package jalview.datamodel;\r
\r
-import jalview.jbgui.*;\r
import java.util.*;\r
\r
/** Data structure to hold and manipulate a multiple sequence alignment\r
public int getWidth() ;\r
public int getMaxIdLength() ;\r
\r
+ public boolean isAligned();\r
+\r
public Vector getSequences();\r
public SequenceI getSequenceAt(int i);\r
\r
public void sortByPID(SequenceI s) ;\r
public void sortByID() ;\r
\r
+ //Annotations\r
+ public void addAnnotation(AlignmentAnnotation aa);\r
+ public void deleteAnnotation(AlignmentAnnotation aa);\r
+ public AlignmentAnnotation [] getAlignmentAnnotation();\r
+\r
public void setGapCharacter(char gc);\r
public char getGapCharacter();\r
\r
- public Vector getAAFrequency();\r
+ public Vector getAAFrequency();\r
}\r
\r
\r