Package org.biojava.nbio.core.sequence.template

Interface LightweightProfile<S extends Sequence<C>,C extends Compound>

Type Parameters:

S - each element of the alignment profile is of type S

C - each element of an Sequence is a Compound of type C

All Known Implementing Classes:

MultipleSequenceAlignment

public interface LightweightProfile<S extends Sequence<C>,C extends Compound>

Defines a minimal data structure for reading and writing a sequence alignment. The full Profile data structure in the alignment module provides additional functionality.

Author:

Mark Chapman

Nested Class Summary

Nested Classes

Modifier and Type	Interface	Description
static class	LightweightProfile.StringFormat	List of output formats.

Method Summary

Modifier and Type	Method	Description
S	getAlignedSequence(int listIndex)	Returns Sequence at given index.
List<S>	getAlignedSequences()	Returns a List containing the individual Sequences of this alignment.
List<C>	getCompoundsAt(int alignmentIndex)	Returns the Compound elements of the original Sequences at the given column.
CompoundSet<C>	getCompoundSet()	Returns CompoundSet of all Sequences
int	getLength()	Returns the number of columns in the alignment profile.
int	getSize()	Returns the number of rows in this profile.
String	toString()	Returns a simple view of the alignment profile.
String	toString(int width)	Returns a formatted view of the alignment profile.
String	toString(LightweightProfile.StringFormat format)	Returns a formatted view of the alignment profile.

Method Detail

getAlignedSequence

S getAlignedSequence(int listIndex)

Returns Sequence at given index.

Parameters:

listIndex - index of sequence in profile

Returns:

desired sequence

Throws:

IndexOutOfBoundsException - if listIndex < 1 or listIndex > number of sequences

getAlignedSequences

List<S> getAlignedSequences()

Returns a List containing the individual Sequences of this alignment.

Returns:

list of aligned sequences

getCompoundsAt

List<C> getCompoundsAt(int alignmentIndex)

Returns the Compound elements of the original Sequences at the given column.

Parameters:

alignmentIndex - column index within an alignment

Returns:

the sequence elements

Throws:

IndexOutOfBoundsException - if alignmentIndex < 1 or alignmentIndex > getLength()

getCompoundSet

CompoundSet<C> getCompoundSet()

Returns CompoundSet of all Sequences

Returns:

set of Compounds in contained sequences

getLength

int getLength()

Returns the number of columns in the alignment profile.

Returns:

the number of columns

getSize

int getSize()

Returns the number of rows in this profile. If any Sequences are circular and overlap within the alignment, the returned size will be greater than the number of sequences, otherwise the numbers will be equal.

Returns:

number of rows

toString

String toString()

Returns a simple view of the alignment profile. This shows each sequence on a separate line (or multiple lines, if circular) and nothing more. This should result in getSize() lines with getLength() Compounds per line.

Overrides:

toString in class Object

Returns:

a simple view of the alignment profile

toString

String toString(int width)

Returns a formatted view of the alignment profile. This shows the start and end indices of the profile for each group of lines of the given width. Each line may also be labeled.

Parameters:

width - limit on the line length

Returns:

a formatted view of the alignment profile

toString

String toString(LightweightProfile.StringFormat format)

Returns a formatted view of the alignment profile. Details depend on the format given.

Parameters:

format - output format

Returns:

a formatted view of the alignment profile