import java.util.*;
-import java.awt.*;
-
/**
* DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
- public String getSequence();
+ public String getSequenceAsString();
/**
* DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
- public String getSequence(int start, int end);
+ public String getSequenceAsString(int start, int end);
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public char [] getSequence();
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param start DOCUMENT ME!
+ * @param end DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public char [] getSequence(int start, int end);
/**
* create a new sequence object from start to end of this sequence
* @param start int
*/
public void deleteChars(int i, int j);
- /**
- * DOCUMENT ME!
- *
- * @param i DOCUMENT ME!
- */
- public void deleteCharAt(int i);
/**
* DOCUMENT ME!
public void insertCharAt(int i, int length, char c);
-
- /**
- * DOCUMENT ME!
- *
- * @param c DOCUMENT ME!
- */
- public void setColor(Color c);
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public Color getColor();
-
/**
* DOCUMENT ME!
*
public void addAlignmentAnnotation(AlignmentAnnotation annotation);
- public SequenceGroup getHiddenSequences();
-
- public void addHiddenSequence(SequenceI seq);
- public void showHiddenSequence(SequenceI seq);
+ /**
+ * Derive a sequence (using this one's dataset or as the dataset)
+ * @return duplicate sequence with valid dataset sequence
+ */
+ public SequenceI deriveSequence();
}