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Searched refs:ali_it1_stop (Results 1 – 17 of 17) sorted by relevance

/dports/biology/seqan1/seqan-1.3.1/apps/splazers/
H A DoutputFormat.h329 …& cigar, TString & mutations, TIter ali_it0, TIter ali_it0_stop, TIter ali_it1, TIter ali_it1_stop) in getCigarLine() argument
344 while(ali_it0 != ali_it0_stop && ali_it1 != ali_it1_stop) in getCigarLine()
349 while(ali_it0!=ali_it0_stop && ali_it1!=ali_it1_stop && !isGap(ali_it0)&& !isGap(ali_it1)) in getCigarLine()
371 while(isGap(ali_it1)&& ali_it1!=ali_it1_stop) in getCigarLine()
391 while(ali_it1 != ali_it1_stop) in getCigarLine()
410 TIter ali_it0, TIter ali_it0_stop, TIter ali_it1, TIter ali_it1_stop) in getCigarLine() argument
424 while(ali_it0 != ali_it0_stop && ali_it1 != ali_it1_stop) in getCigarLine()
429 while(ali_it0!=ali_it0_stop && ali_it1!=ali_it1_stop && !isGap(ali_it0)&& !isGap(ali_it1)) in getCigarLine()
447 while(isGap(ali_it1)&& ali_it1!=ali_it1_stop) in getCigarLine()
465 while(ali_it1 != ali_it1_stop) in getCigarLine()
H A Drazers_spliced.h406 TAlignIterator ali_it1_stop = iter(row(align,1),end_); in countErrorsInAlign() local
410 while(ali_it0 != ali_it0_stop && ali_it1 != ali_it1_stop) in countErrorsInAlign()
412 while(ali_it0!=ali_it0_stop && ali_it1!=ali_it1_stop && !isGap(ali_it0)&& !isGap(ali_it1)) in countErrorsInAlign()
425 while(isGap(ali_it1)&& ali_it1!=ali_it1_stop) in countErrorsInAlign()
437 while(ali_it1 != ali_it1_stop) in countErrorsInAlign()
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/splazers/
H A DoutputFormat.h331 …& cigar, TString & mutations, TIter ali_it0, TIter ali_it0_stop, TIter ali_it1, TIter ali_it1_stop) in getCigarLine() argument
346 while(ali_it0 != ali_it0_stop && ali_it1 != ali_it1_stop) in getCigarLine()
351 while(ali_it0!=ali_it0_stop && ali_it1!=ali_it1_stop && !isGap(ali_it0)&& !isGap(ali_it1)) in getCigarLine()
373 while(isGap(ali_it1)&& ali_it1!=ali_it1_stop) in getCigarLine()
393 while(ali_it1 != ali_it1_stop) in getCigarLine()
412 TIter ali_it0, TIter ali_it0_stop, TIter ali_it1, TIter ali_it1_stop) in getCigarLine() argument
426 while(ali_it0 != ali_it0_stop && ali_it1 != ali_it1_stop) in getCigarLine()
431 while(ali_it0!=ali_it0_stop && ali_it1!=ali_it1_stop && !isGap(ali_it0)&& !isGap(ali_it1)) in getCigarLine()
449 while(isGap(ali_it1)&& ali_it1!=ali_it1_stop) in getCigarLine()
467 while(ali_it1 != ali_it1_stop) in getCigarLine()
H A Drazers_spliced.h560 TAlignIterator ali_it1_stop = iter(row(align,1),end_); in countErrorsInAlign() local
564 while(ali_it0 != ali_it0_stop && ali_it1 != ali_it1_stop) in countErrorsInAlign()
566 while(ali_it0!=ali_it0_stop && ali_it1!=ali_it1_stop && !isGap(ali_it0)&& !isGap(ali_it1)) in countErrorsInAlign()
579 while(isGap(ali_it1)&& ali_it1!=ali_it1_stop) in countErrorsInAlign()
591 while(ali_it1 != ali_it1_stop) in countErrorsInAlign()
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/bs_tools/
H A Dcasbar.h816 TAlignIterator ali_it1_stop = iter(row(align,1),endPosition(cols(align)));
825 while(ali_it0 != ali_it0_stop && ali_it1 != ali_it1_stop)
827 while(ali_it0!=ali_it0_stop && ali_it1!=ali_it1_stop && !isGap(ali_it0)&& !isGap(ali_it1))
841 while(isGap(ali_it1)&& ali_it1!=ali_it1_stop)
860 TAlignIterator ali_it1_stop = iter(row(align,1),endPosition(cols(align)));
867 while(ali_it0 != ali_it0_stop && ali_it1 != ali_it1_stop && refPos < pos_row1)
869 …while(ali_it0!=ali_it0_stop && ali_it1!=ali_it1_stop && !isGap(ali_it0)&& !isGap(ali_it1) && refP…
882 while(isGap(ali_it1)&& ali_it1!=ali_it1_stop && refPos <= pos_row1)
/dports/biology/seqan/seqan-library-2.4.0/include/seqan/align/
H A Dlocal_alignment_waterman_eggert_impl.h343 TGapsVIter ali_it1_stop = begin(gapsV); in _smithWatermanDeclump() local
409 if(ali_it0==ali_it0_stop && ali_it1==ali_it1_stop) in _smithWatermanDeclump()
428 while(isGap(ali_it1)&& ali_it1!=ali_it1_stop) in _smithWatermanDeclump()
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/align/
H A Dlocal_alignment_waterman_eggert_impl.h343 TGapsVIter ali_it1_stop = begin(gapsV); in _smithWatermanDeclump() local
409 if(ali_it0==ali_it0_stop && ali_it1==ali_it1_stop) in _smithWatermanDeclump()
428 while(isGap(ali_it1)&& ali_it1!=ali_it1_stop) in _smithWatermanDeclump()
/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/align/
H A Dlocal_alignment_waterman_eggert_impl.h341 TGapsVIter ali_it1_stop = begin(gapsV); in _smithWatermanDeclump() local
409 if(ali_it0==ali_it0_stop && ali_it1==ali_it1_stop) in _smithWatermanDeclump()
428 while(isGap(ali_it1)&& ali_it1!=ali_it1_stop) in _smithWatermanDeclump()
/dports/biology/seqan1/seqan-1.3.1/apps/snp_store/
H A Dsnp_store.h872 TAlignIterator ali_it1_stop = iter(row(align,1),endPosition(cols(align)));
881 while(ali_it0 != ali_it0_stop && ali_it1 != ali_it1_stop)
883 while(ali_it0!=ali_it0_stop && ali_it1!=ali_it1_stop && !isGap(ali_it0)&& !isGap(ali_it1))
897 while(isGap(ali_it1)&& ali_it1!=ali_it1_stop)
916 TAlignIterator ali_it1_stop = iter(row(align,1),endPosition(cols(align)));
923 while(ali_it0 != ali_it0_stop && ali_it1 != ali_it1_stop && refPos < pos_row1)
938 while(isGap(ali_it1)&& ali_it1!=ali_it1_stop && refPos <= pos_row1)
2523 TAlignIterator ali_it1_stop = iter(row(align,1),end_);
2528 while(ali_it0 != ali_it0_stop && ali_it1 != ali_it1_stop)
2532 while(ali_it0!=ali_it0_stop && ali_it1!=ali_it1_stop && !isGap(ali_it0)&& !isGap(ali_it1))
[all …]
/dports/biology/seqan1/seqan-1.3.1/apps/razers/
H A DoutputFormat.h329 …& cigar, TString & mutations, TIter ali_it0, TIter ali_it0_stop, TIter ali_it1, TIter ali_it1_stop) in getCigarLine() argument
344 while(ali_it0 != ali_it0_stop && ali_it1 != ali_it1_stop) in getCigarLine()
349 while(ali_it0!=ali_it0_stop && ali_it1!=ali_it1_stop && !isGap(ali_it0)&& !isGap(ali_it1)) in getCigarLine()
371 while(isGap(ali_it1)&& ali_it1!=ali_it1_stop) in getCigarLine()
391 while(ali_it1 != ali_it1_stop) in getCigarLine()
H A Drazers_spliced.h394 TAlignIterator ali_it1_stop = iter(row(align,1),end_); in countErrorsInAlign() local
398 while(ali_it0 != ali_it0_stop && ali_it1 != ali_it1_stop) in countErrorsInAlign()
400 while(ali_it0!=ali_it0_stop && ali_it1!=ali_it1_stop && !isGap(ali_it0)&& !isGap(ali_it1)) in countErrorsInAlign()
413 while(isGap(ali_it1)&& ali_it1!=ali_it1_stop) in countErrorsInAlign()
425 while(ali_it1 != ali_it1_stop) in countErrorsInAlign()
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/razers/
H A DoutputFormat.h335 …& cigar, TString & mutations, TIter ali_it0, TIter ali_it0_stop, TIter ali_it1, TIter ali_it1_stop) in getCigarLine() argument
350 while(ali_it0 != ali_it0_stop && ali_it1 != ali_it1_stop) in getCigarLine()
355 while(ali_it0!=ali_it0_stop && ali_it1!=ali_it1_stop && !isGap(ali_it0)&& !isGap(ali_it1)) in getCigarLine()
377 while(isGap(ali_it1)&& ali_it1!=ali_it1_stop) in getCigarLine()
397 while(ali_it1 != ali_it1_stop) in getCigarLine()
H A Drazers_spliced.h394 TAlignIterator ali_it1_stop = iter(row(align,1),end_); in countErrorsInAlign() local
398 while(ali_it0 != ali_it0_stop && ali_it1 != ali_it1_stop) in countErrorsInAlign()
400 while(ali_it0!=ali_it0_stop && ali_it1!=ali_it1_stop && !isGap(ali_it0)&& !isGap(ali_it1)) in countErrorsInAlign()
413 while(isGap(ali_it1)&& ali_it1!=ali_it1_stop) in countErrorsInAlign()
425 while(ali_it1 != ali_it1_stop) in countErrorsInAlign()
/dports/biology/seqan1/seqan-1.3.1/seqan/align/
H A Dalign_local_dynprog.h367 TAlignIterator ali_it1_stop = iter(row1,beginPosition(row1)); in _smithWatermanDeclump() local
423 if(ali_it0==ali_it0_stop && ali_it1==ali_it1_stop) in _smithWatermanDeclump()
442 while(isGap(ali_it1)&& ali_it1!=ali_it1_stop) in _smithWatermanDeclump()
/dports/biology/seqan1/seqan-1.3.1/apps/razers2/
H A DoutputFormat.h382 TAlignIterator ali_it1_stop = iter(row(align,1),endPosition(cols(align))); in getCigarLine() local
389 while(ali_it0 != ali_it0_stop && ali_it1 != ali_it1_stop) in getCigarLine()
394 while(ali_it0!=ali_it0_stop && ali_it1!=ali_it1_stop && !isGap(ali_it0)&& !isGap(ali_it1)) in getCigarLine()
416 while(isGap(ali_it1)&& ali_it1!=ali_it1_stop) in getCigarLine()
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/razers3/
H A DoutputFormat.h408 TAlignIterator ali_it1_stop = iter(row(align, 1), endPosition(cols(align))); in getCigarLine() local
415 while (ali_it0 != ali_it0_stop && ali_it1 != ali_it1_stop) in getCigarLine()
420 … while (ali_it0 != ali_it0_stop && ali_it1 != ali_it1_stop && !isGap(ali_it0) && !isGap(ali_it1)) in getCigarLine()
446 while (isGap(ali_it1) && ali_it1 != ali_it1_stop) in getCigarLine()
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/snp_store/
H A Dsnp_store.h2218 TAlignIterator ali_it1_stop = iter(row(align,1),endPosition(cols(align)));
2227 while(ali_it0 != ali_it0_stop && ali_it1 != ali_it1_stop)
2229 while(ali_it0!=ali_it0_stop && ali_it1!=ali_it1_stop && !isGap(ali_it0)&& !isGap(ali_it1))
2243 while(isGap(ali_it1)&& ali_it1!=ali_it1_stop)
2262 TAlignIterator ali_it1_stop = iter(row(align,1),endPosition(cols(align)));
2269 while(ali_it0 != ali_it0_stop && ali_it1 != ali_it1_stop && refPos < pos_row1)
2284 while(isGap(ali_it1)&& ali_it1!=ali_it1_stop && refPos <= pos_row1)
4879 TAlignIterator ali_it1_stop = iter(row(align,1),end_);
4884 while(ali_it0 != ali_it0_stop && ali_it1 != ali_it1_stop)
4888 while(ali_it0!=ali_it0_stop && ali_it1!=ali_it1_stop && !isGap(ali_it0)&& !isGap(ali_it1))
[all …]