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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/glb__align_8hpp_source.html below:

NCBI C++ ToolKit: include/algo/gnomon/glb_align.hpp Source File

1 #ifndef ALGO_GNOMON___GLBALIGN__HPP 2 #define ALGO_GNOMON___GLBALIGN__HPP 46  CCigar

(

int

qto = -1,

int

sto = -1) : m_qfrom(qto+1), m_qto(qto), m_sfrom(sto+1), m_sto(sto) {}

47  CCigar

(

string

& cigar_string,

int

qfrom,

int

sfrom);

53  void

PushFront(

const SElement

& el);

55  string

CigarString(

int

qstart,

int

qlen)

const

;

56  string

DetailedCigarString(

int

qstart,

int

qlen,

const char

*

query

,

const char

*

subject

)

const

;

61  int

Matches(

const char

*

query

,

const char

*

subject

)

const

;

63  int

Score(

const char

*

query

,

const char

*

subject

,

int

gopen,

int

gapextend,

const char delta

[256][256])

const

;

64  const

list<SElement>&

Elements

() {

return

m_elements; }

68  int

m_qfrom, m_qto, m_sfrom,

m_sto

;

78 CCigar LclAlign

(

const char

*

query

,

int

querylen,

const char

*

subject

,

int

subjectlen,

int

gopen,

int

gapextend,

bool

pinleft,

bool

pinright,

const char delta

[256][256]);

88  char

matrix[256][256];

94  const int

len1 = s1.size(), len2 = s2.size();

95

vector<int> col(len2+1), prevCol(len2+1);

97  for

(

int i

= 0;

i

< (

int

)prevCol.size();

i

++)

99  for

(

int i

= 0;

i

< len1;

i

++) {

101  for

(

int

j = 0; j < len2; j++)

102

col[j+1] =

min

(

min

( 1 + col[j], 1 + prevCol[1 + j]),

103

prevCol[j] + (s1[

i

]==s2[j] ? 0 : 1) );

106  return

prevCol[len2];

111

vector<int> s(

b

.size()+1, 0);

112

vector<int> sm(

b

.size()+1, 0);

114  for

(

int i

= 0;

i

< (

int

)

a

.size() &&

len

< long_enough; ++

i

) {

116  for

(

int

j = 0; j < (

int

)

b

.size() &&

len

< long_enough; ) {

129 double Entropy

(

const string

& seq);

CCigar(int qto=-1, int sto=-1)

TSignedSeqRange SubjectRange() const

list< SElement > m_elements

const list< SElement > & Elements()

TSignedSeqRange QueryRange() const

CCigar VariBandAlign(const char *query, int querylen, const char *subject, int subjectlen, int gopen, int gapextend, const char delta[256][256], const TSignedSeqRange *subject_limits)

double Entropy(const string &seq)

int EditDistance(const T &s1, const T &s2)

CCigar GlbAlign(const char *query, int querylen, const char *subject, int subjectlen, int gopen, int gapextend, const char delta[256][256])

CCigar LclAlign(const char *query, int querylen, const char *subject, int subjectlen, int gopen, int gapextend, const char delta[256][256])

int MaxCommonInterval(const T &a, const T &b, int long_enough=numeric_limits< int >::max())

pair< string, string > TCharAlign

vector< CInDelInfo > TInDels

CRange< TSignedSeqPos > TSignedSeqRange

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

unsigned int

A callback function used to compare two keys in a database.

Magic spell ;-) needed for some weird compilers... very empiric.

Int4 delta(size_t dimension_, const Int4 *score_)

static int match(PCRE2_SPTR start_eptr, PCRE2_SPTR start_ecode, uint16_t top_bracket, PCRE2_SIZE frame_size, pcre2_match_data *match_data, match_block *mb)

static SLJIT_INLINE sljit_ins l(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

float Distance(iterator1 iter1, iterator1 end1, iterator2 iter2, iterator2 end2)

Euclidean distance measure.

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