// Open dsm files, which are possibly zipped
void openDsmFile(igzstream& dsm_stream, const std::string& file_name)
{
// Check for a .gz extension
if (!std::regex_match(file_name, gzipped))
{
// Warn
std::cerr << "WARNING: Input file " + file_name
+ " is not gzip compressed, which is recommended\n";
}
dsm_stream.open(file_name.c_str()); // Push binary file into buffer
// Set stream buffer of istream to the one just opened, and check ok
if (!dsm_stream.good())
{
throw std::runtime_error("Could not open kmer file " + file_name + "\n");
}
}
ixstream_t(const char *name)
{
string fname = name;
int len = fname.size();
z = fname.substr(len-3) == ".gz";
if (z)
fz.open(name);
else
fn.open(name);
}
ref_loc_t RefSeq::LoadNextSeq(igzstream &fin) {
char ch[1000]; char c; string s;
if(!param.gz_ref) return 0;
fin>>c; if(fin.eof()) return 0;
string::iterator z=_seq.begin();
_length=0;
fin>>_name; fin.getline(ch, 1000);
while(!fin.eof()) {
fin>>c; if(fin.eof()) break;
fin.unget(); if(c=='>') break;
fin>>s;
if(_length+s.size()>=param.max_dbseq_size) {
param.max_dbseq_size+=param.append_dbseq_size;
_seq.resize(param.max_dbseq_size);
z=_seq.begin()+_length;
//cout<<"_seq size: "<<param.max_dbseq_size<<endl;
}
copy(s.begin(), s.end(), z);
z+=s.size(); _length+=s.size();
}
return _length;
}
void
ScipParaDiffSubproblem::read(
ParaComm *comm,
igzstream &in,
bool onlyBoundChanges
)
{
in.read((char *)&localInfoIncluded, sizeof(int));
in.read((char *)&nBoundChanges, sizeof(int));
indicesAmongSolvers = new int[nBoundChanges];
branchBounds = new SCIP_Real[nBoundChanges];
boundTypes = new SCIP_BOUNDTYPE[nBoundChanges];
for(int i = 0; i < nBoundChanges; i++ )
{
in.read((char *)&indicesAmongSolvers[i], sizeof(int));
in.read((char *)&branchBounds[i], sizeof(SCIP_Real));
in.read((char *)&boundTypes[i], sizeof(int));
}
if( !onlyBoundChanges )
{
in.read((char *)&nLinearConss, sizeof(int));
if( nLinearConss > 0 )
{
linearLhss = new SCIP_Real[nLinearConss];
linearRhss = new SCIP_Real[nLinearConss];
nLinearCoefs = new int[nLinearConss];
linearCoefs = new SCIP_Real*[nLinearConss];
idxLinearCoefsVars = new int*[nLinearConss];
for(int i = 0; i < nLinearConss; i++ )
{
in.read((char *)&linearLhss[i], sizeof(SCIP_Real));
in.read((char *)&linearRhss[i], sizeof(SCIP_Real));
in.read((char *)&nLinearCoefs[i], sizeof(int));
assert(nLinearCoefs[i] > 0);
linearCoefs[i] = new SCIP_Real[nLinearCoefs[i]];
idxLinearCoefsVars[i] = new int[nLinearCoefs[i]];
for(int j = 0; j < nLinearCoefs[i]; j++ )
{
in.read((char *)&linearCoefs[i][j], sizeof(SCIP_Real));
in.read((char *)&idxLinearCoefsVars[i][j], sizeof(int));
}
}
}
#if !( SCIP_VERSION == 211 && SCIP_SUBVERSION == 0 )
in.read((char *)&offset, sizeof(int));
in.read((char *)&nVarBranchStats, sizeof(int));
if( nVarBranchStats > 0 )
{
idxLBranchStatsVars = new int[nVarBranchStats];
downpscost = new SCIP_Real[nVarBranchStats];
uppscost = new SCIP_Real[nVarBranchStats];
downvsids = new SCIP_Real[nVarBranchStats];
upvsids = new SCIP_Real[nVarBranchStats];
downconflen = new SCIP_Real[nVarBranchStats];
upconflen = new SCIP_Real[nVarBranchStats];
downinfer = new SCIP_Real[nVarBranchStats];
upinfer = new SCIP_Real[nVarBranchStats];
downcutoff = new SCIP_Real[nVarBranchStats];
upcutoff = new SCIP_Real[nVarBranchStats];
}
for(int i = 0; i < nVarBranchStats; i++ )
{
in.read((char *)&idxLBranchStatsVars[i], sizeof(int));
in.read((char *)&downpscost[i], sizeof(SCIP_Real));
in.read((char *)&uppscost[i], sizeof(SCIP_Real));
in.read((char *)&downvsids[i], sizeof(SCIP_Real));
in.read((char *)&upvsids[i], sizeof(SCIP_Real));
in.read((char *)&downconflen[i], sizeof(SCIP_Real));
in.read((char *)&upconflen[i], sizeof(SCIP_Real));
in.read((char *)&downinfer[i], sizeof(SCIP_Real));
in.read((char *)&upinfer[i], sizeof(SCIP_Real));
in.read((char *)&downcutoff[i], sizeof(SCIP_Real));
in.read((char *)&upcutoff[i], sizeof(SCIP_Real));
}
#endif
}
else
{
assert( nLinearConss == 0);
SCIP_Real dummyReal;
int dummyInt;
int nConss;
in.read((char *)&nConss, sizeof(int));
if( nConss > 0 )
{
for(int i = 0; i < nConss; i++ )
{
int nCoefs;
in.read((char *)&dummyReal, sizeof(SCIP_Real));
in.read((char *)&dummyReal, sizeof(SCIP_Real));
in.read((char *)&nCoefs, sizeof(int));
assert(nCoefs > 0);
for(int j = 0; j < nCoefs; j++ )
{
in.read((char *)&dummyReal, sizeof(SCIP_Real));
in.read((char *)&dummyInt, sizeof(int));
}
}
}
#if !( SCIP_VERSION == 211 && SCIP_SUBVERSION == 0 )
assert( nVarBranchStats == 0 );
int nStats;
in.read((char *)&dummyInt, sizeof(int));
in.read((char *)&nStats, sizeof(int));
for(int i = 0; i < nStats; i++ )
{
in.read((char *)&dummyInt, sizeof(int));
in.read((char *)&dummyReal, sizeof(SCIP_Real));
in.read((char *)&dummyReal, sizeof(SCIP_Real));
in.read((char *)&dummyReal, sizeof(SCIP_Real));
in.read((char *)&dummyReal, sizeof(SCIP_Real));
in.read((char *)&dummyReal, sizeof(SCIP_Real));
in.read((char *)&dummyReal, sizeof(SCIP_Real));
in.read((char *)&dummyReal, sizeof(SCIP_Real));
in.read((char *)&dummyReal, sizeof(SCIP_Real));
in.read((char *)&dummyReal, sizeof(SCIP_Real));
in.read((char *)&dummyReal, sizeof(SCIP_Real));
}
#endif
}
}
