+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
package jalview.datamodel;\r
\r
-import jalview.jbgui.*;\r
import java.awt.*;\r
\r
-import java.util.Vector;\r
+import java.util.*;\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
+ * 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
- public String getDisplayId();\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public String getName();\r
\r
- public void setEnd(int end);\r
- public int getEnd();\r
\r
- public int getLength();\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param start DOCUMENT ME!\r
+ */\r
+ public void setStart(int start);\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
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public int getStart();\r
\r
- public void setDescription(String desc);\r
- public String getDescription();\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public String getDisplayId(boolean jvsuffix);\r
\r
- public int findIndex(int pos);\r
- public int findPosition(int i);\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param end DOCUMENT ME!\r
+ */\r
+ public void setEnd(int end);\r
\r
- public void deleteChars(int i, int j);\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
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public int getEnd();\r
\r
- public void setColor(Color c);\r
- public Color getColor();\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public int getLength();\r
\r
- public Vector getSequenceFeatures();\r
- public void setSequenceFeatures(Vector v);\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param sequence DOCUMENT ME!\r
+ */\r
+ public void setSequence(String sequence);\r
\r
- public void setPDBId(String id);\r
- public String getPDBId();\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public String getSequence();\r
\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
+ /**\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
+\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 void addPDBId(PDBEntry entry);\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
+ public AlignmentAnnotation [] getAnnotation();\r
+\r
+ public void addAlignmentAnnotation(AlignmentAnnotation annotation);\r
+\r
+ public SequenceGroup getHiddenSequences();\r
+\r
+ public void addHiddenSequence(SequenceI seq);\r
+\r
+ public void showHiddenSequence(SequenceI seq);\r
+\r
+ public void changeCase(boolean toUpper, int start, int end);\r
+\r
+}\r