/* FILE: ciflib_structure.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: Miscellaneous functions. * **************************************************************** */ #include #include "CifFile.h" #include "CifFileIo.h" #include "ciflib_structure.h" #include "ciflib_interface.h" #include "CifErrorCodes.h" extern CifFile *theCifFiles; char *cifGetItemDataTypeCodeByIndex(const int dataBlockIndex, const int categoryIndex, const int itemIndex) /* ------------------------------------------------------------------------- cifGetItemDataTypeCodeByIndex(): Parametrers: const int dataBlockIndex, categoryIndex, itemIndex Return: char *default itemValue ------------------------------------------------------------------------- */ { CifString *dataTypeCode; char *itemValue; itemValue = NULL; dataTypeCode =theCifFiles->GetItemDataTypeCode(dataBlockIndex, categoryIndex, itemIndex); if (dataTypeCode != NULL) { itemValue = (char *) calloc(dataTypeCode->Length()+1, sizeof(char)); strcpy(itemValue, dataTypeCode->Text()); } return itemValue; } char *cifGetItemDataTypeCode(const char *datablockName, const char *categoryName, const char *itemKeyword) /* ------------------------------------------------------------------------- cifGetItemDataTypeCodes(): Parametrers: const int dataBlockIndex, const char *categoryName, itemKeyword Return: char *default itemValue ------------------------------------------------------------------------- */ { int dataBlockIndex; CifCategoryIndex *tableIndex; dataBlockIndex = cifGetDataBlockIndex(datablockName); tableIndex = theCifFiles->GetTableIndex(dataBlockIndex, categoryName, itemKeyword); if (tableIndex == NULL) return NULL; else return cifGetItemDataTypeCodeByIndex(dataBlockIndex, tableIndex->GetCategoryIndex(), tableIndex->GetItemIndex()); } char *cifGetItemPrimitiveCode(const char *datablockName, const char *categoryName, const char *itemKeyword) /* ------------------------------------------------------------------------- cifGetItemDataTypeCodes(): Parametrers: const int dataBlockIndex, const char *categoryName, itemKeyword Return: char *default itemValue ------------------------------------------------------------------------- */ { int dataBlockIndex; CifCategoryIndex *tableIndex; dataBlockIndex = cifGetDataBlockIndex(datablockName); tableIndex = theCifFiles->GetTableIndex(dataBlockIndex, categoryName, itemKeyword); if (tableIndex == NULL) return NULL; else return cifGetItemPrimitiveCodeByIndex(dataBlockIndex, tableIndex->GetCategoryIndex(), tableIndex->GetItemIndex()); } char *cifGetItemPrimitiveCodeByIndex(const int dataBlockIndex, const int categoryIndex, const int itemIndex) /* ------------------------------------------------------------------------- cifGetItemDataTypeCodeByIndex(): Parametrers: const int dataBlockIndex, categoryIndex, itemIndex Return: char *default itemValue ------------------------------------------------------------------------- */ { CifString *dataTypeCode; char *itemValue; itemValue = NULL; dataTypeCode =theCifFiles->GetItemPrimitiveCode(dataBlockIndex, categoryIndex, itemIndex); if (dataTypeCode != NULL) { itemValue = (char *) calloc(dataTypeCode->Length()+1, sizeof(char)); strcpy(itemValue, dataTypeCode->Text()); } return itemValue; } int cifGetItemStructureIndexByIndex(const int datablockIndex, const int categoryIndex, const int itemIndex) /* ------------------------------------------------------------------------- cifGetItemStructureIndexByIndex(): Parametrers: const int datablockIndex, categoryIndex, itemIndex Return: int structure index ------------------------------------------------------------------------- */ { return theCifFiles->GetItemStructureIndex(datablockIndex, categoryIndex, itemIndex); } int cifGetItemStructureIndex(const char *DatablockName, const char *categoryName, const char *itemKeyword) /* ------------------------------------------------------------------------- cifGetItemStructureIndex(): Parametrers: const int datablockIndex, const char * categoryName, itemKeyword Return: int structure index ------------------------------------------------------------------------- */ { CifString category(categoryName), item(itemKeyword); int datablockIndex; datablockIndex = cifGetDataBlockIndex(DatablockName); return theCifFiles->GetItemStructureIndex(datablockIndex, category, item); } int cifGetItemStructureNumValueByIndex(const int datablockIndex, const int categoryIndex, const int itemIndex) /* ------------------------------------------------------------------------- cifGetItemStructureNumValueByIndex(): Parametrers: const int datablockIndex, categoryIndex, itemIndex Return: int number of itemValues ------------------------------------------------------------------------- */ { return theCifFiles->GetItemStructureNumValue(datablockIndex, categoryIndex, itemIndex); } int cifGetItemStructureNumValue(const char *DatablockName, const char *categoryName, const char *itemKeyword) /* ------------------------------------------------------------------------- cifGetItemStructureNumValue(): Parametrers: const int datablockIndex, const char *categoryName, itemKeyword Return: int number of itemValues ------------------------------------------------------------------------- */ { CifString category(categoryName), item(itemKeyword); int datablockIndex; datablockIndex = cifGetDataBlockIndex(DatablockName); return theCifFiles->GetItemStructureNumValue(datablockIndex, category, item); } int cifGetItemStructureDimensionByIndex(const int datablockIndex, const int categoryIndex, const int itemIndex) /* ------------------------------------------------------------------------- cifGetItemStructureDimenstionByIndex(): Parametrers: const int datablockIndex, categoryIndex, itemIndex Return: int structure dimension ------------------------------------------------------------------------- */ { return theCifFiles->GetItemStructureDimension(datablockIndex, categoryIndex, itemIndex); } int cifGetItemStructureDimension(const char *DatablockName, const char *categoryName, const char *itemKeyword) /* ------------------------------------------------------------------------- cifGetItemStructureDimension(): Parametrers: const int datablockIndex, const char *categoryName, itemKeyword Return: int structure dimension ------------------------------------------------------------------------- */ { CifString category(categoryName), item(itemKeyword); int datablockIndex; datablockIndex = cifGetDataBlockIndex(DatablockName); return theCifFiles->GetItemStructureDimension(datablockIndex, category, item); } int cifGetItemStructureOrganizationByIndex(const int datablockIndex, const int categoryIndex, const int itemIndex) /* ------------------------------------------------------------------------- cifGetItemStructureOrganizationByIndex(): Parametrers: const int datablockIndex, categoryIndex, itemIndex Return: int structure organization ------------------------------------------------------------------------- */ { return theCifFiles->GetItemStructureOrganization(datablockIndex, categoryIndex, itemIndex); } int cifGetItemStructureOrganization(const char *DatablockName, const char *categoryName, const char *itemKeyword) /* ------------------------------------------------------------------------- cifGetItemStructureOrganization(): Parametrers: const int datablockIndex, const char *categoryName, itemKeyword Return: int structure organization ------------------------------------------------------------------------- */ { CifString category(categoryName), item(itemKeyword); int datablockIndex; datablockIndex = cifGetDataBlockIndex(DatablockName); return theCifFiles->GetItemStructureOrganization(datablockIndex, category, item); } int cifGetMatrixItemValuesByIndex(char ***itemValue, const int datablockIndex, const int categoryIndex, const int itemIndex, const int rowIndex, int *numItemValue) /* ------------------------------------------------------------------------- cifGetMatrixItemValuesByIndex() Gets a whole matrix itemValues by category and item names Parameter: char **itemValue the address of string itemValue int datablockIndex, categoryIndex, itemIndex, rowIndex, int *numItemValue return number of itemValues Return ItemValue: gets SUCCEED or error code if failed ------------------------------------------------------------------------- */ { CifItemValue *cifItemValue; char **tmpItemValue; int ret; ret = theCifFiles->GetItemValue(&cifItemValue, datablockIndex, categoryIndex, itemIndex, rowIndex); if (ret == CIF_DATA_IS_VALID) { if (cifItemValue->GetStructureNumValue() == 0) { *numItemValue = 1; tmpItemValue = (char **) calloc(1, sizeof(char)); tmpItemValue[0] = (char *) calloc(cifItemValue->_buf.Length() +1, sizeof(char)); strcpy(tmpItemValue[0], cifItemValue->_buf.Text()); } else { *numItemValue = cifItemValue->_data._arrayVal->Length(); tmpItemValue = (char **) calloc(*numItemValue, sizeof(char *)); for (unsigned i = 0; i<*numItemValue; i++) { tmpItemValue[i] = (char *) calloc((*cifItemValue->_data._arrayVal)[i]._buf.Length()+1, sizeof(char)); strcpy(tmpItemValue[i], (*cifItemValue->_data._arrayVal)[i]._buf.Text()); } } } else *itemValue = NULL; *itemValue = tmpItemValue; return ret; } int cifGetMatrixItemValues(char ***itemValue, const char *DatablockName, const char *categoryName, const char *itemKeyword, const int rowIndex, int *numItemValue) /* ------------------------------------------------------------------------- cifGetMatrixItemValues() Gets a whole matrix itemValues by category and item names Parameter: char **itemValue the address of string itemValue int datablockIndex, rowIndex char *categoryname, itemKeyword int *numItemValue return number of itemValues Return ItemValue: gets SUCCEED or error code if failed ------------------------------------------------------------------------- */ { CifCategoryIndex *tableIndex; int datablockIndex; datablockIndex = cifGetDataBlockIndex(DatablockName); tableIndex = theCifFiles->GetTableIndex(datablockIndex, categoryName, itemKeyword); if (tableIndex == NULL) return CIF_KEYWORD_NOT_EXIST; else return cifGetMatrixItemValuesByIndex(itemValue, datablockIndex, tableIndex->GetCategoryIndex(), tableIndex->GetItemIndex(), rowIndex, numItemValue); } int cifUpdateMatrixItemValuesByIndex(char **itemValues, const int datablockIndex, const int categoryIndex, const int itemIndex, const int rowIndex, const int numItemValue) /* ------------------------------------------------------------------------- cifUpdateMatrixItemValues() Gets a itemValue by category and item names Parameter: char **itemValue the address of string itemValue int datablockIndex, categoryIndex, itemIndex, rowIndex Return ItemValue: gets SUCCEED or error code if failed ------------------------------------------------------------------------- */ { CifItemValue *cifItemValue = NULL, *finalItemValue; int dataType, StructureNumValue, ret, itemValueNo, caseSensitivity; if (itemValues == NULL) return FAILURE; StructureNumValue = theCifFiles->GetItemStructureNumValue(datablockIndex, categoryIndex, itemIndex); if (StructureNumValue == 1) return cifUpdateItemValueByIndex(itemValues[0], datablockIndex, categoryIndex, itemIndex, rowIndex); dataType = theCifFiles->GetItemDataType(datablockIndex, categoryIndex, itemIndex); caseSensitivity = theCifFiles->GetItemCaseSensitivity(datablockIndex, categoryIndex, itemIndex); if (dataType != CIF_INTEGER_VALUE && dataType != CIF_DOUBLE_VALUE && dataType != CIF_STRING_VALUE) return FAILURE; itemValueNo = 0; finalItemValue = new CifItemValue(dataType, StructureNumValue, caseSensitivity); while (itemValueNo < StructureNumValue && itemValueNo < numItemValue) { if (itemValues[itemValueNo] == (char *) NULL || !strcmp(itemValues[itemValueNo],"")) cifItemValue = new CifItemValue(dataType, caseSensitivity, CIF_DATA_IS_NULL, (char *) NULL); else if (!strcmp(itemValues[itemValueNo], ".")) cifItemValue = new CifItemValue(dataType, caseSensitivity, CIF_DATA_NOT_APPROPRIATE, NULL); else cifItemValue = new CifItemValue(dataType, caseSensitivity, CIF_DATA_IS_VALID, itemValues[itemValueNo]); finalItemValue->_data._arrayVal->Add(*cifItemValue); finalItemValue->_status = CIF_DATA_IS_VALID; delete cifItemValue; itemValueNo ++; } ret = theCifFiles->UpdateItemValue(finalItemValue, datablockIndex, categoryIndex, itemIndex, rowIndex, TRUE); delete finalItemValue; return ret; } int cifUpdateMatrixItemValues(char **itemValues, const char * DatablockName, const char *categoryName, const char *itemKeyword, const int rowIndex, const int numItemValue) /* ------------------------------------------------------------------------- cifUpdateMatrixItemValues() Gets a itemValue by category and item names Parameter: char **itemValue the address of string itemValue int datablockIndex, rowIndex char *categoryName, itemKeyword Return ItemValue: gets SUCCEED or error code if failed ------------------------------------------------------------------------- */ { CifCategoryIndex *tableIndex; int datablockIndex; datablockIndex = cifGetDataBlockIndex(DatablockName); tableIndex = theCifFiles->GetTableIndex(datablockIndex, categoryName, itemKeyword); if (tableIndex == NULL) return CIF_KEYWORD_NOT_EXIST; else return cifUpdateMatrixItemValuesByIndex(itemValues, datablockIndex, tableIndex->GetCategoryIndex(), tableIndex->GetItemIndex(), rowIndex, numItemValue); } int* cifGetParentRow(char ***newItemValues, int *newCategoryIndex, int *newItemIndex, int *newRowIndex, const char *DatablockName, const char *categoryName, const char* itemKeyword, const int parentIndex, const char *mapItemValue, int *numItemValue) /* ------------------------------------------------------------------------- cifGetParentRow() Gets a row of itemValues of parent of given item name Parameters: char ***newItemValues: the address of the string array. int *newCategoryIndex, *newItemIndex, *newRowIndex: the address of the parent's category, item, and row indexes const int dataBlockIndex: which Datablock to process const char *categoryName, itemKeyword: category, and item keyword of the one getting parent itemValues const int parentIndex: the index in link parent list(indicating which parent) const char *mapItemValue: what itemValue of parent to map to int *numItemValue: the address to keep the number of the itemValues, it should be the same as mumber of items in the new category. Return ItemValue: A list of SUCCEED or error codes or NULL if fails ------------------------------------------------------------------------- */ { CifString category(categoryName), item(itemKeyword), tmpMapItemValue; ReVarCifArray *parents = NULL; CifItemValue *newCifItemValue; int *rets, ret, caseSensitivity; int dataBlockIndex; dataBlockIndex = cifGetDataBlockIndex(DatablockName); *newItemValues = NULL; *newCategoryIndex = -1; *newItemIndex = -1; *newRowIndex = -1; *numItemValue = 0; parents = theCifFiles->GetLinkParents(dataBlockIndex, category, item); if (parents == NULL) return NULL; if (parentIndex < 0 || parentIndex >= parents ->Length()) return NULL; *newRowIndex = 0; caseSensitivity = theCifFiles->GetItemCaseSensitivity(dataBlockIndex, (*parents)[parentIndex].GetCategoryIndex(), (*parents)[parentIndex].GetItemIndex()); if (!caseSensitivity) { tmpMapItemValue.Copy(mapItemValue); tmpMapItemValue.ToLower(); } do { ret = theCifFiles->GetItemValue(&newCifItemValue, dataBlockIndex, (*parents)[parentIndex].GetCategoryIndex(), (*parents)[parentIndex].GetItemIndex(), *newRowIndex); if (caseSensitivity && !Compare(newCifItemValue->_buf.Text(), mapItemValue) || !caseSensitivity && !CompareNoCase(newCifItemValue->_buf, tmpMapItemValue)) { *newCategoryIndex = (*parents)[parentIndex].GetCategoryIndex(); *newItemIndex = (*parents)[parentIndex].GetItemIndex(); rets = cifGetRowByIndex(newItemValues, dataBlockIndex, *newCategoryIndex, *newRowIndex, numItemValue); break; } (*newRowIndex) ++; } while ( ret < CIF_OUT_OF_RANGE_ERROR_CODE_START) ; if ( ret > CIF_OUT_OF_RANGE_ERROR_CODE_START) { (*newRowIndex) = -1; *newCategoryIndex = (*parents)[parentIndex].GetCategoryIndex(); *newItemIndex = (*parents)[parentIndex].GetItemIndex(); rets = cifGetRowByIndex(newItemValues, dataBlockIndex, *newCategoryIndex, 0, numItemValue); for (unsigned i=0; i< *numItemValue; i++) { rets[i] = CIF_VALUE_NOT_EXIST; if ((*newItemValues)[i] != NULL) free ((*newItemValues)[i]); (*newItemValues)[i] = NULL; } } return rets; } int* cifGetChildRow(char ***newItemValues, int *newCategoryIndex, int *newItemIndex,int *newRowIndex, const int childRowOrder, const char *DatablockName, const char * categoryName, const char* itemKeyword, const int childIndex, const char *mapItemValue, int *numItemValue) /* ------------------------------------------------------------------------- cifGetChildRow() Gets the row of itemValues of child of given item name which matches its itemValue at the childRowOrder-th times. Parameters: char ***newItemValues: the address of the string array. const int childRowOrder: 1, get the first row of the children matched itemValue, 2, get the second row of the children matched itemValue, int *newCategoryIndex, newItemIndex, newRowIndex: the address of category item, row indexes of the new itemValues. const int dataBlockIndex: which Datablock to process const char *categoryName, itemKeyword: category name and item keyword of the one which is getting child const int childIndex: the index in link child list const char *mapItemValue: which itemValue of the child to map to int *numItemValue: the address to keep the number of the itemValues, it should be the same as mumber of items in the new category. Return ItemValue: gets a list of SUCCEED or error codes or NULL if nothing found Example: errorCodes = cifGetChildRow(&newItemValues, &childCategoryIndex, &childItemIndex, &childRowIndex, 2, 1, "category", "id", 3, "category_group", &numItemValue) this procedure will search the item_list to find the third child of _category.id (third child is _item.category_id in the current ddl) and then map the itemValue "category_group" against table "item" column "category_id" when the second time it matchs the mapItemValue, it copies the itemValues of this row to newItemValues, and makes newCategoryIndex the index of category "item", newItemIndex the index of item "category_id" in category "item", and newRowIndex the new row index of new table "item" ------------------------------------------------------------------------- */ { CifString category(categoryName), item(itemKeyword); ReVarCifArray *children = NULL; CifItemValue *newCifItemValue; int *rets, ret, found, caseSensitivity; CifString tmpMapItemValue; int dataBlockIndex; dataBlockIndex = cifGetDataBlockIndex(DatablockName); *newItemValues = NULL; *newCategoryIndex = -1; *newItemIndex = -1; *newRowIndex = -1; *numItemValue = 0; children = theCifFiles->GetLinkChildren(dataBlockIndex, category, item); if (children == NULL) return NULL; if (childIndex < 0 || childIndex >= children->Length()) return NULL; found = 0; *newRowIndex = 0; caseSensitivity = theCifFiles->GetItemCaseSensitivity(dataBlockIndex, (*children)[childIndex].GetCategoryIndex(), (*children)[childIndex].GetItemIndex()); if (!caseSensitivity) { tmpMapItemValue.Copy(mapItemValue); tmpMapItemValue.ToLower(); } do { ret = theCifFiles->GetItemValue(&newCifItemValue, dataBlockIndex, (*children)[childIndex].GetCategoryIndex(), (*children)[childIndex].GetItemIndex(), *newRowIndex); if (caseSensitivity && !Compare(newCifItemValue->_buf.Text(), mapItemValue) || !caseSensitivity && !CompareNoCase(newCifItemValue->_buf, tmpMapItemValue)) { found ++; if (found == childRowOrder) { *newCategoryIndex = (*children)[childIndex].GetCategoryIndex(); *newItemIndex = (*children)[childIndex].GetItemIndex(); rets = cifGetRowByIndex(newItemValues, dataBlockIndex, *newCategoryIndex, *newRowIndex, numItemValue); break; } } (*newRowIndex) ++; } while ( ret < CIF_OUT_OF_RANGE_ERROR_CODE_START) ; if (ret > CIF_OUT_OF_RANGE_ERROR_CODE_START || found != childRowOrder) { (*newRowIndex) = -1; if (found != 0 && found != childRowOrder) { *newCategoryIndex = (*children)[childIndex].GetCategoryIndex(); *newItemIndex = (*children)[childIndex].GetItemIndex(); rets = cifGetRowByIndex(newItemValues, dataBlockIndex, *newCategoryIndex, 0, numItemValue); for (unsigned i=0; i< *numItemValue; i++) { rets[i] = CIF_VALUE_NOT_EXIST; if ((*newItemValues)[i] != NULL) free ((*newItemValues)[i]); (*newItemValues)[i] = NULL; } } } return rets; } int cifAddDataBlockByIndex(const char *newDatablockName, const int dicdataBlockIndex) /* ------------------------------------------------------------------------- cifAddDataBlockByIndex(): Add a new datablock ------------------------------------------------------------------------- */ { CifDataBlock *datablock; datablock = theCifFiles->AddDatablock(dicdataBlockIndex, newDatablockName); if (datablock == NULL) return -1; else return cifCountDataBlocks()-1; } int cifAddCategoryByIndex(const char *newCategoryName, const int dataBlockIndex) /* ------------------------------------------------------------------------- cifAddCategoryByIndex(): Add a new Category ------------------------------------------------------------------------- */ { CifCategory *category_table; category_table = theCifFiles->AddCategory(dataBlockIndex, newCategoryName); if (category_table == NULL) return -1; else return cifCountCategoriesByIndex(dataBlockIndex)-1; } int cifAddDataItemByIndex(const char *newItemKeyword, const int dataBlockIndex, const int categoryIndex) /* ------------------------------------------------------------------------- cifAddDataItemByIndex(): Add a new itemColumn ------------------------------------------------------------------------- */ { CifDataItem *dataItem; dataItem = theCifFiles->AddDataItem(dataBlockIndex, categoryIndex, newItemKeyword); if (dataItem == NULL) return -1; else return cifCountColumnsByIndex(dataBlockIndex, categoryIndex)-1; } int cifAddRowByIndex(const int dataBlockIndex, const int categoryIndex) /* ------------------------------------------------------------------------- cifAddDataItemByIndex(): Add a new itemColumn ------------------------------------------------------------------------- */ { return theCifFiles->AddRow(dataBlockIndex, categoryIndex); }