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Cytosim
PI
Cytoskeleton Simulator
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Public Member Functions | |
| Interface (Simul &s) | |
| associates with given Simul | |
| virtual | ~Interface () |
| destructor | |
| virtual void | hold () |
| this is called between commands during the execution process More... | |
| virtual void | parse (std::istream &, std::string const &msg)=0 |
| Parse a text containing cytosim commands. More... | |
| Property * | execute_set (std::string const &k, std::string const &n, Glossary &) |
| create a new Property of kind k from options set in Glossary More... | |
| void | execute_change (Property *, Glossary &) |
| change values in Property according to Glossary | |
| Property * | execute_change (std::string const &k, std::string const &n, Glossary &) |
| change values in Property of kind k following options set in Glossary | |
| void | change_display (std::string const &k, std::string const &n, Glossary &) |
| change 'display' (and only this) in corresponding Property More... | |
| ObjectList | execute_new (std::string const &k, std::string const &n, Glossary &) |
| create 1 Object of kind k with name n, following options in Glossary More... | |
| int | execute_new (std::string const &k, std::string const &n, unsigned cnt) |
| create 'cnt' objects of kind k with name n, randomly placed in space (no option) | |
| void | execute_delete (std::string const &k, std::string const &n, Glossary &, int cnt) |
delete cnt objects of kind k with name n, following options in Glossary More... | |
| void | execute_mark (std::string const &k, std::string const &n, Glossary &, int cnt) |
mark cnt objects of kind k with name n, following options in Glossary More... | |
| void | execute_cut (std::string const &k, std::string const &n, Glossary &) |
| cut fibers, following different options in Glossary | |
| void | execute_read (std::string const &file, unsigned index) |
| import objects from another file More... | |
| void | execute_write (std::string &file, std::string const &what, Glossary &) |
| write output file with object coordinates or information on objects More... | |
| void | execute_run (Glossary &opt, unsigned cnt, bool do_write) |
| perform simulation steps | |
Protected Attributes | |
| Simul & | simul |
| associated Simul | |
| void change_display | ( | std::string const & | kind, |
| std::string const & | name, | ||
| Glossary & | def | ||
| ) |
This may change the 'display' field in the Properties corresponding to kind and name. The display value should be specified in def.
| void execute_delete | ( | std::string const & | kind, |
| std::string const & | name, | ||
| Glossary & | opt, | ||
| int | cnt | ||
| ) |
If cnt is specified, this will delete at most 'cnt' objects, chosen randomly
| void execute_mark | ( | std::string const & | kind, |
| std::string const & | name, | ||
| Glossary & | opt, | ||
| int | cnt | ||
| ) |
If cnt is specified, this will mark at most 'cnt' objects, chosen randomly
| ObjectList execute_new | ( | std::string const & | kind, |
| std::string const & | name, | ||
| Glossary & | opt | ||
| ) |
Creates one object of class 'kind' and type 'name'.
| void execute_read | ( | std::string const & | file, |
| unsigned | frame | ||
| ) |
Imports a simulation snapshot from a trajectory file
By default, the first frame in the file is read, but an argument 'frame=INTEGER' can be given in 'opt'.
Property::complete() is called after a property is set. This ensures that inconsistencies are detected as early as possible.
The drawback is that we cannot support cross-dependencies (A needs B and vice-versa). If that is necessary, we could:
| void execute_write | ( | std::string & | file, |
| std::string const & | what, | ||
| Glossary & | opt | ||
| ) |
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inlinevirtual |
The overwritten version should call simul.relax() to make sure that the simulation data structures are coherent. It can perform additional things, for example display the simulation world