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java.lang.Objectorg.biojava3.alignment.SimpleProfile<S,C>
S
- each element of the alignment Profile
is of type SC
- each element of an AlignedSequence
is a Compound
of type Cpublic class SimpleProfile<S extends Sequence<C>,C extends Compound>
Implements a data structure for the results of sequence alignment. Every List
returned is unmodifiable.
Nested Class Summary |
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Nested classes/interfaces inherited from interface org.biojava3.alignment.template.Profile |
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Profile.StringFormat |
Field Summary | |
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protected static SubstitutionMatrix<AminoAcidCompound> |
matrix
|
Constructor Summary | |
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protected |
SimpleProfile(AlignedSequence<S,C> query,
AlignedSequence<S,C> target)
Creates a pair profile for the given already aligned sequences. |
protected |
SimpleProfile(Profile<S,C> query,
Profile<S,C> target,
List<AlignedSequence.Step> sx,
List<AlignedSequence.Step> sy)
Creates a pair profile for the given profiles. |
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SimpleProfile(S sequence)
Creates a profile from a single sequence. |
protected |
SimpleProfile(S query,
S target,
List<AlignedSequence.Step> sx,
int xb,
int xa,
List<AlignedSequence.Step> sy,
int yb,
int ya)
Creates a pair profile for the given sequences. |
Method Summary | |
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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 AlignedSequence s of this alignment. |
List<AlignedSequence<S,C>> |
getAlignedSequences(int... listIndices)
Returns a List containing some of the individual AlignedSequence s of this alignment. |
List<AlignedSequence<S,C>> |
getAlignedSequences(S... sequences)
Returns a List containing some of the individual AlignedSequence s 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 Sequence s at the given column. |
CompoundSet<C> |
getCompoundSet()
Returns CompoundSet of all AlignedSequence s |
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 Sequence s 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 Sequence s 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. |
Iterator<AlignedSequence<S,C>> |
iterator()
|
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 class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Field Detail |
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protected static final SubstitutionMatrix<AminoAcidCompound> matrix
Constructor Detail |
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protected SimpleProfile(AlignedSequence<S,C> query, AlignedSequence<S,C> target)
query
- the first sequence of the pairtarget
- the second sequence of the pair
IllegalArgumentException
- if sequences differ in sizepublic SimpleProfile(S sequence)
sequence
- sequence to seed profileprotected SimpleProfile(S query, S target, List<AlignedSequence.Step> sx, int xb, int xa, List<AlignedSequence.Step> sy, int yb, int ya)
query
- the first sequence of the pairtarget
- the second sequence of the pairsx
- lists whether the query sequence aligns a Compound
or gap at each index of the alignmentxb
- number of Compound
s skipped in the query sequence before the aligned regionxa
- number of Compound
s skipped in the query sequence after the aligned regionsy
- lists whether the target sequence aligns a Compound
or gap at each index of the alignmentyb
- number of Compound
s skipped in the target sequence before the aligned regionya
- number of Compound
s skipped in the target sequence after the aligned region
IllegalArgumentException
- if alignments differ in size or given sequences do not fit in alignmentsprotected SimpleProfile(Profile<S,C> query, Profile<S,C> target, List<AlignedSequence.Step> sx, List<AlignedSequence.Step> sy)
query
- the first profile of the pairtarget
- the second profile of the pairsx
- lists whether the query profile aligns a Compound
or gap at each index of the alignmentsy
- lists whether the target profile aligns a Compound
or gap at each index of the alignment
IllegalArgumentException
- if alignments differ in size or given profiles do not fit in alignmentsMethod Detail |
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public AlignedSequence<S,C> getAlignedSequence(int listIndex)
Profile
AlignedSequence
at given index.
getAlignedSequence
in interface Profile<S extends Sequence<C>,C extends Compound>
listIndex
- index of sequence in profile
public AlignedSequence<S,C> getAlignedSequence(S sequence)
Profile
Sequence
within this alignment profile. Returns the corresponding
AlignedSequence
.
getAlignedSequence
in interface Profile<S extends Sequence<C>,C extends Compound>
sequence
- an original Sequence
AlignedSequence
public List<AlignedSequence<S,C>> getAlignedSequences()
Profile
List
containing the individual AlignedSequence
s of this alignment.
getAlignedSequences
in interface Profile<S extends Sequence<C>,C extends Compound>
public List<AlignedSequence<S,C>> getAlignedSequences(int... listIndices)
Profile
List
containing some of the individual AlignedSequence
s of this alignment.
getAlignedSequences
in interface Profile<S extends Sequence<C>,C extends Compound>
listIndices
- indices of sequences in profile
public List<AlignedSequence<S,C>> getAlignedSequences(S... sequences)
Profile
List
containing some of the individual AlignedSequence
s of this alignment.
getAlignedSequences
in interface Profile<S extends Sequence<C>,C extends Compound>
sequences
- original Sequence
s
public C getCompoundAt(int listIndex, int alignmentIndex)
Profile
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.
getCompoundAt
in interface Profile<S extends Sequence<C>,C extends Compound>
listIndex
- index of sequence in profilealignmentIndex
- column index within an alignment
public C getCompoundAt(S sequence, int alignmentIndex)
Profile
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.
getCompoundAt
in interface Profile<S extends Sequence<C>,C extends Compound>
sequence
- either an AlignedSequence
or an original Sequence
alignmentIndex
- column index within an alignment
public int[] getCompoundCountsAt(int alignmentIndex)
Profile
Compound
in the given column for all compounds in CompoundSet
.
getCompoundCountsAt
in interface Profile<S extends Sequence<C>,C extends Compound>
alignmentIndex
- column index within an alignment
public int[] getCompoundCountsAt(int alignmentIndex, List<C> compounds)
Profile
Compound
in the given column only for compounds in the given list.
getCompoundCountsAt
in interface Profile<S extends Sequence<C>,C extends Compound>
alignmentIndex
- column index within an alignmentcompounds
- list of compounds to count
public List<C> getCompoundsAt(int alignmentIndex)
Profile
Compound
elements of the original Sequence
s at the given column.
getCompoundsAt
in interface Profile<S extends Sequence<C>,C extends Compound>
alignmentIndex
- column index within an alignment
public CompoundSet<C> getCompoundSet()
Profile
CompoundSet
of all AlignedSequence
s
getCompoundSet
in interface Profile<S extends Sequence<C>,C extends Compound>
Compound
s in contained sequencespublic float[] getCompoundWeightsAt(int alignmentIndex)
Profile
Compound
in the given column for all compounds in CompoundSet
.
getCompoundWeightsAt
in interface Profile<S extends Sequence<C>,C extends Compound>
alignmentIndex
- column index within an alignment
public float[] getCompoundWeightsAt(int alignmentIndex, List<C> compounds)
Profile
Compound
in the given column only for compounds in the given list.
getCompoundWeightsAt
in interface Profile<S extends Sequence<C>,C extends Compound>
alignmentIndex
- column index within an alignmentcompounds
- list of compounds to count
public int getIndexOf(C compound)
Profile
Compound
within this alignment profile. Returns column index nearest to the
start of the alignment profile, or -1 if not found.
getIndexOf
in interface Profile<S extends Sequence<C>,C extends Compound>
compound
- search element
public int[] getIndicesAt(int alignmentIndex)
Profile
Sequence
s corresponding to the given column. All indices are
1-indexed and inclusive.
getIndicesAt
in interface Profile<S extends Sequence<C>,C extends Compound>
alignmentIndex
- column index within an alignment
public int getLastIndexOf(C compound)
Profile
Compound
within this alignment profile. Returns column index nearest to the end
of the alignment profile, or -1 if not found.
getLastIndexOf
in interface Profile<S extends Sequence<C>,C extends Compound>
compound
- search element
public int getLength()
Profile
getLength
in interface Profile<S extends Sequence<C>,C extends Compound>
public List<S> getOriginalSequences()
Profile
List
containing the original Sequence
s used for alignment.
getOriginalSequences
in interface Profile<S extends Sequence<C>,C extends Compound>
public int getSize()
Profile
AlignedSequence
s are circular and overlap within the
alignment, the returned size will be greater than the number of sequences, otherwise the numbers will be equal.
getSize
in interface Profile<S extends Sequence<C>,C extends Compound>
public ProfileView<S,C> getSubProfile(Location location)
Profile
ProfileView
windowed to contain only the given Location
. This only includes the
AlignedSequence
s which overlap the location.
getSubProfile
in interface Profile<S extends Sequence<C>,C extends Compound>
location
- portion of profile to view
public boolean hasGap(int alignmentIndex)
Profile
AlignedSequence
has a gap at the given index.
hasGap
in interface Profile<S extends Sequence<C>,C extends Compound>
alignmentIndex
- column index within an alignment
AlignedSequence
has a gap at the given indexpublic boolean isCircular()
Profile
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.
isCircular
in interface Profile<S extends Sequence<C>,C extends Compound>
AlignedSequence
is circularpublic String toString(int width)
Profile
toString
in interface Profile<S extends Sequence<C>,C extends Compound>
width
- limit on the line length
public String toString(Profile.StringFormat format)
Profile
toString
in interface Profile<S extends Sequence<C>,C extends Compound>
format
- output format
public String toString()
Profile
Profile.getSize()
lines with Profile.getLength()
Compound
s per line.
toString
in interface Profile<S extends Sequence<C>,C extends Compound>
toString
in class Object
public Iterator<AlignedSequence<S,C>> iterator()
iterator
in interface Iterable<AlignedSequence<S extends Sequence<C>,C extends Compound>>
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SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |