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Class NxsAssumptionsBlock

Data Members

charBlockPtr, charsets, def_charset, def_exset, def_taxset, exsets, taxa, taxsets

Member Functions

ApplyExSet, GetCharSet, GetCharSetNames, GetDefCharSetName, GetDefExSetName, GetDefTaxSetName, GetExSet, GetExSetNames, GetNumCharSets, GetNumExSets, GetNumTaxSets, GetTaxSet, GetTaxSetNames, HandleCharset, HandleEndblock, HandleExset, HandleTaxset, NxsAssumptionsBlock, ~NxsAssumptionsBlock, Read, ReplaceTaxaBlockPtr, Report, Reset, SetCallback, TaxonLabelToNumber

Class Description

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:

Key to symbols and colors

public, protected, private, A = abstract, C = constructor, D = destructor, I = inline, S = static, V = virtual, F = friend

 

Data Members
     NxsCharactersBlock   *charBlockPtr
       
pointer to the NxsCharactersBlock-derived object to be notified in the event of exset changes
     NxsUnsignedSetMap   charsets
       
the variable storing charsets
     NxsString   def_charset
       
the default charset
     NxsString   def_exset
       
the default exset
     NxsString   def_taxset
       
the default taxset
     NxsUnsignedSetMap   exsets
       
the variable storing exsets
     NxsTaxaBlock   *taxa
       
pointer to the NxsTaxaBlock object
     NxsUnsignedSetMap   taxsets
       
the variable storing taxsets

 

Member Functions
    void   ApplyExSet(NxsString nm)
       
Applies exclusion set having name 'nm' by calling the ApplyExset method of the NxsCharactersBlock or NxsCharactersBlock-derived object stored in the charBlockPtr pointer (which will be whichever block last called the NxsAssumptionsBlock::SetCallback method).
    NxsUnsignedSet   &GetCharSet(NxsString nm)
       
Returns reference to character set having name 'nm'.
    void   GetCharSetNames(NxsStringVector &names)
       
Erases 'names' vector, then fills 'names' with the names of all stored character sets.
    NxsString   GetDefCharSetName()
       
Returns name of default character set. If returned string has zero length, then no default character set was defined in the data set.
    NxsString   GetDefExSetName()
       
Returns name of default exclusion set. If returned string has zero length, then no default exclusion set was defined in the data set.
    NxsString   GetDefTaxSetName()
       
Returns name of default taxon set. If returned string has zero length, then no default taxon set was defined in the data set.
    NxsUnsignedSet   &GetExSet(NxsString nm)
       
Returns reference to exclusion set having name 'nm'.
    void   GetExSetNames(NxsStringVector &names)
       
Erases names, then fills names with the names of all stored exclusion sets.
    int   GetNumCharSets()
       
Returns the number of character sets stored.
    int   GetNumExSets()
       
Returns the number of exclusion sets stored.
    int   GetNumTaxSets()
       
Returns the number of taxon sets stored.
    NxsUnsignedSet   &GetTaxSet(NxsString nm)
       
Returns reference to taxon set having name 'nm'.
    void   GetTaxSetNames(NxsStringVector &names)
       
Erases 'names' vector, then fills 'names' with the names of all stored taxon sets.
    void   HandleCharset(NxsToken &token)
       
Reads and stores information contained in the command CHARSET within an ASSUMPTIONS block.
    void   HandleEndblock(NxsToken &token)
       
Called when the END or ENDBLOCK command needs to be parsed from within the ASSUMPTIONS block. Basically just checks to make sure the next token in the data file is a semicolon.
    void   HandleExset(NxsToken &token)
       
Reads and stores information contained in the command EXSET within an ASSUMPTIONS block. If EXSET keyword is followed by an asterisk, last read NxsCharactersBlock or NxsCharactersBlock-derived object is notified of the characters to be excluded (its ApplyExset function is called).
    void   HandleTaxset(NxsToken &token)
       
Reads and stores information contained in the command TAXSET within an ASSUMPTIONS block.
C     NxsAssumptionsBlock(NxsTaxaBlock *t)
       
Sets id = "ASSUMPTIONS", charBlockPtr = NULL, and taxa = t. Assumes taxa is non-NULL.
D     ~NxsAssumptionsBlock()
       
Nothing needs to be done in the destructor.
V   void   Read(NxsToken &token)
       
This function provides the ability to read everything following the block name (which is read by the NxsReader object) to the end or ENDBLOCK statement. Characters are read from the input stream in. Overrides the pure virtual function in the base class.
    void   ReplaceTaxaBlockPtr(NxsTaxaBlock *tb)
       
Makes data member taxa point to 'tb'. Assumes tb is non-NULL.
V   void   Report(ostream &out)
       
This function outputs a brief report of the contents of this ASSUMPTIONS block. Overrides the pure virtual function in the base class.
V   void   Reset()
       
Prepares for reading a new ASSUMPTIONS block. Overrides the pure virtual function in the base class.
    void   SetCallback(NxsCharactersBlock *p)
       
A CHARACTERS, DATA, or ALLELES block can call this function to specify that it is to receive notification when the current taxon or character set changes (e.g., an "EXSET *" command is read or a program requests that one of the predefined taxon sets, character sets, or exsets be applied). Normally, a NxsCharactersBlock-derived object calls this function upon entering its MATRIX command, since when that happens it becomes the primary data-containing block.
V   unsigned   TaxonLabelToNumber(NxsString s)
       
Converts a taxon label to a number corresponding to the taxon's position within the list maintained by the NxsTaxaBlock object. This method overrides the virtual function of the same name in the NxsBlock base class. If s is not a valid taxon label, returns the value 0.