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/********************************************************************** |
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atom2md.cpp - OpenBabel-based conversion program to OpenMD MD file, |
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atom2md.cpp - OpenBabel-based conversion program to OpenMD file, |
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command-line handling. |
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Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc. |
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Some portions Copyright (C) 2001-2006 by Geoffrey R. Hutchison |
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Some portions Copyright (C) 2004-2006 by Chris Morley |
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Some portions Copyright (C) 2008 by J. Daniel Gezelter |
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Some portions Copyright (C) 2008-2009 by J. Daniel Gezelter |
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This file is part of both the OpenMD and Open Babel projects. |
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For more information, see <http://openmd.net> and <http://openbabel.sourceforge.net/> |
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#if HAVE_CONIO_H |
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#include <conio.h> |
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#endif |
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#include <cstdlib> |
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#if !HAVE_STRNCASECMP |
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extern "C" int strncasecmp(const char *s1, const char *s2, size_t n); |
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#endif |
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#include <openbabel/obconversion.h> |
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#include <openbabel/plugin.h> |
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#include <cstdlib> |
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#include <cstring> |
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using namespace std; |
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using namespace OpenBabel; |
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void DoOption(const char* p, OBConversion& Conv, |
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OBConversion::Option_type typ, int& arg, int argc, |
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char *argv[]); |
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void DoOption(const char* p, OBConversion& Conv, OBConversion::Option_type typ, |
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int& arg, int argc, char *argv[]); |
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void usage(); |
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void help(); |
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bool gotInType = false, gotOutType = false; |
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bool SplitOrBatch=false; |
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char *oext; |
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char *iext; |
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char *oext = NULL; |
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char *iext = NULL; |
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// for use with command name to type conversion |
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string inputExt; |
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string outputExt; |
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gotInType = true; |
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iext = argv[arg] + 2; |
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if(!*iext) |
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iext = argv[++arg]; // space left after -i: use next |
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// argument |
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iext = argv[++arg]; //space left after -i: use next argument |
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if (strncasecmp(iext, "MIME", 4) == 0) |
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{ |
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} |
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else |
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{ |
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// The ID provided by the OBFormat class is used as the |
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// identifying file extension |
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//The ID provided by the OBFormat class is used as the identifying file extension |
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pInFormat = Conv.FindFormat(iext); |
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} |
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if(pInFormat==NULL) |
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{ |
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cerr << program_name << ": cannot read input format!" |
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<< endl; |
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cerr << program_name << ": cannot read input format!" << endl; |
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usage(); |
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} |
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break; |
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gotOutType = true; |
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oext = argv[arg] + 2; |
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if(!*oext) |
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oext = argv[++arg]; // space left after -i: use next |
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// argument |
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oext = argv[++arg]; //space left after -i: use next argument |
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if (strncasecmp(oext, "MIME", 4) == 0) |
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{ |
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if(pOutFormat==NULL) |
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{ |
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cerr << program_name << ": cannot write output format!" |
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<< endl; |
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cerr << program_name << ": cannot write output format!" << endl; |
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usage(); |
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} |
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break; |
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case 'F': |
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/*case 'F': |
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if(!Conv.SetOutFormat("fpt")) |
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cout << "FingerprintFormat needs to be loaded" << endl; |
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else |
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Conv.Write(NULL); |
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} |
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return 0; |
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*/ |
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case 'L': //display a list of plugin type or classes |
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{ |
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const char* param=NULL; |
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if(argc>arg+1) |
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param = argv[arg+2]; |
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OBPlugin::List(argv[arg+1], param); |
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return 0; |
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} |
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case '?': |
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case 'H': |
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if(isalnum(argv[arg][2])) |
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if(isalnum(argv[arg][2]) || arg==argc-2) |
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{ |
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if(strncasecmp(argv[arg]+2,"all",3)) |
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{ |
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OBFormat* pFormat = Conv.FindFormat(argv[arg]+2); |
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const char* pID= (arg==argc-2) ? argv[arg+1] : argv[arg]+2; |
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OBFormat* pFormat = Conv.FindFormat(pID); |
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if(pFormat) |
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{ |
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cout << argv[arg]+2 << " " << pFormat->Description() << endl; |
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cout << pID << " " << pFormat->Description() << endl; |
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if(pFormat->Flags() & NOTWRITABLE) |
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cout << " This format is Read-only" << endl; |
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if(pFormat->Flags() & NOTREADABLE) |
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cout << " This format is Write-only" << endl; |
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if(strlen(pFormat->SpecificationURL())) |
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cout << "Specification at: " << pFormat->SpecificationURL() << endl; |
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} |
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else |
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cout << "Format type: " << argv[arg]+2 << " was not recognized" <<endl; |
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cout << "Format type: " << pID << " was not recognized" <<endl; |
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} |
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else |
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{ |
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Formatpos pos; |
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OBFormat* pFormat; |
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const char* str=NULL; |
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while(OBConversion::GetNextFormat(pos,str,pFormat)) |
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{ |
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if((pFormat->Flags() & NOTWRITABLE) && (pFormat->Flags() & NOTREADABLE)) |
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continue; |
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cout << str << endl; |
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const char* p = strchr(pFormat->Description(),'\n'); |
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cout << p+1; //second line of description |
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if(strlen(pFormat->SpecificationURL())) |
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cout << "Specification at: " << pFormat->SpecificationURL(); |
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cout << endl << endl; |
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} |
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OBPlugin::List("formats","verbose"); |
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} |
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} |
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else |
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help(); |
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exit(0); |
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return 0; |
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case '-': //long option --name text |
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{ |
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} |
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// user didn't specify input and output format in commandline option |
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// try to parse it from program name (pdb2mdin means input format is pdb, |
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// output format is mdin) |
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// try to parse it from program name (pdb2md means input format is pdb, |
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// output format is md) |
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string formatName(program_name); |
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pos = formatName.find_first_of("2"); |
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outputExt = tmpExt; |
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} |
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} |
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} |
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} |
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if(!gotOutType) //the last file is the output |
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{ |
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if(FileList.empty()) |
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{ |
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cerr << "No output file or format spec!" << endl; |
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usage(); |
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} |
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OutputFileName = FileList.back(); |
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FileList.pop_back(); |
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} |
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#ifdef _WIN32 |
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//Expand wildcards in input filenames and add to FileList |
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vector<string> tempFileList(FileList); |
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FileList.clear(); |
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vector<string>::iterator itr; |
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for(itr=tempFileList.begin();itr!=tempFileList.end();++itr) |
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DLHandler::findFiles (FileList, *itr); |
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#endif |
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if (!gotInType) |
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{ |
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usage(); |
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} |
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} |
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if (!gotOutType) |
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if (!gotOutType) |
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{ |
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pOutFormat = Conv.FormatFromExt(OutputFileName.c_str()); |
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if(pOutFormat==NULL) |
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} |
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} |
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Conv.SetInAndOutFormats(pInFormat, pOutFormat); |
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if(!Conv.SetInFormat(pInFormat)) |
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{ |
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cerr << "Invalid input format" << endl; |
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usage(); |
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} |
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if(!Conv.SetOutFormat(pOutFormat)) |
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{ |
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cerr << "Invalid output format" << endl; |
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usage(); |
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} |
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if(SplitOrBatch) |
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{ |
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//Put * into output file name before extension (or ext.gz) |
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if(OutputFileName.empty()) |
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{ |
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OutputFileName = "*."; |
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OutputFileName += oext; |
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if (oext != NULL) |
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OutputFileName += oext; |
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} |
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else |
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{ |
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} |
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int count = Conv.FullConvert(FileList, OutputFileName, OutputFileList); |
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// send info message to clog -- don't mess up cerr or cout for user programs |
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//Get the last word on the first line of the description which should |
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//be "molecules", "reactions", etc and remove the s if only one object converted |
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std::string objectname(pOutFormat->TargetClassDescription()); |
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pos = objectname.find('\n'); |
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if(count==1) --pos; |
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objectname.erase(pos); |
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pos = objectname.rfind(' '); |
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if(pos==std::string::npos) |
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pos=0; |
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std::clog << count << objectname.substr(pos) << " converted" << endl; |
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Conv.ReportNumberConverted(count); |
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if(OutputFileList.size()>1) |
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{ |
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clog << OutputFileList.size() << " files output. The first is " << OutputFileList[0] <<endl; |
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} |
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std::string messageSummary = obErrorLog.GetMessageSummary(); |
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if (messageSummary.size()) |
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{ |
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cout << "Press any key to finish" <<endl; |
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getch(); |
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#endif |
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return 0; |
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} |
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cout << "Usage: " << program_name |
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<< " [-i<input-type>] <name> [-o<output-type>] <name>" << endl; |
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cout << "Try -H option for more information." << endl; |
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/* |
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#ifdef _DEBUG |
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//CM keep window open |
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cout << "Press any key to finish" <<endl; |
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getch(); |
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#endif |
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*/ |
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exit (0); |
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} |
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