void IndexInitial()
{
MsgFunction("IndexInitial");
FILE* pFile = NULL;
MsgRead(pchProteinIndexFile);
if (pFile = fopen(pchProteinIndexFile, "r"))
{
int step_i = 0;
for (step_i = 0; step_i <= INDEX_PROTEINS - 1; ++step_i)
{
fscanf(pFile, "%s %d", selectProteins[step_i].chName,
&(selectProteins[step_i].iID));
}
fclose(pFile);
}
else
{
MsgError(pchProteinIndexFile);
}
MsgRead(pchPhenotypeIndexFile);
if (pFile = fopen(pchPhenotypeIndexFile, "r"))
{
int step_i = 0;
for (step_i = 0; step_i <= INDEX_PHENOTYPES - 1; ++step_i)
{
fscanf(pFile, "%s %d", selectPhenotypes[step_i].chName,
&(selectPhenotypes[step_i].iID));
}
fclose(pFile);
}
else
{
MsgError(pchPhenotypeIndexFile);
}
MsgRead(pchGeneIndexFile);
if (pFile = fopen(pchGeneIndexFile, "r"))
{
int step_i = 0;
for (step_i = 0; step_i <= INDEX_GENES - 1; ++step_i)
{
fscanf(pFile, "%s %d", selectGenes[step_i].chName,
&(selectGenes[step_i].iID));
//debug
//if(strcmp(selectGenes[step_i].chName, "613733")==0)
//{
// cout << "";
//}
}
fclose(pFile);
}
else
{
MsgError(pchGeneIndexFile);
}
}
static int
MsgCmd(int ac, char **av)
{
char *buf;
char *path, *cmdstr;
int i, len;
/* Get arguments */
if (ac < 3)
return (CMDRTN_USAGE);
path = av[1];
cmdstr = av[2];
/* Put command and arguments back together as one string */
for (len = 1, i = 3; i < ac; i++)
len += strlen(av[i]) + 1;
if ((buf = malloc(len)) == NULL) {
warn("malloc");
return (CMDRTN_ERROR);
}
for (*buf = '\0', i = 3; i < ac; i++) {
snprintf(buf + strlen(buf),
len - strlen(buf), " %s", av[i]);
}
/* Send it */
if (NgSendAsciiMsg(csock, path, "%s%s", cmdstr, buf) < 0) {
free(buf);
warn("send msg");
return (CMDRTN_ERROR);
}
free(buf);
/* See if a synchronous reply awaits */
{
struct timeval tv;
fd_set rfds;
FD_ZERO(&rfds);
FD_SET(csock, &rfds);
memset(&tv, 0, sizeof(tv));
switch (select(csock + 1, &rfds, NULL, NULL, &tv)) {
case -1:
err(EX_OSERR, "select");
case 0:
break;
default:
MsgRead();
break;
}
}
/* Done */
return (CMDRTN_OK);
}
int
io_console_write(resmgr_context_t *ctp, io_write_t *msg, iofunc_ocb_t *ocb) {
int n;
int off;
int len;
int ret;
int cnt;
int status;
int nonblock;
char *cptr;
ret = EOK;
cptr = (char *) (sizeof(msg->i) + (char *)&msg->i);
off = 0;
len = msg->i.nbytes;
// Is device open for write?
if((status = iofunc_write_verify(ctp, msg, ocb, &nonblock)) != EOK)
return status;
// No special xtypes
if((msg->i.xtype & _IO_XTYPE_MASK) != _IO_XTYPE_NONE)
return(EINVAL);
while(off < len) {
/* Limit write to max payload, NULL terminate the string,
* and figure out how many ints we're writing.
*/
n = min(len - off, _SLOG_MAXSIZE - _SLOG_HDRINTS*sizeof(int) - 1);
cptr[n] = '\0';
cnt = n/sizeof(int) +1;
/* put it in the log */
ret = _io_write_log(ctp, msg, ocb, cnt, 1);
if(ret != EOK)
break;
off += n;
//skip the MsgRead() if we're done.
if (off == len)
break;
ret = MsgRead(ctp->rcvid, cptr, n, off + sizeof(msg->i));
if(ret <= 0)
break;
}
_IO_SET_WRITE_NBYTES(ctp, off);
return(ret);
}
int das_tmr_scan_msg( resmgr_context_t *ctp, RESMGR_OCB_T *pocb,
int num_entries )
{
int num_read;
char plist[QMM10XT_N_TIMERS]; // hold scan list read from second part
num_read = MsgRead(ctp->rcvid, plist, num_entries, sizeof(das_msg_t));
if( qmm10xt_tmr_set_scan( pmain_board, plist, num_entries ) == TRUE )
return ( EOK );
else
return ( EINVAL );
}
void ReadIDFile()
{
MsgFunction("ReadIDFile");
FILE* pFile = NULL;
MsgRead(pchProteinIDFile);
if (pFile = fopen(pchProteinIDFile, "r"))
{
int step_i = 0;
for (step_i = 0; step_i < TOTAL_PROTEINS; ++step_i)
{
fscanf(pFile, "%s %d", TotalProteins[step_i].chName,
&(TotalProteins[step_i].iID));
}
fclose(pFile);
}
else
{
printf("File %s open error\n", pchProteinIDFile);
}
MsgRead(pchPhenotypeIDFile);
if (pFile = fopen(pchPhenotypeIDFile, "r"))
{
int step_i = 0;
for (step_i = 0; step_i < TOTAL_PHENOTYPES; ++step_i)
{
fscanf(pFile, "%s %d", TotalPhenotypes[step_i].chName,
&(TotalPhenotypes[step_i].iID));
}
fclose(pFile);
}
else
{
printf("File %s open error\n", pchPhenotypeIDFile);
}
}
int resmgr_msg_again(resmgr_context_t *ctp, int rcvid) {
if(MsgInfo(rcvid, &ctp->info) == -1) {
return -1;
}
if((ctp->info.msglen = MsgRead(ctp->rcvid = rcvid, ctp->msg, ctp->msg_max_size, 0)) == -1) {
return -1;
}
(void)MsgCurrent(rcvid);
_resmgr_handler(ctp);
return 0;
}
void ReadPhenotypeSimiIndex()
{
MsgRead(pchIndexFile);
FILE* fin = fopen(pchIndexFile, "r");
if (fin)
{
int i = 0;
for (i = 0; i <= iMaxPhenotype - 1; i++)
{
char aLine[PHENOTYPE_LENGTH] = {'\0'};
fscanf(fin, "%s", aLine);
strcpy(phenotypeSimiIndex[i].chName, aLine);
phenotypeSimiIndex[i].iID = i;
}
fclose(fin);
}
else
{}
}
void CreateSelectFile()
{
MsgFunction("CreateSelectFile");
CreateIndexGeneProtein();
CreateIndexPhenotype();
ReadGeneProtein();
memset(selectPhenotypeProtein, CAUSE_PROTEIN_END, sizeof(selectPhenotypeProtein));
//Phenotype tempPhenotype;
MsgRead(morbidMapFile);
FILE* fin = fopen(morbidMapFile, "r");
if (fin)
{
int w = 0;
for(w = 0; w <= iMax -1 && !feof(fin); w++)
{
char aLine[LINE_LENGTH] = {'\0'};
fgets(aLine, LINE_LENGTH, fin);
*(aLine+strlen(aLine)-1) = '\0';
char* posP = aLine;
char* posG = aLine;
char* p = ExtractPhenotypeID(aLine);
char* g = ExtractGeneID(aLine);
while (p != NULL)
{
Phenotype tempPhenotype;
strcpy(tempPhenotype.chName, p);
Phenotype* pPh = NULL;
pPh = (Phenotype*) bsearch(&tempPhenotype, selectPhenotypes, INDEX_PHENOTYPES, sizeof(Phenotype), PhenotypeCompare);
if (pPh != NULL)
{
int phenotypePos = pPh -> iID;
while(g != NULL) //in fact 一行一个G
{
Phenotype tempGene;
strcpy(tempGene.chName, g);
Gene* pG = NULL;
pG = (Gene*) bsearch(&tempGene, selectGenes, INDEX_GENES, sizeof(Gene), GeneCompare);
if (pG != NULL)
{
int genePos = pG -> iID;
int end = 0;
int k = 0;
for (k = 0;k <= CAUSE_PROTEINS - 1 ; k++ )// j <= RELATE_PROTEINS - 1
{
if (selectPhenotypeProtein[phenotypePos][k]== CAUSE_PROTEIN_END)
{
end = k;
break;
}
else
{}
}
int m = 0;
for (m = 0; m <= RELATE_PROTEINS - 1 && GeneProtein[genePos][m] != CAUSE_PROTEIN_END; m++ )
{
bool isExist = false;
int n = 0;
for (n = 0; n <= RELATE_PROTEINS - 1 && selectPhenotypeProtein[phenotypePos][n] != CAUSE_PROTEIN_END ; n++)
{
if (selectPhenotypeProtein[phenotypePos][n] == GeneProtein[genePos][m])
{
isExist = true;
break;
}
else
{}
}
if (isExist == false)
{
selectPhenotypeProtein[phenotypePos][end] = GeneProtein[genePos][m];
end++;
}
else
{}
}
selectPhenotypeProtein[phenotypePos][end] = CAUSE_PROTEIN_END;
}
else
{}
//strcpy(phenotypes[i].chName, rs[j].str().substr(1,6).c_str());
//i++ ;
posG = strstr(aLine, g);
posG = posG + GENE_LENGTH - 1;
if (posG <= aLine + strlen(aLine) )
{
g = ExtractPhenotypeID(posG);
}
else
{}
}
}
else
{}
posP = strstr(aLine, p);
posP = posP + PHENOTYPE_LENGTH - 1;
if (posP <= aLine + strlen(aLine) )
{
p = ExtractPhenotypeID(posP);
}
}
}
fclose(fin);
}
else
{}
//test
/*ofstream fout1("Data\\test\\selected.test", ios::out);
for (i = 0; i <= TOTAL_PHENOTYPES -1 ; i++)
{
if (selectPhenotypeProtein[i][0] == CAUSE_PROTEIN_END)
{
continue;
}
else
{}
if (strcmp(selectPhenotypes[i].chName, NOSIMIINFO) == 0)
{
break;
}
else
{}
bool isHG = false;
for (k = 0; k <= CAUSE_PROTEINS - 1 && selectPhenotypeProtein[i][k] != CAUSE_PROTEIN_END; k++)
{
string proteinLoc = proteinMaps[selectPhenotypeProtein[i][k]].pos.oriString;
if (proteinLoc.find('H') != string::npos || proteinLoc.find('G') != string::npos)
{
isHG = true;
break;
}
else
{}
}
if (isHG == false)
{
for (j = 0; j <= CAUSE_PROTEINS - 1; j++)
{
fout1 << selectPhenotypeProtein[i][j] << ",";
if (selectPhenotypeProtein[i][j] == CAUSE_PROTEIN_END)
{
break;
}
else
{}
}
fout1<<endl;
}
else
{}
}
fout1.flush();
fout1.close();*/
//609033以下的，没有表型相似度了，break
//去掉没有蛋白质的
//去掉蛋白质区间是H,G表示的
//output selected.txt
ReadProteinMap(proteinMaps, selectProteins, INDEX_PROTEINS);
ReadPhenotypeSimiIndex();
MsgWrite(selectedFile);
FILE* fout = fopen(selectedFile, "w");
if (fout)
{
int available = 0;
int i = 0;
for (i = 0; i <= INDEX_PHENOTYPES -1; i++)
{
Phenotype tempPhenotype = selectPhenotypes[i];
Phenotype* pPh = NULL;
pPh = (Phenotype*) bsearch(&tempPhenotype, phenotypeSimiIndex, iMaxPhenotype, sizeof(Phenotype), PhenotypeCompare);
if (pPh == NULL)
{
continue;
}
else
{}
//去掉没有找到蛋白质的
if (strcmp(selectPhenotypes[i].chName, NOSIMIINFO) == 0)
{
break;
}
else
{}
//以下没有表型相似度
if (selectPhenotypeProtein[i][0] == CAUSE_PROTEIN_END)
{
continue;
}
else
{}
//去掉没有区间信息的(蛋白质区间没有，或者编码以H,G开头的)
bool isHG = false;
int k = 0;
for (k = 0; k <= CAUSE_PROTEINS - 1 && selectPhenotypeProtein[i][k] != CAUSE_PROTEIN_END; k++)
{
//debug
//cout << proteinMaps[selectPhenotypeProtein[i][k]].chName << endl;
//cout << i <<endl;
//string proteinPosStr = proteinMaps[selectPhenotypeProtein[i][k]].oriString;
//if (proteinPosStr.at(0) == 'G' || proteinPosStr.at(0) == 'H')
int proteinLoc = proteinMaps[selectPhenotypeProtein[i][k]].pos;
if (proteinLoc == UNNORMAL_POS)
{
isHG = true;
break;
}
else
{}
}
if (isHG == false)
{
available++;
//fout << selectPhenotypes[i].chName << " ";
fprintf(fout, "%s ", selectPhenotypes[i].chName);
int j = 0;
for (j = 0; j <= CAUSE_PROTEINS - 1 && selectPhenotypeProtein[i][j] != CAUSE_PROTEIN_END; j++)
{
//fout << selectProteins[selectPhenotypeProtein[i][j]].chName << ",";
fprintf(fout, "%s,", selectProteins[selectPhenotypeProtein[i][j]].chName);
//fout << selectPhenotypeProtein[i][j] << ",";
}
//fout << endl;
fprintf(fout, "\n");
}
else //含有'H','G'开头的不规则蛋白质区间编码，表型不要了
{}
}
printf("->sMax:%d\n", available);
fflush(fout);
fclose(fout);
}
else
{
MsgError(selectedFile);
}
}
//static const int gpMax = 2773; //bio_g->p 行数
void CreateIndexGeneProtein()
{
MsgFunction("CreateIndexGeneProtein");
char proteinTemp[LINE_LENGTH] = {'\0'};
char gene[PHENOTYPE_LENGTH] = {'\0'};
//char protein[PROTEIN_LENGTH] = {'\0'};
int m = 0;
int n = 0;
MsgRead(geneProteinFile);
FILE* fin = fopen(geneProteinFile, "r");
if (fin)
{
int i = 0;
for(i = 0; !feof(fin) && i <= gpMax - 1; i++)
{
fscanf(fin, "%s %s", gene, proteinTemp);
//debug
//if (strcmp(gene, "609062") == 0)
//{
// cout<< gene;
//}
strcpy(genes[m].chName, gene);
m++;
char* pProteinNameHead = proteinTemp;
int current = 0;
for (current = 0; current <= strlen(proteinTemp) - 1 ; current += PROTEIN_LENGTH)
{
pProteinNameHead = proteinTemp + current;
strncpy(proteins[n].chName, pProteinNameHead, PROTEIN_LENGTH - 1);
n++;
}
}
fclose(fin);
}
else
{
MsgError(selectedFile);
}
qsort (genes, m, sizeof(Gene), GeneCompare);
qsort (proteins, n, sizeof(Protein), ProteinCompare);
MsgWrite(pchGeneIndexFile);
FILE* fout = fopen(pchGeneIndexFile, "w");
if (fout)
{
int j = 0;
for (j = 0; j <= m - 1; j++)
{
fprintf(fout, "%s %d\n", genes[j].chName, j);
}
printf("->INDEX_GENES:%d\n", j);
fflush(fout);
fclose(fout);
}
else
{
MsgError(pchPhenotypeIDFile);
}
MsgWrite(pchProteinIDFile);
fout = fopen(pchProteinIndexFile, "w");
if (fout)
{
char last [PROTEIN_LENGTH] = {'\0'};
int k = 0;
int j = 0;
for (j = 0; j <= n - 1; j++)
{
if (strcmp(proteins[j].chName, last) != 0)
{
fprintf(fout, "%s %d\n", proteins[j].chName, k);
k++;
}
else
{}
strcpy(last, proteins[j].chName);
}
printf("->INDEX_PROTEINS:%d", k);
fflush(fout);
fclose(fout);
}
else
{
MsgError(pchProteinIDFile);
}
}
void ReadGeneProtein()
{
MsgFunction("ReadGeneProtein");
IndexInitial();
char gene[PHENOTYPE_LENGTH] = {'\0'};
char protein[PROTEIN_LENGTH] = {'\0'};
char proteinTemp[LINE_LENGTH] = {'\0'};
MsgRead(geneProteinFile);
FILE* pFile = fopen(geneProteinFile, "r");
if (pFile)
{
while (!feof(pFile))
{
fscanf(pFile, "%s %s", gene, proteinTemp);//可以跳过空行
Phenotype tempGene;
strcpy(tempGene.chName, gene);
//debug
//if (strcmp(gene, "613733") == 0)
//{
//cout << gene;
//}
Gene* pResult = NULL;
pResult = (Gene*) bsearch(&tempGene, selectGenes, INDEX_GENES, sizeof(Gene), GeneCompare);
if (pResult != NULL)
{
int genePos = pResult - selectGenes;
int i = 0;
char* pProteinNameHead = proteinTemp;
int current = 0;
for (current = 0; current <= strlen(proteinTemp) - 1 ; current += PROTEIN_LENGTH)
{
pProteinNameHead = proteinTemp + current;
strncpy(protein, pProteinNameHead, PROTEIN_LENGTH - 1);
protein[PROTEIN_LENGTH - 1] = '\0';
Protein tempProtein;
strcpy(tempProtein.chName, protein);
Protein* pResult = NULL;
pResult = (Protein*) bsearch(&tempProtein, selectProteins, INDEX_PROTEINS, sizeof(Protein), ProteinCompare);
if (pResult != NULL)
{
int proteinPos = pResult - selectProteins;
GeneProtein[genePos][i] = proteinPos;
i++;
}
else
{
MsgError("error: protein index:");
MsgError(tempProtein.chName);
}
}
GeneProtein[genePos][i] = CAUSE_PROTEIN_END;
}
else
{
MsgError("error gene index");
MsgError(tempGene.chName);
}
}
fclose(pFile);
}
else
{
MsgError(geneProteinFile);
}
//test
//ofstream fout("Data\\test\\selectedGeneProtein.test", ios::out);
//for (i = 0; i <= INDEX_GENES -1 ; i++)
//{
// for (j = 0; j <= CAUSE_PROTEINS - 1; j++)
// {
// fout << GeneProtein[i][j] << ",";
// if (GeneProtein[i][j] == CAUSE_PROTEIN_END)
// {
// break;
// }
// }
// fout<<endl;
//}
//fout.flush();
//fout.close();
}
void CreateIndexPhenotype()
{
MsgFunction("CreateIndexPhenotype");
int i = 0;
//Phenotype tempPhenotype;
Phenotype phenotypes[iMax];//从morbidmap->index
MsgRead(morbidMapFile);
FILE* fin = fopen(morbidMapFile, "r");
if (fin)
{
int j = 0;
for(j = 0; j <= iMax -1 && !feof(fin); j++)
{
char aLine[LINE_LENGTH] = {'\0'};
fgets(aLine, LINE_LENGTH, fin);
*(aLine+strlen(aLine)-1) = '\0';
char* posP = aLine;
char* p = ExtractPhenotypeID(aLine);
while (p != NULL)
{
strcpy(phenotypes[i].chName, p);
i++;
posP = strstr(aLine, p);
posP = posP + PHENOTYPE_LENGTH - 1;
if (posP <= aLine + strlen(aLine) )
{
p = ExtractPhenotypeID(posP);
}
else
{
p = NULL;
}
}
}
qsort(phenotypes, i, sizeof(Phenotype), PhenotypeCompare);
}
else
{}
FILE* fout = fopen(pchPhenotypeIndexFile, "w");
if (fout)
{
//string last = "";
char last[PHENOTYPE_LENGTH] = {'\0'};
int k = 0;
int j = 0;
for (j = 0; j <= i - 1; j++)
{
if (strcmp(phenotypes[j].chName, last) != 0)
{
//fout << phenotypes[j].chName << " " << k << endl;
fprintf(fout, "%s %d\n",phenotypes[j].chName, k);
k++;
}
else
{}
strcpy(last, phenotypes[j].chName);
}
printf("->INDEX_PHENOTYPES:%d\n", k);
fflush(fout);
fclose(fout);
}
else
{}
}
void ReadMorbidMap()
{
MsgFunction("ReadMorbidMap");
int i = 0;
for (i = 0; i<=TOTAL_PHENOTYPES-1; i++)
{
int j =0;
for (j =0; j<=CAUSE_LOCATIONS-1; j++)
{
strcpy(TotalMorbidMaps[i][j].chName, "");
}
}
char name[PROTEIN_LENGTH] = {'\0'};
char location[16] = {'\0'};
Phenotype tempPhenotype;
MsgRead(morbidMapFile);
FILE* fin = fopen(morbidMapFile, "r");
if (fin)
{
int i = 0;
for (i = 0; i <= iMax -1 && !feof(fin); i++ )
{
char aLine[LINE_LENGTH] = {'\0'};
fgets(aLine, LINE_LENGTH, fin);
*(aLine+strlen(aLine)-1) = '\0'; //'\n'也读进来了
char* posP = aLine;
char* p = ExtractPhenotypeID(aLine);
while (p!= NULL)
{
//debug
//if (strcpy(name,"210210") == 0)
//{
// cout << "210210";
//}
//cout << "debug ReadMorbidMap" << name << endl;
strcpy(name, p);
strcpy(tempPhenotype.chName, name);
char* last = strrchr(aLine, '|');
strcpy(location, last + 1);
Phenotype* pResult = NULL;
pResult = (Phenotype*) bsearch(&tempPhenotype, TotalPhenotypes, TOTAL_PHENOTYPES, sizeof(Phenotype), PhenotypeCompare);
if (pResult != NULL)
{
int pos = pResult -> iID;
int i = 0;
for (i = 0; i <= CAUSE_LOCATIONS - 1; i++)
{
if (strcmp(TotalMorbidMaps[pos][i].chName, "") == 0)
{
strcpy(TotalMorbidMaps[pos][i].chName, name);
StrToLocation(location, &TotalMorbidMaps[pos][i]);
break;
}
else
{}
}
}
else
{}
posP = strstr(aLine, p);
posP = posP + PHENOTYPE_LENGTH-1;
if (posP <= aLine + strlen(aLine) )
{
p = ExtractPhenotypeID(posP);
}
else
{}
}
}
fclose(fin);
}
else
{
MsgError(morbidMapFile);
}
//test
//ofstream fout("Data\\test\\morbidmap.test", ios::out);
//if (fout)
//{
// for (pos = 0; pos <= TOTAL_PHENOTYPES - 1; pos++)
// {
// fout << TotalMorbidMaps[pos][0].chName << " ";
// for (i = 0; i <= CAUSE_LOCATIONS - 1; i++)
//
// {
// fout << "[" << BitToLocation(TotalMorbidMaps[pos][i].start) << "," << BitToLocation(TotalMorbidMaps[pos][i].end) << "] ";
// }
// fout << "\n";
// /*fout << morbidMap[pos].at(0).chName << " ";
// for (vector<MorbidMap>::iterator iter = morbidMap[pos].begin() ; iter <= morbidMap[pos].begin()- 1; iter++)
// {
// fout << "[" + (*iter).start.oriString << "," << (*iter).end.oriString << "] ";
// }
// fout << "\n";*/
// }
// fout.flush();
// fout.close();
//}
//else
//{}
}
void ReadPhenotypeProteinRelationFile()
{
MsgFunction("ReadPhenotypeProteinRelationFile");
char phenotypes[PHENOTYPE_LENGTH];
char protein[PROTEIN_LENGTH];
char proteinTemp[LINE_LENGTH];
int phenotypeID = 0;
int proteinID = 0;
MsgRead(selectedFile);
FILE* pFile = fopen(selectedFile, "r");
if (pFile)
{
while (!feof(pFile))
{
//debug
/*if (strcmp(phenotypes, "202400") == 0)
{
cout << phenotypes;
}*/
fscanf(pFile, "%s %s", phenotypes, proteinTemp);//©иртлЬ╧Щ©упп
phenotypeID = PhenotypeNameToID(phenotypes);
int i = 0;
char* pProteinNameHead = proteinTemp;
int current = 0;
for (current = 0; current <= strlen(proteinTemp) - 1 ; current += PROTEIN_LENGTH)
{
pProteinNameHead = proteinTemp + current;
strncpy(protein, pProteinNameHead, PROTEIN_LENGTH - 1);
protein[PROTEIN_LENGTH - 1] = '\0';
proteinID = ProteinNameToID(protein);
phenotypeProtein[phenotypeID][i] = proteinID;
i++;
}
phenotypeProtein[phenotypeID][i] = CAUSE_PROTEIN_END;
}
fclose(pFile);
}
else
{
printf("File %s open error\n", selectedFile);
}
//test
//ofstream fout("Data\\test\\selected.test", ios::out);
//for (i = 0; i <= TOTAL_PHENOTYPES -1 ; i++)
//{
// for (j = 0; j <= TOTAL_PROTEINS - 1; j++)
// {
// fout << phenotypeProtein[i][j] << ",";
// if (phenotypeProtein[i][j] == CAUSE_PROTEIN_END)
// {
// break;
// }
// }
// fout<<endl;
//}
//fout.flush();
//fout.close();
}
int _resmgr_mount_handler(resmgr_context_t *ctp, resmgr_iomsgs_t *msg, struct link *link, io_mount_extra_t *extra,
int (*func)(resmgr_context_t *ctp, resmgr_iomsgs_t *msg, void *handle, void *extra)) {
struct binding *binding = NULL;
int status = EOK;
io_mount_extra_t *newextra;
if ( msg->link.connect.extra_type == _IO_CONNECT_EXTRA_MOUNT_OCB) {
// Lookup passed in handle to send an ocb if required
if((binding = (struct binding *)_resmgr_handle(&extra->extra.cl.info, 0, _RESMGR_HANDLE_FIND_LOCK)) == (void *)-1) {
return ENXIO;
}
// Make sure they are from the same process
/*
if((status = _resmgr_access(ctp, &extra->node.info, 0, 0, 0, 0)) != EOK) {
return status;
}
*/
}
//We need to find a faster/more elegant way to make sure that we have the whole
//sized buffer to slurp in. For now, just allocate a new buffer
if (!(newextra = (io_mount_extra_t *)malloc(extra->nbytes))) {
if(binding) _resmgr_handle(&extra->extra.cl.info, 0, _RESMGR_HANDLE_UNLOCK);
return(ENOMEM);
}
//Copy the structure following the message (extra + data) into our allocated buffer.
if ((status = MsgRead(ctp->rcvid, newextra, extra->nbytes, (char *)extra - (char *)msg)) != extra->nbytes) {
if(binding) _resmgr_handle(&extra->extra.cl.info, 0, _RESMGR_HANDLE_UNLOCK);
free(newextra);
return(errno);
}
//Now that we have the buffer, set the pointers to the data, type and special device string
memset(&newextra->extra, 0, sizeof(newextra->extra));
if (binding) {
newextra->extra.srv.ocb = binding->ocb;
}
if (newextra->datalen) {
newextra->extra.srv.data = (void *)(newextra +1);
}
newextra->extra.srv.type =
newextra->extra.srv.special = (char *)(newextra + 1) + newextra->datalen;
if ((status = ((newextra->nbytes - sizeof(io_mount_extra_t))
- newextra->datalen)
- (strlen(newextra->extra.srv.type) +1)) > 0) {
newextra->extra.srv.special += strlen(newextra->extra.srv.type) + 1;
}
else {
newextra->extra.srv.special = NULL;
}
//Actually perform the mount callout
status = func(ctp, msg, link->handle, newextra);
free(newextra);
if(binding)_resmgr_handle(&extra->extra.cl.info, 0, _RESMGR_HANDLE_UNLOCK);
return(status);
}
//static const int sMax = 1897;//2042; //selected.txt行数
void CreateIDFile()
{
MsgFunction("CreateIDFile");
//char aLine[LINE_LENGTH] = {'\0'};
char proteinTemp[LINE_LENGTH] = "";
char phenotype[PHENOTYPE_LENGTH] = "";
char protein[PROTEIN_LENGTH] = "";
int m = 0;
int n = 0;
MsgRead(selectedFile);
FILE* fin = fopen(selectedFile, "r");
if (fin)
{
int i = 0;
for (i = 0; !feof(fin) && i <= sMax-1; i++)
{
fscanf(fin, "%s %s", phenotype, proteinTemp);
//debug
/*if (strcmp(phenotype, "202400") == 0)
{
cout<< aLine;
}*/
if (strcmp(phenotype, "") != 0)
{
strcpy(phenotypesOut[m].chName, phenotype);
m++;
char* pProteinNameHead = proteinTemp;
int current = 0;
for (current = 0; current <= strlen(proteinTemp) - 1 ; current += PROTEIN_LENGTH)
{
pProteinNameHead = proteinTemp + current;
strncpy(proteinsOut[n].chName, pProteinNameHead, PROTEIN_LENGTH - 1);
n++;
}
}
else
{}
}
fclose(fin);
}
else
{
MsgError(selectedFile);
}
qsort(phenotypesOut, m, sizeof(Phenotype), PhenotypeCompare);
qsort(proteinsOut, n, sizeof(Protein), ProteinCompare);
MsgWrite(pchPhenotypeIDFile);
FILE* fout = fopen(pchPhenotypeIDFile, "w");
if (fout)
{
//string last = "";
int j = 0;
for (j = 0; j <= m - 1; j++)
{
fprintf(fout, "%s %d\n", phenotypesOut[j].chName, j);
}
printf("->TOTAL_PHENOTYPES:%d\n", j);
fflush(fout);
fclose(fout);
}
else
{
MsgError(pchPhenotypeIDFile);
}
/*MsgWrite(pchProteinIDFile);
fout = fopen(pchProteinIDFile, "w");
if (fout)
{
char last[PROTEIN_LENGTH] = {'\0'};
int k = 0;
int j = 0;
for (j = 0; j <= n - 1; j++)
{
if (strcmp(proteinsOut[j].chName, last) != 0)
{
fprintf(fout, "%s %d\n", proteinsOut[j].chName, k);
k++;
}
else
{}
strcpy(last, proteinsOut[j].chName);
}
printf("->TOTAL_PROTEINS:%d\n", k);
fflush(fout);
fclose(fout);
}
else
{
MsgError(pchProteinIDFile);
}*/
CreateProteinIDNew();
}
void CreateProteinIDNew()
{
MsgFunction("CreateProteinIDNew");
//Protein tempProtein;
MsgRead(proteinMapFile);
FILE* fin = fopen(proteinMapFile, "r");
if (fin)
{
int i = 0;
int pos = 0;
for (i = 0; i <= BIGLINE - 1 && !feof(fin); i++ )
{
char aLine[LINE_LENGTH];
fgets(aLine, LINE_LENGTH, fin);
char* del = ",";
char* LF = "\n";
char* name = strtok(aLine, del);
char* chromosome = strtok(NULL, del);
char* band = strtok(NULL, LF);
if (!name || !chromosome || !band)
{
continue;
}
else if (chromosome[0] == 'G' ||chromosome[0] == 'H')
{
continue;
}
else if (i == 0)
{
continue;
}
else
{
//pTempArray[pos].iID = pos;
strcpy(pTempArray[pos].chName, name);
pos++;
}
}
printf("->TOTAL_PROTEINS:%d\n", pos);
qsort(pTempArray, pos, sizeof(Protein), ProteinCompare);
FILE* fout = fopen(pchProteinIDFile, "w");
MsgWrite(pchProteinIDFile);
if (fout)
{
int i = 0;
for (i = 0; i<=pos-1;i++)
{
fprintf(fout, "%s %d\n", pTempArray[i].chName, i);
}
}
else
{
MsgError(pchProteinIDFile);
}
fclose(fin);
fclose(fout);
}
else
{
MsgError(proteinMapFile);
}
}
void CreatePhenotypeSimilarityFile()
{
MsgRead(pchIndexFile);
FILE* fin = fopen(pchIndexFile, "r");
if (fin)
{
int i = 0;
for (i = 0; i <= iMaxPhenotype - 1; i++)
{
char aLine[PHENOTYPE_LENGTH] = {'\0'};
fscanf(fin, "%s", aLine);
strcpy(PhenotypeIDIndex[i].chName, aLine);
PhenotypeIDIndex[i].iID = i;
}
fclose(fin);
}
else
{}
MsgRead(pchDataFile);
fin = fopen(pchDataFile, "r");
if (fin)
{
int i = 0;
for (i = 0; i <= iMaxPhenotype - 1; i++)
{
int head = 0;
char aLine[iMaxRowLength+10] = {'\0'};
fscanf(fin, "%s", aLine);
int j = 0;
for (j = 0; j <= iMaxPhenotype - 1; j++)
{
char simiStr[simiLength] = {'\0'};
strncpy(simiStr, aLine + head, simiLength - 1);
simiStr[simiLength - 1] = '\0';
TotalSimilarity[i][j] = atof(simiStr);
head += simiLength;
}
}
fclose(fin);
}
else
{
MsgError(pchDataFile);
}
int i = 0;
for (i = 0; i <= TOTAL_PHENOTYPES - 1; i++)
{
Phenotype* pI = NULL;
pI = (Phenotype*) bsearch(&TotalPhenotypes[i], PhenotypeIDIndex, iMaxPhenotype, sizeof(Phenotype), PhenotypeCompare);
int j = 0;
for (j = 0; j <= TOTAL_PHENOTYPES - 1 && j <= i; j++)
{
Phenotype* pJ = NULL;
pJ = (Phenotype*) bsearch(&TotalPhenotypes[j], PhenotypeIDIndex, iMaxPhenotype, sizeof(Phenotype), PhenotypeCompare);
if (pI != NULL && pJ != NULL)
{
phenotypesSimilarity[i][j] = TotalSimilarity[pI->iID][pJ->iID];
phenotypesSimilarity[j][i] = phenotypesSimilarity[i][j];
}
else
{}
}
}
MsgWrite(phenotypeSimilarityFileBin);
FILE* pFile = fopen(phenotypeSimilarityFileBin, "wb");
if (pFile)
{
fwrite(phenotypesSimilarity, sizeof(float), TOTAL_PHENOTYPES * TOTAL_PHENOTYPES, pFile);
fflush(pFile);
fclose(pFile);
}
else
{
MsgError(phenotypeSimilarityFileBin);
}
}
