6.21. Handling Maths

6.21.1. Introduction

EMBOSS provides a basic maths library that includes functions for datatype conversion, random number generation, rounding and other basics.

6.21.2. AJAX Library Files

AJAX library files for handling maths are listed in the table (Table 6.36, “AJAX Library Files for Handling Maths”). Library file documentation, including a complete description of datatypes and functions, is available at:

Table 6.36. AJAX Library Files for Handling Maths
Library File DocumentationDescription
ajmathGeneral maths functions
ajvectorFunctions for handling vectors

ajmath.h/cGeneral maths functions for rounding numbers, coordinate conversion, random number generation etc.

ajvector.h/cData structures and functions for handling vectors in 3D space. The library is not described here and you should see the library documentation online for further information.

6.21.3. ACD Datatypes

There are no ACD datatypes dedicated for maths.

6.21.4. AJAX Datatypes

There are no AJAX datatypes dedicated for maths.

6.21.5. Conversion Functions

Functions are provided for converting one datatype to another. These all have the prefix ajCvt. To interconvert polar and cartesian coordinates, to convert radians to degrees or return a probability given a Gaussian distribution use:

float  ajCvtDegToRad (float degrees);
void  ajCvtPolToRec (float radius, float angle, float* Px, float* Py);
float  ajCvtRadToDeg (float radians);
void   ajCvtRecToPol (float x, float y, float* Pradius, float* Pangle);
double  ajCvtGaussToProb (float mean, float sd, float score);

Sequence positions are often specified by the user on the command line. EMBOSS supports negative values for sequence positions which are interpreted as an offset from the end of the sequence. Two functions are provided to convert an EMBOSS sequence position to a true position which, for instance, could be used to index into the sequence itself. The functions return an integer between 0 (the start of the sequence) and the length of the sequence minus 1:

ajint  ajCvtSposToPos (ajint len, ajint ipos);
ajint  ajCvtSposToPosStart (ajint len, ajint imin, ajint ipos);

In both cases, len is the length of the sequence and ipos is the position. A value of 0 means the start of the sequence whereas negative numbers indicate an offset from the end of the sequence. A minimum relative position (imin) can be specified.

6.21.6. Random Number Functions

There are three functions for random number generation. These are based on dprand and sdprand and used with the permission of N.M. Maclaren (Copyright, The University of Cambridge). ajRandomSeed initialises random number generation and must be called before ajRandomNumber (returns a random integer between 0-32767) and ajRandomDouble (returns a random double precision value between 0.0 and 1.0):

void  ajRandomSeed (void);
double  ajRandomNumber (void);
double  ajRandomDouble (void);

6.21.7. Rounding

Two functions are for rounding off numbers, either a float to an int or a float to a float with a specified number of bits left for cumulative addition:

ajint  ajRound (ajint i, ajint round);
float  ajRoundFloat (float f, ajint nbits);

6.21.8. Miscellaneous Functions

Various miscellaneous functions are provided, for instance, to calculate a geometric mean, the modulo of two numbers or a 32 or 64 bit SwissProt-style checksum for a protein sequence:

float  ajMathGmean (const float* Parr, ajint n);
ajint  ajMathModulo (ajint i1, ajint i2);
ajuint ajMathCrc32 (const AjPStr str);
unsigned long long  ajMathCrc64 (const AjPStr str);