int main(int argc,char *argv[])
{
/* 读入目标串和模式串 初始化 */
int i,j;
char *subjfname=0,*quryfname=0;
time_t start, finish;
double elapsed_time;
int n, m;
int isGene = 0;
//void (* matchalg[20])(char * text,char * pat);
//void (* matchalg2[20])(char * text,char * pat,int n, int m);
//char * matchalgstr[20]={0};
//int boolmatch[20];
matchTest match[ALLALG ];
double time_used[ALLALG ];
FILE *fp;
int verbose = 0;
//FILE *fp;
_U64 startrdt,endrdt;
if(argc==1)
{
printf("match [-t text_file|-s text] [-a pattern| -q pattern_file] -v n\n");
printf("search pattern in text_file or text\n");
printf("-t text_file :text_file is the text file in which you want to search \n");
printf("-s text :text is the text in which you want to search \n");
printf("-q pattern_file :pattern_file contains the pattern which you want to search \n");
printf("-a pattern :pattern is which you want to search \n");
printf("-v n \n");
printf(" n is 0: the reporter does nothing \n");
printf(" n is 1: the reporter print the matching position\n");
printf("for example: match -s helloworld -a llo -v 1\n");
printf("for example: match -t helloworld.txt -a llo -v 1\n");
exit(0);
//subjfname="sub";
//quryfname="pattern";
}
else
{
int i;
for(i=0; i<argc; i++) {
if(argv[i][0] == '-') {
switch(argv[i][1]) {
case 't':
subjfname=argv[i+1];
isGene = isFastaFile(subjfname);
break;
case 'q':
quryfname=argv[i+1];
break;
case 'a':
Pat=argv[i+1];
break;
case 's':
Text = argv[i+1];
break;
case 'v':
if (i+1 < argc)
verbose = atoi(argv[i+1]);
break;
}
}
}
}
initGroup2(0, 2);
for(i=0; i<ALLALG ; i++)
{
//matchalg[i]=NULL;
//matchalg2[i]=NULL;
match[i].matchalg = NULL;
match[i].matchalg2= NULL;
}
match[0]. matchalg =bfstr;
match[0]. matchalg2 =bfstr2;
match[0]. matchalgstr ="bfstr";
match[1]. matchalg =Sbm;
match[1]. matchalg2 =Sbm2;
match[1]. matchalgstr ="Sbm";
match[2]. matchalg =Sbmh;
match[2]. matchalg2 =Sbmh2;
match[2]. matchalgstr ="Sbmh";
match[3]. matchalg =Sbmhs;
match[3]. matchalg2 =Sbmhs2;
match[3]. matchalgstr ="Sbmhs";
match[4]. matchalg =Ssmith;
match[4]. matchalg2 =Ssmith2;
match[4]. matchalgstr ="Ssmith";
match[5]. matchalg =Smp;
match[5]. matchalg2 =Smp2;
match[5]. matchalgstr ="Smp";
match[6]. matchalg =Skmp;
match[6]. matchalg2 =Skmp2;
match[6]. matchalgstr ="Skmp";
match[7]. matchalg =Sdfa;
match[7]. matchalg2 =Sdfa2;
match[7]. matchalgstr ="Sdfa";
match[8]. matchalg =Sbom;
match[8]. matchalg2 =Sbom2;
match[8]. matchalgstr ="Sbom";
match[9]. matchalg =Sbdm;
match[9]. matchalg2 =Sbdm2;
match[9]. matchalgstr ="Sbdm";
match[10].matchalg =Sbndm;
match[10].matchalg2 =Sbndm2;
match[10].matchalgstr ="Sbndm";
match[11].matchalg =Skr;
match[11].matchalg2 =Skr2;
match[11].matchalgstr ="Skr";
match[12].matchalg =0;//Sbyh;
match[12].matchalg2 =0;//Sbyh2;
match[12].matchalgstr ="Sbyh";
match[13].matchalg =0;//Sskip;
match[13].matchalg2 =0 ;// Sskip2;
match[13].matchalgstr ="Sskip";
match[14].matchalg =Skmpskip;
match[14].matchalg2 =Skmpskip2;
match[14].matchalgstr ="Skmpskip";
match[15].matchalg =Sshiftor;
match[15].matchalg2 =Sshiftor2;
match[15].matchalgstr ="Sshiftor";
match[16].matchalg =Sshiftand;
match[16].matchalg2 =Sshiftand2;
match[16].matchalgstr ="Sshiftand";
match[17].matchalg =SshiftorW;
match[17].matchalg2 =SshiftorW2;
match[17].matchalgstr ="SshiftorW";
match[18].matchalg =strstrsse;
match[18].matchalg2 =0;
match[18].matchalgstr ="strstrsse";
#ifdef TEST_2
match[19].matchalg =lstrstrsseLong;
match[19].matchalg2 =0;
match[19].matchalgstr ="lstrstrsse2";
match[20].matchalg =lstrstr;
match[20].matchalg2 =0;
match[20].matchalgstr ="lstrstr";
#endif
#ifdef SSE4
match[21].matchalg =strstrsse42;
match[21].matchalg2 =0;
match[21].matchalgstr ="strstrsse42";
#endif
match[22].matchalg =strstrmmx;
match[22].matchalg2 =0;
match[22].matchalgstr ="strstrmmx";
for(i=0; i<ALLALG; i++)
{
match[i].boolmatch=1;
}
if((fp=fopen("boolmatch","r"))==NULL)
{
printf("err");
exit(0);
}
{
for(i=0; i<18; i++)
{
char buf[128];
char* ret =fgets(buf, 128,fp);
if(ret ==NULL) break;
sscanf(buf,"%d", &(match[i].boolmatch));
}
}
fclose(fp);
//Pat="Natasha";
if(quryfname !=NULL)
Pat=Getsubjectfromfile(quryfname);
if(subjfname!=NULL) {
if(isGene) {
Text=GetgenefromfileU(subjfname);
} else {
Text=Getsubjectfromfile(subjfname);
}
}
n = strlen(Text);
m = strlen(Pat);
if(Pat[m-1] == '\n') Pat[m-1]=0;
/*fp=fopen("sub","w");
fprintf(fp,"%s",Text);
fclose(fp);
printf("%s\n",Pat);*/
//Pat="ncinc";
// Text="Till today, the lantern ncinchpc festival is Natashastill held each year ncinchpc around the country. Lanterns of various shapes and sizes ncinchpc are hung in the streets, attracting countless visitors. Children will hold self-made or bought lanterns to stroll with on the streets, extremely excite";
occurnum=0;
/* 调用串匹配函数 */
//time( &start );
/*
Mtime(&startrdt);
//for(i=0;i<1;i++)
{
printf("bf:\n");
Sbf(Text,Pat);
printf("mp:\n");
Smp(Text,Pat);
printf("kmp:\n");
Skmp(Text,Pat);
printf("bm:\n");
Sbm(Text,Pat);
printf("bmh:\n");
Sbmh(Text,Pat);
printf("bmhs:\n");
Sbmhs(Text,Pat);
printf("smith:\n");
Ssmith(Text,Pat);
printf("dfa:\n");
Sdfa(Text,Pat);
printf("bdm:\n");
Sbdm(Text,Pat);
printf("byh:\n");
Sbyh(Text,Pat);
printf("kr:\n");
Skr(Text,Pat);
printf("skip:\n");
Sskip(Text,Pat);
printf("kmpskip:\n");
Skmpskip(Text,Pat);
printf("shiftor:\n");
Sshiftor(Text,Pat);
printf("\n");
}
Mtime(&endrdt);*/
//time( &finish );
//elapsed_time= difftime( finish, start );
if((fp=fopen("result","w"))==NULL)
{
printf("open result file err");
exit(0);
}
fprintf(fp,"***********************************************\n");
fprintf(fp,"length of Text:%d\nlength of pattern:%d\n ",strlen(Text),strlen(Pat));
fprintf(stdout,"length of Text:%d\nlength of pattern:%d %s\n ",strlen(Text),strlen(Pat),Pat);
setReportFunc(SEARCH_SILENT);
for(i=0; i<ALLALG; i++)
{
if(match[i].matchalg2 && match[i].boolmatch)
match[i].matchalg2(Text,Pat, n, m);
if(match[i].matchalg && match[i].boolmatch)
match[i].matchalg(Text,Pat);
}
if(verbose ==0)
setReportFunc(SEARCH_SILENT);
else if(verbose == 1)
setReportFunc(SEARCH_ALL);
else
setReportFunc(SEARCH_FIRST);
printf("alg2\n");
for(i=0; i<ALLALG; i++)
{
if(match[i].matchalg2 && match[i].boolmatch)
{
mdtime(0);
int t1 = dlaunch4(match[i].matchalg2)(Text+n/2,Pat, n/2, m);
match[i].matchalg2(Text,Pat, n/2, m);
dsync(t1);
elapsed_time=mdtime(1);
time_used[i] = elapsed_time;
printf("algorithm %15s takes %20f clocks.\n",match[i].matchalgstr, elapsed_time );
fprintf(fp,"%20.15f seconds:algorithm %s takes \n ", elapsed_time, match[i].matchalgstr);
}
}//end for
printf("alg\n");
for(i=0; i<ALLALG; i++)
{
if(match[i].matchalg&& match[i].boolmatch)
{
char* pcur;
mdtime(0);
pcur = match[i].matchalg(Text,Pat);
elapsed_time=mdtime(1);
time_used[i] = elapsed_time;
if(verbose ==2)
printf("(%d)", pcur - Text);
printf("algorithm %15s takes %20f clocks.\n",match[i].matchalgstr, elapsed_time );
fprintf(fp,"%20.15f seconds:algorithm %s takes \n ", elapsed_time, match[i].matchalgstr);
}
}//end for
fclose(fp);
printf("speedup to bfStr :%f\n", time_used[0] / time_used[18]);
printf("speedup to bmStr :%f\n", time_used[1] / time_used[18]);
printf("speedup to bmhStr:%f\n", time_used[2] / time_used[18]);
/* 输出结果 */
printf("%f\n%f\n%f\n%f\n%f\n%f\n",time_used[18], time_used[1], time_used[2], time_used[0],time_used[6],time_used[15]);
for(i=0; i<occurnum; i++)
printf("%d,",occurrenceint[i]);
//printf("\nalgorithm takes %6.2f seconds.\n", elapsed_time );
// elapsed_time =Mdifftime(startrdt,endrdt);
//printf("\nalgorithm takes %20.15f seconds.\n", elapsed_time );
}
int main(int argc,char **argv) {
FILE *input,*good,*bad = NULL,*missing=NULL;
Reader *input;
Writer *good;
fastap linker1,linker2;
int ind,isFasta;
int wantProgressMeter = 0;
int cTrimmed=0,cUnTrimmed=0,cLinker=0,cQual=0;
/* process the command-line options */
ind = readOptions(argc,argv);
if (isatty(fileno(stderr))) {
wantProgressMeter = 1;
}
/* check the linker file, read linkers */
if (!isFastaFile(argv[ind])) {
fprintf(stderr,"linker file '%s' does not exist or does not appear to be a Fasta file.\n",argv[ind]);
exit(-1);
}
linker1 = fa_alloc(LINELENGTH);
linker2 = fa_alloc(LINELENGTH);
getLinker(argv[ind],linker1,linker2);
/* check that the input file looks good, get its type */
if (ind + 1 >= argc) {
fprintf(stderr,USAGE);
exit(-1);
}
if (!fileExists(argv[ind+1])) {
fprintf(stderr,"input file '%s' does not exist (or some other error occurred).\n",argv[ind+1]);
exit(-1);
}
input = bode::Reader::open(std::string(argv[ind+1]))
/*
if (isFastaFile(argv[ind+1])) {
isFasta = 1;
} else if (isFastqFile(argv[ind+1])) {
isFasta = 0;
} else {
fprintf(stderr,"input file '%s' does not appear to be Fasta or Fastq.\n",argv[ind+1]);
exit(-1);
}
input = fopen(argv[ind+1],"r");
*/
/* check that output file doesn't exist, open it */
if (ind + 2 >= argc) {
fprintf(stderr,USAGE);
exit(-1);
}
if (fileExists(argv[ind+2]) && !overwrite) {
fprintf(stderr,"output file '%s' exists, will not overwrite.\n",argv[ind+2]);
exit(-1);
}
good = input->getWriter();
good = good->open(argv[ind+2],input->header());
/* missing linker output file */
/*
if (missingLinkerOutputFile != NULL) {
if (fileExists(missingLinkerOutputFile)) {
fprintf(stderr,"missing linker output file '%s' exists, will not overwrite.\n",missingLinkerOutputFile);
exit(-1);
}
missing = fopen(missingLinkerOutputFile,"w");
}
*/
/* set up the alignment stuff */
calignInit(LINELENGTH,2,-2,-6,-1);
processFile(linker1,linker2,input,good,bad,missing,&cTrimmed,&cUnTrimmed,&cLinker,wantProgressMeter);
fprintf(stdout,"trimmed=%d untrimmed=%d linker=%d lowqual=%d\n",
cTrimmed,cUnTrimmed,cLinker,cQual);
return 0;
}
