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#include <algorithm>
#include <cassert>
#include <utility>
#include <memory>
#include "Alignment/Geners/interface/ContiguousCatalog.hh"
#include "Alignment/Geners/interface/IOException.hh"
#include "Alignment/Geners/interface/binaryIO.hh"
namespace gs {
void ContiguousCatalog::findByName(const NameMap &m,
const SearchSpecifier &namePattern,
std::vector<unsigned long long> *found) const {
typedef NameMap::const_iterator Nameiter;
if (namePattern.useRegex()) {
const Nameiter itend = m.end();
for (Nameiter it = m.begin(); it != itend; ++it)
if (namePattern.matches(it->first))
found->push_back(it->second);
} else {
const std::pair<Nameiter, Nameiter> limits = m.equal_range(namePattern.pattern());
for (Nameiter it = limits.first; it != limits.second; ++it)
found->push_back(it->second);
}
}
unsigned long long ContiguousCatalog::makeEntry(const ItemDescriptor &descriptor,
const unsigned compressionCode,
const unsigned long long itemLength,
const ItemLocation &loc,
const unsigned long long offset) {
const unsigned long long nextId = records_.size() + firstId_;
lastEntry_ = SPtr(new CatalogEntry(descriptor, nextId, compressionCode, itemLength, loc, offset));
records_.push_back(lastEntry_);
recordMap_[descriptor.category()].insert(std::make_pair(descriptor.name(), nextId));
return nextId;
}
void ContiguousCatalog::search(const SearchSpecifier &namePattern,
const SearchSpecifier &categoryPattern,
std::vector<unsigned long long> *found) const {
typedef RecordMap::const_iterator Mapiter;
assert(found);
found->clear();
const Mapiter endMap = recordMap_.end();
if (categoryPattern.useRegex()) {
for (Mapiter it = recordMap_.begin(); it != endMap; ++it)
if (categoryPattern.matches(it->first))
findByName(it->second, namePattern, found);
} else {
Mapiter it = recordMap_.find(categoryPattern.pattern());
if (it != endMap)
findByName(it->second, namePattern, found);
}
std::sort(found->begin(), found->end());
}
bool ContiguousCatalog::isEqual(const AbsCatalog &other) const {
if ((void *)this == (void *)(&other))
return true;
const ContiguousCatalog &r = static_cast<const ContiguousCatalog &>(other);
if (firstId_ != r.firstId_)
return false;
if (recordMap_ != r.recordMap_)
return false;
const unsigned long nRecords = records_.size();
if (nRecords != r.records_.size())
return false;
for (unsigned long i = 0; i < nRecords; ++i)
if (*records_[i] != *r.records_[i])
return false;
return true;
}
// Version 1 write function
// bool ContiguousCatalog::write(std::ostream& os) const
// {
// bool status = ClassId::makeId<CatalogEntry>().write(os) &&
// ClassId::makeId<ItemLocation>().write(os);
// const unsigned long long sz = records_.size();
// for (unsigned long long i=0; i<sz && status; ++i)
// status = records_[i]->write(os);
// return status;
// }
bool ContiguousCatalog::write(std::ostream &os) const {
const unsigned long long sz = records_.size();
long long nRecords = sz;
write_pod(os, nRecords);
bool status = !os.fail() && ClassId::makeId<CatalogEntry>().write(os) && ClassId::makeId<ItemLocation>().write(os);
for (unsigned long long i = 0; i < sz && status; ++i)
status = records_[i]->write(os);
return status;
}
ContiguousCatalog *ContiguousCatalog::read(const ClassId &cid, std::istream &in) {
static const ClassId current(ClassId::makeId<ContiguousCatalog>());
cid.ensureSameName(current);
cid.ensureVersionInRange(1, version());
if (cid.version() == 1)
return read_v1(in);
long long nRecords;
read_pod(in, &nRecords);
if (nRecords < 0)
return read_v1(in);
ClassId rId(in, 1);
ClassId locId(in, 1);
std::unique_ptr<ContiguousCatalog> catalog(new ContiguousCatalog());
bool firstEntry = true;
for (long long recnum = 0; recnum < nRecords; ++recnum) {
CatalogEntry *rec = CatalogEntry::read(rId, locId, in);
if (rec) {
const unsigned long long id = rec->id();
if (firstEntry) {
catalog->firstId_ = id;
firstEntry = false;
} else {
const unsigned long long nextId = catalog->records_.size() + catalog->firstId_;
if (id != nextId) {
delete rec;
throw IOInvalidData(
"In gs::ContiguousCatalog::read:"
" unexpected item id. "
"Catalog is corrupted.");
}
}
catalog->records_.push_back(SPtr(rec));
catalog->recordMap_[rec->category()].insert(std::make_pair(rec->name(), id));
} else
throw IOInvalidData(
"In gs::ContiguousCatalog::read:"
" failed to read catalog entry");
}
return catalog.release();
}
ContiguousCatalog *ContiguousCatalog::read_v1(std::istream &in) {
ClassId rId(in, 1);
ClassId locId(in, 1);
std::unique_ptr<ContiguousCatalog> catalog(new ContiguousCatalog());
bool firstEntry = true;
for (in.peek(); !in.eof(); in.peek()) {
CatalogEntry *rec = CatalogEntry::read(rId, locId, in);
if (rec) {
const unsigned long long id = rec->id();
if (firstEntry) {
catalog->firstId_ = id;
firstEntry = false;
} else {
const unsigned long long nextId = catalog->records_.size() + catalog->firstId_;
if (id != nextId) {
delete rec;
throw IOInvalidData(
"In gs::ContiguousCatalog::read_v1:"
" unexpected item id. "
"Catalog is corrupted.");
}
}
catalog->records_.push_back(SPtr(rec));
catalog->recordMap_[rec->category()].insert(std::make_pair(rec->name(), id));
} else
throw IOInvalidData(
"In gs::ContiguousCatalog::read_v1:"
" failed to read catalog entry");
}
return catalog.release();
}
std::shared_ptr<const CatalogEntry> ContiguousCatalog::retrieveEntry(const unsigned long long id) const {
if (id >= firstId_ && id < records_.size() + firstId_)
return records_[id - firstId_];
else {
CatalogEntry *ptr = nullptr;
return std::shared_ptr<const CatalogEntry>(ptr);
}
}
bool ContiguousCatalog::retrieveStreampos(unsigned long long id,
unsigned *compressionCode,
unsigned long long *length,
std::streampos *pos) const {
assert(compressionCode);
assert(length);
assert(pos);
if (id >= firstId_ && id < records_.size() + firstId_) {
const std::shared_ptr<const CatalogEntry> &rec(records_[id - firstId_]);
*compressionCode = rec->compressionCode();
*length = rec->itemLength();
*pos = rec->location().streamPosition();
return true;
} else
return false;
}
} // namespace gs
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