Property Object Model (v2.0)


Class DB

Provides intarface to the database which is essentially directory or set of directories with database files. This class must be created before doing anything else.

DB(char *path=NULL) - constructor for the database class, path - specifies directory with database files, default is NULL and implies current directory.

void setPath(char *path) - setting path for the database directory.

void addPath(char *path) - adding path for the database directory.

Class Property

Provides representation of property as an object consisting of items (constructed according to one of suggested designs) organized according to integer index representing items sequential number within Property object. Incremental updating of the database is allowed by adding new data objects to Property object at the end with index assigned as next sequential number corresponding to this data item in the Property object. Updating of items is possible if either size is not changes or object is loaded in the memory.

Property() - constructor.

Property(char *name) - constructor, opens property file name.

Property(char *name, int load_in_memory) - constructor, opens property file name with load_in_memory mode overriding default mode. load_in_memory=1 - load, load_in_memory=0 - don't load.

Property(char *name, DB *db) - constructor, opens property file name in database db.

Property(char *name, int load_in_memory, DB *db) - constructor, opens property file name with load_in_memory mode overriding default mode. load_in_memory=1 - load, load_in_memory=0 - don't load in database db.

void create (char *name, DataType type, int4 size, int load_in_memory=1) - creates property with name name of type type and size of array representing object size, and load_in_memory mode 1(default) for loading in memory and 0 for not loading.

type can be one of the following:

size can be either fixed (specified as integer number) or variable (specified as 0).

void create (char *name, DataType type, int4 size, int load_in_memory=1, DB *db) - creates property with name name of type type and size of array representing object size, and load_in_memory mode 1(default) for loading in memory and 0 for not loading, in database db.

void clear() - deletes all objects in the Property object.

void open(char *name) - opens property file name.

void open(char *name, int load_in_memory) - opens property file name with load_in_memory mode overriding default mode. load_in_memory=1 - load, load_in_memory=0 - don't load.

void open(char *name, int load_in_memory, DB *db) - opens property file name with load_in_memory mode overriding default mode. load_in_memory=1 - load, load_in_memory=0 - don't load, in database db.

void close() - closes property, there is no need to use this method, because property is closed when goes out of scope or another property is opened with the same Property object.

void addItem(int1 item) - adds item of type int1 represented by a single value item. This method can be used only if size equals 1.

void addItem(int2 item) - adds item of type int2 represented by a single value item. This method can be used only if size equals 1.

void addItem(int4 item) - adds item of type int4 represented by a single value item. This method can be used only if size equals 1.

void addItem(flt4 item) - adds item of type flt4 represented by a single value item. This method can be used only if size equals 1.

void addItem(flt8 item) - adds item of type flt8 represented by a single value item. This method can be used only if size equals 1.

void addItem(int1 *item) - adds item represented by character string (terminated by '\0') as a type int1 provided as item item.

void addItem(int2 *item) - adds item of type int2* represented by array item. This method can be used only if size is fixed.

void addItem(int4 *item) - adds item of type int4* represented by array item. This method can be used only if size is fixed.

void addItem(flt4 *item) - adds items of type flt4* represented by array item. This method can be used only if size is fixed.

void addItem(int1 *item, int4 nValues) - adds item consisting of nValues data values of type int1 represented by array item.

void addItem(int2 *item, int4 nValues) - adds item consisting of nValues data values of type int2 represented by array item.

void addItem(int4 *item, int4 nValues) - adds item consisting of nValues data values of type int4 represented by array item.

void addItem(flt4 *item, int4 nValues) - adds item consisting of nValues data values of type flt4 represented by array item.

void addItem(flt8 *item, int4 nValues) - adds item consisting of nValues data values of type flt8 represented by array item.

void addItem() - adds item consisting of 0 data values of any type.

void setItem(int4 index, int1 item) - sets item index of type int1 to item.

void setItem(int4 index, int2 item) - sets item index of type int2 to item.

void setItem(int4 index, int4 item) - sets item index of type int4 to item.

void setItem(int4 index, flt4 item) - sets item index of type flt4 to item.

void setItem(int4 index, flt8 item) - sets item index of type flt8 to item.

void setItem(int4 index, int1* item) - sets item index of type int1 to item.

void setItem(int4 index, int2* item) - sets item index of type int2 to item.

void setItem(int4 index, int4* item) - sets item index of type int4 to item.

void setItem(int4 index, flt4* item) - sets item index of type flt4 to item.

void setItem(int4 index, flt8* item) - sets item index of type flt8 to item.

void setItem(int4 index, int1* item, int4 nValues) - sets item index of type int1 to item of size nValues.

void setItem(int4 index, int2* item, int4 nValues) - sets item index of type int2 to item of size nValues.

void setItem(int4 index, int4* item, int4 nValues) - sets item index of type int4 to item of size nValues.

void setItem(int4 index, flt4* item, int4 nValues) - sets item index of type flt4 to item of size nValues.

void setItem(int4 index, flt8* item, int4 nValues) - sets item index of type flt8 to item of size nValues.

void extendItem(int4 index, int1 *item) - extends item index of type int1 with item represented by character string (terminated by '\0').

void extendItem(int4 index, int1 *item, int4 nValues) - extends item index of type int1 with item of size nValues.

void extendItem(int4 index, int4 item) - extends item index of type int4 with item.

void extendItem(int4 index, int4 item, int4 nValues) - extends item index of type int4 with item of size nValues.

DataType getType() - returns type attribute of Property object.

int4 getSize() - returns size attribute of Property object.

int4 getItemSize(int4 index) - returns size of a particular item with index index.

int4 getObjectSize() - returns number of items in a given Property object.

int4 getPropertySize() - returns number of values in a given Property object.

int1* item1(int4 index, int copy_array=0) - returns item indexof type int1. See note 2 for details on optional parameter copy_array.

int2* item2(int4 index, int copy_array=0) - returns item indexof type int2. See note 2 for details on optional parameter copy_array.

int4* item4(int4 index, int copy_array=0) - returns item indexof type int4. See note 2 for details on optional parameter copy_array.

flt4* itemf(flt4 index, int copy_array=0) - returns item indexof type flt4. See note 2 for details on optional parameter copy_array.

flt8* itemd(flt8 index, int copy_array=0) - returns item indexof type flt8. See note 2 for details on optional parameter copy_array.

int1* item1n(int4 index, int4& nValues, int copy_array=0) - returns item indexof type int1 and its size as nValues. See note 2 for details on optional parameter copy_array.

int2* item2n(int4 index, int4& nValues, int copy_array=0) - returns item indexof type int2 and its size as nValues. See note 2 for details on optional parameter copy_array.

int4* item4n(int4 index, int4& nValues, int copy_array=0) - returns item indexof type int4 and its size as nValues. See note 2 for details on optional parameter copy_array.

flt4* itemfn(flt4 index, int4& nValues, int copy_array=0) - returns item indexof type flt4 and its size as nValues. See note 2 for details on optional parameter copy_array.

flt8* itemdn(flt8 index, int4& nValues, int copy_array=0) - returns item indexof type flt8 and its size as nValues. See note 2 for details on optional parameter copy_array.

int4 find(int1 *text) - searches for string text in Property object without mismatches. Returns index of the object or (-1) if not successful.

int4 find(int1 *textint mismatches) - searches for string text in Property object with mismatchesmismatches. Returns index of the object or (-1) if not successful.

int4 find(int1 *text, int mismatches, int4& pos, int& next=0) - searches for string text in Property object with mismatches mismatches. Returns index of the object and position in the string pos or (-1) if not successful. next specifies whether to search from the beginning (next=0, default) or continue search from the previously found match (next=1).

int4 find(int1 t1, int1 t2, int& next=0) - searches for value of int1 type in Property object within range from t1 to t2. Returns index of the object or (-1) if not successful. next specifies whether to search from the beginning (next=0, default) or continue search from the previously found match (next=1).

int4 find(int2 t1, int2 t2, int& next=0) - searches for value of int2 type in Property object within range from t1 to t2. Returns index of the object or (-1) if not successful. next specifies whether to search from the beginning (next=0, default) or continue search from the previously found match (next=1).

int4 find(int4 t1, int4 t2, int& next=0) - searches for value of int4 type in Property object within range from t1 to t2. Returns index of the object or (-1) if not successful. next specifies whether to search from the beginning (next=0, default) or continue search from the previously found match (next=1).

int4 find(flt4 t1, flt4 t2, int& next=0) - searches for value of flt4 type in Property object within range from t1 to t2. Returns index of the object or (-1) if not successful. next specifies whether to search from the beginning (next=0, default) or continue search from the previously found match (next=1).

Class Collection

Provides representation of properties as a set of numbers (indexes) organized according to another Set Index of fixed size. Incremental updating of the database is allowed by adding new numbers (indexes) to Collection object extending one of sets with corresponding Set Index.

Collection() - constructor.

Collection(char *name) - constructor, opens collection file name.

void create (char *name, DataType type, int4 nClasses) - creates collection with name name of type type and size of Set Index of nClasses. type can be one of the following:

void clear() - deletes all sets in the collection.

void open(char *name) - opens collection file name.

void open(char *name, int load_in_memory) - opens collection file name with load_in_memory mode as: load_in_memory=1 - load (default), load_in_memory=0 - don't load.

void close() - close collection, there is no need to use this method, because collection is closed when goes out of scope or another collection is opened with the same Collection object.

void add(int4 index, int2 item) - adds number (index) of type int2 represented by item to the set with index index.

void add(int4 index, int4 item) - adds number (index) of type int4 represented by item to the set with index index.

void add(int4 index, int2 *items, int4 nValues) - adds nValues numbers (indexes) of type int2 represented by items to the set with index index.

void add(int4 index, int4 *items, int4 nValues) - adds nValues numbers (indexes) of type int4 represented by items to the set with index index.

DataType getType() - returns type attribute of Collection object.

int4 getCollectionSize() - returns number of sets in a given Collection object.

int4 getClassSize(int4 index) - returns size of a set with index index in a given Collection object.

int4* getClassSize() - returns sizes of all sets in a given Collection item.

int2 itemValue2(int4 index, int4 itemIndex) - returns value of type int2 from the set index and index in the set itemIndex in a given Collection object.

int4 itemValue4(int4 index, int4 itemIndex) - returns value of type int4 from the set index and index in the set itemIndex in a given Collection object.

int2* item2(int4 index) - returns values of type int2 from the set index in a given Collection object.

int4* item4(int4 index) - returns values of type int4 from the set index in a given Collection object.

int2* item2n(int4 index, int4& nValues) - returns values of type int2 and number of values nValues from the set index in a given Collection object.

int4* item4n(int4 index, int4& nValues) - returns values of type int4 and number of values nValues from the set index in a given Collection object.

Notes

  1. Alternative data types have been introduced for multiplatform compatibility:
    • int1 - 1-byte integer;
    • int2 - 2-byte integer;
    • int4 - 4-byte integer;
    • flt4 - 4-byte floating point number;
    • flt8 - 8-byte floating point number;

  2. Parameter copy_array for methods item1, item1n etc. specifies whether returned array is created as new array (copy_array=1) or not (copy_array=0, default). In the default mode user gets pointer to the data represented internally in the Property object. This pointer may become invalid when Property object releases memory related to a specified object, which only occurs in two cases: (i) Property object is destroyed; (ii) Property object with load_in_memory flag set to 0 has been requested for another item object.
    In the mode (copy_array=1) user gets a copy of item object which will never be destroyed by Property object. In this case user assumes responsibility for releasing memory associated with this pointer when necessary.

  3. Other classes of the library which are not described here: XYZ, AminoacidProperty, Monomers, Entities, IEntity, Isubentity, IAtom, IMonomer, IBond.

Examples

1. Reading item.

// Reading sequence with index iEntity from the Property object "seq.enp" DB db("seqdb"); Property sequence("seq.enp"); char *seq=sequence.item1(iEntity);

2. Creating new Property object and adding item.

// Adding sequence to the Property object "seq.enp" DB db("seqdb"); Property sequence; sequence.create("seq.enp", D_INT1, 0, LOAD_IN_MEMORY_ON); sequence.add(seq);

3. Using composite containers and iterators.

// Printing atom CA-coordinates for compound with index iCom DB db("/user/user1/db"); Entities entities; entities.addCom("4HHB"); for(IEntity ientity(&entities); ientity; ++ientity) for(ISubentity isubentity(ientity); isubentity; ++isubentity) for(IAtom iatom(isubentity); iatom; ++iatom) if(!strcmp(iatom.name(), " CA ")) printf("%8.3f %8.3f %8.3f\n", iatom.x(), iatom.y(), iatom.z());