This class handles reading and storage for the NEXUS block TREES. More...
#include <nxstreesblock.h>
Public Member Functions | |
| NxsTreesBlock (NxsTaxaBlockAPI *tb) | |
| virtual | ~NxsTreesBlock () |
| void | ReplaceTaxaBlockPtr (NxsTaxaBlockAPI *tb) |
| unsigned | GetNumDefaultTree () |
| unsigned | GetNumTrees () |
| unsigned | GetNumTrees () const |
| const NxsFullTreeDescription & | GetFullTreeDescription (unsigned i) const |
| unsigned | TreeLabelToNumber (const std::string &name) const |
| NxsString | GetTreeName (unsigned i) |
| NxsString | GetTreeDescription (unsigned i) |
| NxsString | GetTranslatedTreeDescription (unsigned i) |
| bool | IsDefaultTree (unsigned i) |
| bool | IsRootedTree (unsigned i) |
| virtual void | Report (std::ostream &out) NCL_COULD_BE_CONST |
| virtual void | BriefReport (NxsString &s) NCL_COULD_BE_CONST |
| virtual void | Reset () |
| void | SetNexus (NxsReader *nxsptr) |
| virtual const std::string & | GetBlockName () const |
| void | WriteAsNexus (std::ostream &out) const |
| virtual VecBlockPtr | GetImpliedBlocks () |
| virtual void | HandleLinkCommand (NxsToken &token) |
| virtual void | WriteLinkCommand (std::ostream &out) const |
| unsigned | GetIndicesForLabel (const std::string &label, NxsUnsignedSet *inds) const |
| bool | AddNewPartition (const std::string &label, const NxsPartition &inds) |
| bool | GetProcessAllTreesDuringParse () const |
| void | SetProcessAllTreesDuringParse (bool s) |
| void | setValidationCallbacks (ProcessedTreeValidationFunction func, void *blob) |
Protected Member Functions | |
| virtual void | Read (NxsToken &token) |
Protected Attributes | |
| bool | processAllTreesDuringParse |
| bool | constructingTaxaBlock |
| bool | writeFromNodeEdgeDataStructure |
| std::vector < NxsFullTreeDescription > | trees |
This class handles reading and storage for the NEXUS block TREES.
The class can read the TRANSLATE and TREE commands.
The tree is validated during the parse and then stored as a NxsFullTreeDescription object which will hold the newick string. This newick string will have numbers rather than names. The numbers in the tree string start at 1 (like other NEXUS numbering), but they are simply 1 + the taxon index.
In previous versions of NCL (before v2.1), the client code would have to use the translate table to convert the newick string into the taxon numbers.
As of v2.1, NCL now does this translation.
Definition at line 553 of file nxstreesblock.h.
1.6.3
