NCBI C++ Toolkit Cross Reference


/* $Id: cApiDisc.cpp 63807 2014-07-28 14:38:25Z chenj $ * ========================================================================= * * PUBLIC DOMAIN NOTICE * National Center for Biotechnology Information * * This software/database is a "United States Government Work" under the * terms of the United States Copyright Act. It was written as part of * the author's official duties as a United States Government employee and * thus cannot be copyrighted. This software/database is freely available * to the public for use. The National Library of Medicine and the U.S. * Government have not placed any restriction on its use or reproduction. * * Although all reasonable efforts have been taken to ensure the accuracy * and reliability of the software and data, the NLM and the U.S. * Government do not and cannot warrant the performance or results that * may be obtained by using this software or data. The NLM and the U.S. * Government disclaim all warranties, express or implied, including * warranties of performance, merchantability or fitness for any particular * purpose. * * Please cite the author in any work or product based on this material. * * ========================================================================= * * Author: Jie Chen * * File Description: * Example of integrated discrepancy report * */ #include <ncbi_pch.hpp> #include <corelib/ncbistd.hpp> #include <corelib/ncbiapp.hpp> #include <corelib/ncbiargs.hpp> #include <corelib/metareg.hpp> #include <corelib/ncbireg.hpp> // Object Manager includes #include <objmgr/object_manager.hpp> #include <objmgr/scope.hpp> #include <misc/discrepancy_report/hDiscRep_config.hpp> USING_NCBI_SCOPE; USING_SCOPE(DiscRepNmSpc); ///////////////////////////////////////////////////////////////////////////// // MAIN // void GetDiscrepancyReport(int argc, const char* argv[]) { if (argc < 2) { NCBI_THROW(CException, eUnknown, "Input path or input file must be specified"); } vector <string> arr; string in_file(kEmptyStr); for (int i=1; i< argc; i++) { arr = NStr::Tokenize(argv[i], "=", arr); if (arr[0] == "i") { in_file = arr[1]; break; } } if (in_file.empty()) { NCBI_THROW(CException, eUnknown, "Input path or input file must be specified"); } auto_ptr <CObjectIStream> ois(CObjectIStream::Open(eSerial_AsnText,in_file)); string strtmp = ois->ReadFileHeader(); ois->SetStreamPos(0); CRef <CSeq_submit> seq_submit (new CSeq_submit); CRef <CSeq_entry> seq_entry (new CSeq_entry); if (strtmp == "Seq-submit") { *ois >> *seq_submit; if (seq_submit->IsEntrys()) { NON_CONST_ITERATE (list <CRef <CSeq_entry> >, it, seq_submit->SetData().SetEntrys()) { seq_entry.Reset(&(**it)); } } } else if (strtmp == "Seq-entry") { *ois >> *seq_entry; } ois->Close(); CRef<CObjectManager> object_manager = CObjectManager::GetInstance(); CRef <CScope> scope (new CScope(*object_manager)); CSeq_entry_Handle seq_handle = scope->AddTopLevelSeqEntry(*seq_entry); CRef <CRepConfig> config (CRepConfig::factory(fOncaller, &seq_handle)); /* CRef <CRepConfig> config (CRepConfig::factory(fDiscrepancy, &seq_handle)); CRef <CRepConfig> config (CRepConfig::factory(fMegaReport, &seq_handle)); */ CRef <IRWRegistry> reg(0); if (CFile("disc_report.ini").Exists()) { CMetaRegistry:: SEntry entry = CMetaRegistry :: Load("disc_report.ini"); reg.Reset(entry.registry); } config->InitParams(reg); config->CollectTests(); config->Run(); vector <CRef <CClickableText> > item_list; CDiscRepOutput output_obj; output_obj.Export(item_list); }; int main(int argc, const char* argv[]) { // Usage disc_report i=data_file try { SetDiagPostLevel(eDiag_Error); GetDiscrepancyReport(argc, argv); cerr << "Program existed normally\n"; } catch (CException& eu) { string err_msg(eu.GetMsg()); if (err_msg == "Input path or input file must be specified") { err_msg = "You need to supply an input file (i=myfild)"; // err_msg = "You need to supply at least an input file (i=) or a path in which to find input files (p=). Please see 'asndisc -help' for additional details, and use the format arg=arg_value to input arguments."; } ERR_POST(err_msg); }; }

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