seqio_status seqio_read_all(seqio_sequence sequence,
char **buffer,
uint64_t *buffer_length,
uint64_t *read_length) {
check_null(sequence);
check_null(buffer);
check_null(buffer_length);
check_null(read_length);
ISequence *iseq = (ISequence *)sequence;
try {
if(*buffer == nullptr) {
*buffer_length = INITIAL_READ_ALL_BUFFER_LENGTH;
*buffer = (char *)malloc(*buffer_length);
if(*buffer == nullptr)
raise_oom("Cannot allocate %zu bytes", size_t(*buffer_length));
}
auto grow_to = [=] (uint64_t new_length) {
char *buffer_ = (char *)realloc(*buffer, new_length);
if(buffer_ == nullptr) {
raise_oom("Cannot allocate %zu bytes", size_t(new_length));
}
*buffer = buffer_;
*buffer_length = new_length;
};
uint64_t nread;
uint64_t nread_total = 0;
while( (nread = iseq->read(*buffer + nread_total, *buffer_length - nread_total)) != 0) {
nread_total += nread;
if(nread_total == *buffer_length) {
grow_to(*buffer_length * 2);
}
}
if(nread_total == *buffer_length) {
grow_to(*buffer_length + 1);
}
(*buffer)[nread_total] = '\0';
*read_length = nread_total;
} catch(Exception x) {
*read_length = 0;
return err_handler(x.err_info);
}
return SEQIO_SUCCESS;
}
SequenceContainer * SequenceApplicationTools::getSequenceContainer(
const Alphabet * alpha,
map<string, string> & params,
const string & suffix,
bool suffixIsOptional,
bool verbose)
{
string sequenceFilePath = ApplicationTools::getAFilePath("sequence.file",params, true, true, suffix, suffixIsOptional);
string sequenceFormat = ApplicationTools::getStringParameter("sequence.format", params, "Fasta", suffix, suffixIsOptional);
if(verbose) ApplicationTools::displayResult("Sequence format " + suffix, sequenceFormat);
ISequence * iSeq = NULL;
if(sequenceFormat == "Mase")
{
iSeq = new Mase();
}
else if(sequenceFormat == "Phylip")
{
bool sequential = true, extended = true;
string split = " ";
if(params.find("sequence.format_phylip.order") != params.end())
{
if(params["sequence.format_phylip.order"] == "sequential" ) sequential = true;
else if(params["sequence.format_phylip.order"] == "interleaved") sequential = false;
else ApplicationTools::displayWarning("Argument '" +
params["sequence.format_phylip.order"] +
"' for parameter 'sequence.format_phylip.order' is unknown. " +
"Default used instead: sequential.");
}
else ApplicationTools::displayWarning("Argument 'sequence.format_phylip.order' not found. Default used instead: sequential.");
if(params.find("sequence.format_phylip.ext") != params.end())
{
if(params["sequence.format_phylip.ext"] == "extended")
{
extended = true;
split = ApplicationTools::getStringParameter("sequence.format_phylip.extended.split", params, "spaces", suffix, suffixIsOptional);
if(split == "spaces") split = " ";
else if(split == "tab") split = "\t";
else throw Exception("Unknown option for sequence.format_phylip.extended.split: " + split);
}
else if(params["sequence.format_phylip.ext"] == "classic" ) extended = false;
else ApplicationTools::displayWarning("Argument '" +
params["sequence.format_phylip.ext"] +
"' for parameter 'sequence.format_phylip.ext' is unknown. " +
"Default used instead: extended.");
}
else ApplicationTools::displayWarning("Argument 'sequence.format_phylip.ext' not found. Default used instead: extended.");
iSeq = new Phylip(extended, sequential, 100, true, split);
}
else if(sequenceFormat == "Fasta") iSeq = new Fasta();
else if(sequenceFormat == "Clustal") iSeq = new Clustal();
else
{
ApplicationTools::displayError("Unknown sequence format.");
exit(-1);
}
SequenceContainer * sequences = iSeq->read(sequenceFilePath, alpha);
delete iSeq;
if(verbose) ApplicationTools::displayResult("Sequence file " + suffix, sequenceFilePath);
return sequences;
}
VectorSiteContainer * SequenceApplicationTools::getSiteContainer(
const Alphabet * alpha,
map<string, string> & params,
const string & suffix,
bool suffixIsOptional,
bool verbose)
{
string sequenceFilePath = ApplicationTools::getAFilePath("sequence.file",params, true, true, suffix, suffixIsOptional);
string sequenceFormat = ApplicationTools::getStringParameter("sequence.format", params, "Fasta", suffix, suffixIsOptional);
if(verbose) ApplicationTools::displayResult("Sequence format " + suffix, sequenceFormat);
ISequence * iSeq = NULL;
if(sequenceFormat == "Mase")
{
iSeq = new Mase();
}
else if(sequenceFormat == "Phylip")
{
bool sequential = true, extended = true;
string split = " ";
if(params.find("sequence.format_phylip.order") != params.end())
{
if(params["sequence.format_phylip.order"] == "sequential" ) sequential = true;
else if(params["sequence.format_phylip.order"] == "interleaved") sequential = false;
else ApplicationTools::displayWarning("Argument '" +
params["sequence.format_phylip.order"] +
"' for parameter 'sequence.format_phylip.order' is unknown. " +
"Default used instead: sequential.");
}
else ApplicationTools::displayWarning("Argument 'sequence.format_phylip.order' not found. Default used instead: sequential.");
if(params.find("sequence.format_phylip.ext") != params.end())
{
if(params["sequence.format_phylip.ext"] == "extended")
{
extended = true;
split = ApplicationTools::getStringParameter("sequence.format_phylip.extended.split", params, "spaces", suffix, suffixIsOptional);
if(split == "spaces") split = " ";
else if(split == "tab") split = "\t";
else throw Exception("Unknown option for sequence.format_phylip.extended.split: " + split);
}
else if(params["sequence.format_phylip.ext"] == "classic" ) extended = false;
else ApplicationTools::displayWarning("Argument '" +
params["sequence.format_phylip.ext"] +
"' for parameter 'sequence.format_phylip.ext' is unknown. " +
"Default used instead: extended.");
}
else ApplicationTools::displayWarning("Argument 'sequence.format_phylip.ext' not found. Default used instead: extended.");
iSeq = new Phylip(extended, sequential, 100, true, split);
}
else if(sequenceFormat == "Fasta") iSeq = new Fasta();
else if(sequenceFormat == "Clustal") iSeq = new Clustal();
else
{
ApplicationTools::displayError("Unknown sequence format.");
exit(-1);
}
const SequenceContainer * seqCont = iSeq->read(sequenceFilePath, alpha);
VectorSiteContainer * sites = new VectorSiteContainer(* dynamic_cast<const OrderedSequenceContainer *>(seqCont));
delete seqCont;
delete iSeq;
if(verbose) ApplicationTools::displayResult("Sequence file " + suffix, sequenceFilePath);
// Look for site selection:
if(sequenceFormat == "Mase")
{
//getting site set:
string siteSet = ApplicationTools::getStringParameter("sequence.format_mase.site_selection", params, "none", suffix, suffixIsOptional, false);
if(siteSet != "none")
{
VectorSiteContainer * selectedSites;
try
{
selectedSites = dynamic_cast<VectorSiteContainer *>(MaseTools::getSelectedSites(* sites, siteSet));
if(verbose) ApplicationTools::displayResult("Set found", TextTools::toString(siteSet) + " sites.");
}
catch(IOException ioe)
{
ApplicationTools::displayError("Site Set '" + siteSet + "' not found.");
exit(-1);
}
if(selectedSites->getNumberOfSites() == 0)
{
ApplicationTools::displayError("Site Set '" + siteSet + "' is empty.");
exit(-1);
}
delete sites;
sites = selectedSites;
}
}
return sites;
}