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NCBI C++ ToolKit: src/algo/blast/composition_adjustment/compo_mode_condition.c Source File

39 #define HALF_CIRCLE_DEGREES 180 41 #define PI 3.1415926543 43 #define QUERY_MATCH_DISTANCE_THRESHOLD 0.16 44 #define LENGTH_RATIO_THRESHOLD 3.0 45 #define ANGLE_DEGREE_THRESHOLD 70.0 46 #define HIGH_PAIR_THRESHOLD 0.4 47 #define LENGTH_LOWER_THRESHOLD 50 72  if

(letterProbs[

i

] > second) {

73

second = letterProbs[

i

];

74  if

(letterProbs[

i

] >

max

) {

76  max

= letterProbs[

i

];

88  const double

* P_match,

int

length2)

95  return

result1 || result2;

102  const double

* P_query,

const double

* P_match,

103  const char

*matrix_name)

119  const double

* P_query,

const double

* P_match,

120  const char

*matrix_name)

139  const double

* P_query,

140  const double

* P_match,

141  const char

*matrix_name)

162  const double

* P_query,

163  const double

* P_match,

164  const char

*matrix_name)

172  const double

*p_matrix;

174  double

D_m_mat, D_q_mat, D_m_q;

178  double

corr_factor = 0.0;

183  double

len_large, len_small;

191

p_query[

i

] = P_query[

i

];

192

p_match[

i

] = P_match[

i

];

194

(p_query[

i

] - p_matrix[

i

]) * (p_match[

i

] - p_matrix[

i

]);

201

acos((D_m_mat * D_m_mat + D_q_mat * D_q_mat -

202

D_m_q * D_m_q) / 2.0 / D_m_mat / D_q_mat);

206

len_q = 1.0 * Len_query;

207

len_m = 1.0 * Len_match;

246  const double

* probArray1,

247  const double

* probArray2,

248  const char

*matrixName,

251  int

testFunctionIndex = (

int

) composition_adjust_mode;

254  Cond_func

[testFunctionIndex] (length1, length2,

255

probArray1, probArray2, matrixName);

EMatrixAdjustRule(* Condition)(int, int, const double *, const double *, const char *)

type of function used to choose a mode for composition-based statistics.

#define ANGLE_DEGREE_THRESHOLD

static EMatrixAdjustRule s_JustScaleOldMatrix(int Len_query, int Len_match, const double *P_query, const double *P_match, const char *matrix_name)

Return eCompoScaleOldMatrix unconditionally.

#define QUERY_MATCH_DISTANCE_THRESHOLD

#define PI

some digits of PI

static Condition Cond_func[]

An array of functions that can be used to decide which optimization formulation should be used for sc...

#define HALF_CIRCLE_DEGREES

180 degrees in half a circle

static int s_HighPairFrequencies(const double *letterProbs, int length)

Return true if length > 50 and the two most frequent letters occur a total of more that 40% of the ti...

static EMatrixAdjustRule s_TestToApplyREAdjustmentUnconditional(int Len_query, int Len_match, const double *P_query, const double *P_match, const char *matrix_name)

A function used to choose a mode for composition-based statistics.

EMatrixAdjustRule Blast_ChooseMatrixAdjustRule(int length1, int length2, const double *probArray1, const double *probArray2, const char *matrixName, ECompoAdjustModes composition_adjust_mode)

Choose how the relative entropy should be constrained based on properties of the two sequences to be ...

static EMatrixAdjustRule s_NeverAdjustMatrix(int Len_query, int Len_match, const double *P_query, const double *P_match, const char *matrix_name)

Return eDontAdjustMatrix unconditionally.

#define HIGH_PAIR_THRESHOLD

static EMatrixAdjustRule s_TestToApplyREAdjustmentConditional(int Len_query, int Len_match, const double *P_query, const double *P_match, const char *matrix_name)

A function used to choose a mode for composition-based statistics.

static int s_HighPairEitherSeq(const double *P_query, int length1, const double *P_match, int length2)

Return true if either the query or the matching sequences passes the test in s_HighPairFrequencies.

#define LENGTH_LOWER_THRESHOLD

#define LENGTH_RATIO_THRESHOLD

Declarations of functions used to choose the mode for composition-based statistics.

Definitions used in compositional score matrix adjustment.

double Blast_GetRelativeEntropy(const double A[], const double B[])

Compute the symmetric form of the relative entropy of two probability vectors.

ECompoAdjustModes

An collection of constants that specify all permissible modes of composition adjustment.

#define COMPO_NUM_TRUE_AA

Number of standard amino acids.

EMatrixAdjustRule

An collection of constants that specify all rules that may be used to generate a compositionally adju...

@ eUserSpecifiedRelEntropy

unsigned int

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

Definitions used to get joint probabilities for a scoring matrix.

const double * Blast_GetMatrixBackgroundFreq(const char *matrix_name)

Return true if frequency data is available for the given matrix name.

Type and macro definitions from C toolkit that are not defined in C++ toolkit.

#define FALSE

bool replacment for C indicating false.

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