*/
package jalview.datamodel;
+import jalview.datamodel.Sequence.DBModList;
import jalview.datamodel.features.SequenceFeaturesI;
import jalview.util.MapList;
import jalview.ws.params.InvalidArgumentException;
* get a range on the sequence as a string
*
* @param start
- * position relative to start of sequence including gaps (from 0)
+ * (inclusive) position relative to start of sequence including gaps
+ * (from 0)
* @param end
- * position relative to start of sequence including gaps (from 0)
+ * (exclusive) position relative to start of sequence including gaps
+ * (from 0)
*
* @return String containing all gap and symbols in specified range
*/
* - last column, base 1
* @return
*/
- public Range findPositions(int fromColum, int toColumn);
+ public ContiguousI findPositions(int fromColum, int toColumn);
/**
* Returns an int array where indices correspond to each residue in the
/**
* set the array of Database references for the sequence.
*
- * BH 2019.01.25 added throw
+ * BH 2019.02.04 changes param to DBModlist
*
* @param dbs
- * @throws InvalidArgumentException
* @deprecated - use is discouraged since side-effects may occur if DBRefEntry
* set are not normalised.
* @throws InvalidArgumentException if the is not one created by Sequence itself
*/
@Deprecated
- public void setDBRefs(List<DBRefEntry> dbs) throws InvalidArgumentException;
+ public void setDBRefs(DBModList<DBRefEntry> dbs);
- public List<DBRefEntry> getDBRefs();
-
- public void getDBRefsFrom(SequenceI seq);
+ public DBModList<DBRefEntry> getDBRefs();
/**
* add the given entry to the list of DBRefs for this sequence, or replace a
*/
public int firstResidueOutsideIterator(Iterator<int[]> it);
+ /**
+ * @author Bob Hanson 2019.07.30
+ *
+ * get a 4-byte color, with caching
+ *
+ */
+ public int getColor(int i);
+
+ /**
+ * @author Bob Hanson 2019.07.30
+ *
+ * set a 4-byte color, with caching
+ *
+ */
+ public int setColor(int i, int argb);
+
+ /**
+ * @author Bob Hanson 2019.07.30
+ *
+ * allows resetting the color cache
+ *
+ */
+ public void resetColors();
+
+ /**
+ * allows passing the result ArrayList as a parameter to avoid unnecessary
+ * construction
+ *
+ * @author Bob Hanson 2019.07.30
+ *
+ *
+ */
+ List<SequenceFeature> findFeatures(int column, String type,
+ List<SequenceFeature> result);
+
+ /**
+ * allows early intervention for renderer if false
+ *
+ * @author Bob Hanson 2019.07.30
+ *
+ */
+ public boolean hasFeatures(String type);
+
}