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 insertColumns(SequenceI[] seqs, int pos) ;\r
\r
public SequenceI findName(String name) ;\r
- public SequenceI findbyDisplayId(String name);\r
+ public SequenceI findbyDisplayId(String name);\r
\r
public int findIndex(SequenceI s) ;\r
\r
public void addToGroup(SequenceGroup g, SequenceI s) ;\r
public void removeFromGroup(SequenceGroup g,SequenceI s) ;\r
public void addGroup(SequenceGroup sg) ;\r
- public SequenceGroup addGroup() ;\r
public void deleteGroup(SequenceGroup g) ;\r
public Vector getGroups();\r
+ public void deleteAllGroups();\r
+\r
+ public void addSuperGroup(SuperGroup sg);\r
+ public void removeSuperGroup(SuperGroup sg);\r
+ public SuperGroup getSuperGroup(SequenceGroup sg);\r
\r
// Sorting\r
public void sortGroups() ;\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