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Public Member Functions

jalview::datamodel::AlignmentI Interface Reference

Inheritance diagram for jalview::datamodel::AlignmentI:
Inheritance graph

List of all members.

Public Member Functions

void addAnnotation (AlignmentAnnotation aa)
void addAnnotation (AlignmentAnnotation consensus, int i)
void addCodonFrame (AlignedCodonFrame codons)
void addGroup (SequenceGroup sg)
void addSequence (SequenceI seq)
void append (AlignmentI toappend)
void deleteAllGroups ()
boolean deleteAnnotation (AlignmentAnnotation aa)
boolean deleteAnnotation (AlignmentAnnotation aa, boolean unhook)
void deleteGroup (SequenceGroup g)
void deleteSequence (SequenceI s)
void deleteSequence (int i)
SequenceGroup[] findAllGroups (SequenceI s)
SequenceGroup findGroup (SequenceI s)
int findIndex (SearchResults results)
int findIndex (SequenceI s)
SequenceI findName (String token, boolean b)
SequenceI findName (SequenceI startAfter, String token, boolean b)
SequenceI findName (String name)
SequenceI[] findSequenceMatch (String name)
AlignmentAnnotation[] getAlignmentAnnotation ()
AlignedCodonFrame[] getCodonFrame (SequenceI seq)
AlignedCodonFrame getCodonFrame (int index)
AlignedCodonFrame[] getCodonFrames ()
CigarArray getCompactAlignment ()
Alignment getDataset ()
char getGapCharacter ()
Vector getGroups ()
int getHeight ()
HiddenSequences getHiddenSequences ()
Hashtable getProperties ()
Object getProperty (Object key)
SequenceI getSequenceAt (int i)
Vector getSequences ()
SequenceI[] getSequencesArray ()
int getWidth ()
boolean isAligned (boolean includeHidden)
boolean isAligned ()
boolean isNucleotide ()
boolean justify (boolean right)
boolean padGaps ()
boolean removeCodonFrame (AlignedCodonFrame codons)
void setAnnotationIndex (AlignmentAnnotation aa, int index)
void setDataset (Alignment dataset)
void setGapCharacter (char gc)
void setNucleotide (boolean b)
void setProperty (Object key, Object value)
void setSequenceAt (int i, SequenceI seq)

Detailed Description

Data structure to hold and manipulate a multiple sequence alignment

Definition at line 25 of file AlignmentI.java.

The documentation for this interface was generated from the following file:

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