CScope& CAlnMrgApp::GetScope(void) const
{
if (!m_Scope) {
m_ObjMgr = CObjectManager::GetInstance();
CGBDataLoader::RegisterInObjectManager(*m_ObjMgr);
m_Scope = new CScope(*m_ObjMgr);
m_Scope->AddDefaults();
}
return *m_Scope;
}
CScope& GetScope(void)
{
static CRef<CScope> s_Scope;
if ( !s_Scope ) {
CRef<CObjectManager> objmgr = CObjectManager::GetInstance();
CGBDataLoader::RegisterInObjectManager(*objmgr);
s_Scope.Reset(new CScope(*objmgr));
s_Scope->AddDefaults();
}
return *s_Scope;
}
int ReadFastaQueries(const string& filename,
vector< CRef<objects::CSeq_loc> >& seqs,
CRef<objects::CScope>& scope,
bool parse_deflines /* = false*/,
objects::CSeqIdGenerator* id_generator /* = NULL*/)
{
seqs.clear();
CNcbiIfstream instream(filename.c_str());
if (!instream) {
return -1;
}
CStreamLineReader line_reader(instream);
CFastaReader::TFlags flags = CFastaReader::fAssumeProt |
CFastaReader::fForceType;
if (!parse_deflines) {
flags |= CFastaReader::fNoParseID;
}
CFastaReader fasta_reader(line_reader, flags);
if (id_generator) {
fasta_reader.SetIDGenerator(*id_generator);
}
scope->AddDefaults();
while (!line_reader.AtEOF()) {
CRef<CSeq_entry> entry = fasta_reader.ReadOneSeq();
if (entry == 0) {
return -1;
}
scope->AddTopLevelSeqEntry(*entry);
CTypeConstIterator<CBioseq> itr(ConstBegin(*entry));
CRef<CSeq_loc> seqloc(new CSeq_loc());
seqloc->SetWhole().Assign(*itr->GetId().front());
seqs.push_back(seqloc);
}
return 0;
}
bool CCSRATestApp::TestApp_Init(void)
{
SetDiagPostLevel(eDiag_Info);
const CArgs& args = GetArgs();
m_Verbose = args["verbose"];
m_ErrorCount = 0;
m_Seed = args["seed"]? args["seed"].AsInteger(): int(time(0));
if ( m_Verbose ) {
LOG_POST(Info<<"Seed: "<<m_Seed);
}
NStr::Split(args["accs"].AsString(), ",", m_Accession);
if ( args["accs-file"] ) {
m_Accession.clear();
CNcbiIstream& in = args["accs-file"].AsInputFile();
string acc;
while ( in >> acc ) {
m_Accession.push_back(acc);
}
}
if ( m_Accession.empty() ) {
ERR_POST(Fatal<<"empty accession list");
}
m_IterCount = args["iter-count"].AsInteger();
m_IterSize = args["iter-size"].AsInteger();
m_MaxSpotId.assign(m_Accession.size(), 0);
m_OM = CObjectManager::GetInstance();
CCSRADataLoader::RegisterInObjectManager(*m_OM, CObjectManager::eDefault);
if ( args["shared-scope"] ) {
m_SharedScope = new CScope(*m_OM);
m_SharedScope->AddDefaults();
}
m_ResetHistory = args["reset-history"];
m_TestRefSeqs = args["reference-sequences"];
m_FullSeq = args["full-seq"];
if ( m_TestRefSeqs ) {
LoadRefSeqs();
}
if ( args["preload"] ) {
Thread_Run(-1);
}
return true;
}
int CNgAlignTest::Run()
{
//const CArgs& args = GetArgs();
CRef<CObjectManager> obj_mgr = CObjectManager::GetInstance();
CGBDataLoader::RegisterInObjectManager(*obj_mgr);
m_Scope.Reset(new CScope(*obj_mgr));
m_Scope->AddDefaults();
//string TestCaseIni = "/home/boukn/code/toolkit/c++/src/algo/align/uberalign/test/testcases.ini";
string TestCaseIni = "/panfs/pan1.be-md.ncbi.nlm.nih.gov/genome_maint/work/uberalign/test/testcases.ini";
CNcbiIfstream TestCaseFile(TestCaseIni.c_str());
CNcbiRegistry TestCases(TestCaseFile);
string CasesStr = TestCases.Get("caselist", "cases");
list<string> Cases;
NStr::Split(CasesStr, " \t\r\n,", Cases);
ITERATE(list<string>, CaseIter, Cases) {
string Type = TestCases.Get(*CaseIter, "type");
if(Type == "one_to_one") {
x_OneToOneCase(&TestCases, *CaseIter);
} else if(Type == "one_to_blastdb") {
x_OneToBlastDbCase(&TestCases, *CaseIter);
} else if(Type == "list_to_blastdb") {
x_ListToBlastDbCase(&TestCases, *CaseIter);
} else if(Type == "split_one_to_blastdb") {
x_SplitOneToBlastDbCase(&TestCases, *CaseIter);
} else if(Type == "split_list_to_blastdb") {
x_SplitListToBlastDbCase(&TestCases, *CaseIter);
} else if(Type == "overlap_one_to_blastdb") {
x_OverlapOneToBlastDbCase(&TestCases, *CaseIter);
} else if(Type == "overlap_list_to_blastdb") {
x_OverlapListToBlastDbCase(&TestCases, *CaseIter);
}
}
// --------------------------------------------------------------------------
int CAsn2FastaApp::Run(void)
// --------------------------------------------------------------------------
{
// initialize conn library
CONNECT_Init(&GetConfig());
const CArgs& args = GetArgs();
// create object manager
m_Objmgr = CObjectManager::GetInstance();
if ( !m_Objmgr ) {
NCBI_THROW(CException, eUnknown,
"Could not create object manager");
}
CGBDataLoader::RegisterInObjectManager(*m_Objmgr);
m_Scope.Reset(new CScope(*m_Objmgr));
m_Scope->AddDefaults();
// open the output stream
m_Os = args["o"] ? &(args["o"].AsOutputFile()) : &cout;
if ( m_Os == 0 ) {
NCBI_THROW(CException, eUnknown, "Could not open output stream");
}
auto_ptr<CObjectIStream> is;
is.reset( x_OpenIStream( args ) );
if (is.get() == NULL) {
string msg = args["i"]? "Unable to open input file" + args["i"].AsString() :
"Unable to read data from stdin";
NCBI_THROW(CException, eUnknown, msg);
}
m_DeflineOnly = args["defline-only"];
if ( args["batch"] ) {
CGBReleaseFile in(*is.release());
in.RegisterHandler(this);
in.Read(); // HandleSeqEntry will be called from this function
}
else {
if ( args["id"] ) {
//
// Implies gbload; otherwise this feature would be pretty
// useless...
//
m_Scope->AddDefaults();
string seqID = args["id"].AsString();
HandleSeqID( seqID );
} else {
string asn_type = args["type"].AsString();
CSeq_entry_Handle seh;
if ( asn_type == "seq-entry" ) {
//
// Straight through processing: Read a seq_entry, then process
// a seq_entry:
//
seh = ObtainSeqEntryFromSeqEntry(*is);
while (seh) {
try {
HandleSeqEntry(seh);
}
catch (...) {
cerr << "Resolution error: Sequence dropped." << endl;
}
m_Scope->RemoveTopLevelSeqEntry(seh);
seh = ObtainSeqEntryFromSeqEntry(*is);
}
return 0;
}
else if ( asn_type == "bioseq" ) {
//
// Read object as a bioseq, wrap it into a seq_entry, then
// process the wrapped bioseq as a seq_entry:
//
seh = ObtainSeqEntryFromBioseq(*is);
if ( !seh ) {
NCBI_THROW(CException, eUnknown,
"Unable to construct Seq-entry object" );
}
HandleSeqEntry(seh);
}
else if ( asn_type == "bioseq-set" ) {
//
// Read object as a bioseq_set, wrap it into a seq_entry, then
// process the wrapped bioseq_set as a seq_entry:
//
seh = ObtainSeqEntryFromBioseqSet(*is);
if ( !seh ) {
NCBI_THROW(CException, eUnknown,
"Unable to construct Seq-entry object" );
}
HandleSeqEntry(seh);
}
else if ( asn_type == "any" ) {
//
// Try the first three in turn:
//
size_t streampos = is->GetStreamPos();
while (!is->EndOfData()) {
seh = ObtainSeqEntryFromSeqEntry(*is);
if (!seh) {
if (is->EndOfData()) {
break;
}
is->ClearFailFlags(-1);
is->SetStreamPos(streampos);
seh = ObtainSeqEntryFromBioseqSet(*is);
}
if (!seh) {
if (is->EndOfData()) {
break;
}
is->ClearFailFlags(-1);
is->SetStreamPos(streampos);
seh = ObtainSeqEntryFromBioseq(*is);
}
if (!seh) {
NCBI_THROW(CException, eUnknown,
"Unable to construct Seq-entry object" );
}
HandleSeqEntry(seh);
m_Scope->RemoveTopLevelSeqEntry(seh);
streampos = is->GetStreamPos();
}
}
}
}
m_Os->flush();
is.reset();
return 0;
}