/* FILE: CifFile.C */ /* VERSION: 4 */ /* DATE: 6/17/2002 */ /* Comments and Questions to: sw-help@rcsb.rutgers.edu */ /* COPYRIGHT 1999-2002 Rutgers - The State University of New Jersey This software is provided WITHOUT WARRANTY OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE OR ANY OTHER WARRANTY, EXPRESS OR IMPLIED. RUTGERS MAKE NO REPRESENTATION OR WARRANTY THAT THE SOFTWARE WILL NOT INFRINGE ANY PATENT, COPYRIGHT OR OTHER PROPRIETARY RIGHT. The user of this software shall indemnify, hold harmless and defend Rutgers, its governors, trustees, officers, employees, students, agents and the authors against any and all claims, suits, losses, liabilities, damages, costs, fees, and expenses including reasonable attorneys' fees resulting from or arising out of the use of this software. 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TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT WILL LICENSOR BE LIABLE FOR ANY INDIRECT, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OF OR INABILITY TO USE THE SOFTWARE, INCLUDING, WITHOUT LIMITATION, DAMAGES FOR LOSS OF GOODWILL, WORK STOPPAGE, COMPUTER FAILURE OR MALFUNCTION, OR ANY AND ALL OTHER COMMERCIAL DAMAGES OR LOSSES, EVEN IF ADVISED OF THE POSSIBILITY THEREOF. */ /* **************************************************************** * PURPOSE: This file contains the methods for class CifFile and the anonymous function: AddADicItem(ReVarCifArray *newdata,const CifString keyword, const CifString value, const CifString relation_label) * **************************************************************** */ #include "CifFile.h" // ********************************************************************* // CifFile // ********************************************************************* CifString*CifFile::GetItemDataTypeCode(const int dataBlockIndex, const int categoryIndex, const int itemIndex) { if (dataBlockIndex < 0 || dataBlockIndex >= _dataBlocks.Length()) return NULL; else return _dataBlocks[dataBlockIndex].GetItemDataTypeCode(categoryIndex, itemIndex); } CifString*CifFile::GetItemDataTypeCode(const int dataBlockIndex, const CifString category, const CifString item) { if (dataBlockIndex < 0 || dataBlockIndex >= _dataBlocks.Length()) return NULL; else return _dataBlocks[dataBlockIndex].GetItemDataTypeCode(category, item); } int CifFile::GetItemDataType(const int dataBlockIndex, const int categoryIndex, const int itemIndex) { if (dataBlockIndex < 0 || dataBlockIndex >= _dataBlocks.Length()) return CIF_DATABLOCK_NOT_EXIST ; else return _dataBlocks[dataBlockIndex].GetItemDataType(categoryIndex, itemIndex); } int CifFile::GetItemDataType(const int dataBlockIndex, const CifString categoryName, const CifString itemName) { if (dataBlockIndex < 0 || dataBlockIndex >= _dataBlocks.Length()) return CIF_DATABLOCK_NOT_EXIST ; else return _dataBlocks[dataBlockIndex].GetItemDataType(categoryName, itemName); } int CifFile::GetIndex(const char *datablock_name) // ---------------------------------------------------------------------- // GetIndex() Finds the index of the datablock_namein dics array, // -1 if not found // --------------------------------------------------------------------- { int i; CifString Datablock_label(datablock_name); Datablock_label.ToLower(); for (i=0; i< _dataBlocks.Length(); i++) if (!CompareNoCase(_dataBlocks[i]._dataBlockName, Datablock_label)) break; if (i != _dataBlocks.Length()) return i; else return -1; } void CifFile::Print() const // ---------------------------------------------------------------------- // Print(): Dump the structure // --------------------------------------------------------------------- { unsigned i; PrintLine("File"); for (i=0; i<_dataBlocks.Length(); i++) _dataBlocks[i].Print(); } void CifFile::PrintDetails() const // ---------------------------------------------------------------------- // Print(): Dump the structure // --------------------------------------------------------------------- { unsigned i; cout << "GLOBALS: " << endl; _globalInformation.Print(); for (i=0; i<_dataBlocks.Length(); i++) { cout << "datablocks: " << i << ' '; _dataBlocks[i].PrintDetails(); } PrintLine(); } void CifFile::PrintTable() const // ---------------------------------------------------------------------- // Print(): Dump the structure // --------------------------------------------------------------------- { unsigned i; cout << "GLOBALS: " << endl; _globalInformation.Print(); for (i=0; i<_dataBlocks.Length(); i++) { cout << "datablocks: " << i << ' '; _dataBlocks[i].PrintTable(); } } void CifFile::PrintDiagnostics() { int i,j; // // Output error and warning messages .... // for (i=0; i < _dataBlocks.Length(); i++) { cout << endl << "There are " << _dataBlocks[i].CountErrors() << " errors in block " << _dataBlocks[i]._dataBlockName.Text() << " [" << i << "]" << endl << endl; for (j=0; j < _dataBlocks[i].CountErrors(); j++) { cout << _dataBlocks[i].GetError(j)->Text() << endl; } cout << endl << "There are " << _dataBlocks[i].CountWarnings() << " warnings in block " << _dataBlocks[i]._dataBlockName.Text() << " [" << i << "]" << endl << endl; for (j=0; j < _dataBlocks[i].CountWarnings(); j++) { cout << _dataBlocks[i].GetWarning(j)->Text() << endl; } } } CifFile &CifFile::Copy(const CifFile &file) { // file_name.Copy(file.file_name); _globalInformation.Copy(file._globalInformation); _dataBlocks.Clear(); for (unsigned i=0; i < file._dataBlocks.Length(); i++) _dataBlocks.Add(file._dataBlocks[i]); return *this; } CifString *CifFile::GetItemPrimitiveCode(const int dataBlockIndex, const int categoryIndex, const int itemIndex) { if (dataBlockIndex < 0 || dataBlockIndex >= _dataBlocks.Length()) return NULL; else return _dataBlocks[dataBlockIndex].GetItemPrimitiveCode(categoryIndex, itemIndex); } CifString*CifFile::GetItemPrimitiveCode(const int dataBlockIndex, const CifString category, const CifString item) { if (dataBlockIndex < 0 || dataBlockIndex >= _dataBlocks.Length()) return NULL; else return _dataBlocks[dataBlockIndex].GetItemPrimitiveCode(category, item); } int CifFile:: ReadFile(const char *filename, const char *dicDataBlockName, const int verify) { int ret, i,type, dicDataBlockNo = -1, index; CifFileIo *newCifFile; CifCategory newCategory; CifDataBlock cifDatablock, *dic; CifString label, message; if (dicDataBlockName != NULL) dicDataBlockNo = GetIndex(dicDataBlockName); // Look for an existing persistent object version of the this file. if (dicDataBlockNo != -1 && dicDataBlockName != NULL) { if (PermanentRead(filename, _dataBlocks[dicDataBlockNo]._fileName.Text(), _dataBlocks[dicDataBlockNo]._dataBlockName.Text())) { return TRUE; } } else if (PermanentRead(filename)) { return TRUE; } // Open given CIF text filename for reading ret = FILE_OPERATION_SUCCEED; newCifFile = new CifFileIo; if ((ret = newCifFile->OpenFile(filename, 'r'))!= FILE_OPERATION_SUCCEED ) { delete newCifFile; cout << filename << " can not be opened" << endl; return ret; } if (dicDataBlockNo != -1) { dic = &_dataBlocks[dicDataBlockNo]; } else { dic = NULL; } // Get the first token, if data_ is the keyword, store the label cifDatablock._fileName.Copy(newCifFile->GetFileName()); cifDatablock._fileOffset = newCifFile->GetInMemoryOffset(); type = newCifFile->GetNextCifToken(&cifDatablock, dic); if (type == CIF_KEYWORD_DATA) { if ((index = GetIndex(&newCifFile->GetTokenValue()->Text()[5])) != -1) { message.Clear(); message += "Repeated datablock name at index "; message += index; message += " in file \'"; message += _dataBlocks[index]._fileName; message += "\'"; cifDatablock.ErrorMessage(CIF_ERROR, newCifFile->GetCurrLineNo(), message); } cifDatablock.SetDatablockName(&newCifFile->GetTokenValue()->Text()[5]); newCifFile->GetNextCifToken(&cifDatablock, dic); } while (type == CIF_KEYWORD_GLOBAL || type == CIF_KEYWORD_DATA || type == CIF_KEYWORD_INCLUDE || type == CIF_KEYWORD_ALIAS || type == CIF_DEFINITION_CATEGORY || type == CIF_DEFINITION_ITEM || type == CIF_ITEM_NAME || type == CIF_KEYWORD_LOOP) { // Copy down the label for further usage if (type == CIF_KEYWORD_GLOBAL) { for (i=0; iGetTokenValue()->Length(); i++) { if (newCifFile->GetTokenValue()->Text()[i] == CIF_DATA_PREFIX_CHARACTER) break; } if (i != newCifFile->GetTokenValue()->Length()) label.Copy(&(newCifFile->GetTokenValue()->Text()[i+1])); newCifFile->GetNextCifToken(&cifDatablock, dic); do { if ( newCifFile->GetTokenType() == CIF_KEYWORD_LOOP || newCifFile->GetTokenType() == CIF_ITEM_NAME) { if (newCifFile->GetTokenType() == CIF_KEYWORD_LOOP) { newCifFile->GetCifLoopedValue(NULL, &_globalInformation, &newCategory ); } else { newCifFile->GetCifNonLoopedValue(NULL, &_globalInformation, &newCategory); } _globalInformation.InsertRowsFromFile(&_dataBlocks[dicDataBlockNo], verify, newCifFile->GetCurrLineNo(), newCifFile->GetSaveOffset(), &newCategory, NULL, NULL, NULL); if (newCategory._items.Length() != 0) newCategory.DeleteElement(); } } while (newCifFile->GetTokenType() == CIF_ITEM_NAME || newCifFile->GetTokenType() == CIF_KEYWORD_LOOP); } else { if (dicDataBlockNo != -1) { cifDatablock.ReadDatablock(newCifFile, &_globalInformation, &_dataBlocks[dicDataBlockNo], verify); cifDatablock._dictionaryIndex = dicDataBlockNo; } else { cifDatablock.ReadDatablock(newCifFile, &_globalInformation, &cifDatablock, verify); cifDatablock._dictionaryIndex = _dataBlocks.Length(); } _dataBlocks.Add(cifDatablock); cifDatablock.DeleteElement(); cifDatablock._fileName.Copy(newCifFile->GetFileName()); cifDatablock._fileOffset = (long) newCifFile->GetInMemoryOffset() - (long) newCifFile->GetTokenValue()->Length(); } type = newCifFile->GetTokenType(); } // end while PermanentWrite(newCifFile->GetFileName()->Text()); if (newCifFile->GetTokenType() != EOF) { delete newCifFile; return FAILURE; } delete newCifFile; return SUCCEED; } int CifFile:: WriteFile(const char *filename, const char *outputFileName, const char type, const int write_comment, const int esdFlag, const char *dictionary, const char *version) { int ret, i; CifFileIo *newCifFile; CifString *dic, *dic_version; ret = FILE_OPERATION_SUCCEED; if (type != 'w' && type != 'W' && type != 'a' && type != 'A') return FILE_OPERATION_TYPE_DISALLOW ; // Open given filename for reading newCifFile = new CifFileIo; if ((ret = newCifFile->OpenFile(outputFileName, type))!= FILE_OPERATION_SUCCEED ) { delete newCifFile; return ret; } if (dictionary != NULL && strcmp(dictionary, "")) dic = new CifString(dictionary); else dic = NULL; if (version != NULL && strcmp(version,"")) dic_version = new CifString(version); else dic_version = NULL; if (_globalInformation._categories.Length() > 0) { newCifFile->FileIo::PrintF("%s%s\n", CIF_RESERVED_KEYWORD_GLOBAL, _globalInformation._dataBlockName.Text()); _globalInformation.WriteDataBlock(newCifFile, write_comment, esdFlag, dic, dic_version); } for (i=0; i< _dataBlocks.Length(); i++) { if (!strcmp(_dataBlocks[i]._fileName.Text(), filename)) _dataBlocks[i].WriteDataBlock(newCifFile, write_comment, esdFlag, dic, dic_version, &_dataBlocks[_dataBlocks[i]._dictionaryIndex]); } newCifFile->CloseFile(); delete newCifFile; if (dic != NULL) delete dic; if (dic_version != NULL) delete dic_version; return SUCCEED; } int CifFile:: WriteDataBlock(const char *filename, const char type, const char *datablock_name, const int write_comment, const int esdFlag, const char *dictionary, const char *version ) { int ret, dic_no, datablock_no; CifFileIo *newCifFile; CifString *dic, *dic_version; ret = FILE_OPERATION_SUCCEED; if (type != 'w' && type != 'W' && type != 'a' && type != 'A') return FILE_OPERATION_TYPE_DISALLOW ; // Open given filename for reading newCifFile = new CifFileIo; if ((ret = newCifFile->OpenFile(filename, type))!= FILE_OPERATION_SUCCEED ) { delete newCifFile; return ret; } datablock_no = GetIndex(datablock_name); if (datablock_no == -1) return CIF_DATABLOCK_NOT_EXIST; dic_no = GetDataBlockDictionaryIndex(datablock_no); if (dictionary != NULL && strcmp(dictionary,"")) dic = new CifString(dictionary); else dic = NULL; if (version != NULL && strcmp(version,"")) dic_version = new CifString(version); else dic_version = NULL; if (dic_no != -1) _dataBlocks[datablock_no].WriteDataBlock(newCifFile, write_comment, esdFlag, dic, dic_version, &_dataBlocks[dic_no]); else _dataBlocks[datablock_no].WriteDataBlock(newCifFile, write_comment,esdFlag, dic, dic_version); newCifFile->CloseFile(); delete newCifFile; if (dic != NULL) delete dic; if (dic_version != NULL) delete dic_version; return SUCCEED; } int CifFile:: MergeDataBlock(const char *new_blockname, const int index1, const int index2) { CifDataBlock *newblock; CifString message; int index; if (index1 < 0 || index1 >= _dataBlocks.Length() || index2 < 0 || index2 >= _dataBlocks.Length() || GetDataBlockDictionaryIndex(index1) != GetDataBlockDictionaryIndex(index2) ) return -1; else { newblock = new CifDataBlock(_dataBlocks[index1]); if ((index = GetIndex(new_blockname)) != -1) { message.Clear(); message += "Repeated datablock name at index "; message += index; message += "in file \'"; message += _dataBlocks[index]._fileName; message += "\'"; _dataBlocks[index].ErrorMessage(CIF_ERROR, -1, message); } newblock->SetDatablockName(new_blockname); newblock->Merge(&_dataBlocks[_dataBlocks[index1]._dictionaryIndex], &_dataBlocks[index2]); if (_dataBlocks[index1]._fileName != _dataBlocks[index2]._fileName ) newblock->_fileName.Clear(); newblock->_fileOffset = 0; _dataBlocks.Add(*newblock); delete newblock; return _dataBlocks.Length()-1; /* _dataBlocks[index1].SetDatablockName(new_blockname); _dataBlocks[index1].Merge(&_dataBlocks[index2]); _dataBlocks.DeleteAt(index2, 1); return SUCCEED; */ } } void CifFile:: DeleteDataBlock(const int index) { if (index < 0 || index >= _dataBlocks.Length()) return; _dataBlocks.DeleteAt(index, 1); for (unsigned i=0; i< _dataBlocks.Length(); i++) { if (_dataBlocks[i]._dictionaryIndex == index) { _dataBlocks[i]._dictionaryIndex = -1; _dataBlocks[i]._dictionaryName.Copy(""); } else if (_dataBlocks[i]._dictionaryIndex > index) _dataBlocks[i]._dictionaryIndex--; } } void CifFile:: CheckDataBlock(const int index) { CifDataBlock *dic; if (index < 0 || index >= _dataBlocks.Length()) return; dic = GetDictionaryDataBlock(index); if (dic != NULL) _dataBlocks[index].CheckDataBlock(dic, FALSE); else return; } CifDataBlock *CifFile::GetDictionaryDataBlock(const int index) { int dicIndex; dicIndex = _dataBlocks[index]._dictionaryIndex; if ((dicIndex >=0 || dicIndex < _dataBlocks.Length() ) && !CompareNoCase(_dataBlocks[dicIndex]._dataBlockName, _dataBlocks[index]._dictionaryName)) return &_dataBlocks[dicIndex]; else return NULL; } void CifFile::PermanentWrite(const char *fileName) { int i, len, dicIndex; FILE *fp; DIR *dirp; CifString perFileName, dicFileName, dicName, message, dirName; dicName.Clear(); for (i=0; i< _dataBlocks.Length(); i++) { if (!strcmp(_dataBlocks[i]._fileName.Text(), fileName)) { if (!strcmp(dicName.Text(),"")) dicName.Copy(_dataBlocks[i]._dictionaryName); else { if (CompareNoCase(dicName, _dataBlocks[i]._dictionaryName)) { message.Clear(); message += "Different dictionary name from the other datablock with the same file name"; _dataBlocks[i].ErrorMessage(CIF_ERROR, -1, message.Text()); break; } } } } if (i != _dataBlocks.Length()) return; dicIndex = GetIndex(dicName); if (dicIndex != -1) dicFileName.Copy(_dataBlocks[dicIndex]._fileName); else dicFileName.Clear(); GetPermanentFileName(fileName, dicFileName, &perFileName, &dirName); dirp = opendir(dirName.Text()); if (dirp == NULL) { i = mkdir(dirName.Text(), 0777); if (i == -1) { fprintf(stderr, "Creating directory %s failed\n", dirName.Text()); return; } chmod (dirName.Text(), 0777); } else closedir(dirp); fp = fopen(perFileName.Text(), "w"); if (fp != NULL) { // _globalInformation.PermanentWrite(fp); len = 0; for (i=0; i< _dataBlocks.Length(); i++) if (!strcmp(_dataBlocks[i]._fileName.Text(), fileName)) len ++; fprintf(fp, "%d\n", len); for (i=0; i< _dataBlocks.Length(); i++) { if (!strcmp(_dataBlocks[i]._fileName.Text(), fileName)) _dataBlocks[i].PermanentWrite(fp); } fclose(fp); chmod (perFileName.Text(), 0666); } else fprintf(stderr, "Writing permanent file %s failed\n", perFileName.Text()); } int CifFile::PermanentRead(const char *fileName, const char *dicFileName, const char *dicDataBlockName) { struct stat stat1, stat2, dicStat1, dicStat2; int i, j, ret_stat1 = 1, ret_stat2 = 1, dicIndex, dicIndex1; CifString perFileName, dicPerFileName, dirName, dicName; FILE *fp; int tmplen; CifDataBlock tmpblock; if (dicFileName == NULL || !strcmp(dicFileName,"")) dicName.Clear(); else dicName.Copy(dicFileName); GetPermanentFileName(fileName, dicName, &perFileName, &dirName); if (stat(perFileName.Text(), &stat1) == 0 && stat(fileName, &stat2) == 0 ) { if (dicDataBlockName != NULL && strcmp(dicDataBlockName,"") ) { dicIndex = GetIndex(dicDataBlockName); if (dicIndex != -1) { ret_stat1 = stat(_dataBlocks[dicIndex]._fileName.Text(), &dicStat1); dicIndex1 = GetIndex(_dataBlocks[dicIndex]._dictionaryName); if (dicIndex1 != -1) GetPermanentFileName(_dataBlocks[dicIndex]._fileName.Text(), _dataBlocks[dicIndex1]._fileName, &dicPerFileName, &dirName); ret_stat2 = stat(dicPerFileName.Text(), &dicStat2); } } if (stat1.st_mtime >= stat2.st_mtime && (dicDataBlockName == NULL || ret_stat1 == 0 && dicStat1.st_mtime <= stat1.st_mtime && ret_stat2 == 0 && dicStat2.st_mtime <= stat1.st_mtime )) { fp = fopen(perFileName.Text(), "r"); if (fp != NULL) { fscanf(fp, "%d\n", &tmplen); if (tmplen > 0) _dataBlocks.GrowBy(tmplen); for (i=0; i< tmplen; i++) { tmpblock.DeleteElement(); tmpblock.PermanentRead(fp); _dataBlocks.Add(tmpblock); } fclose(fp); for (i=0; i<_dataBlocks.Length(); i++) { for (j=0; j<_dataBlocks.Length(); j++) if (!CompareNoCase(_dataBlocks[i]._dictionaryName, _dataBlocks[j]._dataBlockName)) break; if (j != _dataBlocks.Length()) _dataBlocks[i]._dictionaryIndex = j; else return FALSE; } return TRUE; } } } return FALSE; } CifDataBlock *CifFile::AddDatablock(const int dictionaryIndex, const char *datablockName) { CifDataBlock *datablock; CifString message, *title; // int index; if (datablockName == NULL || !strcmp(datablockName, "")) return NULL; if ( GetIndex(datablockName) != -1) { /* if ((index = GetIndex(datablockName)) != -1) { message.Clear(); message += "Datablock \'"; message += datablockName; message += "\' has existed already"; _dataBlocks[index].ErrorMessage(CIF_ERROR, "", datablockName, -1, message.Text()); */ return (CifDataBlock *) NULL; } else { if (dictionaryIndex< 0 || dictionaryIndex >= _dataBlocks.Length()) { message.Clear(); message += "Dictionary does not exist"; _dataBlocks[0].ErrorMessage(CIF_ERROR, -1, message.Text()); return (CifDataBlock *) NULL; } else { datablock = new CifDataBlock; datablock->_dataBlockName.Copy(datablockName); datablock->_dictionaryIndex = dictionaryIndex; title = _dataBlocks[dictionaryIndex].GetDictionaryTitle(); if (title != NULL) datablock->_dictionaryName.Copy(title->Text()); title = _dataBlocks[dictionaryIndex].GetDictionaryVersion(); if (title != NULL) datablock->_dictionaryVersion.Copy(title->Text()); _dataBlocks.Add(*datablock); delete datablock; return &_dataBlocks[_dataBlocks.Length()-1]; } } } CifCategory *CifFile::AddCategory(const int datablockIndex, const char *categoryName) { // CifString message; if (categoryName == NULL || !strcmp(categoryName,"")) return (CifCategory *) NULL; if (datablockIndex< 0 || datablockIndex >= _dataBlocks.Length()) return (CifCategory *) NULL; return _dataBlocks[datablockIndex]. AddCategory(&_dataBlocks[_dataBlocks[datablockIndex]._dictionaryIndex], categoryName); } CifDataItem *CifFile::AddDataItem(const int datablockIndex, const int categoryIndex, const char *itemName) { // CifString message; if (itemName == NULL || !strcmp(itemName,"")) return (CifDataItem *) NULL; if (datablockIndex< 0 || datablockIndex >= _dataBlocks.Length()) { return (CifDataItem *) NULL; } return _dataBlocks[datablockIndex]. AddDataItem(&_dataBlocks[_dataBlocks[datablockIndex]._dictionaryIndex], categoryIndex, itemName); } int CifFile::AddRow(const int dataBlockIndex, const int categoryIndex) // ---------------------------------------------------------------------- // AddDataItem() Gets itemValue from itemValues array // --------------------------------------------------------------------- { if (dataBlockIndex< 0 || dataBlockIndex >= _dataBlocks.Length()) { return -1; } return _dataBlocks[dataBlockIndex].AddRow(categoryIndex); }