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calSOV.cpp
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calSOV.cpp
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/*
* =====================================================================================
*
* Filename: calSOV.cpp
*
* Description: calculate the SOV score and Q3 score given a prediction
*
* Version: 1.0
* Created: 07/23/2009 03:49:05 PM CEST
* Revision: none
* Compiler: gcc
*
* Author: Nanjiang Shu (Shu), [email protected]
* Company: Department of Biochemistry and Biophysics, Stockholm Univesity
*
* =====================================================================================
*/
/* ChangeLog 2009-10-26
* The confidence normalization function,
* a1, a2 and a3 can be modified from argument
* */
#include <stdio.h>
#include <string.h>
#include <math.h>
#include <stdlib.h>
#include <algorithm>
#include <set>
#include <list>
#include <vector>
#include <utility>
#include "array.h"
#include "mytemplate.h"
/*#include "myfunc.h"*/
using namespace std;
#if defined(_Windows) || defined(__WINDOWS__) || \
defined(__WIN32__) || defined(WIN32) || \
defined(__WINNT__) || defined(__NT__)
# ifndef WINDOWS
# define WINDOWS
# endif
#endif
#define NUM_HSR_STATE 3
int method_HSR = 1 ;
bool isStatQ3Conf = false; /*whether analyze the Q3 for residues at each confidence bin*/
int typeConfidence = 0; /*default using the raw confidence*/
char HSRalphabet[] = "HSR-";
double binWidth = 1.0; /*halfBinWidth*/
int maxSeqLength = MAX_SEQ_LENGTH +1 ;
bool isProofReading = false; /*2009-08-03*/
int method_ProofReading = 0;
/*parameters for the function
* normConf = a1 * rawConf*rawConf + a2 * rawConf + a3
* 2009-10-26*/
double poly_a1 = -0.0071;
double poly_a2 = 1.8084;
double poly_a3 = -11.4;
void PrintHelp(char** argv)
{
fprintf(stdout,"Usage: calSOV [options] file1 file2 ...\n");
fprintf(stdout,"OPTIONS:\n");
fprintf(stdout," -o, --out <outfile> : output the result to outfile, (default = stdout)\n");
fprintf(stdout," -l, --list listfile : set the file containing a list of predicted files\n");
fprintf(stdout," -f, --format 0|1|2|3 : set the format of the input file, (default = 1)\n");
fprintf(stdout," -q3, --isOutQ3 yes|no: wheter output q3, (default = yes)\n");
fprintf(stdout," -m, --method 0|1|2|3: set the method to get predicted secondary structure state from Res file, (default = 1)\n");
fprintf(stdout," -statq3 : anylyze the Q3 for residues predicted at different confidences \n");
fprintf(stdout," -chkfstdir : folder to which Res from checkfirst program are stored, this need to be supplied when -statq3 is enabled \n");
fprintf(stdout," -selconf 0|1 : selection of the confidence, (default = 0) \n");
fprintf(stdout," : 0 -- raw confidence, 1 -- normalized confidence \n");
fprintf(stdout," -binwidth <real> : set halfbinwidth, (default = 1.0) \n");
fprintf(stdout," -max, --max-length : set the max length of the sequence, (default = %d)\n", maxSeqLength-1);
fprintf(stdout," -proof, --proof : enable proof reading\n");
fprintf(stdout," -proofmethod int : set the method for proof reading, (default = 0)\n");
fprintf(stdout," -polypara a1 a2 a3 : input three parameters for polynormail function which normalize the confidence\n");
fprintf(stdout," : default a1=%8.6lf , a2 = %8.6lf , a3 = %8.6lf \n", poly_a1, poly_a2 ,poly_a3);
fprintf(stdout," -h, --help : print this help message and exit\n");
fprintf(stdout,"\n");
fprintf(stdout,"Created on 2009-07-23, updated 2016-11-03, Nanjiang Shu\n");
fprintf(stdout,"\nFormat description of input file:\n");
fprintf(stdout," Format 0: prediction Res* file\n");
fprintf(stdout," Format 1: AA OSEC PSEC NUM\n");
fprintf(stdout," Format 2: Fasta format, >AA, >OSEC, >PSEC, order not important\n");
fprintf(stdout,"\nExamples:\n");
fprintf(stdout," %s -f 1 test/16VPA.psipred.format_1.txt\n", argv[0]);
fprintf(stdout," %s -f 2 test/16VPA.psipred.format_2.txt\n", argv[0]);
}
void PrintVerboseHelp() { }
int coverage(int a1, int b1, int a2, int b2)
/*
return the coverage of two intervals
a1, b1, a2, b2 are integers
when the return value <=0, it means there is no coverage
*/
{
return (min(b1,b2)-max(a1,a2));
}
int my_strcpy(char* to, const char* from, int max)/*{{{*/
/******************************************************************************
* my modification of strcpy
* copy max characters from "from" to "to", add NULL terminator automatically
* updated 2008-04-23, memcpy win in speed when the copying string is long
* updated 2011-10-27:
* since calling strlen will be time consuming for very large from string,
* e.g. when "from" is the buffer of a whole trunk of file. Therefore, strlen
* part is removed.
*****************************************************************************/
{
if(max < 200) {
strncpy(to,from,max);
} else {
memcpy(to,from,max);
}
to[max] = '\0';
return max;
}/*}}}*/
char *rootname(const char* filename, char* rtname, int max_rtname /*= MAX_PATH*/)/*{{{*/
/*****************************************************************************
* rootname
* given the file name,
* return the rootname of the filename
****************************************************************************/
{
const char *pch;
char *pstr;
if((pch = strrchr(filename,'/')) != NULL)
pstr = (char*) pch+1;
else
pstr = (char*) filename;
if((pch = strrchr(pstr,'.')) != NULL)
my_strcpy(rtname,pstr, min((int)(pch - pstr), max_rtname));
else
rtname = pstr;
return rtname;
}
/*}}}*/
int option_parser_filename(int argc, char **argv, int beg, char *filename)/*{{{*/
/*****************************************************************************
* beg is the current index of argument list, e.g., argv[i] = "--out"
****************************************************************************/
{
int i ;
bool isNonOptionArg = false;
bool isFileNameSet = false;
for(i = beg +1 ; i < argc ; i++)
{
if(argv[i][0] == '-' && strcmp(argv[i], "--") != 0 && !isNonOptionArg)
{
fprintf(stderr,"option '%s' must be followed by a filename, not option\n", argv[beg]);
return -1;
}
else if(strcmp(argv[i], "--") == 0 && !isNonOptionArg)
{
isNonOptionArg = true;
}
else
{
my_strcpy(filename, argv[i], MAX_PATH-1);
isFileNameSet = true;
break;
}
}
if(!isFileNameSet)
{
fprintf(stderr,"option '%s' must be followed by a filename\n", argv[beg]);
return -1;
}
else
{
return i+1;
}
}
/*}}}*/
template <class T> int option_parser_numeric(int argc, char **argv, int beg, T &x, bool isRangeSet /*= false*/, T min /*= MIN_INT*/, T max /*= MAX_INT*/)/*{{{*/
/*****************************************************************************
* beg is the current index of argument list, e.g., argv[i] = "--value"
****************************************************************************/
{
int i ;
bool isValueSet = false;
double tmp;
i = beg +1;
if (i < argc)
{
if(IsNumeric(argv[i]))
{
tmp = atof(argv[i]);
if(isRangeSet)
{
if(tmp < min || tmp > max)
{
fprintf(stderr,"Invalid value! Value after option '%s' must be in the range of [%g %g]\n", argv[beg], double(min), double(max));
return -1;
}
}
x = T(tmp);
isValueSet = true;
}
}
if(!isValueSet)
{
fprintf(stderr,"option '%s' must be followed by a numerical value\n", argv[beg]);
return -1;
}
else
{
return i+1;
}
}
template int option_parser_numeric<int> (int argc, char **argv, int beg, int &x , bool isRangeSet /*= false*/, int min /*= MIN_INT*/ , int max/* = MAX_INT*/);
template int option_parser_numeric<float> (int argc, char **argv, int beg, float &x , bool isRangeSet /*= false*/, float min /*= MIN_FLOAT*/ , float max /*= MAX_FLOAT*/);
template int option_parser_numeric<double>(int argc, char **argv, int beg, double &x, bool isRangeSet /*= false*/, double min/* = MIN_DOUBLE*/, double max /*= MAX_DOUBLE*/);
template int option_parser_numeric<int8>(int argc, char **argv, int beg, int8 &x, bool isRangeSet /*= false*/, int8 min/* = MIN_DOUBLE*/, int8 max /*= MAX_DOUBLE*/);
/*}}}*/
int ReadNextSeq_FASTA(FILE *fp, char* seq, int *pSeq_type /*= NULL*/, int maxlength /*= LONGEST_SEQ*/, char* annotationLine/*=NULL*/, int maxSizeAnnotationLine /*=50*/)/*{{{*/
/****************************************************************************
* ReadNextSeq_FASTA()
* read in the fasta format sequence from the file stream
* return the length of the sequence if successful
* return 0 or minus value if no more sequence can be read from the file stream
* The leading white spaces are ignored
* check the type (DNA or AA) of fasta sequence file based the annotation line
* Last modified, 2007-02-12, Nanjiang Shu
* Updated 2010-04-22: the annotation line (without the leading ">") can be
* read in, note that the maxSizeAnnotationLine must be supplied
***************************************************************************/
{
int c;
int i;
do{ /* ignore the leading white spaces */
c = getc(fp);
}while(isspace(c));
if(pSeq_type != NULL)
*pSeq_type = UNKNOWN_SEQ_TYPE; /* initializing sequence type*/
if(c == '>')
{
Array1D <char> line_1darray(maxSizeAnnotationLine +1);
char *line = line_1darray.array1D;
fgetline(fp,line,maxSizeAnnotationLine);
if( pSeq_type != NULL)
{
if(strstr(line, "protein") != NULL)
*pSeq_type = AA_SEQ;
else if( strstr(line,"nucleic") != NULL)
*pSeq_type = DNA_SEQ;
else if( strstr(line,"shape") != NULL)
*pSeq_type = SHAPE_SEQ;
else
*pSeq_type = UNKNOWN_SEQ_TYPE;
}
if (annotationLine != NULL)
{
my_strcpy(annotationLine,line, maxSizeAnnotationLine-1); /*read in the annotation line*/
}
}
else
{
fseek(fp, -1, SEEK_CUR); /* backward 1 byte of file stream if there is no annotation line*/
}
i = 0 ;
while((c = getc(fp)) != EOF)
{
if(c == '>')
{
fseek(fp, -1, SEEK_CUR); /* backward 1 byte of file stream*/
break; /* read in the first sequence if there are multiple sequences in the file*/
}
if(! isspace(c)) /* neglect white spaces and return characters in sequence region*/
{
seq[i] = c ; i ++ ;
if(i >= maxlength)
{
fprintf(stderr,"Error, sequence longer then maxlength = %d\n", maxlength);
return 1;
}
}
}
seq[i] = '\0' ;
if(c == EOF && i == 0)
return EOF;
else
return i; /* return the length of sequence*/
}/*}}}*/
bool IsNumeric(const char* str)/*{{{*/
//**********************************************************************
//IsNumeric(char*)
//check if a string is a numeric number
{
int i = 0;
int cntdot = 0;
while(str[i] != '\0')
{
if( i == 0)
{
if(!isdigit(str[i]) && str[i] != '+' && str[i] != '-' && str[i] != '.' )
return false;
if(str[i] == '.')
cntdot ++;
}
else
{
if(! isdigit(str[i]) && str[i] != '.')
return false;
if(str[i] == '.')
cntdot ++;
}
i ++;
}
if(cntdot >= 2)
return false;
else
return true;
}
/*}}}*/
bool IsInCharSet(const char ch, const char *charSet, int n /*= 0 */)/*{{{*/
/*****************************************************************************
* check if the character "ch" is in charSet,
****************************************************************************/
{
if(n == 0)
n = strlen(charSet);
int i;
for(i = 0 ;i < n ; i ++)
{
if(ch == charSet[i])
return true;
}
return false;
}/*}}}*/
int fgetline(FILE* fp, char* line, int max/* = 0x7FFFFFFF*/)/*{{{*/
/*****************************************************************************
* Read one line from fp, copying it to line array (but no more than max
* chars). Does not place terminating \n in line array.
* it can be called without "max" flag, but should make sure the allocated
* memory for "line" is larger than the longest line.
*
* Returns: line length, or 0 for empty line, or "EOF" for end-of-file.
*
* since fgetc(), getc(), getchar(), returns int value,always use an int
* variable to store the result of the fgetc(), getc() and getchar().
* getc() is faster than fgetc()
* LOG: 2006-04-26 16:31:29 Wednesday Week 17 <nanjiang@shu>
* bug fixed for '\n' return keys,
* now it is valid for both dos and unix
****************************************************************************/
{
int nch = 0; /* record number of characters actually read */
int c;
max = max - 1; /* leave room for '\0' */
while((c = getc(fp)) != EOF)
{
if(c == 0x0d ) continue; /* in unix, '\n'= 0x0a, thus 0x0d will be cheated as another character*/
if(c == '\n') break; /* in dos, '\n' is also equal to 0x0a, but the preceding 0x0d will not be read*/
if(nch < max)
{
line[nch] = c;
nch = nch + 1;
}
}
line[nch] = '\0';
if(c == EOF && nch == 0) return EOF;
else return nch;
}/*}}}*/
int checkfilestream(FILE *fp, const char* filename, const char *mode, bool isAssert /*= false*/)/*{{{*/
{
if( fp == NULL)
{
fprintf(stderr,"Can not open file '%s' with mode '%s'\n", filename,mode);
if(isAssert)
{
assert(fp != NULL);
}
return -1;
}
else
return 0;
}
/*}}}*/
double GetRawHSRConfidence(int probH, int probS, int probR)/*{{{*/
/*Determine raw confidence of the prediction based on the probability on H, S
* and R
* 2009-07-21, Nanjiang*/
{
double sumHSR = double(probH+probS+probR) + 1e-6; /*plus 1e-6 to avoid division by zero*/
double maxHSR = double (max (max(probH, probS), probR ));
double rawConf = maxHSR/sumHSR;
return rawConf;
}/*}}}*/
float GetNormHSRConfidence(int probH, int probS, int probR)/*{{{*/
/*Determine normalized confidence of the prediction based on the probability on H, S
* and R, parameters were obtained by polynormial regression (order 2) of the
* raw confidence and two Q3 at different raw confidence bins
* 2009-08-02
* */
{
double sumHSR = double(probH+probS+probR) + 1e-6; /*plus 0.00001 to avoid division by zero*/
double maxHSR = double (max (max(probH, probS), probR ));
double rawConf =(maxHSR/sumHSR)*100.0;
double normConf = poly_a1 * rawConf*rawConf + poly_a2 * rawConf + poly_a3;
/*method 2, three order regression, 2009-08-02 */
//y = -0.0001x3 + 0.0225x2 - 0.1356x + 28.889
//double a1 =-0.0001;
//double a2 = 0.0225;
//double a3 = -0.1356;
//double a4 =28.889;
//double normConf = a1 * rawConf*rawConf*rawConf + a2 * rawConf*rawConf + a3*rawConf + a4;
normConf /= 100.0;
if (normConf < 0.0)
{
normConf = 0.0;
}
else if (normConf> 1.0)
{
normConf = 1.0;
}
return normConf;
}/*}}}*/
int GetHSRState(int probH, int probS, int probR, int method_HSR /*= 1*/)/*{{{*/
/*Determine the state of secondary structure based on the probability on H, S
* and R
* the return value is 0 or 1 or 2, representing H, S and R respectively
* 2009-07-13, Nanjiang*/
{
int hsrState = 2;
if (method_HSR == 0)
{
if ( (probS>=probH) && (probS>=probR) ) { hsrState = 1; }
else if ((probH>=probS) && (probH>=probR) ) { hsrState = 0; }
else { hsrState = 2; }
}
else if (method_HSR == 1)
{
if ( (probR>=probH) && (probR>=probS) ) { hsrState = 2; }
else if ((probS>=probH) && (probS>=probR) ) { hsrState = 1; }
else { hsrState = 0; }
}
else
{
if ( (probR>=probH) && (probR>=probS) ) { hsrState = 2; }
else if ((probH>=probS) && (probH>=probR) ) { hsrState = 0; }
else { hsrState = 1; }
}
return hsrState;
}/*}}}*/
int ReadInSecPredFile(const char *infile, char *aaSeq, char *obsSec, char *predSec, double *predConf, int typeConfidence, int fileFormat)/*{{{*/
{
int linesize;
int maxline = 400;
Array1D <char> line_1darray(maxline+1);
char *line = line_1darray.array1D;
char aa;
char obs_sec;
char pred_sec;
int status_sscanf = 0;
int seqLength = 0;
FILE *fp = fopen(infile, "r");
checkfilestream(fp, infile, "r", true);
if (fileFormat == 0) /*Res file format*//*{{{*/
{
int num ;
char shape;
int probH;
int probS;
int probR;
int predHSRstate = 0; /*predicted HSR state, 0 -- H, 1 -- S, 2 -- R*/
int cntRes = 0;
while((linesize=fgetline(fp, line, maxline)) != EOF)
{
status_sscanf = sscanf(line,"%d %c %c %c %d %d %d" , &num,&aa,&shape, &obs_sec,&probH,&probS,&probR);
if (status_sscanf != 7)
{
fprintf(stderr,"sscanf error!");
fprintf(stderr,"File: %s\n", infile);
fprintf(stderr,"line: %s\n", line);
assert (status_sscanf == 7);
}
predHSRstate = GetHSRState(probH, probS, probR, method_HSR);
aaSeq[cntRes] = aa;
obsSec[cntRes] = obs_sec;
predSec[cntRes] = HSRalphabet[predHSRstate];
if (typeConfidence == 0) /*Raw confidence*/
{
predConf[cntRes] = GetRawHSRConfidence(probH, probS, probR);
}
else
{
predConf[cntRes] = GetNormHSRConfidence(probH, probS, probR);
}
cntRes ++;
}
seqLength = cntRes;
}/*}}}*/
else if (fileFormat == 1) /*AA OSEC PSEC NUM*//*{{{*/
{
/*AA OSEC PSEC NUM*/
linesize=fgetline(fp,line,maxline); /*neglect the header line*/
int cntRes = 0;
while((linesize=fgetline(fp, line, maxline)) != EOF)
{
status_sscanf = sscanf(line," %c %c %c" , &aa,&obs_sec,&pred_sec);
if (status_sscanf != 3)
{
fprintf(stderr,"sscanf error!");
fprintf(stderr,"File: %s\n", infile);
fprintf(stderr,"line: %s\n", line);
assert (status_sscanf == 3);
}
if (obs_sec == 'E' ) { obs_sec = 'S'; }
else if (obs_sec == 'C' || obs_sec == 'L') { obs_sec = 'R'; }
if (pred_sec == 'E' ) { pred_sec = 'S'; }
else if (pred_sec == 'C' || pred_sec == 'L') { pred_sec = 'R'; }
aaSeq[cntRes] = aa;
obsSec[cntRes] = obs_sec;
predSec[cntRes] = pred_sec;
#ifdef DEBUG
fprintf(stdout, "line=%s\n", line);
fprintf(stdout, "cntRes=%d\n", cntRes);
#endif
cntRes ++;
if (cntRes >= maxSeqLength){
fprintf(stdout,"Number of residues in the input file exceeds the maxSeqLength (%d). Please check your input file. Exit.\n", maxSeqLength);
assert(cntRes<maxSeqLength);
}
}
seqLength = cntRes;
}/*}}}*/
else if (fileFormat == 2) /*Fasta format >AA, >OSEC, >PSEC*//*{{{*/
{
int maxSizeAnno = 100;
Array1D <char> anno_1darray(maxSizeAnno+1);
Array1D <char> tmpSeq_1darray(maxSeqLength+1);
char *tmpSeq = tmpSeq_1darray.array1D;
char *anno = anno_1darray.array1D;
int seqlength = 0;
/*>AA >OSEC >PSEC*/
int cntSeq = 0;
while((seqlength = ReadNextSeq_FASTA(fp, tmpSeq, NULL, maxSeqLength, anno, maxSizeAnno))!= EOF)
{
if(strstr(anno, "AA") != NULL){
my_strcpy(aaSeq,tmpSeq, maxSeqLength-1);
}else if(strstr(anno, "OSEC") != NULL){
my_strcpy(obsSec,tmpSeq, maxSeqLength-1);
}else if(strstr(anno, "PSEC") != NULL){
my_strcpy(predSec,tmpSeq, maxSeqLength-1);
}
cntSeq ++;
if (cntSeq>3){
fprintf(stderr, "You input file contains more than 3 sequences. Please check the format of your input file\n");
assert(cntSeq<=3);
}
}
int i = 0;
seqlength = strlen(obsSec);
for (i = 0; i<seqlength; i++){
if (obsSec[i] == 'E' ) { obsSec[i] = 'S'; }
else if (obsSec[i] == 'C' || obsSec[i] == 'L') { obsSec[i] = 'R'; }
}
seqlength = strlen(predSec);
for (i = 0; i<seqlength; i++){
if (predSec[i] == 'E' ) { predSec[i] = 'S'; }
else if (predSec[i] == 'C' || predSec[i] == 'L') { predSec[i] = 'R'; }
}
seqLength = strlen(aaSeq);
}/*}}}*/
if (fp != NULL) { fclose(fp); }
return seqLength;
}/*}}}*/
int ProofReading(char *predSec, int seqLength, int method_ProofReading = 0)/*{{{*/
{
//proof reading for predicted result, for 1 long strand (sheet)
int Part1;
int Part2;
int ik;
int ij;
if (method_ProofReading == 0)/*{{{*/
{
int NShe = 0;
for (ik=0; ik<seqLength; ik++)
{
if ( predSec[ik] == 'S' )
{
NShe++;
}
else
{
if ( NShe == 1 )
{
//previous
Part1 = ik-3;
Part2 = ik +1 ;
if ( (Part1>=0) && (predSec[Part1]=='S') )
{
predSec[Part1+1] = 'S';
}
else if ( (Part2<seqLength) && (predSec[Part2]=='S') )
{
predSec[Part2-1] = 'S';
}
else
{
for (ij=ik-NShe; ij<ik; ij++)
{
predSec[ij] = 'R';
}
}
}
NShe = 0;
}
}
//proof reading for predicted result, for 1 or 2 long helix
int NHel = 0;
for (ik=0; ik<seqLength; ik++)
{
if ( predSec[ik] == 'H' )
{
NHel++;
}
else
{
if ( (NHel>=1) && (NHel<=2) )
{
//previous
Part1 = ik-NHel-2;
Part2 = ik +1 ;
if ( (Part1>=0) && (predSec[Part1]=='H') )
{
predSec[Part1+1] = 'H';
}
else if ( (Part2<seqLength) && (predSec[Part2]=='H') )
{
predSec[Part2-1] = 'H';
}
else
{
for (ij=ik-NHel; ij<ik; ij++)
{
predSec[ij] = 'R';
}
}
}
NHel = 0;
}
}
}/*}}}*/
else if (method_ProofReading == 1)/*{{{*/
{ /*do not proof reading single residue sheet, when using the DSSP8to3 scheme BE --> Sheet, 2009-10-29*/
//proof reading for predicted result, for 1 or 2 long helix
int NHel = 0;
for (ik=0; ik<seqLength; ik++)
{
if ( predSec[ik] == 'H' )
{
NHel++;
}
else
{
if ( (NHel>=1) && (NHel<=2) )
{
//previous
Part1 = ik-NHel-2;
Part2 = ik +1 ;
if ( (Part1>=0) && (predSec[Part1]=='H') )
{
predSec[Part1+1] = 'H';
}
else if ( (Part2<seqLength) && (predSec[Part2]=='H') )
{
predSec[Part2-1] = 'H';
}
else
{
for (ij=ik-NHel; ij<ik; ij++)
{
predSec[ij] = 'R';
}
}
}
NHel = 0;
}
}
}/*}}}*/
return seqLength;
}/*}}}*/
int ReadConf(const char *infile, double *predConf, int typeConfidence)/*{{{*/
{
int linesize;
int maxline = 400;
Array1D <char> line_1darray(maxline+1);
char *line = line_1darray.array1D;
char aa;
char obs_sec;
int status_sscanf = 0;
int seqLength = 0;
FILE *fp = fopen(infile, "r");
checkfilestream(fp, infile, "r", true);
int num ;
char shape;
int probH;
int probS;
int probR;
int cntRes = 0;
while((linesize=fgetline(fp, line, maxline)) != EOF)
{
status_sscanf = sscanf(line,"%d %c %c %c %d %d %d" , &num,&aa,&shape, &obs_sec,&probH,&probS,&probR);
if (status_sscanf != 7)
{
fprintf(stderr,"sscanf error!");
fprintf(stderr,"File: %s\n", infile);
fprintf(stderr,"line: %s\n", line);
assert (status_sscanf == 7);
}
if (typeConfidence == 0) /*Raw confidence*/
{
predConf[cntRes] = GetRawHSRConfidence(probH, probS, probR);
}
else
{
predConf[cntRes] = GetNormHSRConfidence(probH, probS, probR);
}
cntRes ++;
}
seqLength = cntRes;
if (fp != NULL) { fclose(fp); }
return seqLength;
}/*}}}*/
list < pair <int, int > > GetSecSeg(char *seq, char state, int seqLength)/*{{{*/
/*Get segment list for a certain secondary structure state*/
{
list < pair <int,int> > segList;
pair <int, int> seg;
int i,j;
i = 0;
while (i < seqLength)
{
int b, e;
if (seq[i] == state)
{
b = i;
j = i;
while (j < seqLength && seq[j] == state)
{
j ++;
}
e = j;
i = j;
seg = make_pair(b,e);
segList.push_back(seg);
}
else
{
i ++;
}
}
return segList;
}
/*}}}*/
int CalSOV(char *obsSec, char *predSec, int seqLength, double *numCorrectHSR, int *numHSR, double *sovHSR, int numState = 3)/*{{{*/
{
list <list <pair <int, int> > > segment_obs;
list <list <pair <int, int> > > segment_pred;
list <list <pair <int, int> > >::iterator it_sl_1;
list <list <pair <int, int> > >::iterator it_sl_2;
list <pair <int, int> > ::iterator it_seg_1;
list <pair <int, int> > ::iterator it_seg_2;
int i = 0;
for (i = 0; i < 3; i ++) /*iterator for secondary structure states*/
{
list <pair <int, int> > segList;
segList = GetSecSeg(obsSec, HSRalphabet[i], seqLength);
segment_obs.push_back(segList);
segList = GetSecSeg(predSec, HSRalphabet[i], seqLength);
segment_pred.push_back(segList);
}
vector <int> N(3,0); /*Normalization value*/
vector <double> sum_un_norm(3,0.0); /*sum of un-normalized score*/
int total_N = 0;
double total_sum_un_norm = 0.0;
int b1, e1, b2, e2, minov, maxov, delta, len_seg1, len_seg2;
double score;
for (i = 0; i < 3; i ++) /*iterator for secondary structure states*/
{
/*For all segments of the observed secondary structure*/
it_sl_1 = segment_obs.begin();
advance( it_sl_1, i );
it_sl_2 = segment_pred.begin();
advance( it_sl_2, i );
for (it_seg_1 = (*it_sl_1).begin(); it_seg_1 != (*it_sl_1).end(); ++it_seg_1)
{
b1 = (*it_seg_1).first;
e1 = (*it_seg_1).second;
len_seg1 = e1-b1;
bool isOverlap = false;
for (it_seg_2 = (*it_sl_2).begin(); it_seg_2 != (*it_sl_2).end(); ++it_seg_2)
{
b2 = (*it_seg_2).first;
e2 = (*it_seg_2).second;
len_seg2 = e2-b2;
minov = coverage(b1, e1, b2, e2);
if (minov > 0) {
maxov = max(e1,e2) - min(b1,b2);
} else {
maxov = 0;
}
if (minov > 0)
{
isOverlap = true;
double min1 = min(maxov - minov, minov);
double min2 = min(int(len_seg1/2), int(len_seg2/2));
delta = min(min1, min2);
score = (minov + delta)/double(maxov)*len_seg1;
sum_un_norm[i] += score;
N[i] += len_seg1;
}
}
if (isOverlap == false) {
N[i] += len_seg1;
}
}
sovHSR[i] = sum_un_norm[i]/N[i];
total_sum_un_norm += sum_un_norm[i];
total_N += N[i];
numHSR[i] = N[i];
}
sovHSR[numState] = total_sum_un_norm/total_N;
numHSR[numState] = total_N;
return numHSR[numState];
}/*}}}*/
int CalSOV_obsolete(char *obsSec, char *predSec, int seqLength, double *numCorrectHSR, int *numHSR, double *sovHSR, int numState = 3)/*{{{*/
/*=======================================================================
* numHSR[4] Helix, Sheet, Coil, All
* sovHSR[4]
* numState = 3 by default
*====================================================================*/
{
int Min_overlap[500] ;
int Max_extend[500] ;
int LenSeg_pred[500];
int All_HSRLen[3];
double All_Sum[3];
int iterHSRState = 0; /*iterator for the HSR state, H, S and R*/
char thisHSRstate = ' '; /*current HSR state*/
int i = 0;
int j = 0;
for (i=0;i<3;i++)
{
All_HSRLen[i] = 0;
All_Sum[i] = 0.0;
}
int Length = seqLength +1 ; /*Here Length is 1 residue longer than seqLength*/
for (iterHSRState=0; iterHSRState<3; iterHSRState++)//corrsponding to H, S, R
{
//for helix
int HSRLen = 0;/*iterator for secondary structure elements*/
thisHSRstate = HSRalphabet[iterHSRState];
for(i=0; i<Length; i++)
{
if ( obsSec[i] == thisHSRstate )
{
HSRLen++;
}
else
{
if ( HSRLen >= 1 )
{
int Num_Segment = 0;//the number of segments in an observed element
int SubLen = 0; /*length of the sub segment*/
//Min_overlap[]--the length of overlapping
//Mam_extend[] -- the extended length of two segments to be compared
for (j=i-HSRLen; j<i; j++)
{
if ( predSec[j] == thisHSRstate )
{
SubLen++;
}
else
{
if ( SubLen >= 1 )
{
Min_overlap[Num_Segment] = SubLen;
Num_Segment++;
}
SubLen = 0;
}
}
if ( SubLen >= 1 )
{
Min_overlap[Num_Segment] = SubLen;
Num_Segment++;
}
double sum = 0;
int beg = 0;
int Nextend = 0;
int Num_HSRLen = HSRLen;
if ( Num_Segment >= 1 )
{
for (j=0; j<Num_Segment; j++)
{
Max_extend[j] = HSRLen;
LenSeg_pred[j] = Min_overlap[j];
}
//for first segment
if ( predSec[i-HSRLen] == thisHSRstate )
{
beg = i - HSRLen - 1;
Nextend = 0;
while ( (beg>=0) && (predSec[beg]==thisHSRstate) && (obsSec[beg]!=thisHSRstate) )
{
Nextend++;
beg--;
}
Max_extend[0] = Max_extend[0] + Nextend;
LenSeg_pred[0] = LenSeg_pred[0] + Nextend;
}
//for last segment
if ( predSec[i-1] == thisHSRstate )
{
beg = i;
Nextend = 0;
while ( (beg<Length) && (predSec[beg]==thisHSRstate) && (obsSec[beg]!=thisHSRstate) )
{
Nextend++;
beg++;
}
Max_extend[Num_Segment-1] = Max_extend[Num_Segment-1] + Nextend;
LenSeg_pred[Num_Segment-1] = LenSeg_pred[Num_Segment-1] + Nextend;
}
for (j=0; j<Num_Segment; j++)
{
int Nmin1 = min( (Max_extend[j]-Min_overlap[j]), Min_overlap[j]);
int Nmin2 = min( HSRLen/2, LenSeg_pred[j]/2);
int Nmin = min(Nmin1, Nmin2);
double score_seg = (Min_overlap[j]+Nmin)*1.0/double(Max_extend[j]) ;
sum = sum + score_seg;
}
sum = sum*HSRLen;
Num_HSRLen = HSRLen*Num_Segment;
}
All_HSRLen[iterHSRState] = All_HSRLen[iterHSRState] + Num_HSRLen;
All_Sum[iterHSRState] = All_Sum[iterHSRState] + sum;
}
HSRLen = 0;
}
}
}
double sumOverlap = 0;
int sumAllRes = 0;
for (i=0; i<numState; i++)
{
numHSR[i] = All_HSRLen[i];