Package org.biojava.nbio.core.alignment.template

Interface Profile<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 AlignedSequence is a Compound of type C

All Superinterfaces:

Iterable<AlignedSequence<S,C>>

All Known Subinterfaces:

MutableProfile<S,C>, MutableProfilePair<S,C>, MutableSequencePair<S,C>, ProfilePair<S,C>, ProfileView<S,C>, SequencePair<S,C>

All Known Implementing Classes:

SimpleProfile, SimpleProfilePair, SimpleSequencePair

public interface Profile<S extends Sequence<C>,C extends Compound>
extends Iterable<AlignedSequence<S,C>>

Defines a data structure for the results of sequence alignment. Every List returned is unmodifiable unless the class implements the subinterface MutableProfile.

Author:

Mark Chapman, Paolo Pavan

Nested Class Summary

Nested Classes

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

Method Summary

Modifier and Type	Method	Description
AlignedSequence<S,C>	getAlignedSequence(int listIndex)	Returns AlignedSequence at given index.
AlignedSequence<S,C>	getAlignedSequence(S sequence)	Searches for the given Sequence within this alignment profile.
List<AlignedSequence<S,C>>	getAlignedSequences()	Returns a List containing the individual AlignedSequences of this alignment.
List<AlignedSequence<S,C>>	getAlignedSequences(int... listIndices)	Returns a List containing some of the individual AlignedSequences of this alignment.
List<AlignedSequence<S,C>>	getAlignedSequences(S... sequences)	Returns a List containing some of the individual AlignedSequences of this alignment.
C	getCompoundAt(int listIndex, int alignmentIndex)	Returns the Compound at row of given sequence and column of alignment index.
C	getCompoundAt(S sequence, int alignmentIndex)	Returns the Compound at row of given sequence and column of alignment index.
int[]	getCompoundCountsAt(int alignmentIndex)	Returns the number of each Compound in the given column for all compounds in CompoundSet.
int[]	getCompoundCountsAt(int alignmentIndex, List<C> compounds)	Returns the number of each Compound in the given column only for compounds in the given list.
List<C>	getCompoundsAt(int alignmentIndex)	Returns the Compound elements of the original Sequences at the given column.
CompoundSet<C>	getCompoundSet()	Returns CompoundSet of all AlignedSequences
float[]	getCompoundWeightsAt(int alignmentIndex)	Returns the fraction of each Compound in the given column for all compounds in CompoundSet.
float[]	getCompoundWeightsAt(int alignmentIndex, List<C> compounds)	Returns the fraction of each Compound in the given column only for compounds in the given list.
int	getIndexOf(C compound)	Searches for the given Compound within this alignment profile.
int[]	getIndicesAt(int alignmentIndex)	Returns the indices in the original Sequences corresponding to the given column.
int	getLastIndexOf(C compound)	Searches for the given Compound within this alignment profile.
int	getLength()	Returns the number of columns in the alignment profile.
List<S>	getOriginalSequences()	Returns a List containing the original Sequences used for alignment.
int	getSize()	Returns the number of rows in this profile.
ProfileView<S,C>	getSubProfile(Location location)	Returns a ProfileView windowed to contain only the given Location.
boolean	hasGap(int alignmentIndex)	Returns true if any AlignedSequence has a gap at the given index.
boolean	isCircular()	Returns true if any AlignedSequence is circular.
String	toString()	Returns a simple view of the alignment profile.
String	toString(int width)	Returns a formatted view of the alignment profile.
String	toString(Profile.StringFormat format)	Returns a formatted view of the alignment profile.

Methods inherited from interface java.lang.Iterable

forEach, iterator, spliterator

Method Detail

getAlignedSequence

AlignedSequence<S,C> getAlignedSequence(int listIndex)

Returns AlignedSequence at given index.

Parameters:

listIndex - index of sequence in profile

Returns:

desired sequence

Throws:

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

getAlignedSequence

AlignedSequence<S,C> getAlignedSequence(S sequence)

Searches for the given Sequence within this alignment profile. Returns the corresponding AlignedSequence.

Parameters:

sequence - an original Sequence

Returns:

the corresponding AlignedSequence

getAlignedSequences

List<AlignedSequence<S,C>> getAlignedSequences()

Returns a List containing the individual AlignedSequences of this alignment.

Returns:

list of aligned sequences

getAlignedSequences

List<AlignedSequence<S,C>> getAlignedSequences(int... listIndices)

Returns a List containing some of the individual AlignedSequences of this alignment.

Parameters:

listIndices - indices of sequences in profile

Returns:

list of aligned sequences

getAlignedSequences

List<AlignedSequence<S,C>> getAlignedSequences(S... sequences)

Returns a List containing some of the individual AlignedSequences of this alignment.

Parameters:

sequences - original Sequences

Returns:

list of aligned sequences

getCompoundAt

C getCompoundAt(int listIndex,
                int alignmentIndex)

Returns the Compound at row of given sequence and column of alignment index. If the given sequence has overlap, this will return the Compound from the top row of the sequence.

Parameters:

listIndex - index of sequence in profile

alignmentIndex - column index within an alignment

Returns:

the sequence element

Throws:

IndexOutOfBoundsException - if listIndex < 1, listIndex > number of sequences, alignmentIndex < 1, or alignmentIndex > getLength()

getCompoundAt

C getCompoundAt(S sequence,
                int alignmentIndex)

Returns the Compound at row of given sequence and column of alignment index. If the given sequence has overlap, this will return the Compound from the top row of the sequence.

Parameters:

sequence - either an AlignedSequence or an original Sequence

alignmentIndex - column index within an alignment

Returns:

the sequence element

Throws:

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

getCompoundCountsAt

int[] getCompoundCountsAt(int alignmentIndex)

Returns the number of each Compound in the given column for all compounds in CompoundSet.

Parameters:

alignmentIndex - column index within an alignment

Returns:

list of counts

Throws:

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

getCompoundCountsAt

int[] getCompoundCountsAt(int alignmentIndex,
                          List<C> compounds)

Returns the number of each Compound in the given column only for compounds in the given list.

Parameters:

alignmentIndex - column index within an alignment

compounds - list of compounds to count

Returns:

corresponding list of counts

Throws:

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

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 AlignedSequences

Returns:

set of Compounds in contained sequences

getCompoundWeightsAt

float[] getCompoundWeightsAt(int alignmentIndex)

Returns the fraction of each Compound in the given column for all compounds in CompoundSet.

Parameters:

alignmentIndex - column index within an alignment

Returns:

list of fractional weights

Throws:

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

getCompoundWeightsAt

float[] getCompoundWeightsAt(int alignmentIndex,
                             List<C> compounds)

Returns the fraction of each Compound in the given column only for compounds in the given list.

Parameters:

alignmentIndex - column index within an alignment

compounds - list of compounds to count

Returns:

corresponding list of fractional weights

Throws:

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

getIndicesAt

int[] getIndicesAt(int alignmentIndex)

Returns the indices in the original Sequences corresponding to the given column. All indices are 1-indexed and inclusive.

Parameters:

alignmentIndex - column index within an alignment

Returns:

the sequence indices

Throws:

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

getIndexOf

int getIndexOf(C compound)

Searches for the given Compound within this alignment profile. Returns column index nearest to the start of the alignment profile, or -1 if not found.

Parameters:

compound - search element

Returns:

index of column containing search element nearest to the start of the alignment profile

getLastIndexOf

int getLastIndexOf(C compound)

Searches for the given Compound within this alignment profile. Returns column index nearest to the end of the alignment profile, or -1 if not found.

Parameters:

compound - search element

Returns:

index of column containing search element nearest to the end of the alignment profile

getLength

int getLength()

Returns the number of columns in the alignment profile.

Returns:

the number of columns

getOriginalSequences

List<S> getOriginalSequences()

Returns a List containing the original Sequences used for alignment.

Returns:

list of original sequences

getSize

int getSize()

Returns the number of rows in this profile. If any AlignedSequences 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

getSubProfile

ProfileView<S,C> getSubProfile(Location location)

Returns a ProfileView windowed to contain only the given Location. This only includes the AlignedSequences which overlap the location.

Parameters:

location - portion of profile to view

Returns:

a windowed view of the profile

Throws:

IllegalArgumentException - if location is invalid

hasGap

boolean hasGap(int alignmentIndex)

Returns true if any AlignedSequence has a gap at the given index.

Parameters:

alignmentIndex - column index within an alignment

Returns:

true if any AlignedSequence has a gap at the given index

Throws:

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

isCircular

boolean isCircular()

Returns true if any AlignedSequence is circular. If so, sequences may simply wrap around from the end to the start of the alignment or they may contribute multiple overlapping lines to the profile.

Returns:

true if any AlignedSequence is circular

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 and each sequence 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(Profile.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