Interface Functions Detail
void assignSource(gaps, seq);
Assign the source of a gaps object, copying data.
Parameters
gaps
|
The Gaps object to assign the source of. |
seq
|
The sequence to assign to the underlying string. |
Data Races
Thread safety unknown!
TPos beginPosition(gaps);
Return the clipping begin position as a source position.
Parameters
gaps
|
The Gaps object to query. |
Returns
TPos |
The clipping begin position in the source (Metafunction: Position). |
Example
In the following gaps configuration, the result of beginPosition(gaps) is $1$. The clipping starts in a
gap and the source position of the first non-gap character right of the clipping begin has source position 1.
clipping [ )
(half-open interval)
gapped sequence: X--XXX-XX-
source position: 0111234456
unclipped view position: 0123456789
clipped view position: 0123456
Data Races
Thread safety unknown!
void clearClipping(gaps);
Clear clipping from Gaps objects.
Parameters
gaps
|
Object to clear clipping from. |
Data Races
Thread safety unknown!
void clearGaps(gaps);
Clear gaps from Gaps objects.
Parameters
gaps
|
Object to clear gaps from. |
Data Races
Thread safety unknown!
TPos clippedBeginPosition(gaps);
Return begin position of the clipping.
Parameters
gaps
|
The Gaps object to query. |
Returns
TPos |
The begin position of the unclipped view (Metafunction: Position). |
Example
In the following gaps configuration, the result of clippedBeginPosition(gaps) is 1.
clipping [ )
(half-open interval)
gapped sequence: X--XXX-XX-
source position: 0111234456
unclipped view position: 0123456789
clipped view position: 0123456
Data Races
Thread safety unknown!
TPos clippedEndPosition(gaps);
Return end position of the clipping.
Parameters
gaps
|
The Gaps object to query. |
Returns
TPos |
The end position of the unclipped view (Metafunction: Position). |
Example
In the following gaps configuration, the result of clippedEndPosition(gaps) is 7.
clipping [ )
(half-open interval)
gapped sequence: X--XXX-XX-
source position: 0111234456
unclipped view position: 0123456789
clipped view position: 0123456
Data Races
Thread safety unknown!
void clipSemiGlobal(global, local);
Clip the Gaps objects to reflect a semi-global alignment.
Parameters
global
|
The global Gaps object. |
local
|
The local Gaps object. |
Leading and trailing gaps are clipped in the local Gaps object. The global Gaps object is updated accordingly.
Data Races
Thread safety unknown!
void copyClipping(dest, source);
Copy clipping information from one Gaps object to another.
Parameters
dest
|
The destination Gaps object. |
source
|
The source Gaps object. |
Data Races
Thread safety unknown!
void copyGaps(dest, source);
Copy gaps from one Gaps object to another (in the clipped view of both argumetns).
Parameters
dest
|
The destination Gaps object (appropriate clipping, no gaps). |
source
|
The source Gaps object. |
The user is resposible for ensuring that the gaps are over sequences of same length and appropriate clipping.
Data Races
Thread safety unknown!
TSize countCharacters(gaps, viewPos[, dir]);
The number of characters following a position.
Parameters
gaps
|
The Gaps object to query. |
viewPos
|
View position (including clipping and gaps) to query at. |
dir
|
A tag to specify the counting direction. One of GapDirectionTags.
Defaults to RightOfViewPos. |
Returns
TSize |
The number of non-gaps characters characters at viewPos (Metafunction: Size). |
If the the direction tag is RightOfViewPos the current view position will be
included in the count, and excluded when LeftOfViewPos is selected.
Data Races
Thread safety unknown!
TSize countGapExtensions(gaps);
The number of gap extensions.
Parameters
gaps
|
The Gaps object to query. |
Returns
TSize |
The total number of gap extensions (Metafunction: Size). |
Data Races
Thread safety unknown!
TSize countGapOpens(gaps);
The number of gap openings.
Parameters
gaps
|
The Gaps object to query. |
Returns
TSize |
The total number of gap openings (Metafunction: Size). |
Data Races
Thread safety unknown!
TSize countGaps(gaps, viewPos[, dir]);
The number of gaps following a position.
Parameters
gaps
|
The Gaps object to query. |
viewPos
|
View position (including clipping and gaps) to query at. |
dir
|
A tag to specify the counting direction. One of GapDirectionTags.
Defaults to RightOfViewPos. |
Returns
TSize |
The number of gap characters at viewPos (Metafunction: Size). |
If the the direction tag is RightOfViewPos the current view position will be
included in the count, and excluded when LeftOfViewPos is selected.
Data Races
Thread safety unknown!
TSize countLeadingGaps(gaps);
The number of leading gaps.
Parameters
gaps
|
The Gaps object to query. |
Returns
TSize |
The number of leading gap characters (Metafunction: Size). |
Data Races
Thread safety unknown!
TSize countTrailingGaps(gaps);
The number of trailing gaps.
Parameters
gaps
|
The Gaps object to query. |
Returns
TSize |
The number of trailing gap characters (Metafunction: Size). |
Data Races
Thread safety unknown!
TPos endPosition(gaps);
Return the clipping end position as a source position.
Parameters
gaps
|
The Gaps object to query for the end position as a source position. |
Returns
TPos |
The end position as a source position (Metafunction: Position). |
Example
In the following gaps configuration, the result of endPositioN(gaps) is 4.
clipping [ )
(half-open interval)
gapped sequence: X--XXX-XX-
source position: 0111234456
unclipped view position: 0123456789
clipped view position: 0123456
Data Races
Thread safety unknown!
void insertGap(gaps, viewPos);
Insert one gap character.
Parameters
gaps
|
The Gaps object to insert gap into. |
viewPos
|
The view position (including clipping and gaps) to insert the gap at. |
Data Races
Thread safety unknown!
void insertGaps(gaps, viewPos, count);
Parameters
gaps
|
The Gaps object to insert gaps into. |
viewPos
|
The view position (including clipping and gaps) to insert gaps at. |
count
|
The number of gaps to insert. |
Data Races
Thread safety unknown!
bool isGap(gaps, viewPos);
Query positions in a Gaps object for being a character.
Parameters
gaps
|
The Gaps object to query. |
viewPos
|
The view position (including clipping and gaps). |
Returns
Data Races
Thread safety unknown!
bool isGap(gaps, viewPos);
Query positions in a Gaps object for being a gap.
Parameters
gaps
|
The Gaps object to query. |
viewPos
|
The view position (including clipping and gaps). |
Returns
Data Races
Thread safety unknown!
TIterator iter(gaps, viewPos[, tag]);
Return an iterator to a specific position in the current clipping.
Parameters
gaps
|
The Gaps object to get an iterator into. |
viewPos
|
View position to get an iterator to (Metafunction: Position). |
tag
|
An optional tag for selecting the iterator type. |
Returns
TIterator |
The resulting iterator. The type is Iterator<TGaps, TTag>::Type where TTag is
the type of tag. |
Data Races
Thread safety unknown!
TSize length(gaps);
Return number of gap and characters between the beginning and the end of the clipping.
Parameters
gaps
|
The Gaps object to query for its length. |
Returns
TSize |
The number of gaps and characters between the beginning and the end of the clipping (Metafunction:
Size). |
Data Races
Thread safety unknown!
TSize removeGap(gaps, viewPos);
Remove one gap from a Gaps object.
Parameters
gaps
|
The gaps object to remove one gap character from. |
viewPos
|
The view positions to remove one gap character from. |
Returns
TSize |
The number of gap characters removed (Metafunction: Size). |
Data Races
Thread safety unknown!
TSize removeGaps(gaps, viewPos, count);
Remove gaps from a Gaps object.
Parameters
gaps
|
The gaps object to remove gap characters from. |
viewPos
|
The view positions to remove gap characters from. |
count
|
The number of gap characters to remove. |
Returns
TSize |
The number of gap characters removed (Metafunction: Size). |
Data Races
Thread safety unknown!
void setBeginPosition(gaps, sourcePos);
Set the begin position of the clipped gapped sequence, given a source position.
Parameters
gaps
|
The Gaps object to set the begin position in. |
sourcePos
|
Position in the underlying sequence to set clipping to. |
Data Races
Thread safety unknown!
void setClippedBeginPosition(gaps, unclippedViewPos);
Set the begin position of the clipping.
Parameters
gaps
|
The Gaps object to set the clipping begin position of. |
unclippedViewPos
|
View position (including gaps but excluding clipping) to set the clipping begin to. |
Data Races
Thread safety unknown!
void setClippedEndPosition(gaps, unclippedViewPos);
Set the end position of the clipping.
Parameters
gaps
|
The Gaps object to set the clipping end position of. |
unclippedViewPos
|
View position (including gaps but excluding clipping) to set the clipping end to. |
Data Races
Thread safety unknown!
void setEndPosition(gaps, sourcePos);
Set the end position of the clipped gapped sequence, given a source position.
Parameters
gaps
|
The Gaps object to set the end position in. |
sourcePos
|
Position in the underlying sequence to set clipping to. |
Data Races
Thread safety unknown!
TSource source(gaps);
Return underlying object.
Parameters
gaps
|
The Gaps object to return the underling sequence for. |
Returns
TSource |
Reference to the source of the Gaps. |
Data Races
Thread safety unknown!
TPos toSourcePosition(gaps, viewPos);
Conversion from view position (including gaps and clipping) to source (without gaps or clipping).
Parameters
gaps
|
The gaps object to use for translation. |
sourcePos
|
The view position (including gaps and clipping) to translate. |
Returns
TPos |
The resulting position in the underlying sequence (Metafunction: Position). |
Data Races
Thread safety unknown!
TPos toViewPosition(gaps, sourcePos);
Conversion from source (without gaps or clipping) to view position (including gaps and clipping).
Parameters
gaps
|
The gaps object to use for translation. |
sourcePos
|
The source position (in the underlying sequence) to translate. |
Returns
TPos |
The resulting position in the view (Metafunction: Position). |
Data Races
Thread safety unknown!
TSize unclippedLength(gaps);
Return length of the gapped sequence without clipping.
Parameters
gaps
|
The Gaps object to query. |
Returns
TSize |
The result (Metafunction: Size). |
Data Races
Thread safety unknown!