+/*\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
+\r
import java.awt.*;\r
\r
import java.util.Vector;\r
\r
+\r
public interface SequenceI {\r
- public void setName(String name);\r
- public String getName();\r
+ public void setName(String name);\r
+\r
+ public String getName();\r
+\r
+ public void setStart(int start);\r
+\r
+ public int getStart();\r
\r
- public void setStart(int start);\r
- public int getStart();\r
+ public String getDisplayId();\r
\r
- public String getDisplayId();\r
+ public void setEnd(int end);\r
\r
- public void setEnd(int end);\r
- public int getEnd();\r
+ public int getEnd();\r
\r
- public int getLength();\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
+ public void setSequence(String sequence);\r
\r
- public void setDescription(String desc);\r
- public String getDescription();\r
+ public String getSequence();\r
\r
- public int findIndex(int pos);\r
- public int findPosition(int i);\r
+ public String getSequence(int start, 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
+ public char getCharAt(int i);\r
\r
- public void setColor(Color c);\r
- public Color getColor();\r
+ public void setDescription(String desc);\r
\r
- public Vector getSequenceFeatures();\r
- public void setSequenceFeatures(Vector v);\r
+ public String getDescription();\r
\r
- public void setPDBId(String id);\r
- public String getPDBId();\r
+ public int findIndex(int pos);\r
\r
- }\r
+ public int findPosition(int i);\r
\r
+ public int[] gapMap();\r
\r
+ public void deleteChars(int i, int j);\r
\r
+ public void deleteCharAt(int i);\r
\r
+ public void insertCharAt(int i, char c);\r
\r
+ public void insertCharAt(int i, char c, boolean chop);\r
\r
+ public void setColor(Color c);\r
\r
+ public Color getColor();\r
\r
+ public Vector getSequenceFeatures();\r
\r
+ public void setSequenceFeatures(Vector v);\r
\r
+ public void setPDBId(String id);\r
\r
+ public String getPDBId();\r
+}\r