void axtToPsl(char *inName, char *tSizeFile, char *qSizeFile, char *outName)
/* axtToPsl - Convert axt to psl format. */
{
struct hash *tSizeHash = readSizes(tSizeFile);
struct hash *qSizeHash = readSizes(qSizeFile);
struct lineFile *lf = lineFileOpen(inName, TRUE);
char strand[2];
FILE *f = mustOpen(outName, "w");
struct psl* psl;
struct axt *axt;
strand[1] = '\0';
while ((axt = axtRead(lf)) != NULL)
{
int qSize = findSize(qSizeHash, axt->qName);
int qStart = axt->qStart;
int qEnd = axt->qEnd;
if (axt->qStrand == '-')
reverseIntRange(&qStart, &qEnd, qSize);
strand[0] = axt->qStrand;
psl = pslFromAlign(axt->qName, qSize, qStart, qEnd, axt->qSym,
axt->tName, findSize(tSizeHash, axt->tName),
axt->tStart, axt->tEnd, axt->tSym, strand,
PSL_IS_SOFTMASK);
if (psl != NULL)
{
pslTabOut(psl, f);
pslFree(&psl);
}
axtFree(&axt);
}
lineFileClose(&lf);
carefulClose(&f);
}
void chainToPsl(char *inName, char *tSizeFile, char *qSizeFile, char *targetList, char *queryList, char *outName)
/* chainToPsl - Convert chain file to psl format. */
{
struct hash *tSizeHash = readSizes(tSizeFile);
struct hash *qSizeHash = readSizes(qSizeFile);
struct lineFile *lf = lineFileOpen(inName, TRUE);
FILE *f = mustOpen(outName, "w");
struct hash *fileHash = newHash(0); /* No value. */
struct hash *tHash = newHash(20); /* seqFilePos value. */
struct hash *qHash = newHash(20); /* seqFilePos value. */
struct dlList *fileCache = newDlList();
struct chain *chain;
int q,t;
verbose(1, "Scanning %s\n", targetList);
hashFileList(targetList, fileHash, tHash);
verbose(1, "Scanning %s\n", queryList);
hashFileList(queryList, fileHash, qHash);
verbose(1, "Converting %s\n", inName);
while ((chain = chainRead(lf)) != NULL)
{
//uglyf("chain %s %s \n",chain->tName,chain->qName);
q = findSize(qSizeHash, chain->qName);
t = findSize(tSizeHash, chain->tName);
aliStringToPsl(lf, chain->qName, chain->tName, chain->qSize, chain->tSize,
min(chain->tEnd-chain->tStart, chain->qEnd-chain->qStart), chain->qStart, chain->qEnd, chain->tStart, chain->tEnd,
chain->qStrand, f, chain, tHash, qHash, fileCache);
chainFree(&chain);
}
lineFileClose(&lf);
carefulClose(&f);
}
/*
* Constructor: std::vector<int> B64coder::KeyToDecimal(char* key)
*
* Purpose: Finds the decimal value for each char in key with respect to cypher
*
* Arguments: char* key = starting address of a char array
*
* Returns: std::vector<int> = each int corresponds to a single values decimal value
*/
std::vector<int> B64coder::KeyToDecimal(char* key)
{
int length = findSize(key);
std::vector<int> DecCy(length);
int loc;
for ( int i = 0; i < length; i++ )
{
loc = B64->cypherIndex(*key);
DecCy[i] = loc;
key++;
}
return DecCy;
}
Node * Shell_Sort(Node *list)
{
long Size; //store the size of the integer list
Size = findSize(list); //find the size
int q = largest_index(3, Size); //find the largest value for q less than size
long j, l;
int count1;
Node * head = list;
int pow1, pow2, k;
for (pow1 = q; pow1 >= 0; pow1--)
{
for (pow2 = pow1; pow2 >= 0 ; pow2--)
{
Node * cur = head;
k = power(3, pow2) * power(2, pow1 - pow2); //use this formula to calculate the sequence elements
for (j = 1; j <= (Size - k); j++)
{
List * dhead = NULL;
dhead = List_Insert(dhead, cur); //insert starting from the first j'th value
Node * tmp1 = cur;
for (l = j + k; l <= Size; l = l + k)
{ //printf("\nj+k=%ld\n", l);
count1 = 0;
while (count1 != k)
{
tmp1 = tmp1 -> next; //keep on iterating till you reach the correct node
count1++;
}
dhead = List_Insert(dhead, tmp1); //insert node into the sublist
}
Insertion_Sort(dhead); //implement insertion sort
cur = cur -> next; //make current as the next node
while (dhead != NULL) //free memory due to each sublist before the next iteration
{
List * tmp = dhead;
dhead = dhead -> next;
free(tmp);
}
}
}
}
return head; //return the list of integers that has been sorted
}
int main(int argc,char *argv[]){
/*input file pointer*/
FILE *fpInp;
/*Toplam bulunan string sayisi*/
int intTotalNumber=0;
/*String Size*/
int intStrSize=0;
/*Arguman kontrolu*/
/*Program ismi-txt file-aranacak string
3 arguman olmasi gerekiyor*/
if(argc!=3){
if(argc>3)
printf("Fazla Argüman\n");
else
printf("Eksik Argüman\n");
printf("---Programin dogru kullanim sekli---\n");
usage();
exit(0);
}
/*dosyayi aciyoruz*/
/*kontrollerimizi yapiyoruz*/
if((fpInp=fopen(argv[1],"r"))==NULL){
printf("Dosya Hatasi : %s\n",strerror(errno));
exit(0);
}
/*dosyayi kapatiyoruz*/
fclose(fpInp);
/*Size'ı belirliyoruz*/
intStrSize=findSize(fpInp,argv[1]);
/*printf("size : %d",intStrSize);*/
intTotalNumber=findString(fpInp,argv[1],intStrSize,argv[2]);
/*Kac kez bulundugunu ekrana basiyoruz*/
printf("Kelimenin text dosyasindaki toplam sayisi : %d\n",intTotalNumber);
return 0;
}
void axtDropOverlap(char *inName, char *tSizeFile, char *qSizeFile, char *outName)
/* used for cleaning up self alignments - deletes all overlapping self alignments */
{
struct hash *qSizeHash = readSizes(qSizeFile);
struct lineFile *lf = lineFileOpen(inName, TRUE);
FILE *f = mustOpen(outName, "w");
struct axt *axt;
int totMatch = 0;
int totSkip = 0;
int totLines = 0;
while ((axt = axtRead(lf)) != NULL)
{
totLines++;
totMatch += axt->score;
if (sameString(axt->qName, axt->tName))
{
int qs = axt->qStart;
int qe = axt->qEnd;
if (axt->qStrand == '-')
reverseIntRange(&qs, &qe, findSize(qSizeHash, axt->qName));
if (axt->tStart == qs && axt->tEnd == qe)
{
/*
printf( "skip %c\t%s\t%d\t%d\t%d\t%s\t%d\t%d\t%d\n",
axt->qStrand,
axt->qName, axt->symCount, axt->qStart, axt->qEnd,
axt->tName, axt->symCount, axt->tStart, axt->tEnd
);
*/
totSkip++;
continue;
}
}
axtWrite(axt, f);
axtFree(&axt);
}
fclose(f);
lineFileClose(&lf);
}
int fileOperations(FILE *outputFile,int* fd,char *directoryName,char *findString){
DIR *openFile;
FILE *inputFile=NULL;
struct dirent *input;
char directory[MAX];
char fullDirectory[MAX];
struct stat statFile;
pid_t pid;
char strPipe[MAX];
char readpipe[MAX];
char arr[MAX];
int stat = 0;
int size = 0;
int fifo2;
int in;
openFile = opendir(directoryName);
if(openFile == NULL){
printf("Dosya acilamadi\n");
closedir(openFile);
exit (1);
}
strncpy(directory,directoryName, MAX - 1);
//signal(SIGINT, &ctrlcSignal);
/*Directory okudum*/
while((input = readdir(openFile)) != NULL){
if(strcmp(input->d_name,".")!=0 && strcmp(input->d_name,"..")!=0){
/*Directory ve altindaki dosyayi bir arraye attim*/
sprintf(fullDirectory, "%s/%s",directory, input -> d_name );
if (lstat(fullDirectory,&statFile) < 0){
perror(fullDirectory);
}
/*Dosya mi directory mi oldugunu kontrol ettim dosya ise*/
if (S_ISDIR(statFile.st_mode) == 0){
/*Dosya sayimi artirdim*/
totalFile = totalFile + 1;
if((pid = fork())== -1){
perror("Not fork\n");
exit (1);
}if(pid == 0){
size = findSize(inputFile,fullDirectory);
totalW += myGrep(inputFile,outputFile,strPipe,fd,size,fullDirectory,findString);
exit (totalW);
}else{
// while (r_wait(NULL) > 0);
/*Asagidaki fonksiyonlari http://www.kaanaslan.com/resource/article/display_article.php?id=87
* sitesinden referans alarak kullandim */
wait(&stat);
totalW = WEXITSTATUS(stat);
}
/*Childlari topladim*/
totalChild = totalChild + 1;
}else{/*Dosya degil ise recursive olarak fonksiyonumu tekrar cagirdim ki dosyayi bulsun*/
/*Directory sayimi buldum*/
totalDirectory = totalDirectory + 1;
if((pid = fork())== -1){
perror("Not fork\n");
exit (1);
}
if(pid == 0){
fileOperations(outputFile,fd,fullDirectory,findString);
if((in= read(fd[0], readpipe,MAX)> 0)){
if(in<=0){
perror("read error \n");
exit(1);
}
//close(fd[0]);
if((fifo2 = open(myfifo, O_RDWR ))==-1){
perror("Not fifo");
exit(1);
}
if(write(fifo2,readpipe,sizeof(char)*MAX)<0)
{
perror("Failed to write");
exit(1);
}
close(fifo2);
if((fifo2 = open(myfifo,O_RDONLY))==-1){
perror("Not fifo");
exit(1);
}
in = read( fifo2, arr,sizeof(char)*MAX);
if(in<=0)
{
perror("not read");
exit(1);
}
fprintf(outputFile,"%s\n",arr);
exit(1);
}
}else{
//while (r_wait(NULL) > 0);
//close(fd[1]);
//unlink("myfifo");
}
}
}
}
//close(fifo2);
closedir(openFile);
return 0;
}
Link::Link(Node *n) {
h = n;
size = findSize();
}
Link::Link(int v, Node *n) {
h = new Node(v,n);
size = findSize();
}
Link::Link(int v) { h = new Node(v); size = findSize(); }
Link::Link() { h = 0; size = findSize(); }
