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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/struct__dp__demo_8cpp_source.html below:

NCBI C++ ToolKit: src/algo/structure/struct_dp/demo/struct_dp_demo.cpp Source File

51 #define ERROR_MESSAGE(s) ERR_POST(Error << "struct_dp_demo: "

<< s << '!')

52 #define INFO_MESSAGE(s) ERR_POST(Info << "struct_dp_demo: "

<< s)

60  int

ch =

toupper

((

unsigned char

) original);

62  case 'A'

:

case 'R'

:

case 'N'

:

case 'D'

:

case 'C'

:

63  case 'Q'

:

case 'E'

:

case 'G'

:

case 'H'

:

case 'I'

:

64  case 'L'

:

case 'K'

:

case 'M'

:

case 'F'

:

case 'P'

:

65  case 'S'

:

case 'T'

:

case 'W'

:

case 'Y'

:

case 'V'

:

77  static bool

unpacked =

false

;

114  subject

=

"PTVEYLNYEVVDDNGWDMYDDDVFGEASDMDLDDEDYGSLEVNEGEYILEAAEAQGYDWPFSC" 115  "RAGACANCAAIVLEGDIDMDMQQILSDEEVEDKNVRLTCIGSPDADEVKIVYNAKHLDYLQNRVI"

;

145  query

=

"ASYQVRLINKKQDIDTTIEIDEETTILDGAEENGIELPFSCHSGSCSSCVGKVVEGEVDQSDQ" 146  "IFLDDEQMGKGFALLCVTYPRSNCTIKTHQEPYLA"

;

154

<<

" for "

<< alignment->

nBlocks

<<

" blocks"

);

156  for

(block=0; block<alignment->

nBlocks

; block++) {

162  "Block "

<< (block + alignment->

firstBlock

+ 1) <<

", score " 164

<<

"S: "

<<

subject

.substr(subjectStart, blockSize)

165

<<

' '

<< (subjectStart + 1) <<

'-'

<< (subjectStart + blockSize) <<

'\n' 166

<<

"Q: "

<<

query

.substr(queryStart, blockSize)

167

<<

' '

<< (queryStart + 1) <<

'-'

<< (queryStart + blockSize)

192 int main

(

int

argc,

const char

* argv[])

Include a standard set of the NCBI C++ Toolkit most basic headers.

EDiagSev SetDiagPostLevel(EDiagSev post_sev=eDiag_Error)

Set the threshold severity for posting the messages.

void SetDiagStream(CNcbiOstream *os, bool quick_flush=true, FDiagCleanup cleanup=0, void *cleanup_data=0, const string &stream_name="")

Set diagnostic stream.

@ eDS_Default

Try standard log file (app.name + ".log") in /log/, use stderr on failure.

@ eDiag_Info

Informational message.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_SCOPE(ns)

Define a new scope.

const SNCBIPackedScoreMatrix NCBISM_Blosum62

void NCBISM_Unpack(const SNCBIPackedScoreMatrix *psm, SNCBIFullScoreMatrix *fsm)

Expand a packed score matrix into an unpacked one, which callers can proceed to index directly by sta...

unsigned int * blockPositions

unsigned int * blockPositions

unsigned int * blockSizes

int DP_LocalBlockAlign(const DP_BlockInfo *blocks, DP_BlockScoreFunction BlockScore, unsigned int queryFrom, unsigned int queryTo, DP_AlignmentResult **alignment)

void DP_DestroyBlockInfo(DP_BlockInfo *blocks)

#define STRUCT_DP_FOUND_ALIGNMENT

#define STRUCT_DP_PARAMETER_ERROR

#define STRUCT_DP_ALGORITHM_ERROR

static const int DP_NEGATIVE_INFINITY

#define STRUCT_DP_NO_ALIGNMENT

void DP_DestroyAlignmentResult(DP_AlignmentResult *alignment)

DP_BlockInfo * DP_CreateBlockInfo(unsigned int nBlocks)

static unsigned int ScreenResidueCharacter(char original)

static DP_BlockInfo * blocks

static int GetBLOSUM62Score(char a, char b)

int ScoreByBlosum62(unsigned int block, unsigned int queryPos)

int main(int argc, const char *argv[])

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