|
Cytosim
PI
Cytoskeleton Simulator
|
This is the interface used for writing / reading from a file.
Three functions identify an Object:
These three qualities are concatenated in reference() and writeReference().
Objects are stored in ObjectSet.
Public Member Functions | |
| Object () | |
| constructor | |
| virtual Tag | tag () const =0 |
| an ASCII character identifying the ObjectSet corresponding to this object | |
| virtual const Property * | property () const =0 |
| Property associated with the Object. | |
| virtual void | write (OutputWrapper &) const =0 |
| write Object data to file | |
| virtual void | read (InputWrapper &, Simul &)=0 |
| read Object from file, within the Simul | |
| std::string | reference () const |
| concatenation of [ tag(), property()->index(), number() ] in plain ascii More... | |
| void | writeReference (OutputWrapper &) const |
| write a reference that identifies the Object uniquely More... | |
| void | writeReference (OutputWrapper &, Tag tag) const |
| write a reference, but using the provided Tag More... | |
| int | mark () const |
| birth mark value | |
| void | mark (int m) |
| set birth mark | |
| int | fleck () const |
| fleck value (not stored in trajectory files) | |
| void | fleck (int f) const |
| set fleck (the value is not stored in trajectory files) | |
| Object * | next () const |
| extends Node::next(), with a cast to preserve type | |
| Object * | prev () const |
| extends Node::prev(), with a cast to preserve type | |
Public Member Functions inherited from Node | |
| Node () | |
| constructor set as unlinked | |
| virtual | ~Node () |
| destructor More... | |
| bool | linked () const |
| true if Node is linked | |
| Node * | next () const |
| the next Node in the list, or zero if this is last | |
| Node * | prev () const |
| the previous Node in the list, or zero if this is first | |
| NodeList * | list () const |
| the list where the object is linked, or zero | |
| ObjectSet * | objset () const |
| return associated ObjectSet | |
Public Member Functions inherited from Inventoried | |
| Inventoried () | |
| initialize (name=0) | |
| ~Inventoried () | |
| destructor | |
| void | number (Number n) |
| change the serial number | |
| Number | number () const |
| serial number : a integer identifier, unique within each class | |
Public Member Functions inherited from Movable | |
| Movable () | |
| constructor | |
| virtual | ~Movable () |
| destructor | |
| virtual Vector | position () const |
| return the position in space of the object | |
| virtual void | setPosition (Vector const &) |
| move object to specified position More... | |
| virtual bool | translatable () const |
| true if object accepts translations (default=false) | |
| virtual void | translate (Vector const &) |
| move the object ( position += given vector ) More... | |
| virtual bool | rotatable () const |
| true if object accepts rotations (default=false) | |
| virtual void | rotate (Rotation const &) |
| rotate the object around the origin of coordinates More... | |
| virtual void | rotateP (Rotation const &) |
| rotate the object around its current position More... | |
| virtual void | foldPosition (Modulo const *) |
| perform modulo for periodic boundary conditions More... | |
Static Public Member Functions | |
| static std::string | strReference (char, int, Number, int) |
| build a string reference by concatenating (tag, property_index, number, mark) More... | |
| static void | readReference (InputWrapper &, int &, Number &, int &, char pretag) |
| read a reference (property_index, number, mark) from input More... | |
| static void | writeNullReference (OutputWrapper &) |
| write a reference that does not refer to any Object | |
Static Public Member Functions inherited from Movable | |
| static Vector | readPrimitive (std::istream &, const Space *) |
| read a position specified with primitives, such as 'circle 5', etc. More... | |
| static Vector | readPosition (std::istream &, const Space *) |
| read a position in space More... | |
| static Vector | readDirection (std::istream &, const Vector &, const Space *) |
| read an orientation, and return a normalized vector More... | |
| static Rotation | readRotation (std::istream &, const Vector &, const Space *) |
| read a rotation specified in is, at position pos More... | |
Static Public Attributes | |
| static const Tag | TAG = 'v' |
| Object::TAG = 'v' represents the 'void' pointer. | |
Friends | |
| class | ObjectSet |
Additional Inherited Members | |
Protected Attributes inherited from Node | |
| Node * | nNext |
| the next Node in the list | |
| Node * | nPrev |
| the previous Node in the list | |
Protected Attributes inherited from Inventoried | |
| Number | nNumber |
| object identifier, unique within the class defined by tag() | |
|
static |
This must be able to read the formats written by Object::writeReference()
| std::string reference | ( | ) | const |
The ASCII reference has the format XP:N or XP:N:M, where:
For example 'f0:21' is the fiber of property 0, number 21
|
static |
The ASCII reference has the format XP:N or XP:N:M, where:
For example 'f0:21' is the fiber of property 0, number 21
| void writeReference | ( | OutputWrapper & | out | ) | const |
Two binary formats are used:
There is only one ascii based format, as returned by reference(). All formats are read by ObjectSet::readReference()
| void writeReference | ( | OutputWrapper & | out, |
| Tag | g | ||
| ) | const |
Same as writeReference(OutputWrapper&), excepts that tag() is replaced by 'g' given as argument.