/dports/biology/seqan1/seqan-1.3.1/apps/splazers/ |
H A D | outputFormat.h | 329 …& 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()
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H A D | razers_spliced.h | 406 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()
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/splazers/ |
H A D | outputFormat.h | 331 …& 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()
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H A D | razers_spliced.h | 560 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()
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/bs_tools/ |
H A D | casbar.h | 816 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)
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/dports/biology/seqan/seqan-library-2.4.0/include/seqan/align/ |
H A D | local_alignment_waterman_eggert_impl.h | 343 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()
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/align/ |
H A D | local_alignment_waterman_eggert_impl.h | 343 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()
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/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/align/ |
H A D | local_alignment_waterman_eggert_impl.h | 341 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()
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/dports/biology/seqan1/seqan-1.3.1/apps/snp_store/ |
H A D | snp_store.h | 872 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 …]
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/dports/biology/seqan1/seqan-1.3.1/apps/razers/ |
H A D | outputFormat.h | 329 …& 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()
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H A D | razers_spliced.h | 394 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()
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/razers/ |
H A D | outputFormat.h | 335 …& 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()
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H A D | razers_spliced.h | 394 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()
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/dports/biology/seqan1/seqan-1.3.1/seqan/align/ |
H A D | align_local_dynprog.h | 367 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()
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/dports/biology/seqan1/seqan-1.3.1/apps/razers2/ |
H A D | outputFormat.h | 382 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()
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/razers3/ |
H A D | outputFormat.h | 408 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()
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/snp_store/ |
H A D | snp_store.h | 2218 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 …]
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