00001 /********************************************************************** 00002 obconversion.h - Handle file conversions. Declaration of OBFormat, OBConversion 00003 00004 Copyright (C) 2004-2005 by Chris Morley 00005 00006 This file is part of the Open Babel project. 00007 For more information, see <http://openbabel.sourceforge.net/> 00008 00009 This program is free software; you can redistribute it and/or modify 00010 it under the terms of the GNU General Public License as published by 00011 the Free Software Foundation version 2 of the License. 00012 00013 This program is distributed in the hope that it will be useful, 00014 but WITHOUT ANY WARRANTY; without even the implied warranty of 00015 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 00016 GNU General Public License for more details. 00017 ***********************************************************************/ 00018 00019 #ifndef OB_CONV_H 00020 #define OB_CONV_H 00021 00022 #include <openbabel/babelconfig.h> 00023 00024 #include <iostream> 00025 #include <fstream> 00026 #include <sstream> 00027 00028 #include <string> 00029 #include <vector> 00030 #include <map> 00031 00032 #include <openbabel/dlhandler.h> 00033 #include <openbabel/oberror.h> 00034 00035 // These macros are used in DLL builds. If they have not 00036 // been set in babelconfig.h, define them as nothing. 00037 #ifndef OBCONV 00038 #define OBCONV 00039 #endif 00040 #ifndef OBDLL 00041 #define OBDLL 00042 #endif 00043 00044 //using namespace std; 00045 namespace OpenBabel { 00046 00047 00048 class OBBase; 00049 class OBConversion; 00050 OBERROR extern OBMessageHandler obErrorLog; 00051 00052 //************************************************* 00053 00055 // class introduction in obconversion.cpp 00056 class OBCONV OBFormat 00057 { 00058 public: 00060 00064 virtual bool ReadMolecule(OBBase* /*pOb*/, OBConversion* /*pConv*/) 00065 { std::cerr << "Not a valid input format"; return false;} 00066 00068 00072 virtual bool ReadChemObject(OBConversion* /*pConv*/) 00073 { std::cerr << "Not a valid input format"; return false;} 00074 00076 00081 virtual bool WriteMolecule(OBBase* /*pOb*/, OBConversion* /*pConv*/) 00082 { std::cerr << "Not a valid output format"; return false;} 00083 00085 00089 virtual bool WriteChemObject(OBConversion* /*pConv*/) 00090 { std::cerr << "Not a valid output format"; return false;} 00091 00093 00097 virtual const char* Description()=0; 00098 00100 00102 virtual const char* TargetClassDescription(); 00103 00105 00108 virtual const std::type_info& GetType(); 00109 00111 virtual const char* SpecificationURL() { return ""; } 00112 00114 virtual const char* GetMIMEType() { return ""; } 00115 00117 00121 virtual unsigned int Flags() { return 0;}; 00122 00124 00126 virtual int SkipObjects(int /*n*/, OBConversion* /*pConv*/) 00127 { 00128 return 0; //shows not implemented in the format class 00129 }; 00130 00132 00136 virtual OBFormat* MakeNewInstance() 00137 { 00138 return NULL; //shows not implemented in the format class 00139 } 00140 00142 virtual ~OBFormat(){}; 00143 }; 00144 00145 //************************************************* 00148 struct CharPtrLess : public std::binary_function<const char*,const char*, bool> 00149 { 00150 bool operator()(const char* p1,const char* p2) const 00151 { return strcasecmp(p1,p2)<0; } 00152 }; 00153 00154 typedef std::map<const char*,OBFormat*,CharPtrLess > FMapType; 00155 typedef FMapType::iterator Formatpos; 00156 00157 //************************************************* 00159 // Class introduction in obconversion.cpp 00160 class OBCONV OBConversion 00161 { 00163 public: 00165 00166 OBConversion(std::istream* is=NULL, std::ostream* os=NULL); 00168 OBConversion(const OBConversion& o); 00169 virtual ~OBConversion(); 00171 00172 00173 00174 static int RegisterFormat(const char* ID, OBFormat* pFormat, const char* MIME = NULL); 00176 static OBFormat* FindFormat(const char* ID); 00178 static OBFormat* FormatFromExt(const char* filename); 00180 static OBFormat* FormatFromMIME(const char* MIME); 00181 00183 static bool GetNextFormat(Formatpos& itr, const char*& str,OBFormat*& pFormat); 00185 00187 00188 static const char* Description(); //generic conversion options 00190 00192 00193 std::istream* GetInStream() const {return pInStream;}; 00194 std::ostream* GetOutStream() const {return pOutStream;}; 00195 void SetInStream(std::istream* pIn) 00196 { 00197 if (pInStream && NeedToFreeInStream) { 00198 delete pInStream; NeedToFreeInStream = false; 00199 } 00200 pInStream=pIn; 00201 CheckedForGzip = false; // haven't tried to gzip decode this stream 00202 }; 00203 void SetOutStream(std::ostream* pOut) 00204 { 00205 if (pOutStream && NeedToFreeOutStream) { 00206 delete pOutStream; NeedToFreeOutStream = false; 00207 } 00208 pOutStream=pOut; 00209 }; 00211 bool SetInAndOutFormats(const char* inID, const char* outID); 00212 bool SetInAndOutFormats(OBFormat* pIn, OBFormat* pOut); 00214 bool SetInFormat(const char* inID); 00215 bool SetInFormat(OBFormat* pIn); 00217 bool SetOutFormat(const char* outID); 00218 bool SetOutFormat(OBFormat* pOut); 00219 00220 OBFormat* GetInFormat() const{return pInFormat;}; 00221 OBFormat* GetOutFormat() const{return pOutFormat;}; 00222 std::string GetInFilename() const{return InFilename;}; 00223 00225 std::streampos GetInPos()const{return wInpos;}; 00226 00228 size_t GetInLen()const{return wInlen;}; 00229 00231 const char* GetTitle() const; 00232 00234 OBConversion* GetAuxConv() const {return pAuxConv;}; 00235 void SetAuxConv(OBConversion* pConv) {pAuxConv=pConv;}; 00237 00238 00239 00240 enum Option_type { INOPTIONS, OUTOPTIONS, GENOPTIONS }; 00241 00243 const char* IsOption(const char* opt,Option_type opttyp=OUTOPTIONS); 00244 00246 const std::map<std::string,std::string>* GetOptions(Option_type opttyp) 00247 { return &OptionsArray[opttyp];}; 00248 00250 void AddOption(const char* opt, Option_type opttyp, const char* txt=NULL); 00251 00252 bool RemoveOption(const char* opt, Option_type optype); 00253 00255 void SetOptions(const char* options, Option_type opttyp); 00256 00258 static void RegisterOptionParam(std::string name, OBFormat* pFormat, 00259 int numberParams=0, Option_type typ=OUTOPTIONS); 00260 00262 static int GetOptionParams(std::string name, Option_type typ); 00264 00266 00267 // @brief Set and return the list of supported input format 00268 std::vector<std::string> GetSupportedInputFormat(); 00269 // @brief Set and return the list of supported output format 00270 std::vector<std::string> GetSupportedOutputFormat(); 00272 00274 00275 00276 int Convert(std::istream* is, std::ostream* os); 00277 00279 int Convert(); 00280 00283 int FullConvert(std::vector<std::string>& FileList, 00284 std::string& OutputFileName, std::vector<std::string>& OutputFileList); 00286 00288 00289 bool AddChemObject(OBBase* pOb); 00290 OBBase* GetChemObject(); 00291 bool IsLast(); 00292 bool IsFirstInput(); 00293 int GetOutputIndex() const ; 00294 void SetOutputIndex(int indx); 00295 void SetMoreFilesToCome(); 00296 void SetOneObjectOnly(bool b=true); 00297 void SetLast(bool b){SetOneObjectOnly(b);} 00298 00299 00300 00301 00302 static OBFormat* GetDefaultFormat(){return pDefaultFormat;}; 00303 00305 00308 bool Write(OBBase* pOb, std::ostream* pout=NULL); 00309 00311 00317 std::string WriteString(OBBase* pOb, bool trimWhitespace = false); 00318 00320 00325 bool WriteFile(OBBase* pOb, std::string filePath); 00326 00331 void CloseOutFile(); 00332 00334 00338 bool Read(OBBase* pOb, std::istream* pin=NULL); 00339 00341 00345 bool ReadString(OBBase* pOb, std::string input); 00346 00348 00354 bool ReadFile(OBBase* pOb, std::string filePath); 00355 00356 protected: 00358 static std::string BatchFileName(std::string& BaseName, std::string& InFile); 00360 static std::string IncrementedFileName(std::string& BaseName, const int Count); 00362 static bool CheckForUnintendedBatch(const std::string& infile, const std::string& outfile); 00363 00365 00366 protected: 00367 bool SetStartAndEnd(); 00368 static FMapType& FormatsMap(); 00369 static FMapType& FormatsMIMEMap(); 00370 typedef std::map<std::string,int> OPAMapType; 00371 static OPAMapType& OptionParamArray(Option_type typ); 00372 static int LoadFormatFiles(); 00373 bool OpenAndSetFormat(bool SetFormat, std::ifstream* is); 00374 00375 std::string InFilename; 00376 std::istream* pInStream; 00377 std::ostream* pOutStream; 00378 static OBFormat* pDefaultFormat; 00379 OBFormat* pInFormat; 00380 OBFormat* pOutFormat; 00381 00382 std::map<std::string,std::string> OptionsArray[3]; 00383 00384 int Index; 00385 unsigned int StartNumber; 00386 unsigned int EndNumber; 00387 int Count; 00388 bool m_IsFirstInput; 00389 bool m_IsLast; 00390 bool MoreFilesToCome; 00391 bool OneObjectOnly; 00392 bool ReadyToInput; 00393 bool CheckedForGzip; 00394 bool NeedToFreeInStream; 00395 bool NeedToFreeOutStream; 00396 00397 static int FormatFilesLoaded; 00398 OBBase* pOb1; 00399 std::streampos wInpos; 00400 std::streampos rInpos; 00401 size_t wInlen; 00402 size_t rInlen; 00403 00404 OBConversion* pAuxConv; 00405 00406 std::vector<std::string> SupportedInputFormat; 00407 std::vector<std::string> SupportedOutputFormat; 00408 00409 }; 00410 00412 #define NOTREADABLE 0x01 00413 #define READONEONLY 0x02 00414 #define READBINARY 0x04 00415 #define ZEROATOMSOK 0x08 00416 #define NOTWRITABLE 0x10 00417 #define WRITEONEONLY 0x20 00418 #define WRITEBINARY 0x40 00419 #define READXML 0x80 00420 #define DEFAULTFORMAT 0x4000 00421 00422 } //namespace OpenBabel 00423 #endif //OB_CONV_H 00424 00427 00428
This file is part of the documentation for Open Babel, version 2.1.0.
1.5.2.