- /**
- * DOCUMENT ME!
- *
- * @param name DOCUMENT ME!
- */
- public void setName(String name);
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public String getName();
-
-
- /**
- * DOCUMENT ME!
- *
- * @param start DOCUMENT ME!
- */
- public void setStart(int start);
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int getStart();
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public String getDisplayId(boolean jvsuffix);
-
- /**
- * DOCUMENT ME!
- *
- * @param end DOCUMENT ME!
- */
- public void setEnd(int end);
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int getEnd();
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int getLength();
-
- /**
- * DOCUMENT ME!
- *
- * @param sequence DOCUMENT ME!
- */
- public void setSequence(String sequence);
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public String getSequence();
-
- /**
- * DOCUMENT ME!
- *
- * @param start DOCUMENT ME!
- * @param end DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public String getSequence(int start, int end);
- /**
- * create a new sequence object from start to end of this sequence
- * @param start int
- * @param end int
- * @return SequenceI
- */
- public SequenceI getSubSequence(int start, int end);
- /**
- * DOCUMENT ME!
- *
- * @param i DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public char getCharAt(int i);
-
- /**
- * DOCUMENT ME!
- *
- * @param desc DOCUMENT ME!
- */
- public void setDescription(String desc);
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public String getDescription();
-
- /**
- * DOCUMENT ME!
- *
- * @param pos DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int findIndex(int pos);
-
- /**
- * Returns the sequence position for an alignment position
- *
- * @param i column index in alignment (from 1)
- *
- * @return residue number for residue (left of and) nearest ith column
- */
- public int findPosition(int i);
-
- /**
- * Returns an int array where indices correspond to each residue in the sequence and the element value gives its position in the alignment
- *
- * @return int[SequenceI.getEnd()-SequenceI.getStart()+1] or null if no residues in SequenceI object
- */
- public int[] gapMap();
-
- /**
- * DOCUMENT ME!
- *
- * @param i DOCUMENT ME!
- * @param j DOCUMENT ME!
- */
- public void deleteChars(int i, int j);
-
- /**
- * DOCUMENT ME!
- *
- * @param i DOCUMENT ME!
- */
- public void deleteCharAt(int i);
-
- /**
- * DOCUMENT ME!
- *
- * @param i DOCUMENT ME!
- * @param c DOCUMENT ME!
- */
- public void insertCharAt(int i, char c);
-
-
- /**
- * DOCUMENT ME!
- *
- * @param c DOCUMENT ME!
- */
- public void setColor(Color c);
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public Color getColor();
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public SequenceFeature[] getSequenceFeatures();
-
- /**
- * DOCUMENT ME!
- *
- * @param v DOCUMENT ME!
- */
- public void setSequenceFeatures(SequenceFeature [] features);
-
- /**
- * DOCUMENT ME!
- *
- * @param id DOCUMENT ME!
- */
- public void setPDBId(Vector ids);
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public Vector getPDBId();
-
- public void addPDBId(PDBEntry entry);
-
- public String getVamsasId();
-
- public void setVamsasId(String id);
-
- public void setDBRef(DBRefEntry[] dbs);
-
- public DBRefEntry [] getDBRef();
-
- public void addDBRef(DBRefEntry entry);
-
- public void addSequenceFeature(SequenceFeature sf);