gclib/tophat_cpp/GBase.h

#ifndef G_BASE_DEFINED
#define G_BASE_DEFINED
#ifndef _POSIX_SOURCE
//mostly for MinGW
#define _POSIX_SOURCE
#endif
#ifdef HAVE_CONFIG_H
#include "config.h"
#endif
#include <string.h>
#include <stdlib.h>
#include <stdio.h>
#include <math.h>
#include <limits.h>
#include <sys/types.h>
#include <sys/stat.h>
#include <stdint.h>

#if defined __WIN32__ || defined WIN32 || defined _WIN32 || defined _WIN32_
  #ifndef __WIN32__
    #define __WIN32__
  #endif
  #include <windows.h>
  #include <io.h>
  #define CHPATHSEP '\\'
  #undef off_t
  #define off_t int64_t
  #ifdef _fseeki64
    #define fseeko(stream, offset, origin) _fseeki64(stream, offset, origin)
  #else
    /*
    #define _DEFINE_WIN32_FSEEKO
    int fseeko(FILE *stream, off_t offset, int whence);
    */
    #define fseeko fseek
  #endif
  #ifdef _ftelli64
    #define ftello(stream) _ftelli64(stream)
  #else
    /*
    #define _DEFINE_WIN32_FTELLO
    off_t ftello(FILE *stream);
    */
    #define ftello ftell
  #endif
 #else
  #define CHPATHSEP '/'
  #include <unistd.h>
#endif


#ifdef DEBUG
#undef NDEBUG
#endif

typedef int32_t int32;
typedef uint32_t uint32;

typedef unsigned char uchar;
typedef unsigned char byte;

#ifndef MAXUINT
#define MAXUINT ((unsigned int)-1)
#endif

#ifndef MAXINT
#define MAXINT INT_MAX
#endif

#ifndef MAX_UINT
#define MAX_UINT ((unsigned int)-1)
#endif

#ifndef MAX_INT
#define MAX_INT INT_MAX
#endif

typedef int64_t int64;
typedef uint64_t uint64;

/****************************************************************************/

#ifndef EXIT_FAILURE
#define EXIT_FAILURE 1
#endif

#ifndef EXIT_SUCCESS
#define EXIT_SUCCESS 0
#endif

/****************************************************************************/
#define ERR_ALLOC "Error allocating memory.\n"

//-------------------

// Debug helpers
#ifndef NDEBUG
 #define GASSERT(exp) ((exp)?((void)0):(void)GAssert(#exp,__FILE__,__LINE__))
 #ifdef TRACE
  #define GTRACE(exp)  (GMessage exp)
 #else
  #define GTRACE(exp)  ((void)0)
 #endif
#else
 #define GASSERT(exp) ((void)0)
 #define GTRACE(exp)  ((void)0)
#endif

#define GERROR(exp) (GError exp)
/**********************************  Macros  ***********************************/
// Abolute value
#define GABS(val) (((val)>=0)?(val):-(val))

// Min and Max
#define GMAX(a,b) (((a)>(b))?(a):(b))
#define GMIN(a,b) (((a)>(b))?(b):(a))

// Min of three
#define GMIN3(x,y,z) ((x)<(y)?GMIN(x,z):GMIN(y,z))

// Max of three
#define GMAX3(x,y,z) ((x)>(y)?GMAX(x,z):GMAX(y,z))

// Return minimum and maximum of a, b
#define GMINMAX(lo,hi,a,b) ((a)<(b)?((lo)=(a),(hi)=(b)):((lo)=(b),(hi)=(a)))

// Clamp value x to range [lo..hi]
#define GCLAMP(lo,x,hi) ((x)<(lo)?(lo):((x)>(hi)?(hi):(x)))

typedef void* pointer;
typedef unsigned int uint;

typedef int GCompareProc(const pointer item1, const pointer item2);
typedef void GFreeProc(pointer item); //usually just delete,
      //but may also support structures with embedded dynamic members

#define GMALLOC(ptr,size)  if (!GMalloc((pointer*)(&ptr),size)) \
                                     GError(ERR_ALLOC)
#define GCALLOC(ptr,size)  if (!GCalloc((pointer*)(&ptr),size)) \
                                     GError(ERR_ALLOC)
#define GREALLOC(ptr,size) if (!GRealloc((pointer*)(&ptr),size)) \
                                     GError(ERR_ALLOC)
#define GFREE(ptr)       GFree((pointer*)(&ptr))

inline char* strMin(char *arg1, char *arg2) {
    return (strcmp(arg1, arg2) < 0)? arg1 : arg2;
}

inline char* strMax(char *arg1, char *arg2) {
    return (strcmp(arg2, arg1) < 0)? arg1 : arg2;
}

inline int iround(double x) {
   return (int)floor(x + 0.5);
}

/****************************************************************************/

inline int Gintcmp(int a, int b) {
 //return (a>b)? 1 : ((a==b)?0:-1);
  return a-b;
}

int Gstrcmp(char* a, char* b);
//same as strcmp but doesn't crash on NULL pointers

int Gstricmp(const char* a, const char* b);

inline void swap(int &arg1, int &arg2){
 //arg1 ^= arg2;
 //arg2 ^= arg1;
 //arg1 ^= arg2;
 register int swp=arg1;
 arg1=arg2; arg2=swp;
 }

inline void swap(char* &arg1, char* &arg2){ //swap pointers!
 register char* swp=arg1;
 arg1=arg2; arg2=swp;
 }

inline void swap(uint &arg1, uint &arg2) {
  register uint swp=arg1;
  arg1=arg2; arg2=swp;
  }

inline void swap(short &arg1, short &arg2) {
  register short swp=arg1;
  arg1=arg2; arg2=swp;
  }

inline void swap(unsigned short &arg1, unsigned short &arg2) {
  register unsigned short swp=arg1;
  arg1=arg2; arg2=swp;
  }

inline void swap(long &arg1, long &arg2) {
  register long swp=arg1;
  arg1=arg2; arg2=swp;
  }

inline void swap(unsigned long &arg1, unsigned long &arg2) {
  register unsigned long swp=arg1;
  arg1=arg2; arg2=swp;
  }


inline void swap(char &arg1, char &arg2) {
  register char swp=arg1;
  arg1=arg2; arg2=swp;
  }

inline void swap(unsigned char &arg1, unsigned char &arg2) {
  register unsigned char swp=arg1;
  arg1=arg2; arg2=swp;
  }

/**************** Memory management ***************************/

bool GMalloc(pointer* ptr, unsigned long size); // Allocate memory
bool GCalloc(pointer* ptr, unsigned long size); // Allocate and initialize memory
bool GRealloc(pointer* ptr,unsigned long size); // Resize memory
void GFree(pointer* ptr); // Free memory, resets ptr to NULL


int saprintf(char **retp, const char *fmt, ...);

void GError(const char* format,...); // Error routine (aborts program)
void GMessage(const char* format,...);// Log message to stderr
// Assert failed routine:- usually not called directly but through GASSERT
void GAssert(const char* expression, const char* filename, unsigned int lineno);

// ****************** string manipulation *************************
char *Gstrdup(const char* str);
//duplicate a string by allocating a copy for it and returning it
char* Gstrdup(const char* sfrom, const char* sto);
//same as GStrdup, but with an early termination (e.g. on delimiter)

char* Gsubstr(const char* str, char* from, char* to=NULL);
//extracts a substring, allocating it, including boundaries (from/to)

int strsplit(char* str, char** fields, int maxfields, const char* delim);
int strsplit(char* str, char** fields, int maxfields, const char delim);
int strsplit(char* str, char** fields, int maxfields); //splits by tab or space

char* replaceStr(char* &str, char* newvalue);

//conversion: to Lower/Upper case
// creating a new string:
char* upCase(const char* str);
char* loCase(const char* str);
// changing string in place:
char* strlower(char * str);
char* strupper(char * str);

//strstr but for memory zones: scans a memory region
//for a substring:
void* Gmemscan(void *mem, unsigned int len,
                  void *part, unsigned int partlen);

// test if a char is in a string:
bool chrInStr(char c, const char* str);

char* rstrchr(char* str, char ch);
/* returns a pointer to the rightmost
  occurence of ch in str - like rindex for platforms missing it*/

char* strchrs(const char* s, const char* chrs);
//strchr but with a set of chars instead of only one

char* rstrfind(const char* str, const char *substr); /* like rindex() but for strings
or like the right side version of strstr()
*/
//reverse character string or
char* reverseChars(char* str, int slen=0);

char* rstrstr(const char* rstart, const char *lend, const char* substr);
/*the reversed, rightside equivalent of strstr: starts searching
 from right end (rstart), going back to left end (lend) and returns
 a pointer to the last (right) matching character in str */

char* strifind(const char* str,  const char* substr);
// the case insensitive version of strstr -- finding a string within a strin


//Determines if a string begins with a given prefix
//(returns false when any of the params is NULL,
// but true when prefix is '' (empty string)!)
bool startsWith(const char* s, const char* prefix);

bool endsWith(const char* s, const char* suffix);
//Note: returns true if suffix is empty string, but false if it's NULL


// ELF hash function for strings
int strhash(const char* str);


//---- generic base GSeg : genomic segment (interval) --
// coordinates are considered 1-based (so 0 is invalid)
class GSeg {
 public:
  uint start; //start<end always!
  uint end;
  GSeg(uint s=0,uint e=0) {
    if (s>e) { start=e;end=s; }
        else { start=s;end=e; }
    }
  //check for overlap with other segment
  uint len() { return end-start+1; }
  bool overlap(GSeg* d) {
     //return start<d->start ? (d->start<=end) : (start<=d->end);
     return (start<=d->end && end>=d->start);
     }

  bool overlap(GSeg& d) {
     //return start<d.start ? (d.start<=end) : (start<=d.end);
     return (start<=d.end && end>=d.start);
     }

  bool overlap(GSeg& d, int fuzz) {
     //return start<d.start ? (d.start<=end+fuzz) : (start<=d.end+fuzz);
     return (start<=d.end+fuzz && end+fuzz>=d.start);
     }

  bool overlap(uint s, uint e) {
     if (s>e) { swap(s,e); }
     //return start<s ? (s<=end) : (start<=e);
     return (start<=e && end>=s);
     }

  //return the length of overlap between two segments
  int overlapLen(GSeg* r) {
     if (start<r->start) {
        if (r->start>end) return 0;
        return (r->end>end) ? end-r->start+1 : r->end-r->start+1;
        }
       else { //r->start<=start
        if (start>r->end) return 0;
        return (r->end<end)? r->end-start+1 : end-start+1;
        }
     }
  int overlapLen(uint rstart, uint rend) {
     if (rstart>rend) { swap(rstart,rend); }
     if (start<rstart) {
        if (rstart>end) return 0;
        return (rend>end) ? end-rstart+1 : rend-rstart+1;
        }
       else { //rstart<=start
        if (start>rend) return 0;
        return (rend<end)? rend-start+1 : end-start+1;
        }
     }

  //fuzzy coordinate matching:
  bool coordMatch(GSeg* s, uint fuzz=0) {
    if (fuzz==0) return (start==s->start && end==s->end);
    uint sd = (start>s->start) ? start-s->start : s->start-start;
    uint ed = (end>s->end) ? end-s->end : s->end-end;
    return (sd<=fuzz && ed<=fuzz);
    }
  //comparison operators required for sorting
  bool operator==(GSeg& d){
      return (start==d.start && end==d.end);
      }
  bool operator>(GSeg& d){
     return (start==d.start)?(end>d.end):(start>d.start);
     }
  bool operator<(GSeg& d){
     return (start==d.start)?(end<d.end):(start<d.start);
     }
};


//--------------------------------------------------------
// ************** simple line reading class for text files

//GLineReader -- text line reading/buffering class
class GLineReader {
   bool closeFile;
   int len;
   int allocated;
   char* buf;
   bool isEOF;
   FILE* file;
   off_t filepos; //current position
   bool pushed; //pushed back
   int lcount; //line counter (read lines)
 public:
   char* chars() { return buf; }
   char* line() { return buf; }
   int readcount() { return lcount; } //number of lines read
   void setFile(FILE* stream) { file=stream; }
   int length() { return len; }
   int size() { return len; } //same as size();
   bool isEof() {return isEOF; }
   bool eof() { return isEOF; }
   off_t getfpos() { return filepos; }
   off_t getFpos() { return filepos; }
   char* nextLine() { return getLine(); }
   char* getLine() { if (pushed) { pushed=false; return buf; }
                            else return getLine(file);  }
   char* getLine(FILE* stream) {
                 if (pushed) { pushed=false; return buf; }
                          else return getLine(stream, filepos); }
   char* getLine(FILE* stream, off_t& f_pos); //read a line from a stream and update
                           // the given file position
   void pushBack() { if (lcount>0) pushed=true; } // "undo" the last getLine request
            // so the next call will in fact return the same line
   GLineReader(const char* fname) {
      FILE* f=fopen(fname, "rb");
      if (f==NULL) GError("Error opening file '%s'!\n",fname);
      closeFile=true;
      init(f);
      }
   GLineReader(FILE* stream=NULL, off_t fpos=0) {
     closeFile=false;
     init(stream,fpos);
     }
   void init(FILE* stream, off_t fpos=0) {
     len=0;
     isEOF=false;
     allocated=1024;
     GMALLOC(buf,allocated);
     lcount=0;
     buf[0]=0;
     file=stream;
     filepos=fpos;
     pushed=false;
     }
   ~GLineReader() {
     GFREE(buf);
     if (closeFile) fclose(file);
     }
};


/* extended fgets() -  to read one full line from a file and
  update the file position correctly !
  buf will be reallocated as necessary, to fit the whole line
  */
char* fgetline(char* & buf, int& buflen, FILE* stream, off_t* f_pos=NULL, int* linelen=NULL);


//print int/values nicely formatted in 3-digit groups
char* commaprint(uint64 n);

/*********************** File management functions *********************/

// removes the last part (file or directory name) of a full path
// WARNING: this is a destructive operation for the given string!
void delFileName(char* filepath);

// returns a pointer to the last file or directory name in a full path
const char* getFileName(const char* filepath);
// returns a pointer to the file "extension" part in a filename
const char* getFileExt(const char* filepath);


int fileExists(const char* fname);
//returns 0 if file entry doesn't exist
//        1 if it's a directory
//        2 if it's a regular file
//        3 otherwise (?)

int64 fileSize(const char* fpath);

//write a formatted fasta record, fasta formatted
void writeFasta(FILE *fw, const char* seqid, const char* descr,
        const char* seq, int linelen=60, int seqlen=0);

//parses the next number found in a string at the current position
//until a non-digit (and not a '.', 'e','E','-','+') is encountered;
//updates the char* pointer to be after the last digit parsed
bool parseNumber(char* &p, double& v);
bool parseDouble(char* &p, double& v); //just an alias for parseNumber

bool parseInt(char* &p, int& i);
bool parseUInt(char* &p, uint& i);
bool parseHex(char* &p,  uint& i);

#endif /* G_BASE_DEFINED */
Revision:	29
Committed:	Tue Aug 2 21:24:54 2011 UTC (13 years, 1 month ago) by gpertea
File size:	13918 byte(s)
Log Message:	adding tophat source work
Line	User	Rev	File contents
1	gpertea	29	#ifndef G_BASE_DEFINED
2			#define G_BASE_DEFINED
3			#ifndef _POSIX_SOURCE
4			//mostly for MinGW
5			#define _POSIX_SOURCE
6			#endif
7			#ifdef HAVE_CONFIG_H
8			#include "config.h"
9			#endif
10			#include <string.h>
11			#include <stdlib.h>
12			#include <stdio.h>
13			#include <math.h>
14			#include <limits.h>
15			#include <sys/types.h>
16			#include <sys/stat.h>
17			#include <stdint.h>
18
19			#if defined __WIN32__ \|\| defined WIN32 \|\| defined _WIN32 \|\| defined _WIN32_
20			#ifndef __WIN32__
21			#define __WIN32__
22			#endif
23			#include <windows.h>
24			#include <io.h>
25			#define CHPATHSEP '\\'
26			#undef off_t
27			#define off_t int64_t
28			#ifdef _fseeki64
29			#define fseeko(stream, offset, origin) _fseeki64(stream, offset, origin)
30			#else
31			/*
32			#define _DEFINE_WIN32_FSEEKO
33			int fseeko(FILE *stream, off_t offset, int whence);
34			*/
35			#define fseeko fseek
36			#endif
37			#ifdef _ftelli64
38			#define ftello(stream) _ftelli64(stream)
39			#else
40			/*
41			#define _DEFINE_WIN32_FTELLO
42			off_t ftello(FILE *stream);
43			*/
44			#define ftello ftell
45			#endif
46			#else
47			#define CHPATHSEP '/'
48			#include <unistd.h>
49			#endif
50
51
52			#ifdef DEBUG
53			#undef NDEBUG
54			#endif
55
56			typedef int32_t int32;
57			typedef uint32_t uint32;
58
59			typedef unsigned char uchar;
60			typedef unsigned char byte;
61
62			#ifndef MAXUINT
63			#define MAXUINT ((unsigned int)-1)
64			#endif
65
66			#ifndef MAXINT
67			#define MAXINT INT_MAX
68			#endif
69
70			#ifndef MAX_UINT
71			#define MAX_UINT ((unsigned int)-1)
72			#endif
73
74			#ifndef MAX_INT
75			#define MAX_INT INT_MAX
76			#endif
77
78			typedef int64_t int64;
79			typedef uint64_t uint64;
80
81			/****************************************************************************/
82
83			#ifndef EXIT_FAILURE
84			#define EXIT_FAILURE 1
85			#endif
86
87			#ifndef EXIT_SUCCESS
88			#define EXIT_SUCCESS 0
89			#endif
90
91			/****************************************************************************/
92			#define ERR_ALLOC "Error allocating memory.\n"
93
94			//-------------------
95
96			// Debug helpers
97			#ifndef NDEBUG
98			#define GASSERT(exp) ((exp)?((void)0):(void)GAssert(#exp,__FILE__,__LINE__))
99			#ifdef TRACE
100			#define GTRACE(exp) (GMessage exp)
101			#else
102			#define GTRACE(exp) ((void)0)
103			#endif
104			#else
105			#define GASSERT(exp) ((void)0)
106			#define GTRACE(exp) ((void)0)
107			#endif
108
109			#define GERROR(exp) (GError exp)
110			/******************************** Macros *********************************/
111			// Abolute value
112			#define GABS(val) (((val)>=0)?(val):-(val))
113
114			// Min and Max
115			#define GMAX(a,b) (((a)>(b))?(a):(b))
116			#define GMIN(a,b) (((a)>(b))?(b):(a))
117
118			// Min of three
119			#define GMIN3(x,y,z) ((x)<(y)?GMIN(x,z):GMIN(y,z))
120
121			// Max of three
122			#define GMAX3(x,y,z) ((x)>(y)?GMAX(x,z):GMAX(y,z))
123
124			// Return minimum and maximum of a, b
125			#define GMINMAX(lo,hi,a,b) ((a)<(b)?((lo)=(a),(hi)=(b)):((lo)=(b),(hi)=(a)))
126
127			// Clamp value x to range [lo..hi]
128			#define GCLAMP(lo,x,hi) ((x)<(lo)?(lo):((x)>(hi)?(hi):(x)))
129
130			typedef void* pointer;
131			typedef unsigned int uint;
132
133			typedef int GCompareProc(const pointer item1, const pointer item2);
134			typedef void GFreeProc(pointer item); //usually just delete,
135			//but may also support structures with embedded dynamic members
136
137			#define GMALLOC(ptr,size) if (!GMalloc((pointer*)(&ptr),size)) \
138			GError(ERR_ALLOC)
139			#define GCALLOC(ptr,size) if (!GCalloc((pointer*)(&ptr),size)) \
140			GError(ERR_ALLOC)
141			#define GREALLOC(ptr,size) if (!GRealloc((pointer*)(&ptr),size)) \
142			GError(ERR_ALLOC)
143			#define GFREE(ptr) GFree((pointer*)(&ptr))
144
145			inline char* strMin(char arg1, char arg2) {
146			return (strcmp(arg1, arg2) < 0)? arg1 : arg2;
147			}
148
149			inline char* strMax(char arg1, char arg2) {
150			return (strcmp(arg2, arg1) < 0)? arg1 : arg2;
151			}
152
153			inline int iround(double x) {
154			return (int)floor(x + 0.5);
155			}
156
157			/****************************************************************************/
158
159			inline int Gintcmp(int a, int b) {
160			//return (a>b)? 1 : ((a==b)?0:-1);
161			return a-b;
162			}
163
164			int Gstrcmp(char* a, char* b);
165			//same as strcmp but doesn't crash on NULL pointers
166
167			int Gstricmp(const char* a, const char* b);
168
169			inline void swap(int &arg1, int &arg2){
170			//arg1 ^= arg2;
171			//arg2 ^= arg1;
172			//arg1 ^= arg2;
173			register int swp=arg1;
174			arg1=arg2; arg2=swp;
175			}
176
177			inline void swap(char* &arg1, char* &arg2){ //swap pointers!
178			register char* swp=arg1;
179			arg1=arg2; arg2=swp;
180			}
181
182			inline void swap(uint &arg1, uint &arg2) {
183			register uint swp=arg1;
184			arg1=arg2; arg2=swp;
185			}
186
187			inline void swap(short &arg1, short &arg2) {
188			register short swp=arg1;
189			arg1=arg2; arg2=swp;
190			}
191
192			inline void swap(unsigned short &arg1, unsigned short &arg2) {
193			register unsigned short swp=arg1;
194			arg1=arg2; arg2=swp;
195			}
196
197			inline void swap(long &arg1, long &arg2) {
198			register long swp=arg1;
199			arg1=arg2; arg2=swp;
200			}
201
202			inline void swap(unsigned long &arg1, unsigned long &arg2) {
203			register unsigned long swp=arg1;
204			arg1=arg2; arg2=swp;
205			}
206
207
208			inline void swap(char &arg1, char &arg2) {
209			register char swp=arg1;
210			arg1=arg2; arg2=swp;
211			}
212
213			inline void swap(unsigned char &arg1, unsigned char &arg2) {
214			register unsigned char swp=arg1;
215			arg1=arg2; arg2=swp;
216			}
217
218			/************** Memory management *************************/
219
220			bool GMalloc(pointer* ptr, unsigned long size); // Allocate memory
221			bool GCalloc(pointer* ptr, unsigned long size); // Allocate and initialize memory
222			bool GRealloc(pointer* ptr,unsigned long size); // Resize memory
223			void GFree(pointer* ptr); // Free memory, resets ptr to NULL
224
225
226			int saprintf(char *retp, const char fmt, ...);
227
228			void GError(const char* format,...); // Error routine (aborts program)
229			void GMessage(const char* format,...);// Log message to stderr
230			// Assert failed routine:- usually not called directly but through GASSERT
231			void GAssert(const char* expression, const char* filename, unsigned int lineno);
232
233			// **************** string manipulation ***********************
234			char Gstrdup(const char str);
235			//duplicate a string by allocating a copy for it and returning it
236			char* Gstrdup(const char* sfrom, const char* sto);
237			//same as GStrdup, but with an early termination (e.g. on delimiter)
238
239			char* Gsubstr(const char* str, char* from, char* to=NULL);
240			//extracts a substring, allocating it, including boundaries (from/to)
241
242			int strsplit(char* str, char** fields, int maxfields, const char* delim);
243			int strsplit(char* str, char** fields, int maxfields, const char delim);
244			int strsplit(char* str, char** fields, int maxfields); //splits by tab or space
245
246			char* replaceStr(char* &str, char* newvalue);
247
248			//conversion: to Lower/Upper case
249			// creating a new string:
250			char* upCase(const char* str);
251			char* loCase(const char* str);
252			// changing string in place:
253			char* strlower(char * str);
254			char* strupper(char * str);
255
256			//strstr but for memory zones: scans a memory region
257			//for a substring:
258			void* Gmemscan(void *mem, unsigned int len,
259			void *part, unsigned int partlen);
260
261			// test if a char is in a string:
262			bool chrInStr(char c, const char* str);
263
264			char* rstrchr(char* str, char ch);
265			/* returns a pointer to the rightmost
266			occurence of ch in str - like rindex for platforms missing it*/
267
268			char* strchrs(const char* s, const char* chrs);
269			//strchr but with a set of chars instead of only one
270
271			char* rstrfind(const char* str, const char substr); / like rindex() but for strings
272			or like the right side version of strstr()
273			*/
274			//reverse character string or
275			char* reverseChars(char* str, int slen=0);
276
277			char* rstrstr(const char* rstart, const char lend, const char substr);
278			/*the reversed, rightside equivalent of strstr: starts searching
279			from right end (rstart), going back to left end (lend) and returns
280			a pointer to the last (right) matching character in str */
281
282			char* strifind(const char* str, const char* substr);
283			// the case insensitive version of strstr -- finding a string within a strin
284
285
286			//Determines if a string begins with a given prefix
287			//(returns false when any of the params is NULL,
288			// but true when prefix is '' (empty string)!)
289			bool startsWith(const char* s, const char* prefix);
290
291			bool endsWith(const char* s, const char* suffix);
292			//Note: returns true if suffix is empty string, but false if it's NULL
293
294
295			// ELF hash function for strings
296			int strhash(const char* str);
297
298
299
300			//---- generic base GSeg : genomic segment (interval) --
301			// coordinates are considered 1-based (so 0 is invalid)
302			class GSeg {
303			public:
304			uint start; //start<end always!
305			uint end;
306			GSeg(uint s=0,uint e=0) {
307			if (s>e) { start=e;end=s; }
308			else { start=s;end=e; }
309			}
310			//check for overlap with other segment
311			uint len() { return end-start+1; }
312			bool overlap(GSeg* d) {
313			//return start<d->start ? (d->start<=end) : (start<=d->end);
314			return (start<=d->end && end>=d->start);
315			}
316
317			bool overlap(GSeg& d) {
318			//return start<d.start ? (d.start<=end) : (start<=d.end);
319			return (start<=d.end && end>=d.start);
320			}
321
322			bool overlap(GSeg& d, int fuzz) {
323			//return start<d.start ? (d.start<=end+fuzz) : (start<=d.end+fuzz);
324			return (start<=d.end+fuzz && end+fuzz>=d.start);
325			}
326
327			bool overlap(uint s, uint e) {
328			if (s>e) { swap(s,e); }
329			//return start<s ? (s<=end) : (start<=e);
330			return (start<=e && end>=s);
331			}
332
333			//return the length of overlap between two segments
334			int overlapLen(GSeg* r) {
335			if (start<r->start) {
336			if (r->start>end) return 0;
337			return (r->end>end) ? end-r->start+1 : r->end-r->start+1;
338			}
339			else { //r->start<=start
340			if (start>r->end) return 0;
341			return (r->end<end)? r->end-start+1 : end-start+1;
342			}
343			}
344			int overlapLen(uint rstart, uint rend) {
345			if (rstart>rend) { swap(rstart,rend); }
346			if (start<rstart) {
347			if (rstart>end) return 0;
348			return (rend>end) ? end-rstart+1 : rend-rstart+1;
349			}
350			else { //rstart<=start
351			if (start>rend) return 0;
352			return (rend<end)? rend-start+1 : end-start+1;
353			}
354			}
355
356			//fuzzy coordinate matching:
357			bool coordMatch(GSeg* s, uint fuzz=0) {
358			if (fuzz==0) return (start==s->start && end==s->end);
359			uint sd = (start>s->start) ? start-s->start : s->start-start;
360			uint ed = (end>s->end) ? end-s->end : s->end-end;
361			return (sd<=fuzz && ed<=fuzz);
362			}
363			//comparison operators required for sorting
364			bool operator==(GSeg& d){
365			return (start==d.start && end==d.end);
366			}
367			bool operator>(GSeg& d){
368			return (start==d.start)?(end>d.end):(start>d.start);
369			}
370			bool operator<(GSeg& d){
371			return (start==d.start)?(end<d.end):(start<d.start);
372			}
373			};
374
375
376
377			//--------------------------------------------------------
378			// ************** simple line reading class for text files
379
380			//GLineReader -- text line reading/buffering class
381			class GLineReader {
382			bool closeFile;
383			int len;
384			int allocated;
385			char* buf;
386			bool isEOF;
387			FILE* file;
388			off_t filepos; //current position
389			bool pushed; //pushed back
390			int lcount; //line counter (read lines)
391			public:
392			char* chars() { return buf; }
393			char* line() { return buf; }
394			int readcount() { return lcount; } //number of lines read
395			void setFile(FILE* stream) { file=stream; }
396			int length() { return len; }
397			int size() { return len; } //same as size();
398			bool isEof() {return isEOF; }
399			bool eof() { return isEOF; }
400			off_t getfpos() { return filepos; }
401			off_t getFpos() { return filepos; }
402			char* nextLine() { return getLine(); }
403			char* getLine() { if (pushed) { pushed=false; return buf; }
404			else return getLine(file); }
405			char* getLine(FILE* stream) {
406			if (pushed) { pushed=false; return buf; }
407			else return getLine(stream, filepos); }
408			char* getLine(FILE* stream, off_t& f_pos); //read a line from a stream and update
409			// the given file position
410			void pushBack() { if (lcount>0) pushed=true; } // "undo" the last getLine request
411			// so the next call will in fact return the same line
412			GLineReader(const char* fname) {
413			FILE* f=fopen(fname, "rb");
414			if (f==NULL) GError("Error opening file '%s'!\n",fname);
415			closeFile=true;
416			init(f);
417			}
418			GLineReader(FILE* stream=NULL, off_t fpos=0) {
419			closeFile=false;
420			init(stream,fpos);
421			}
422			void init(FILE* stream, off_t fpos=0) {
423			len=0;
424			isEOF=false;
425			allocated=1024;
426			GMALLOC(buf,allocated);
427			lcount=0;
428			buf[0]=0;
429			file=stream;
430			filepos=fpos;
431			pushed=false;
432			}
433			~GLineReader() {
434			GFREE(buf);
435			if (closeFile) fclose(file);
436			}
437			};
438
439
440			/* extended fgets() - to read one full line from a file and
441			update the file position correctly !
442			buf will be reallocated as necessary, to fit the whole line
443			*/
444			char* fgetline(char* & buf, int& buflen, FILE* stream, off_t* f_pos=NULL, int* linelen=NULL);
445
446
447			//print int/values nicely formatted in 3-digit groups
448			char* commaprint(uint64 n);
449
450			/********************* File management functions *******************/
451
452			// removes the last part (file or directory name) of a full path
453			// WARNING: this is a destructive operation for the given string!
454			void delFileName(char* filepath);
455
456			// returns a pointer to the last file or directory name in a full path
457			const char* getFileName(const char* filepath);
458			// returns a pointer to the file "extension" part in a filename
459			const char* getFileExt(const char* filepath);
460
461
462			int fileExists(const char* fname);
463			//returns 0 if file entry doesn't exist
464			// 1 if it's a directory
465			// 2 if it's a regular file
466			// 3 otherwise (?)
467
468			int64 fileSize(const char* fpath);
469
470			//write a formatted fasta record, fasta formatted
471			void writeFasta(FILE fw, const char seqid, const char* descr,
472			const char* seq, int linelen=60, int seqlen=0);
473
474			//parses the next number found in a string at the current position
475			//until a non-digit (and not a '.', 'e','E','-','+') is encountered;
476			//updates the char* pointer to be after the last digit parsed
477			bool parseNumber(char* &p, double& v);
478			bool parseDouble(char* &p, double& v); //just an alias for parseNumber
479
480			bool parseInt(char* &p, int& i);
481			bool parseUInt(char* &p, uint& i);
482			bool parseHex(char* &p, uint& i);
483
484			#endif /* G_BASE_DEFINED */