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Searched refs:fillLimited (Results 1 – 25 of 30) sorted by relevance

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/dports/devel/capnproto/capnproto-0.9.0/c++/src/kj/
H A Dstring.h302 inline char* fillLimited(char* ptr, char* limit) { return ptr; } in fillLimited() function
337 char* fillLimited(char* __restrict__ target, char* limit, const First& first, Rest&&... rest) { in fillLimited() function
344 return fillLimited(target, limit, kj::fwd<Rest>(rest)...); in fillLimited()
354 char* fillLimited(char* __restrict__ target, char* limit, Delimited<T>&& first,Rest&&... rest);
358 char* fillLimited(char* __restrict__ target, char* limit, Delimited<T>& first,Rest&&... rest);
514 char* end = _::fillLimited(buffer.begin(), buffer.end() - 1, in strPreallocated()
702 target = fillLimited(target, limit, delimiter); in flattenTo()
704 target = fillLimited(target, limit, kj::toCharSequence(elem)); in flattenTo()
730 return fillLimited(target, limit, kj::fwd<Rest>(rest)...); in fillLimited()
738 char* fillLimited(char* __restrict__ target, char* limit, Delimited<T>& first, Rest&&... rest) { in fillLimited() function
[all …]
H A Dstring-tree.h128 char* fillLimited(char* __restrict__ target, char* limit, const StringTree& first, Rest&&... rest) { in fillLimited() function
132 return fillLimited(target + first.size(), limit, kj::fwd<Rest>(rest)...); in fillLimited()
H A Dexception.c++423 ptr = _::fillLimited(ptr, limit, kj::StringPtr(info.dli_fname), "@0x"_kj, hex(offset)); in stringifyStackTraceAddresses()
425 ptr = _::fillLimited(ptr, limit, toCharSequence(addr)); in stringifyStackTraceAddresses()
428 ptr = _::fillLimited(ptr, limit, " "_kj); in stringifyStackTraceAddresses()
/dports/devel/capnproto080/capnproto-0.8.0/c++/src/kj/
H A Dstring.h265 inline char* fillLimited(char* ptr, char* limit) { return ptr; } in fillLimited() function
270 char* fillLimited(char* __restrict__ target, char* limit, const StringTree& first, Rest&&... rest);
300 char* fillLimited(char* __restrict__ target, char* limit, const First& first, Rest&&... rest) { in fillLimited() function
307 return fillLimited(target, limit, kj::fwd<Rest>(rest)...); in fillLimited()
317 char* fillLimited(char* __restrict__ target, char* limit, Delimited<T> first,Rest&&... rest);
463 char* end = _::fillLimited(buffer.begin(), buffer.end() - 1, in strPreallocated()
655 target = fillLimited(target, limit, delimiter); in flattenTo()
657 target = fillLimited(target, limit, kj::toCharSequence(elem)); in flattenTo()
681 char* fillLimited(char* __restrict__ target, char* limit, Delimited<T> first, Rest&&... rest) { in fillLimited() function
683 return fillLimited(target, limit, kj::fwd<Rest>(rest)...); in fillLimited()
H A Dstring-tree.h128 char* fillLimited(char* __restrict__ target, char* limit, const StringTree& first, Rest&&... rest) { in fillLimited() function
132 return fillLimited(target + first.size(), limit, kj::fwd<Rest>(rest)...); in fillLimited()
H A Dexception.c++396 ptr = _::fillLimited(ptr, limit, kj::StringPtr(info.dli_fname), "@0x"_kj, hex(offset)); in stringifyStackTraceAddresses()
398 ptr = _::fillLimited(ptr, limit, toCharSequence(addr)); in stringifyStackTraceAddresses()
401 ptr = _::fillLimited(ptr, limit, " "_kj); in stringifyStackTraceAddresses()
/dports/biology/bbmap/bbmap/current/aligner/
H A DAligner.java7 int[] fillLimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minScore); in fillLimited() method
H A DSingleStateAlignerPacBioAdapter.java69 …public final int[] fillLimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minSco… in fillLimited() method in SingleStateAlignerPacBioAdapter
310 int[] max=fillLimited(read, ref, a, b, minScore);
H A DSingleStateAlignerFlat.java94 …public final int[] fillLimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minSco… in fillLimited() method in SingleStateAlignerFlat
424 int[] max=fillLimited(read, ref, a, b, minScore);
H A DSingleStateAlignerFlat2_1D.java68 …public final int[] fillLimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minSco… in fillLimited() method in SingleStateAlignerFlat2_1D
409 int[] max=fillLimited(read, ref, a, b, minScore); in fillAndScoreLimited()
H A DSingleStateAlignerFlat2.java79 …public final int[] fillLimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minSco… in fillLimited() method in SingleStateAlignerFlat2
426 int[] max=fillLimited(read, ref, a, b, minScore); in fillAndScoreLimited()
H A DSingleStateAlignerFlat3.java79 …public final int[] fillLimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minSco… in fillLimited() method in SingleStateAlignerFlat3
424 int[] max=fillLimited(read, ref, a, b, minScore); in fillAndScoreLimited()
H A DSingleStateAlignerFlat2Amino.java78 …public final int[] fillLimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minSco… in fillLimited() method in SingleStateAlignerFlat2Amino
494 int[] max=fillLimited(read, ref, a, b, minScore); in fillAndScoreLimited()
H A DSingleStateAlignerFlatFloat.java79 …public final int[] fillLimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minSco… in fillLimited() method in SingleStateAlignerFlatFloat
467 int[] max=fillLimited(read, ref, a, b, minScore); in fillAndScoreLimited()
H A DMultiStateAligner9PacBioAdapter_WithBarriers.java38 int[] max=msa.fillLimited(read, ref, 0, ref.length-1, 0, null); in main()
114 …public final int[] fillLimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minSco… in fillLimited() method in MultiStateAligner9PacBioAdapter_WithBarriers
1342 int[] max=fillLimited(read, ref, a, b, minScore, gaps);
1346 int[] max=fillLimited(read, ref, a, b, minScore, gaps);
H A DMultiStateAligner9PacBioAdapter.java82 …public final int[] fillLimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minSco… in fillLimited() method in MultiStateAligner9PacBioAdapter
957 int[] max=fillLimited(read, ref, a, b, minScore);
H A DMultiStateAligner9PacBioAdapter2.java141 …public final int[] fillLimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minSco… in fillLimited() method in MultiStateAligner9PacBioAdapter2
1138 int[] max=fillLimited(read, ref, a, b, minScore);
H A DMultiStateAligner9PacBioAdapter3.java78 …public final int[] fillLimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minSco… in fillLimited() method in MultiStateAligner9PacBioAdapter3
963 int[] max=fillLimited(read, ref, a, b, minScore); in fillAndScoreLimited()
/dports/biology/bbmap/bbmap/current/var2/
H A DRealigner.java86 max=msa.fillLimited(qbases, rbases, a, b, minScore, null); in realign()
/dports/biology/bbmap/bbmap/current/align2/
H A DTranslateColorspaceRead.java132 int[] max=msa.fillLimited(r.bases, chacs.array, minLoc, maxLoc, scoreNoIndel, r.gaps); in realignByReversingRef()
188 int[] max=msa.fillLimited(r.bases, ref, 0, ref.length-1, scoreNoIndel, r.gaps); in realignByReversingRef()
370 …max=msa.fillLimited(bases, chacs.array, minLoc, maxLoc, Tools.max(scoreNoIndel, minValidScore), ss… in realign_new()
413 …max=msa.fillLimited(bases, chacs.array, minLoc, maxLoc, Tools.max(scoreNoIndel, minValidScore), ss… in realign_new()
450 …max=msa.fillLimited(bases, chacs.array, minLoc, maxLoc, Tools.max(scoreNoIndel, minValidScore), ss… in realign_new()
522 …int[] max=msa.fillLimited(bases, chacs.array, minLoc, maxLoc, Tools.max(scoreNoIndel, minValidScor… in realign_new()
562 …max=msa.fillLimited(bases, chacs.array, minLoc, maxLoc, Tools.max(scoreNoIndel, minValidScore), ss… in realign_new()
597 …max=msa.fillLimited(bases, chacs.array, minLoc, maxLoc, Tools.max(scoreNoIndel, minValidScore), ss… in realign_new()
H A DMSA.java53 …public abstract int[] fillLimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int min… in fillLimited() method in MSA
105 int[] max=fillLimited(read, ref, a, b, minScore, gaps); in fillAndScoreLimited()
109 int[] max=fillLimited(read, ref, a, b, minScore, gaps); in fillAndScoreLimited()
H A DMultiStateAligner11tsJNI.java31 int[] max=msa.fillLimited(read, ref, 0, ref.length-1, 0, null); in main()
75 …public final int[] fillLimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minSco… in fillLimited() method in MultiStateAligner11tsJNI
H A DMultiStateAligner9XFlat.java27 int[] max=msa.fillLimited(read, ref, 0, ref.length-1, 0, null); in main()
91 …public final int[] fillLimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minSco… in fillLimited() method in MultiStateAligner9XFlat
H A DMultiStateAligner9ts.java30 int[] max=msa.fillLimited(read, ref, 0, ref.length-1, 0, null); in main()
93 …public final int[] fillLimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minSco… in fillLimited() method in MultiStateAligner9ts
/dports/biology/bbmap/bbmap/current/jgi/
H A DFindPrimers_old.java195 max=msa.fillLimited(query.bases, r.bases, a, b, -9999, null); in process()

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