mafBlock_t* maf_readAll(mafFileApi_t *mfa) {
// read an entire mfa, creating a linked list of mafBlock_t, returning the head.
mafBlock_t *head = maf_readBlock(mfa);
mafBlock_t *mb = head;
mafBlock_t *tmp = NULL;
while ((tmp = maf_readBlock(mfa)) != NULL) {
mb->next = tmp;
mb = tmp;
}
return head;
}
void processBody(mafFileApi_t *mfa) {
// walk the body of the maf file and process it, block by block.
mafBlock_t *thisBlock = NULL;
thisBlock = maf_readBlock(mfa); // unused
maf_destroyMafBlockList(thisBlock);
while((thisBlock = maf_readBlock(mfa)) != NULL) {
correctSpeciesNames(thisBlock);
checkBlock(thisBlock);
maf_destroyMafBlockList(thisBlock);
}
}
void processBody(mafFileApi_t *mfa, char *seq, char strand) {
// walk the body of the maf file and process it, block by block.
mafBlock_t *thisBlock = NULL;
thisBlock = maf_readBlock(mfa); // header block, unused
maf_destroyMafBlockList(thisBlock);
printHeader();
while((thisBlock = maf_readBlock(mfa)) != NULL) {
checkBlock(thisBlock, seq, strand);
maf_mafBlock_print(thisBlock);
maf_destroyMafBlockList(thisBlock);
}
}
void searchInput(mafFileApi_t *mfa, char *fullname, unsigned long pos) {
mafBlock_t *thisBlock = NULL;
while ((thisBlock = maf_readBlock(mfa)) != NULL) {
checkBlock(thisBlock, fullname, pos);
maf_destroyMafBlockList(thisBlock);
}
}
void processBody(mafFileApi_t *mfa, char *seq, uint32_t start, uint32_t stop) {
mafBlock_t *thisBlock = NULL;
bool printedHeader = false;
while ((thisBlock = maf_readBlock(mfa)) != NULL) {
checkBlock(thisBlock, seq, start, stop, &printedHeader);
maf_destroyMafBlockList(thisBlock);
}
}
void processBody(mafFileApi_t *mfa, char *seq, uint64_t start, uint64_t stop, bool isSoft) {
mafBlock_t *thisBlock = NULL;
bool printedHeader = false;
uint64_t blockNumber = 0;
while ((thisBlock = maf_readBlock(mfa)) != NULL) {
checkBlock(thisBlock, blockNumber, seq, start, stop, &printedHeader, isSoft);
maf_destroyMafBlockList(thisBlock);
++blockNumber;
}
if (!printedHeader) {
// this makes the output valid even when no data was output
printHeader();
}
}
