Delete unneeded directory

[jabaws.git] / website / archive / binaries / mac / src / clustalw / src / general / Stats.h

diff --git a/website/archive/binaries/mac/src/clustalw/src/general/Stats.h b/website/archive/binaries/mac/src/clustalw/src/general/Stats.h
deleted file mode 100644 (file)
index bf9768d..0000000
--- a/website/archive/binaries/mac/src/clustalw/src/general/Stats.h
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@@ -1,131 +0,0 @@
-/**
- * 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