails = new HashMap<String, Object>();
+ otherDetails = new HashMap<>();
}
otherDetails.put(key, value);
@Override
public boolean isContactFeature()
{
- // TODO abstract one day to a FeatureType class
- if ("disulfide bond".equalsIgnoreCase(type)
- || "disulphide bond".equalsIgnoreCase(type))
- {
- return true;
- }
- return false;
+ return contactFeature;
}
/**
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();
+ }
+}