+++ /dev/null
-/* -*- mode: c; tab-width: 4; c-basic-offset: 4; indent-tabs-mode: nil -*- */
-
-/*********************************************************************
- * Clustal Omega - Multiple sequence alignment
- *
- * Copyright (C) 2010 University College Dublin
- *
- * Clustal-Omega is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License as
- * published by the Free Software Foundation; either version 2 of the
- * License, or (at your option) any later version.
- *
- * This file is part of Clustal-Omega.
- *
- ********************************************************************/
-
-/*
- * RCS $Id: util-C.h 155 2010-11-17 12:18:47Z fabian $
- */
-
-// Utility subroutines
-
-
-#ifndef MAIN
-#include <iostream> // cin, cout, cerr
-#include <fstream> // ofstream, ifstream
-#include <cstdio> // printf
-#include <stdlib.h> // exit
-#include <time.h> // clock
-#endif
-#include <sys/time.h>
-
-/////////////////////////////////////////////////////////////////////////////////////
-// Arithmetics
-/////////////////////////////////////////////////////////////////////////////////////
-
-//// max and min
-inline double dmax(double x, double y) { return (x>y? x : y);}
-inline double dmin(double x, double y) { return (x<y? x : y);}
-inline int imax(int x, int y) { return (x>y? x : y);}
-inline int imin(int x, int y) { return (x<y? x : y);}
-inline int iabs(int x) { return (x>=0? x : -x);}
-
-// Rounding up, rounding down and rounding to nearest integer
-inline int iceil(double x) {return int(ceil(x));}
-inline int ifloor(double x) {return int(floor(x));}
-inline int iround(double x) {return int(floor(x+0.5));}
-
-//// Generalized mean: d=0: sqrt(x*y) d=1: (x+y)/2 d->-inf: min(x,y) d->+inf: max(x,y)
-inline double fmean(double x, double y, double d) { return pow( (pow(x,d)+pow(y,d))/2 ,1./d);}
-
-// log base 2
-inline float log2(float x) {return (x<=0? (float)(-100000):1.442695041*log(x));}
-inline float log10(float x) {return (x<=0? (float)(-100000):0.434294481*log(x));}
-
-
-/////////////////////////////////////////////////////////////////////////////////////
-// fast log base 2
-/////////////////////////////////////////////////////////////////////////////////////
-
-// This function returns log2 with a max abolute deviation of +/- 1.5E-5 (typically 0.8E-5).
-// It takes 1.42E-8 s whereas log2(x) takes 9.5E-7 s. It is hence 9.4 times faster.
-// It makes use of the representation of 4-byte floating point numbers:
-// seee eeee emmm mmmm mmmm mmmm mmmm mmmm
-// s is the sign,
-// the following 8 bits, eee eee e, give the exponent + 127 (in hex: 0x7f).
-// The following 23 bits, m, give the mantisse, the binary digits behind the decimal point.
-// In summary: x = (-1)^s * 1.mmmmmmmmmmmmmmmmmmmmmm * 2^(eeeeeee-127)
-// The expression (((*(int *)&x) & 0x7f800000 ) >>23 )-0x7f is the exponent eeeeeeee, i.e.
-// the largest integer that is smaller than log2(x) (e.g. -1 for 0.9). *(int *)&x is an integer which
-// contains the bytes as the floating point variable x is represented in memory.
-// Check: assert( sizeof(f) == sizeof(int) );
-// Check: assert( sizeof(f) == 4 );
-inline float fast_log2(float x)
-{
- static float lg2[1025]; // lg2[i] = log2[1+x/1024]
- static float diff[1025]; // diff[i]= (lg2[i+1]-lg2[i])/8096 (for interpolation)
- static char initialized;
- if (x<=0) return -100000;
- if (!initialized) //First fill in the arrays lg2[i] and diff[i]
- {
- float prev = 0.0f;
- lg2[0] = 0.0f;
- for (int i=1; i<=1024; ++i)
- {
- lg2[i] = log(float(1024+i))*1.442695041-10.0f;
- diff[i-1] = (lg2[i]-prev)*1.2352E-4;
- prev = lg2[i];
- }
- initialized=1;
- }
- int a = (((*((int *)&x)) & 0x7F800000) >>23 )-0x7f;
- int b = ((*((int *)&x)) & 0x007FE000) >>13;
- int c = ((*((int *)&x)) & 0x00001FFF);
- return a + lg2[b] + diff[b]*(float)(c);
-}
-
-/////////////////////////////////////////////////////////////////////////////////////
-// fast 2^x
-// ATTENTION: need to compile with g++ -fno-strict-aliasing when using -O2 or -O3!!!
-// Relative deviation < 1.5E-4
-/////////////////////////////////////////////////////////////////////////////////////
-inline float fpow2(float x)
-{
- if (x>=128) return FLT_MAX;
- if (x<=-128) return FLT_MIN;
- int *px = (int*)(&x); // store address of float as pointer to long
- float tx = (x-0.5f) + (3<<22); // temporary value for truncation: x-0.5 is added to a large integer (3<<22)
- int lx = *((int*)&tx) - 0x4b400000; // integer value of x
- float dx = x-(float)(lx); // float remainder of x
- x = 1.0f + dx*(0.6960656421638072f // cubic apporoximation of 2^x
- + dx*(0.224494337302845f // for x in the range [0, 1]
- + dx*(0.07944023841053369f)));
- *px += (lx<<23); // add integer power of 2 to exponent
- return x;
-}
-
-/////////////////////////////////////////////////////////////////////////////////////
-// ATTENTION:
-// Can't be used with -O2/-O3 optimization on some compilers !
-// Works with g++ version 4.1, but not with 3.4, in which case it returns values
-// that are a factor 1.002179942 too low
-//
-// Fast pow2 routine (Johannes Soeding)
-// Same speed as fpow2(), but *relative* deviation < 1.2E-7
-// Makes use of the binary representation of floats in memory:
-// x = (-1)^s * 1.mmmmmmmmmmmmmmmmmmmmmm * 2^(eeeeeee-127)
-// is represented as
-// 31 23 7654 3210
-// seee eeee emmm mmmm mmmm mmmm mmmm mmmm
-// s is the sign, the 8 bits eee eee e are the exponent + 127 (in hex: 0x7f),
-// and the following 23 bits m give the mantisse.
-// We decompose the argument x = a + b, with integer a and 0 <= b < 1
-// Therefore 2^x = 2^a * 2^b where a is the binary exponent of 2^x
-// and 1 <= 2^b < 2, i.e. 2^b determines the mantisse uniquely.
-// To calculate 2^b, we split b into the first 10 bits and the last 13 bits,
-// b = b' + c, and then look up the mantisse of 2^b' in a precomputed table.
-// We use the residual c to interpolate between the mantisse for 2^b' and 2(b'+1/1024)
-/////////////////////////////////////////////////////////////////////////////////////
-inline float fast_pow2(float x)
-{
- if (x<=-127) return 5.9E-39;
- if (x>=128) return 3.4E38;
- static char initialized=0;
- static unsigned int pow2[1025];
- static unsigned int diff[1025];
- static int y = 0;
- if (!initialized) //First fill in the pow2-vector
- {
- float f;
- unsigned int prev = 0;
- pow2[0] = 0;
- for (int b=1; b<1024; b++)
- {
- f=pow(2.0,float(b)/1024.0);
- pow2[b]=(*((unsigned int *)(&f)) & 0x7FFFFF); // store the mantisse of 2^(1+b/1024)
- diff[b-1]=pow2[b]-prev;
- prev=pow2[b];
- }
- pow2[1024]=0x7FFFFF;
- diff[1023]=pow2[1024]-prev;
- initialized=1;
- }
-
- int *px = (int *)(&x); // store address of float as pointer to int
- int E = ((*px & 0x7F800000)>>23)-127; // E is exponent of x and is <=6
- unsigned int M=(*px & 0x007FFFFF) | 0x00800000; // M is the mantisse 1.mmm mmmm mmmm mmmm mmmm mmmm
- int a,b,c;
- if (x>=0)
- {
- if (E>=0) {
- a = 0x3F800000 + ((M<<E) & 0x7F800000); // a is exponent of 2^x, beginning at bit 23
- b = ((M<<E) & 0x007FE000)>>13;
- c = ((M<<E) & 0x00001FFF);
- } else {
- a = 0x3F800000; // a = exponent of 2^x = 0
- b = ((M>>(-E)) & 0x007FE000)>>13;
- c = ((M>>(-E)) & 0x00001FFF);
- }
- }
- else
- {
- if (E>=0) {
- a = 0x3F000000 - ((M<<E) & 0x7F800000); // a is exponent of 2^x
- b = (0x00800000-(int)((M<<E) & 0x007FFFFF)) >>13;
- c = (0x00800000-(int)((M<<E) & 0x007FFFFF)) & 0x00001FFF;
- } else {
- a = 0x3F000000; // a = exponent of 2^x = -1
- b = (0x00800000-(int)((M>>(-E)) & 0x007FFFFF)) >>13;
- c = (0x00800000-(int)((M>>(-E)) & 0x007FFFFF)) & 0x00001FFF;
- }
- }
-/* printf("x=%0X\n",*px); */
-/* printf("E=%0X\n",E); */
-/* printf("M=%0X\n",M); */
-/* printf("a=%0X\n",a); */
-/* printf("b=%0X\n",b); */
- y = a | (pow2[b] + ((diff[b]*c)>>13) );
- /* printf("2^x=%0X\n",*px); */
- return *((float*)&y);
-}
-
-
-
-// Normalize a float array such that it sums to one
-// If it sums to 0 then assign def_array elements to array (optional)
-inline float NormalizeTo1(float* array, int length, float* def_array=NULL)
-{
- float sum=0.0f;
- int k;
- for (k=0; k<length; k++) sum+=array[k];
- if (sum!=0.0f)
- {
- float fac=1.0/sum;
- for (k=0; k<length; k++) array[k]*=fac;
- }
- else if (def_array)
- for (k=0; k<length; k++) array[k]=def_array[k];
- return sum;
-}
-
-// Normalize a float array such that it sums to x
-// If it sums to 0 then assign def_array elements to array (optional)
-inline float NormalizeToX(float* array, int length, float x, float* def_array=NULL)
-{
- float sum=0.0;
- int k;
- for (k=0; k<length; k++) sum+=array[k];
- if (sum)
- {
- float fac=x/sum;
- for (k=0; k<length; k++) array[k]*=fac;
- }
- else if (def_array)
- for (k=0; k<length; k++) array[k]=def_array[k];
- return sum;
-}
-
-/////////////////////////////////////////////////////////////////////////////////////
-// Similar to spintf("%*g,w,val), but displays maximum number of digits within width w
-/////////////////////////////////////////////////////////////////////////////////////
-inline char* sprintg(float val, int w)
-{
- static char str[100];
- float log10val = log10(fabs(val));
- int neg = (val<0? 1: 0);
- if (log10val >= w-neg-1 || -log10val > 3)
- {
- // positive exponential 1.234E+06
- // negative exponential 1.234E-06
- int d = w-6-neg;
- sprintf(str,"%*.*e",w,d<1?1:d,val);
- }
- else
- {
- int d = log10val>0? w-2-neg-int(log10val): w-2-neg;
- sprintf(str,"%#*.*f",w,d,val);
- }
- return str;
-}
-
-/////////////////////////////////////////////////////////////////////////////////////
-// String utilities
-/////////////////////////////////////////////////////////////////////////////////////
-
-//the integer. If no integer is found, returns INT_MIN and sets ptr to NULL /* MR1 */
-inline int strtoi(const char*& ptr)
-{
- int i;
- const char* ptr0=ptr;
- if (!ptr) return INT_MIN;
- while (*ptr!='\0' && !(*ptr>='0' && *ptr<='9')) ptr++;
- if (*ptr=='\0') {
- ptr=0;
- return INT_MIN;
- }
- if (*(ptr-1)=='-' && ptr>ptr0) i=-atoi(ptr); else i=atoi(ptr);
- while (*ptr>='0' && *ptr<='9') ptr++;
- return i;
-}
-
-
-//Same as strint, but interpretes '*' as default /* MR1 */
-inline int strtoi_(const char*& ptr, int deflt=INT_MAX)
-{
- int i;
- if (!ptr) return INT_MIN;
- while (*ptr!='\0' && !(*ptr>='0' && *ptr<='9') && *ptr!='*') ptr++;
- if (*ptr=='\0') {
- ptr=0;
- return INT_MIN;
- }
- if (*ptr=='*') {
- ptr++;
- return deflt;
- }
- if (*(ptr-1)=='-') i=atoi(ptr-1);
- else i=atoi(ptr);
- while (*ptr>='0' && *ptr<='9') ptr++;
- return i;
-}
-
-
-// Returns leftmost integer in ptr and sets the pointer to first char after
-// the integer. If no integer is found, returns INT_MIN and sets pt to NULL
-int strint(char*& ptr)
-{
- int i;
- char* ptr0=ptr;
- if (!ptr) return INT_MIN;
- while (*ptr!='\0' && !(*ptr>='0' && *ptr<='9')) ptr++;
- if (*ptr=='\0')
- {
- ptr=0;
- return INT_MIN;
- }
- if (*(ptr-1)=='-' && ptr>ptr0) i=-atoi(ptr); else i=atoi(ptr);
- while (*ptr>='0' && *ptr<='9') ptr++;
- return i;
-}
-
-// Same as strint, but interpretes '*' as default
-int strinta(char*& ptr, int deflt=99999)
-{
- int i;
- if (!ptr) return INT_MIN;
- while (*ptr!='\0' && !(*ptr>='0' && *ptr<='9') && *ptr!='*') ptr++;
- if (*ptr=='\0')
- {
- ptr=0;
- return INT_MIN;
- }
- if (*ptr=='*')
- {
- ptr++;
- return deflt;
- }
- if (*(ptr-1)=='-') i=atoi(ptr-1);
- else i=atoi(ptr);
- while (*ptr>='0' && *ptr<='9') ptr++;
- return i;
-}
-
-// Returns leftmost float in ptr and sets the pointer to first char after
-// the float. If no float is found, returns FLT_MIN and sets pt to NULL /* MR1 */
-float strflt(char*& ptr)
-{
- float i;
- char* ptr0=ptr;
- if (!ptr) return FLT_MIN;
- while (*ptr!='\0' && !(*ptr>='0' && *ptr<='9')) ptr++;
- if (*ptr=='\0')
- {
- ptr=0;
- return FLT_MIN;
- }
- if (ptr>ptr0 && *(ptr-1)=='-') i=-atof(ptr); else i=atof(ptr);
- while ((*ptr>='0' && *ptr<='9') || *ptr=='.') ptr++;
- return i;
-}
-
-// Same as strint, but interpretes '*' as default /* MR1 */
-float strflta(char*& ptr, float deflt=99999)
-{
- float i;
- if (!ptr) return FLT_MIN;
- while (*ptr!='\0' && !(*ptr>='0' && *ptr<='9') && *ptr!='*') ptr++;
- if (*ptr=='\0')
- {
- ptr=0;
- return FLT_MIN;
- }
- if (*ptr=='*')
- {
- ptr++;
- return deflt;
- }
- if (*(ptr-1)=='-') i=-atof(ptr);
- else i=atof(ptr);
- while ((*ptr>='0' && *ptr<='9') || *ptr=='.') ptr++;
- return i;
-}
-
-
-// Removes the newline and other control characters at the end of a string (if present)
-// and returns the new length of the string (-1 if str is NULL)
-inline int chomp(char str[])
-{
- if (!str) return -1;
- int l=0;
- for (l=strlen(str)-1; l>=0 && str[l]<32; l--);
- str[++l]='\0';
- return l;
-}
-
-// Emulates the ifstream::getline method; similar to fgets(str,maxlen,FILE*),
-// but removes the newline at the end and returns NULL if at end of file or read error
-inline char* fgetline(char str[], const int maxlen, FILE* file)
-{
- if (!fgets(str,maxlen,file)) return NULL;
- if (chomp(str)+1>=maxlen) // if line is cut after maxlen characters...
- while (fgetc(file)!='\n'); // ... read in rest of line
- return(str);
-}
-
-// copies substring str[a,b] into substr and returns substr
-char *substr(char* substr, char* str, int a, int b)
-{
- if (b<a) {int i=b; b=a; a=i;}
- if (b-a>1000)
- {printf("Function substr: >1000 chars to copy. Exiting.\n"); exit(6);}
- char* dest=substr;
- char* source=str+a;
- char* send=str+b;
- while (*source!='\0' && source<=send) *(dest++) = *(source++);
- *dest='\0';
- return substr;
-}
-
-
-// Returns pointer to first non-white-space character in str OR to NULL if none found
-inline char* strscn(char* str)
-{
- if (!str) return NULL;
- char* ptr=str;
- while (*ptr!='\0' && *ptr<=32) ptr++;
- return (*ptr=='\0')? NULL: ptr;
-}
-
-// Returns pointer to first white-space character in str OR to NULL if none found /* MR1 */
-inline char* strscn_ws(char* str)
-{
- if (!str) return NULL;
- char* ptr=str;
- while (*ptr!='\0' && *ptr>32) ptr++;
- return (*ptr=='\0')? NULL: ptr;
-}
-
-//Returns pointer to first non-white-space character in str OR to NULL if none found /* MR1 */
-inline const char* strscn_c(const char* str)
-{
- if (!str) return NULL;
- const char* ptr=str;
- while (*ptr!='\0' && isspace(*ptr)) ptr++;
- return (*ptr=='\0') ? NULL : ptr;
-}
-
-// Returns pointer to first non-white-space character in str OR to end of string '\0' if none found
-inline char* strscn_(char* str)
-{
- if (!str) return NULL;
- char* ptr=str;
- while (*ptr!='\0' && *ptr<=32) ptr++;
- return ptr;
-}
-
-// Returns pointer to first non-c character in str OR to NULL if none found
-inline char* strscn(char* str, const char c)
-{
- if (!str) return NULL;
- char* ptr=str;
- while (*ptr!='\0' && *ptr==c) ptr++;
- return (*ptr=='\0')? NULL: ptr;
-}
-
-// Returns pointer to first non-c character in str OR to end of string '\0' if none found
-inline char* strscn_(char* str, const char c)
-{
- if (!str) return NULL;
- char* ptr=str;
- while (*ptr!='\0' && *ptr==c) ptr++;
- return ptr;
-}
-
-// Cuts string at first white space character found by overwriting it with '\0'.
-// Returns pointer to next non-white-space char OR to NULL if no such char found
-inline char* strcut(char* str)
-{
- if (!str) return NULL;
- char* ptr=str;
- while (*ptr!='\0' && *ptr>32) ptr++;
- if (*ptr=='\0') return NULL;
- *ptr='\0';
- ptr++;
- while (*ptr!='\0' && *ptr<=32) ptr++;
- return (*ptr=='\0')? NULL:ptr;
-}
-
-// Cuts string at first white space character found by overwriting it with '\0'.
-// Returns pointer to next non-white-space char OR to end of string '\0' if none found
-inline char* strcut_(char* str)
-{
- if (!str) return NULL;
- char* ptr=str;
- while (*ptr!='\0' && *ptr>32) ptr++;
- if (*ptr=='\0') return ptr;
- *ptr='\0';
- ptr++;
- while (*ptr!='\0' && *ptr<=32) ptr++;
- return ptr;
-}
-
-// Cuts string at first occurence of charcter c, by overwriting it with '\0'.
-// Returns pointer to next char not equal c, OR to NULL if none found
-inline char* strcut(char* str, const char c)
-{
- if (!str) return NULL;
- char* ptr=str;
- while (*ptr!='\0' && *ptr!=c) ptr++;
- if (*ptr=='\0') return NULL;
- *ptr='\0';
- ptr++;
- while (*ptr!='\0' && *ptr==c) ptr++;
- return (*ptr=='\0')? NULL:ptr;
-}
-
-// Cuts string at first occurence of charcter c, by overwriting it with '\0'.
-// Returns pointer to next char not equal c, OR to end of string '\0' if none found
-inline char* strcut_(char* str, const char c)
-{
- if (!str) return NULL;
- char* ptr=str;
- while (*ptr!='\0' && *ptr!=c) ptr++;
- if (*ptr=='\0') return ptr;
- *ptr='\0';
- ptr++;
- while (*ptr!='\0' && *ptr==c) ptr++;
- return ptr;
-}
-
-// Cuts string at first occurence of substr, by overwriting the first letter with '\0'.
-// Returns pointer to next char after occurence of substr, OR to NULL if no such char found
-inline char* strcut(char* str, const char* substr)
-{
- char* ptr; //present location in str being compared to substr
- const char* sptr=substr; //present location in substr being compared to substr
- // while not at end of str and not all of substr is matched yet
- while (1)
- {
- for (ptr=str, sptr=substr; *ptr==*sptr && *ptr!='\0'; ptr++, sptr++) ;
- if (*sptr=='\0') {*str='\0'; return ptr;}
- if (*ptr=='\0') return NULL;
- str++;
- }
-}
-
-// Cuts string at first occurence of substr, by overwriting the first letter with '\0'.
-// Returns pointer to next char after occurence of substr, OR to end of string '\0' if no such char found
-inline char* strcut_(char* str, const char* substr)
-{
- char* ptr; //present location in str being compared to substr
- const char* sptr=substr; //present location in substr being compared to str
- // while not at end of str and not all of substr is matched yet
- while (1)
- {
- for (ptr=str, sptr=substr; *ptr==*sptr && *ptr!='\0'; ptr++, sptr++) ;
- if (*sptr=='\0') {*str='\0'; return ptr;}
- if (*ptr=='\0') return ptr;
- str++;
- }
-}
-
-// Copies first word in ptr to str. In other words, copies first block of non whitespace characters,
-// beginning at ptr, to str. If a word is found, returns address of second word in ptr or, if no second
-// word is found, returns address to end of word ('\0' character) in ptr string. If no word is found
-// in ptr NULL is returned.
-inline char* strwrd(char* str, char* ptr)
-{
- ptr=strscn(ptr); // advance to beginning of next word
- if (ptr)
- {
- while (*ptr!='\0' && *ptr>32) *(str++) = *(ptr++);
- *str='\0';
- while (*ptr!='\0' && *ptr<=32) ptr++;
- return ptr;
- }
- else return NULL;
-}
-
-// Copies first word ***delimited by char c*** in ptr to str. In other words, copies first block of non-c characters,
-// beginning at ptr, to str. If a word is found, returns address of second word in ptr or, if no second
-// word is found, returns address to end of word ('\0' character) in ptr string. If no word is found
-// in ptr NULL is returned.
-inline char* strwrd(char* str, char* ptr, const char c)
-{
- ptr=strscn(ptr,c); // advance to beginning of next word
- if (ptr)
- {
- while (*ptr!='\0' && *ptr!=c) *(str++) = *(ptr++);
- *str='\0';
- while (*ptr!='\0' && *ptr==c) ptr++;
- return ptr;
- }
- else return NULL;
-}
-
-// Similar to Perl's tr/abc/ABC/: Replaces all chars in str found in one list with characters from the second list
-// Returns the number of replaced charactrs
-int strtr(char* str, const char oldchars[], const char newchars[])
-{
- char* ptr;
- const char *plist;
- int ntr=0;
- for (ptr=str; *ptr!='\0'; ptr++)
- for (plist=oldchars; *plist!='\0'; plist++)
- if (*ptr==*plist)
- {
- *ptr=newchars[plist-oldchars];
- ntr++;
- break;
- }
- return ntr;
-}
-
-// Similar to Perl's tr/abc//d: deletes all chars in str found in the list
-// Returns number of removed characters
-int strtrd(char* str, const char chars[])
-{
- char* ptr0=str;
- char* ptr1=str;
- const char *plist;
- while (*ptr1!='\0')
- {
- for (plist=chars; *plist!='\0'; plist++)
- if (*ptr1==*plist) break;
- if (*plist=='\0') {*ptr0=*ptr1; ptr0++;}
- ptr1++;
- }
- return ptr1-ptr0;
-}
-
-// Similar to Perl's tr/a-z//d: deletes all chars in str found in the list
-// Returns number of removed characters
-int strtrd(char* str, char char1, char char2)
-{
- char* ptr0=str;
- char* ptr1=str;
- while (*ptr1!='\0')
- {
- if (*ptr1>=char1 && *ptr1<=char2) {*ptr0=*ptr1; ptr0++;}
- ptr1++;
- }
- return ptr1-ptr0;
-}
-
-// transforms str into an all uppercase string
-char* uprstr(char* str)
-{
- char* s=str;
- while (*s !='\0') {if (*s>='a' && *s<='z') *s+='A'-'a';s++;}
- return(str);
-}
-
-// transforms str into an all uppercase string
-char* lwrstr(char* str)
-{
- char* s=str;
- while (*s !='\0') {if (*s>='A' && *s<='Z') *s+='a'-'A'; s++;}
- return(str);
-}
-
-// transforms chr into an uppercase character
-inline char uprchr(char chr)
-{
- return (chr>='a' && chr<='z')? chr+'A'-'a' : chr;
-}
-
-// transforms chr into an lowercase character
-inline char lwrchr(char chr)
-{
- return (chr>='A' && chr<='Z')? chr-'A'+'a' : chr;
-}
-
-
-// Replaces first occurence of str1 by str2 in str. Returns pointer to first occurence or NULL if not found
-// ATTENTION: if str2 is longer than str1, allocated memory of str must be long enough!!
-inline char* strsubst(char* str, const char str1[], const char str2[])
-{
- char* ptr = strstr(str,str1);
- strcpy(ptr,str2);
- return ptr;
-}
-
-// Gives elapsed time since first call to this function
-inline void ElapsedTimeSinceFirstCall(const char str[])
-{
- timeval t;
- static double tfirst=0;
- if (tfirst==0)
- {
- gettimeofday(&t, NULL);
- tfirst = 1E-6*t.tv_usec + t.tv_sec;
- }
- gettimeofday(&t, NULL);
- printf("Elapsed time since first call:%12.3fs %s\n",1E-6*t.tv_usec + t.tv_sec - tfirst,str);
-}
-
-// Gives elapsed time since last call to this function
-inline void ElapsedTimeSinceLastCall(const char str[])
-{
- timeval t;
- static double tlast=0.0;
- if (tlast==0.0)
- {
- gettimeofday(&t, NULL);
- tlast = 1.0E-6*t.tv_usec + t.tv_sec;
- }
- gettimeofday(&t, NULL);
- printf("Elapsed time since last call:%12.3fs %s\n",1.0E-6*t.tv_usec + t.tv_sec - tlast,str);
- tlast = 1.0E-6*t.tv_usec + t.tv_sec;
-}
-
-inline char* RemovePath(char outname[], char filename[])
-{
- char* ptr;
-#ifdef WINDOWS
- ptr=strrchr(filename,92); //return adress for LAST \ (backslash) in name
-#else
- ptr=strrchr(filename,'/'); //return adress for LAST / in name
-#endif
- if (!ptr) ptr=filename; else ptr++;
- strcpy(outname,ptr);
- return outname;
-}
-
-inline char* RemoveExtension(char outname[], char filename[])
-{
- char *ptr1;
- ptr1=strrchr(filename,'.'); //return adress for LAST '.' in name
- if (ptr1) {*ptr1='\0'; strcpy(outname,filename); *ptr1='.';} else strcpy(outname,filename);
- return outname;
-}
-
-inline char* RemovePathAndExtension(char outname[], char filename[])
-{
- char *ptr, *ptr1;
-#ifdef WINDOWS
- ptr=strrchr(filename,92); //return adress for LAST \ (backslash) in name
-#else
- ptr=strrchr(filename,'/'); //return adress for LAST / in name
-#endif
- if (!ptr) ptr=filename; else ptr++;
- ptr1=strrchr(filename,'.'); //return adress for LAST '.' in name
- if (ptr1) {*ptr1='\0'; strcpy(outname,ptr); *ptr1='.';} else strcpy(outname,ptr);
- return outname;
-}
-
-inline char* Extension(char extension[], char filename[])
-{
- char* ptr;
- ptr=strrchr(filename,'.'); //return adress for LAST '.' in name
- if (ptr) strcpy(extension,ptr+1); else *extension='\0';
- return extension;
-}
-
-// Path includes last '/'
-inline char* Pathname(char pathname[], char filename[])
-{
- char* ptr;
- char chr;
-#ifdef WINDOWS
- ptr=strrchr(filename,92); //return adress for LAST \ (backslash) in name
-#else
- ptr=strrchr(filename,'/'); //return adress for LAST / in name
-#endif
- if (ptr) {chr=*(++ptr); *ptr='\0'; strcpy(pathname,filename); *ptr=chr;} else *pathname='\0';
- return pathname;
-}
-
-// Swaps two integer elements in array k
-inline void swapi(int k[], int i, int j)
-{
- int temp;
- temp=k[i]; k[i]=k[j]; k[j]=temp;
-}
-
-// QSort sorting routine. time complexity of O(N ln(N)) on average
-// Sorts the index array k between elements i='left' and i='right' in such a way that afterwards
-// v[k[i]] is sorted downwards (up=-1) or upwards (up=+1)
-void QSortInt(int v[], int k[], int left, int right, int up=+1)
-{
- int i;
- int last; // last element to have been swapped
-
- if (left>=right) return; // do nothing if less then 2 elements to sort
- // Put pivot element in the middle of the sort range to the side (to position 'left') ...
- swapi(k,left,(left+right)/2);
- last=left;
- // ... and swap all elements i SMALLER than the pivot
- // with an element that is LARGER than the pivot (element last+1):
- if (up==1)
- {
- for (i=left+1; i<=right; i++)
- if (v[k[i]]<v[k[left]]) swapi(k,++last,i);
- }
- else
- for (i=left+1; i<=right; i++)
- if (v[k[i]]>v[k[left]]) swapi(k,++last,i);
-
- // Put the pivot to the right of the elements which are SMALLER, left to elements which are LARGER
- swapi(k,left,last);
-
- // Sort the elements left from the pivot and right from the pivot
- QSortInt(v,k,left,last-1,up);
- QSortInt(v,k,last+1,right,up);
-}
-
-// QSort sorting routine. time complexity of O(N ln(N)) on average
-// Sorts the index array k between elements i='left' and i='right' in such a way that afterwards
-// v[k[i]] is sorted downwards (up=-1) or upwards (up=+1)
-void QSortFloat(float v[], int k[], int left, int right, int up=+1)
-{
- int i;
- int last; // last element to have been swapped
- void swapi(int k[], int i, int j);
-
- if (left>=right) return; // do nothing if less then 2 elements to sort
- // Put pivot element in the middle of the sort range to the side (to position 'left') ...
- swapi(k,left,(left+right)/2);
- last=left;
- // ... and swap all elements i SMALLER than the pivot
- // with an element that is LARGER than the pivot (element last+1):
- if (up==1)
- {
- for (i=left+1; i<=right; i++)
- if (v[k[i]]<v[k[left]]) swapi(k,++last,i);
- }
- else
- for (i=left+1; i<=right; i++)
- if (v[k[i]]>v[k[left]]) swapi(k,++last,i);
-
- // Put the pivot to the right of the elements which are SMALLER, left to elements which are LARGER
- swapi(k,left,last);
-
- // Sort the elements left from the pivot and right from the pivot
- QSortFloat(v,k,left,last-1,up);
- QSortFloat(v,k,last+1,right,up);
-}
-
-/**
- * @brief comparison function for qsort,
- * sorts floating point numbers ascendingly
- *
- * @param cv1 ponter to 1st entry to be sorted
- * @param cv2 ponter to 2nd entry to be sorted
- *
- * @return 0 if entries are equal,
- * +/-1 if 1st greater/smaller than 2nd
- */
-int CompFltAsc(const void *cv1, const void *cv2){
-
- float f1 = *(float *)cv1;
- float f2 = *(float *)cv2;
-
- if (f1 > f2) { return +1; }
- else if (f1 < f2) { return -1; }
- else { return 0; }
-
-} /* this is the end of CompFltAsc() */
-
-//Return random number in the range [0,1]
-inline float frand() { return rand()/(RAND_MAX+1.0); }
-
-
-/////////////////////////////////////////////////////////////////////////////////////
-//// Execute system command
-/////////////////////////////////////////////////////////////////////////////////////
-void runSystem(std::string cmd, int v = 2)
-{
- if (v>2)
- cout << "Command: " << cmd << "!\n";
- int res = system(cmd.c_str());
- if (res!=0)
- {
- cerr << endl << "ERROR when executing: " << cmd << "!\n";
- exit(1);
- }
-
-}
git://source.jalview.org / jabaws.git / blobdiff