Description:

Read the command line options selected by the user, checking incompatibilities among options or problems with the number of input filenames. Every chosen option is represented by raising the corresponding flag (global var).

Briefing:

void printHelp()

Output the list of available options.

void printDTD()

Output the Document Type Definition to validate the XML output (only for best predicted genes).

void readargv (int argc,char* argv[], char* ParamFile, char* SequenceFile, char* ExonsFile, char* HSPFile)

Read the options selected by the user watching incompatibilities (among different options and about number of input filenames), setting the proper global vars (geneid.c) and acquiring the name of different external but optional filenames: parameter, exons (evidences) and similarity to protein regions.

Enrique Blanco Garcia © 2003