src/mmdb_io_file.h
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00001 // $Id: mmdb_io_file.h $ 00002 // ================================================================= 00003 // 00004 // CCP4 Coordinate Library: support of coordinate-related 00005 // functionality in protein crystallography applications. 00006 // 00007 // Copyright (C) Eugene Krissinel 2000-2008. 00008 // 00009 // This library is free software: you can redistribute it and/or 00010 // modify it under the terms of the GNU Lesser General Public 00011 // License version 3, modified in accordance with the provisions 00012 // of the license to address the requirements of UK law. 00013 // 00014 // You should have received a copy of the modified GNU Lesser 00015 // General Public License along with this library. If not, copies 00016 // may be downloaded from http://www.ccp4.ac.uk/ccp4license.php 00017 // 00018 // This program is distributed in the hope that it will be useful, 00019 // but WITHOUT ANY WARRANTY; without even the implied warranty of 00020 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 00021 // GNU Lesser General Public License for more details. 00022 // 00023 // ================================================================= 00024 // 00025 // 11.09.13 <-- Date of Last Modification. 00026 // ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 00027 // ----------------------------------------------------------------- 00028 // 00029 // **** Module : file_ <interface> 00030 // ~~~~~~~~~ 00031 // **** Classes : mmdb::io::File - file I/O Support. 00032 // ~~~~~~~~~ 00033 // 00034 // (C) E. Krissinel 2000-2013 00035 // 00036 // ================================================================= 00037 // 00038 00039 #ifndef __MMDB_IO_File__ 00040 #define __MMDB_IO_File__ 00041 00042 #include <stdio.h> 00043 00044 #include "mmdb_mattype.h" 00045 00046 namespace mmdb { 00047 00048 namespace io { 00049 00050 // ======================== File Class ======================== 00051 00052 enum GZ_MODE { 00053 GZM_NONE = 0, 00054 GZM_CHECK = 1, 00055 GZM_ENFORCE = 2, 00056 GZM_ENFORCE_GZIP = 2, 00057 GZM_ENFORCE_COMPRESS = 3 00058 }; 00059 00060 enum FILE_ERROR { 00061 FileError_NoMemory = 110, 00062 FileError_ShortData = 111, 00063 FileError_NoDataFound = 112, 00064 FileError_NoColumn = 113, 00065 FileError_BadData = 114, 00066 FileError_WrongMemoryAllocation = 115 00067 }; 00068 00069 enum SYSKEY { 00070 syskey_unix = 1, 00071 syskey_win = 2, 00072 syskey_all = 3 00073 }; 00074 00075 extern const char _dir_sep_c; 00076 extern cpstr _dir_sep; 00077 00078 // =================== Auxilary Functions ======================== 00079 00080 00081 extern cpstr GetFPath ( pstr FilePath, SYSKEY syskey=syskey_unix ); 00082 extern cpstr GetFName ( cpstr FilePath, SYSKEY syskey=syskey_unix ); 00083 extern cpstr GetFExt ( cpstr FilePath ); 00084 extern cpstr ChangeExt ( pstr FilePath, cpstr newExt, 00085 SYSKEY syskey=syskey_unix ); 00086 extern cpstr FileError ( int ErrCode ); 00087 extern void RemoveDelimiters ( pstr S, int SLen ); 00088 extern void PickOutNumber ( cpstr S, pstr SV, int SLen, int & j ); 00089 00090 00091 // ========================== File =============================== 00092 00093 DefineClass(File); 00094 00095 class File { 00096 00097 public : 00098 00099 File ( word BufSize=4096 ); 00100 virtual ~File(); 00101 00102 // ---- control functions 00103 // FileName allows for "stdin", "stdout" and "stderr" as 00104 // for standard UNIX streams. 00105 void assign ( cpstr FileName, 00106 bool Text=false, 00107 bool UniB=false, 00108 GZ_MODE gzMode=GZM_NONE ); 00109 // assign for memory IO 00110 void assign ( word poolSize, word sizeInc, pstr filePool ); 00111 void GetFilePool ( pstr & filePool, word & fileSize ); 00112 00113 inline cpstr FileName() { return FName; } 00114 bool reset ( bool ReadOnly=false, int retry=0 ); 00115 // = true if opened, each retry 1 sec sleep 00116 bool erase (); // = true if erased 00117 bool exists (); // = true if exists 00118 bool parse ( cpstr FileName ); // true if filled 00119 bool rename ( cpstr NewFileName ); // true if renamed 00120 bool rewrite (); // = true if opened 00121 bool append (); // = true if opened 00122 bool isOpen (); 00123 long Position (); 00124 inline long FileLength () { return FLength; } 00125 bool seek ( long Position ); 00126 bool FileEnd (); 00127 inline bool Success () { return IOSuccess; } 00128 inline void SetSuccess() { IOSuccess = true; } 00129 void shut (); 00130 00131 // ---- binary I/O 00132 word ReadFile ( void * Buffer, word Count ); 00133 word CreateRead ( pstr & Line ); 00134 word ReadTerLine ( pstr Line, bool longLine=false ); 00135 bool WriteFile ( const void * Buffer, word Count ); 00136 bool CreateWrite ( cpstr Line ); 00137 bool WriteTerLine ( cpstr Line, bool longLine=false ); 00138 00139 // machine-independent binary I/O 00140 bool WriteReal ( realtype * V ); 00141 bool WriteFloat ( realtype * V ); 00142 bool WriteInt ( int * I ); 00143 bool WriteShort ( short * S ); 00144 bool WriteLong ( long * L ); 00145 bool WriteBool ( bool * B ); 00146 bool WriteByte ( byte * B ); 00147 bool WriteWord ( word * W ); 00148 bool ReadReal ( realtype * V ); 00149 bool ReadFloat ( realtype * V ); 00150 bool ReadInt ( int * I ); 00151 bool ReadShort ( short * S ); 00152 bool ReadLong ( long * L ); 00153 bool ReadBool ( bool * B ); 00154 bool ReadByte ( byte * B ); 00155 bool ReadWord ( word * B ); 00156 bool AddReal ( realtype * V ); 00157 bool AddFloat ( realtype * V ); 00158 bool AddInt ( int * I ); 00159 bool AddShort ( short * S ); 00160 bool AddLong ( long * L ); 00161 bool AddByte ( byte * B ); 00162 bool AddWord ( word * B ); 00163 00164 // complex data binary I/O 00165 bool WriteVector ( rvector V, int len, int Shift ); 00166 bool WriteVector ( ivector iV, int len, int Shift ); 00167 bool WriteVector ( lvector lV, int len, int Shift ); 00168 bool WriteVector ( bvector B, int len, int Shift ); 00169 bool ReadVector ( rvector V, int maxlen, int Shift ); 00170 bool ReadVector ( ivector iV, int maxlen, int Shift ); 00171 bool ReadVector ( lvector lV, int maxlen, int Shift ); 00172 bool ReadVector ( bvector B, int maxlen, int Shift ); 00173 bool CreateReadVector ( rvector & V, int & len, int Shift ); 00174 bool CreateReadVector ( ivector & iV, int & len, int Shift ); 00175 bool CreateReadVector ( lvector & lV, int & len, int Shift ); 00176 bool CreateReadVector ( bvector & B, int & len, int Shift ); 00177 bool CreateReadVector ( rvector & V, int Shift ); 00178 bool CreateReadVector ( ivector & iV, int Shift ); 00179 bool CreateReadVector ( lvector & lV, int Shift ); 00180 bool CreateReadVector ( bvector & B, int Shift ); 00181 bool WriteMatrix ( rmatrix & A, int N, int M, 00182 int ShiftN, int ShiftM ); 00183 bool CreateReadMatrix ( rmatrix & A, int ShiftN, int ShiftM ); 00184 bool CreateReadMatrix ( rmatrix & A, int & N, int & M, 00185 int ShiftN, int ShiftM ); 00186 00188 bool Write ( cpstr Line ); 00189 bool Write ( realtype V, int length=10 ); 00190 bool Write ( int iV, int length=5 ); 00191 bool WriteLine ( cpstr Line ); 00192 bool LF (); 00193 word ReadLine ( pstr Line, word MaxLen=255 ); 00194 word ReadNonBlankLine ( pstr S, word MaxLen=255 ); 00195 00197 00198 // writes with spaces and adds LF 00199 bool WriteDataLine ( realtype X, realtype Y, int length=10 ); 00200 00201 bool WriteParameter ( cpstr S, realtype X, // writes parameter 00202 int ParColumn=40, // name S and value X 00203 int length=10 ); // at column ParColumn 00204 // and adds LF. 00205 00206 bool WriteParameters ( cpstr S, int n_X, // writes parameter 00207 rvector X, // name S and n_X values 00208 int ParColumn=40, // X[0..n_X-1] at col 00209 int length=10 ); // ParColumn, ads LF. 00210 00211 bool ReadParameter ( pstr S, realtype & X, // reads parameter 00212 int ParColumn=40 ); // name S and val X 00213 bool ReadParameter ( pstr S, int & X, 00214 int ParColumn=40 ); 00215 00216 bool ReadParameters ( pstr S, int & n_X, // reads parameter 00217 rvector X, // name S, counts the 00218 int MaxLen=255, // of values n_X and 00219 int ParColumn=40 ); // reads X[0..n_X-1]. 00220 // MaxLen gives sizeof(S) 00221 00222 // WriteColumns writes data stored in X, Y and Z in the form 00223 // of columns, adding a blank line in the end. If Z (or Z and Y) 00224 // are set to NULL, then only X and Y (or only X) are written. 00225 // Shift corresponds to the begining of arrays' enumeration 00226 // X[Shift..Shift+len-1]. 00227 bool WriteColumns ( rvector X, rvector Y, rvector Z, 00228 int len, int Shift, int MLength ); 00229 bool WriteColumns ( rvector X, rvector Y, 00230 int len, int Shift, int MLength ); 00231 00232 // ReadColumns reads data stored by WriteColumns. X, Y, and Z 00233 // must be allocated prior to call. 00234 // xCol, yCol and zCol specify the order number of columns 00235 // (starting from 0) to be read into X, Y and Z, correspondingly. 00236 // If zCol (or zCol and yCol) < 0 then Z (or Z and Y) are not read. 00237 // Shift corresponds to the begining of arrays' enumeration 00238 // X[Shift..Shift+len-1]. 00239 // Returns number of lines read. 00240 int ReadColumns ( int maxlen, rvector X, rvector Y, rvector Z, 00241 int xCol, int yCol, int zCol, int Shift ); 00242 int ReadColumns ( int maxlen, rvector X, rvector Y, 00243 int xCol, int yCol, int Shift ); 00244 00245 // CreateReadColumns reads data stored by WriteColumns. X, Y, 00246 // and Z must be set to NULL prior to call. They will be allocated 00247 // within the procedure. 00248 // xCol, yCol and zCol specify the order number of columns 00249 // (starting from 0) to be read into X, Y and Z, correspondingly. 00250 // If zCol (or zCol and yCol) < 0 then Z (or Z and Y) are not read. 00251 // Shift corresponds to the begining of arrays' enumeration 00252 // X[Shift..Shift+len-1]. 00253 // Returns number of lines read, errors are reported by 00254 // ErrorCode(). 00255 int CreateReadColumns ( rvector & X, rvector & Y, rvector & Z, 00256 int xCol, int yCol, int zCol, int Shift ); 00257 int CreateReadColumns ( rvector & X, rvector & Y, 00258 int xCol, int yCol, int Shift ); 00259 00260 // ---- miscellaneous 00261 realtype GetNumber ( cpstr S ); 00262 FILE * GetHandle () { return hFile; } 00263 00264 protected : 00265 word Buf_Size; 00266 bool TextMode,UniBin; 00267 GZ_MODE gzipMode; 00268 pstr IOBuf; 00269 word BufCnt,BufLen,BufInc; 00270 FILE * hFile; 00271 bool EofFile; 00272 pstr FName; 00273 long FLength; 00274 bool IOSuccess; 00275 int ErrCode; 00276 00277 void FreeBuffer (); 00278 void _ReadColumns ( int & DLen, pstr S, int SLen, 00279 rvector X, rvector Y, rvector Z, 00280 int xCol, int yCol, int zCol, int Shift ); 00281 00282 private : 00283 int gzipIO; 00284 bool StdIO,memIO; 00285 00286 }; 00287 00288 00289 extern void SetGZIPPath ( pstr gzipPath, pstr ungzipPath ); 00290 extern void SetCompressPath ( pstr compressPath, pstr uncompressPath ); 00291 00292 extern bool FileExists ( cpstr FileName, PFile f=NULL ); 00293 00294 } 00295 00296 } 00297 00298 00299 #endif 00300
