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#include "refInBinFile.h"
#ifndef REF_IN_BIN_FILE
#define REF_IN_BIN_FILE
const char* check_sum = "End_of_binary_reference";
int readGenomeInBits(FILE* fp, CGenomeInBits& gInBits)
{
int scannedItemNo = fscanf(fp, "%u\n%u\n", &(gInBits.uiGenomeLength), &(gInBits.uiGenomeLengthInWordSize));
if (scannedItemNo != 2) {
printf("%d, %u, %u", scannedItemNo, gInBits.uiGenomeLength, gInBits.uiGenomeLengthInWordSize);
ERR;
}
unsigned int gLength = gInBits.uiGenomeLength;
unsigned int gLengthInWord = gInBits.uiGenomeLengthInWordSize;
myFread(gInBits.pLowerBits, sizeof(WORD_SIZE), gLengthInWord, fp);
myFread(gInBits.pUpperBits, sizeof(WORD_SIZE), gLengthInWord, fp);
unsigned int sizeInByte = size2sizeInByte(gLength);
myFread(gInBits.pNBits->bflag, sizeof(unsigned char), sizeInByte, fp);
return(0);
}
int saveGenomeInBits(FILE* fp, const CGenomeInBits& gInBits)
{
fprintf(fp, "%u\n%u\n", gInBits.uiGenomeLength, gInBits.uiGenomeLengthInWordSize);
unsigned int gLength = gInBits.uiGenomeLength;
unsigned int gLengthInWord = gInBits.uiGenomeLengthInWordSize;
myFwrite(gInBits.pLowerBits, sizeof(WORD_SIZE), gLengthInWord, fp);
myFwrite(gInBits.pUpperBits, sizeof(WORD_SIZE), gLengthInWord, fp);
unsigned int sizeInByte = size2sizeInByte(gLength);
myFwrite(gInBits.pNBits->bflag, sizeof(unsigned char), sizeInByte, fp);
return(0);
}
int readGenesNameVec(FILE* fp, vector<CGene>& gNameV)
{
int noRefInVector = 0;
if (fscanf(fp, "%d\n", &noRefInVector) == 0) {
ERR;
}
gNameV.clear();
gNameV.reserve(noRefInVector);
CGene g;
for (int i = 0; i < noRefInVector; i++) {
char geneName[FILENAME_MAX];
if (fscanf(fp, "%s\n%d\n", geneName, &(g.startIndex)) != 2) {
ERR;
}
g.name = string(geneName);
gNameV.push_back(g);
}
return(noRefInVector);
}
int saveGenesNameVec(FILE* fp, vector<CGene>& gNameV)
{
int noRefInVector = (int)gNameV.size();
fprintf(fp, "%d\n", noRefInVector);
vector<CGene>::iterator it = gNameV.begin();
for (; it != gNameV.end(); it++) {
fprintf(fp, "%s\n%d\n", it->name.c_str(), it->startIndex);
}
return(noRefInVector);
}
int readGIndexConvertTable(FILE* fp, CGenomeNTdata& g)
{
if (fscanf(fp, "%s\n%u\n%u\n", g.refName, &(g.iGenomeSize), &(g.iNo_of_chromosome)) != 3) {
ERR;
return(-1);
}
for (unsigned int i = 0; (i < g.iNo_of_chromosome) && (i < GENOME_CAPACITY); i++) {
if (fscanf(fp, "%u\n", &(g.IndexCovertTable[i])) == 0) {
ERR;
return(-1);
}
}
return(0);
}
int saveGIndexConvertTable(FILE* fp, const CGenomeNTdata& g)
{
fprintf(fp, "%s\n", g.refName);
fprintf(fp, "%u\n", g.iGenomeSize);
fprintf(fp, "%u\n", g.iNo_of_chromosome);
for (unsigned int i = 0; (i < g.iNo_of_chromosome) && (i < GENOME_CAPACITY); i++) {
fprintf(fp, "%u\n", g.IndexCovertTable[i]);
}
return(0);
}
int readRefInBinFile(FILE* fp, CGenomeInBits* gInBits, CGenomeNTdata* g)
{
if (gInBits == NULL || g == NULL) {
ERR;
return(1);
} else {
if (readGIndexConvertTable(fp, *g)) {
ERR;
return(1);
}
gInBits->allocBitStrSpace(g->iGenomeSize);
if (readGenomeInBits(fp, *gInBits)) {
ERR;
return(1);
}
for (unsigned int i = 0; i < g->iNo_of_chromosome; i++) {
// TODO save chromosome info
if (g->paChromosomes[i] == NULL) {
g->paChromosomes[i] = new CchromosomeNTdata();
}
CchromosomeNTdata* pChr = g->paChromosomes[i];
if (fscanf(fp, "%s\n%u\n", pChr->caInputFileName, &(pChr->iChromosome_size)) != 2) {
ERR;
}
if (readGenesNameVec(fp, pChr->geneVec.table) <= 0) {
LOG_INFO("Info %d: ERR reading ref %d's names\n", ERROR_LOG, i);
return(1);
}
}
}
if (!assertFile(fp, check_sum)) {
ERR;
}
return(0);
}
int saveRefInBinFile(FILE* fp, const CGenomeInBits* gInBits, const CGenomeNTdata* g)
{
if (gInBits == NULL || g == NULL) {
ERR;
return(1);
} else {
if (saveGIndexConvertTable(fp, *g)) {
ERR;
return(1);
}
if (saveGenomeInBits(fp, *gInBits)) {
ERR;
return(1);
}
for (unsigned int i = 0; i < g->iNo_of_chromosome; i++) {
CchromosomeNTdata* pChr = g->paChromosomes[i];
if (pChr == NULL) {
ERR;
return(1);
}
fprintf(fp, "%s\n", pChr->caInputFileName);
fprintf(fp, "%u\n", pChr->iChromosome_size);
if (saveGenesNameVec(fp, pChr->geneVec.table) <= 0) {
LOG_INFO("Info %d: ERR saving ref %d's names\n", ERROR_LOG, i);
return(1);
}
}
}
fprintf(fp, "%s\n", check_sum);
return(0);
}
#endif
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