+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
+public interface SequenceI\r
+{\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param name DOCUMENT ME!\r
+ */\r
+ public void setName(String name);\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public String getName();\r
+\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param start DOCUMENT ME!\r
+ */\r
+ public void setStart(int start);\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public int getStart();\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public String getDisplayId(boolean jvsuffix);\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param end DOCUMENT ME!\r
+ */\r
+ public void setEnd(int end);\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public int getEnd();\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public int getLength();\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param sequence DOCUMENT ME!\r
+ */\r
+ public void setSequence(String sequence);\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public String getSequence();\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param start DOCUMENT ME!\r
+ * @param end DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public String getSequence(int start, int end);\r
+ /**\r
+ * create a new sequence object from start to end of this sequence\r
+ * @param start int\r
+ * @param end int\r
+ * @return SequenceI\r
+ */\r
+ public SequenceI getSubSequence(int start, int end);\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param i DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public char getCharAt(int i);\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param desc DOCUMENT ME!\r
+ */\r
+ public void setDescription(String desc);\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public String getDescription();\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param pos DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public int findIndex(int pos);\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param i DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public int findPosition(int i);\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public int[] gapMap();\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param i DOCUMENT ME!\r
+ * @param j DOCUMENT ME!\r
+ */\r
+ public void deleteChars(int i, int j);\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param i DOCUMENT ME!\r
+ */\r
+ public void deleteCharAt(int i);\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param i DOCUMENT ME!\r
+ * @param c DOCUMENT ME!\r
+ */\r
+ public void insertCharAt(int i, char c);\r
+\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param c DOCUMENT ME!\r
+ */\r
+ public void setColor(Color c);\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public Color getColor();\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public SequenceFeature[] getSequenceFeatures();\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param v DOCUMENT ME!\r
+ */\r
+ public void setSequenceFeatures(SequenceFeature [] features);\r