-import java.util.Vector;\r
-\r
-public interface SequenceI {\r
- public void setName(String name);\r
- public String getName();\r
-\r
- public void setStart(int start);\r
- public int getStart();\r
-\r
- public String getDisplayId();\r
-\r
- public void setEnd(int end);\r
- public int getEnd();\r
-\r
- public int getLength();\r
-\r
- public void setSequence(String sequence);\r
- public String getSequence();\r
- public String getSequence(int start,int end);\r
- public char getCharAt(int i);\r
-\r
- public void setDescription(String desc);\r
- public String getDescription();\r
-\r
- public int findIndex(int pos);\r
- public int findPosition(int i);\r
-\r
- public void deleteCharAt(int i);\r
- public void insertCharAt(int i, char c);\r
- public void insertCharAt(int i,char c,boolean chop);\r
-\r
- public void setColor(Color c);\r
- public Color getColor();\r
- }\r
-\r
-\r
-\r
-\r
-\r
-\r
-\r
-\r
-\r
-\r
-\r
+import java.util.*;\r
+\r
+\r
+/**\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
+ * 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 dbref, 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
+ /**\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
+ * DOCUMENT ME!\r
+ *\r
+ * @param i DOCUMENT ME!\r
+ * @param c DOCUMENT ME!\r
+ * @param chop DOCUMENT ME!\r
+ */\r
+ public void insertCharAt(int i, char c, boolean chop);\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 Vector getSequenceFeatures();\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param v DOCUMENT ME!\r
+ */\r
+ public void setSequenceFeatures(Vector v);\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param id DOCUMENT ME!\r
+ */\r
+ public void setPDBId(Vector ids);\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public Vector getPDBId();\r
+\r
+ public String getVamsasId();\r
+\r
+ public void setVamsasId(String id);\r
+\r
+ public void setDBRef(Vector dbs);\r
+\r
+ public Vector getDBRef();\r
+\r
+ public void addDBRef(DBRefEntry entry);\r
+\r
+ public void addSequenceFeature(SequenceFeature sf);\r
+\r
+ public void setDatasetSequence(SequenceI seq);\r
+\r
+ public SequenceI getDatasetSequence();\r
+}\r