Alignment

All Superinterfaces:

IdGroup, java.io.Serializable

All Known Subinterfaces:

AnnotationAlignment

All Known Implementing Classes:

AbstractAlignment, AlignmentReaders.PhylipClustalAlignment, AlignmentReaders.UnalignedAlignment, BootstrappedAlignment, ConcatenatedAlignment, ConcatenatedAnnotatedAlignment, GapBalancedAlignment, IndelAlignment, IndelAnnotatedAlignment, JumbledAlignment, MultiLocusAnnotatedAlignment, ReadAlignment, ReadAlignmentOld, SimpleAlignment, SimpleAnnotatedAlignment, SimulatedAlignment, SitePattern, StrippedAlignment, StrippedAnnotatedAlignment
```
public interface Alignment
extends java.io.Serializable, IdGroup
```
interface for any alignment data.

Version:

$Id: Alignment.java,v 1.15 2003/03/23 00:12:57 matt Exp $

Author:

Alexei Drummond, Korbinian Strimmer

Nested Class Summary
- Nested classes/interfaces inherited from interface pal.misc.IdGroup
  IdGroup.Utils

Field Summary

Fields
Modifier and Type	Field	Description
`static char`	`GAP`	character used to designate gaps
`static java.lang.String`	`GAP_TLA`	A three letter acronym version of a gap.
`static java.lang.String`	`GAPS`	Characters that might be used as gaps
`static char`	`UNKNOWN`	character used to designate unknown characters
`static java.lang.String`	`UNKNOWN_TLA`	character used to designate unknown characters

Method Summary

All Methods Instance Methods Abstract Methods
Modifier and Type	Method	Description
`java.lang.String`	`getAlignedSequenceString(int sequence)`	Returns string representation of single sequence in alignment with gap characters included.
`char`	`getData(int seq, int site)`	sequence alignment at (sequence, site)
`DataType`	`getDataType()`	Return DataType of this alignment.
`int`	`getSequenceCount()`	Return number of sequences in this alignment
`int`	`getSiteCount()`

Methods inherited from interface pal.misc.IdGroup
getIdCount, getIdentifier, setIdentifier, whichIdNumber

- Field Detail
  - GAP
```
static final char GAP
```
    character used to designate gaps
    
    See Also:
    
    Constant Field Values
  - UNKNOWN
```
static final char UNKNOWN
```
    character used to designate unknown characters
    
    See Also:
    
    Constant Field Values
  - UNKNOWN_TLA
```
static final java.lang.String UNKNOWN_TLA
```
    character used to designate unknown characters
    
    See Also:
    
    Constant Field Values
  - GAP_TLA
```
static final java.lang.String GAP_TLA
```
    A three letter acronym version of a gap.
    
    See Also:
    
    Constant Field Values
  - GAPS
```
static final java.lang.String GAPS
```
    Characters that might be used as gaps
    
    See Also:
    
    Constant Field Values
- Method Detail
  - getData
```
char getData(int seq,
             int site)
```
    sequence alignment at (sequence, site)
  - getSiteCount
```
int getSiteCount()
```
    Returns:
    
    number of sites for each sequence in this alignment
  - getSequenceCount
```
int getSequenceCount()
```
    Return number of sequences in this alignment
  - getDataType
```
DataType getDataType()
```
    Return DataType of this alignment.
  - getAlignedSequenceString
```
java.lang.String getAlignedSequenceString(int sequence)
```
    Returns string representation of single sequence in alignment with gap characters included.