|
|||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | ||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
C
- each element of the Sequence
is a Compound
of type Cpublic interface AlignedSequence<S extends Sequence<C>,C extends Compound>
Defines a data structure for a Sequence
within an alignment.
Nested Class Summary | |
---|---|
static class |
AlignedSequence.Step
Defines an alignment step in order to pass alignment information from an Aligner to a constructor. |
Method Summary | |
---|---|
void |
clearCache()
Nullifies cached arrays/objects. |
int |
getAlignmentIndexAt(int sequenceIndex)
Returns the column index within an alignment corresponding to the given index in the original Sequence . |
Point |
getEnd()
Returns the Point within an alignment of the last element of the original Sequence . |
Location |
getLocationInAlignment()
Returns the Location of the original Sequence within an alignment. |
int |
getNumGaps()
Returns number of gaps in the sequence. |
S |
getOriginalSequence()
Returns the original Sequence before alignment. |
int |
getOverlapCount()
Returns the maximum number of elements contributed to a column of an alignment by this Sequence . |
int |
getSequenceIndexAt(int alignmentIndex)
Returns the index in the original Sequence corresponding to the given index within an alignment. |
Point |
getStart()
Returns the Point within an alignment of the first element of the original Sequence . |
boolean |
isCircular()
Returns true if this Sequence wraps around from the last alignment column back to the first. |
boolean |
isGap(int alignmentIndex)
Returns true if this Sequence has a gap at a particular alignment column. |
Methods inherited from interface org.biojava3.core.sequence.template.Sequence |
---|
countCompounds, getAsList, getCompoundAt, getCompoundSet, getIndexOf, getInverse, getLastIndexOf, getLength, getSequenceAsString, getSubSequence |
Methods inherited from interface java.lang.Iterable |
---|
iterator |
Methods inherited from interface org.biojava3.core.sequence.template.Accessioned |
---|
getAccession |
Method Detail |
---|
void clearCache()
int getAlignmentIndexAt(int sequenceIndex)
Sequence
.
Both indices are 1-indexed and inclusive.
sequenceIndex
- index in the original Sequence
IndexOutOfBoundsException
- if sequenceIndex < 1 or sequenceIndex >
getOriginalSequence()
.Sequence.getLength()
Point getEnd()
Point
within an alignment of the last element of the original Sequence
.
Sequence
elementLocation getLocationInAlignment()
Location
of the original Sequence
within an alignment. This provides access to
additional substructure beyond start and end points.
int getNumGaps()
Location
information or from
gap Compound
s, which may not necessarily result in the same number.
S getOriginalSequence()
Sequence
before alignment.
int getOverlapCount()
Sequence
. If
this Sequence
is circular, this number is >= 1. If not, this overlap count is definitely 1.
int getSequenceIndexAt(int alignmentIndex)
Sequence
corresponding to the given index within an alignment. Both
indices are 1-indexed and inclusive.
alignmentIndex
- column index within an alignment
Sequence
IndexOutOfBoundsException
- if alignmentIndex < 1 or alignmentIndex > Sequence.getLength()
Point getStart()
Point
within an alignment of the first element of the original Sequence
.
Sequence
elementboolean isCircular()
Sequence
wraps around from the last alignment column back to the first. This makes
overlap possible, but does not require an overlap count > 1.
boolean isGap(int alignmentIndex)
Sequence
has a gap at a particular alignment column.
alignmentIndex
- column index within an alignment
IndexOutOfBoundsException
- if alignmentIndex < 1 or alignmentIndex > Sequence.getLength()
|
|||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | ||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |