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702ce22305
sequences. It stands for Sequence Search and Alignment by Hashing Algorithm. It achieves its fast search speed by converting sequence information into a `hash table' data structure, which can then be searched very rapidly for matches. WWW: http://www.sanger.ac.uk/Software/analysis/SSAHA/ PR: ports/124525 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> Approved by: gabor (mentor, implicit)
34 lines
1.1 KiB
C++
34 lines
1.1 KiB
C++
--- ./QueryManager/MatchAligner.h.orig 2004-03-01 13:51:29.000000000 -0300
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+++ ./QueryManager/MatchAligner.h 2008-06-12 15:39:31.000000000 -0300
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@@ -315,13 +315,13 @@
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static char getCodon( const char* pChar )
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{
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- return ( ( (ttDNA[ *pChar ] ==nv)
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- || (ttDNA[ *(pChar+1) ] ==nv)
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- || (ttDNA[ *(pChar+2) ] ==nv) )
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+ return ( ( (ttDNA[ (int) *pChar ] ==nv)
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+ || (ttDNA[ (int) *(pChar+1) ] ==nv)
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+ || (ttDNA[ (int) *(pChar+2) ] ==nv) )
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? 'X'
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- : gResidueNames[ ttCodon[ ttDNA[ *(pChar) ] << 4
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- | ttDNA[ *(pChar+1) ] << 2
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- | ttDNA[ *(pChar+2) ] ] ] );
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+ : gResidueNames[ ttCodon[ ttDNA[ (int) *(pChar) ] << 4
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+ | ttDNA[ (int) *(pChar+1) ] << 2
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+ | ttDNA[ (int) *(pChar+2) ] ] ] );
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} // ~getCodon
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@@ -519,8 +519,8 @@
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: public vector<vector<PATH_TYPE> >
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{
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public:
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- typedef pair<vector<vector<PATH_TYPE> >::iterator,
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- vector<PATH_TYPE>::iterator> CellIterator;
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+ typedef pair<typename vector<vector<PATH_TYPE> >::iterator,
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+ typename vector<PATH_TYPE>::iterator> CellIterator;
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template<class MATRIX_FILLER> ScoreType fillIn( MATRIX_FILLER& doMatrix )
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{
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