This class handles reading and storage for the NxsReader block ASSUMPTIONS. More...
#include <nxsassumptionsblock.h>
Public Member Functions | |
| NxsAssumptionsBlock (NxsTaxaBlockAPI *t) | |
| virtual | ~NxsAssumptionsBlock () |
| void | ReplaceTaxaBlockPtr (NxsTaxaBlockAPI *tb) |
| void | SetCallback (NxsCharactersBlockAPI *p) |
| int | GetNumCharSets () const |
| void | GetCharSetNames (NxsStringVector &names) const |
| const NxsUnsignedSet * | GetCharSet (NxsString nm) const |
| int | GetNumCharPartitions () |
| void | GetCharPartitionNames (vector< std::string > &names) |
| const NxsPartition * | GetCharPartition (std::string nm) const |
| int | GetNumTaxSets () |
| void | GetTaxSetNames (NxsStringVector &names) |
| NxsUnsignedSet & | GetTaxSet (NxsString nm) |
| int | GetNumExSets () |
| void | GetExSetNames (NxsStringVector &names) |
| NxsUnsignedSet & | GetExSet (NxsString nm) |
| NxsString | GetDefExSetName () |
| void | ApplyExset (NxsString nm) |
| virtual void | Read (NxsToken &token) |
| virtual void | Report (std::ostream &out) NCL_COULD_BE_CONST |
| virtual void | Reset () |
| virtual void | WriteAsNexus (std::ostream &out) const |
| virtual void | HandleLinkCommand (NxsToken &) |
| virtual void | WriteLinkCommand (std::ostream &out) const |
| virtual VecBlockPtr | GetImpliedBlocks () |
Protected Member Functions | |
| virtual void | ReadCharsetDef (NxsString charset_name, NxsToken &token, bool asterisked) |
| virtual void | ReadExsetDef (NxsString charset_name, NxsToken &token, bool asterisked) |
| virtual void | ReadTreesetDef (NxsString set_name, NxsToken &token, bool asterisked) |
| virtual void | ReadTaxsetDef (NxsString set_name, NxsToken &token, bool asterisked) |
| virtual unsigned | TaxonLabelToNumber (NxsString s) const |
| void | HandleCharPartition (NxsToken &token) |
| void | HandleCharSet (NxsToken &token) |
| void | HandleCodeSet (NxsToken &token) |
| void | HandleCodonPosSet (NxsToken &token) |
| void | HandleExSet (NxsToken &token) |
| void | HandleTaxPartition (NxsToken &token) |
| void | HandleTaxSet (NxsToken &token) |
| void | HandleTreePartition (NxsToken &token) |
| void | HandleTreeSet (NxsToken &token) |
| void | HandleTypeSet (NxsToken &token) |
| void | HandleWeightSet (NxsToken &token) |
This class handles reading and storage for the NxsReader block ASSUMPTIONS.
It overrides the member functions Read and Reset, which are abstract virtual functions in the base class NxsBlock. Adding a new data member? Don't forget to: ~ o Describe it in the class declaration using a C-style comment. o Initialize it (unless it is self-initializing) in the constructor and re-initialize it in the Reset function. o Describe the initial state in the constructor documentation. o Delete memory allocated to it in both the destructor and Reset function. o Report it in some way in the Report function. ~
Definition at line 88 of file nxsassumptionsblock.h.
1.6.3
