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[jalview.git]
/
src
/
jalview
/
datamodel
/
AlignmentI.java
diff --git
a/src/jalview/datamodel/AlignmentI.java
b/src/jalview/datamodel/AlignmentI.java
index
660a4fa
..
b46a1a7
100755
(executable)
--- a/
src/jalview/datamodel/AlignmentI.java
+++ b/
src/jalview/datamodel/AlignmentI.java
@@
-1,6
+1,5
@@
package jalview.datamodel;
\r
\r
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
import java.util.*;
\r
\r
/** Data structure to hold and manipulate a multiple sequence alignment
\r
@@
-11,6
+10,8
@@
public interface AlignmentI {
public int getWidth() ;
\r
public int getMaxIdLength() ;
\r
\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 Vector getSequences();
\r
public SequenceI getSequenceAt(int i);
\r
\r
@@
-29,7
+30,7
@@
public interface AlignmentI {
public void insertColumns(SequenceI[] seqs, int pos) ;
\r
\r
public SequenceI findName(String name) ;
\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
\r
public int findIndex(SequenceI s) ;
\r
\r
@@
-48,19
+49,28
@@
public interface AlignmentI {
public void addToGroup(SequenceGroup g, SequenceI s) ;
\r
public void removeFromGroup(SequenceGroup g,SequenceI s) ;
\r
public void addGroup(SequenceGroup sg) ;
\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 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
\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 void setGapCharacter(char gc);
\r
public char getGapCharacter();
\r
\r
- public Vector getAAFrequency();
\r
+ public Vector getAAFrequency();
\r
}
\r
\r
\r
}
\r
\r
\r