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Public Member Functions | Static Public Member Functions | Public Attributes | Static Public Attributes | Protected Attributes | Package Attributes | Private Member Functions

jalview::datamodel::Alignment Class Reference

Inheritance diagram for jalview::datamodel::Alignment:
Inheritance graph
Collaboration diagram for jalview::datamodel::Alignment:
Collaboration graph

List of all members.

Public Member Functions

void addAnnotation (AlignmentAnnotation aa)
void addAnnotation (AlignmentAnnotation aa, int pos)
void addCodonFrame (AlignedCodonFrame codons)
void addGroup (SequenceGroup sg)
void addSequence (SequenceI snew)
 Alignment (SeqCigar[] alseqs)
 Alignment (SequenceI[] seqs)
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)
void finalize ()
SequenceGroup[] findAllGroups (SequenceI s)
SequenceGroup findGroup (SequenceI s)
int findIndex (SequenceI s)
int findIndex (SearchResults results)
SequenceI findName (String name)
SequenceI findName (String token, boolean b)
SequenceI findName (SequenceI startAfter, String token, boolean b)
SequenceI[] findSequenceMatch (String name)
AlignmentAnnotation[] getAlignmentAnnotation ()
AlignedCodonFrame getCodonFrame (int index)
AlignedCodonFrame[] getCodonFrame (SequenceI seq)
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 isAligned (boolean includeHidden)
boolean isNucleotide ()
boolean justify (boolean right)
boolean padGaps ()
boolean removeCodonFrame (AlignedCodonFrame codons)
void setAnnotationIndex (AlignmentAnnotation aa, int index)
void setDataset (Alignment data)
void setGapCharacter (char gc)
void setNucleotide (boolean b)
void setProperty (Object key, Object value)
void setSequenceAt (int i, SequenceI snew)

Static Public Member Functions

static AlignmentI createAlignment (CigarArray compactAlignment)

Public Attributes

Hashtable alignmentProperties
AlignmentAnnotation[] annotations

Static Public Attributes

static final int NUCLEOTIDE = 1
static final int PROTEIN = 0

Protected Attributes

Alignment dataset
char gapCharacter = '-'
Vector groups = new Vector()
Vector sequences
int type = NUCLEOTIDE

Package Attributes

int alignmentRefs = 0
AlignedCodonFrame[] codonFrameList = null
HiddenSequences hiddenSequences = new HiddenSequences(this)

Private Member Functions

void addAlignmentRef ()
void initAlignment (SequenceI[] seqs)
void removeAlignmentRef ()
void removeAnnotationForGroup (SequenceGroup gp)
void unhookAnnotation (AlignmentAnnotation aa)

Detailed Description

Data structure to hold and manipulate a multiple sequence alignment


Definition at line 31 of file Alignment.java.

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

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