*
* @param sf
*/
- abstract boolean add(SequenceFeature sf);
+ boolean add(SequenceFeature sf);
/**
* Returns a (possibly empty) list of features, optionally restricted to
* @param type
* @return
*/
- abstract List<SequenceFeature> findFeatures(int from, int to,
+ List<SequenceFeature> findFeatures(int from, int to,
String... type);
/**
* @param type
* @return
*/
- abstract List<SequenceFeature> getAllFeatures(String... type);
+ List<SequenceFeature> getAllFeatures(String... type);
/**
* Answers the number of (positional or non-positional) features, optionally
* @param type
* @return
*/
- abstract int getFeatureCount(boolean positional, String... type);
+ int getFeatureCount(boolean positional, String... type);
/**
* Answers the total length of positional features, optionally restricted to
* @param type
* @return
*/
- abstract int getTotalFeatureLength(String... type);
+ int getTotalFeatureLength(String... type);
/**
* Answers a list of all positional features, optionally restricted to
* @param type
* @return
*/
- abstract List<SequenceFeature> getPositionalFeatures(
+ List<SequenceFeature> getPositionalFeatures(
String... type);
/**
*
* @return
*/
- abstract List<SequenceFeature> getContactFeatures(String... type);
+ List<SequenceFeature> getContactFeatures(String... type);
/**
* Answers a list of all non-positional features, optionally restricted to
* if no type is specified, all are returned
* @return
*/
- abstract List<SequenceFeature> getNonPositionalFeatures(
+ List<SequenceFeature> getNonPositionalFeatures(
String... type);
/**
*
* @param sf
*/
- abstract boolean delete(SequenceFeature sf);
+ boolean delete(SequenceFeature sf);
/**
* Answers true if this store contains at least one feature, else false
*
* @return
*/
- abstract boolean hasFeatures();
+ boolean hasFeatures();
/**
* Returns a set of the distinct feature groups present in the collection. The
* @param type
* @return
*/
- abstract Set<String> getFeatureGroups(boolean positionalFeatures,
+ Set<String> getFeatureGroups(boolean positionalFeatures,
String... type);
/**
* @param groups
* @return
*/
- abstract Set<String> getFeatureTypesForGroups(
+ Set<String> getFeatureTypesForGroups(
boolean positionalFeatures, String... groups);
/**
*
* @return
*/
- abstract Set<String> getFeatureTypes();
+ Set<String> getFeatureTypes();
+ /**
+ * Answers the minimum score held for positional or non-positional features
+ * for the specified type. This may be Float.NaN if there are no features, or
+ * none has a non-NaN score.
+ *
+ * @param type
+ * @param positional
+ * @return
+ */
+ float getMinimumScore(String type, boolean positional);
+
+ /**
+ * Answers the maximum score held for positional or non-positional features
+ * for the specified type. This may be Float.NaN if there are no features, or
+ * none has a non-NaN score.
+ *
+ * @param type
+ * @param positional
+ * @return
+ */
+ float getMaximumScore(String type, boolean positional);
}
\ No newline at end of file