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/**
* Author: Andreas Wilm
* Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.
*
*/
#ifndef STATS_H
#define STATS_H
namespace clustalw
{
using namespace std;
/** Log simple statistics about input and output
*
* @section LICENSE
* FIXME: please add license text
*
* @section DESCRIPTION
* The hashing functions have to be enabled at compile/configure time
* otherwise they will not be used.
*
*
*/
class Stats {
public:
/* FUNCTIONS */
/** constructor */
Stats();
/** destructor */
~Stats();
/** set the name of the file where stats are logged to
* @param f filename
*/
void setStatsFile(string f) {logfilename=f;};
/**
* return name of used stats file
* @return file name
*/
string getStatsFile() {return logfilename;};
/** enable stats logging
*/
void setEnabled(bool b) {enabled=b;};
/** check if stats logging is enabled
* @return true if enabled, false otherwise
*/
bool isEnabled() {return enabled;};
/** log the command line arguments
* @param argc number arguments
* @param argv argument array
*/
void logCmdLine(int argc, char **argv);
/** log statistics about sequence input
* @param alnObj: input "alignment" (confusing isn't it?)
*/
void logInputSeqStats(Alignment *alnObj);
/** log statistics about sequence input
* @param alnObj: input "alignment" (confusing isn't it?)
*/
void logAlignedSeqStats(Alignment *alnObj);
/* ATTRIBUTES */
private:
/* FUNCTIONS */
/** Compute pairwise identity of two sequences
*
* Adopted from Sean Eddy'ssquid:aligneval.c
* He defines pairwise identity as fraction:
* idents / min(len1, len2)
*
* Function is case sensitive!
*
* @param alnObj alignment object
* @param s1 index of first sequence
* @param s2 index of first sequence
* @return pairwise identity as float
*/
float pairwiseIdentity(Alignment *alnObj, int s1, int s2);
#ifdef HAVE_MHASH_H
/** compute md5 hash from string
* @param thread string to hash
* @return hash string, or NULL on failure
*/
char * Md5Hash(const char *thread);
/** compute md5 hash for a sequence
* @param alnObj alignment object
* @param s index of sequence
* @return md5 hash string
*/
string Md5ForSeq(Alignment *alnObj, int s);
/** compute md5 hash for all sequences
* sorts and concatenates all sequences beforehand
* thus sequence order doesn't matter
*
* @param alnObj alignment object
* @param s index of sequence
* @return md5 hash string
*/
string ConcatInputHash(Alignment *alnObj);
#endif
/* ATTRIBUTES */
/** the filename used for logging statistics */
string logfilename;
/** logging of statistics enabled */
bool enabled;
};
}
#endif
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