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S
- each element of the alignment profile is of type SC
- each element of an Sequence
is a Compound
of type Cpublic 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.
Nested Class Summary | |
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static class |
LightweightProfile.StringFormat
List of output formats. |
Method Summary | |
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S |
getAlignedSequence(int listIndex)
Returns Sequence at given index. |
List<S> |
getAlignedSequences()
Returns a List containing the individual Sequence s of this alignment. |
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 Sequence s |
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 |
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S getAlignedSequence(int listIndex)
Sequence
at given index.
listIndex
- index of sequence in profile
IndexOutOfBoundsException
- if listIndex < 1 or listIndex > number of sequencesList<S> getAlignedSequences()
List
containing the individual Sequence
s of this alignment.
List<C> getCompoundsAt(int alignmentIndex)
Compound
elements of the original Sequence
s at the given column.
alignmentIndex
- column index within an alignment
IndexOutOfBoundsException
- if alignmentIndex < 1 or alignmentIndex > getLength()
CompoundSet<C> getCompoundSet()
CompoundSet
of all Sequence
s
Compound
s in contained sequencesint getLength()
int getSize()
Sequence
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.
String toString()
getSize()
lines with getLength()
Compound
s per line.
toString
in class Object
String toString(int width)
width
- limit on the line length
String toString(LightweightProfile.StringFormat format)
format
- output format
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