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// Copyright (C) 1999-2003 Paul O. Lewis
//
// This file is part of NCL (Nexus Class Library) version 2.0.
//
// NCL is free software; you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
// the Free Software Foundation; either version 2 of the License, or
// (at your option) any later version.
//
// NCL is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
// GNU General Public License for more details.
//
// You should have received a copy of the GNU General Public License
// along with NCL; if not, write to the Free Software Foundation, Inc.,
// 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
//
#ifndef NCL_NXSTREESBLOCK_H
#define NCL_NXSTREESBLOCK_H
/*----------------------------------------------------------------------------------------------------------------------
| This class handles reading and storage for the NEXUS block TREES. It overrides the member functions Read and Reset,
| which are abstract virtual functions in the base class NxsBlock. The translation table (if one is supplied) is
| stored in the `translateList'. The tree names are stored in `treeName' and the tree descriptions in
| `treeDescription'. Information about rooting of trees is stored in `rooted'. Note that no checking is done to
| ensure that the tree descriptions are valid. The validity of the tree descriptions could be checked after the TREES
| block has been read (but before the next block in the file has been read) by overriding the NxsReader::ExitingBlock
| member function, but no functionality for this is provided by the NCL. Below is a table showing the correspondence
| between the elements of a TREES block and the variables and member functions that can be used to access each piece
| of information stored.
|>
| NEXUS command Data members Member functions
| -----------------------------------------------------
| TRANSLATE translateList
|
| TREE treeName GetTreeName
| GetTreeDescription
| GetNumTrees
| GetNumDefaultTree
| IsDefaultTree
|
| rooted IsRootedTree
| -----------------------------------------------------
|>
*/
class NxsTreesBlock
: public NxsBlock
{
public:
NxsTreesBlock(NxsTaxaBlock *tb);
virtual ~NxsTreesBlock();
void ReplaceTaxaBlockPtr(NxsTaxaBlock *tb);
unsigned GetNumDefaultTree();
unsigned GetNumTrees();
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);
virtual void BriefReport(NxsString &s);
virtual void Reset();
protected :
NxsStringMap translateList; /* storage for translation table (if any) */
NxsStringVector treeName; /* storage for tree names */
NxsStringVector treeDescription; /* storage for tree descriptions */
NxsBoolVector rooted; /* stores information about rooting for each tree */
NxsTaxaBlock *taxa; /* pointer to existing NxsTaxaBlock object */
unsigned ntrees; /* number of trees stored */
unsigned defaultTree; /* 0-offset index of default tree specified by user, or 0 if user failed to specify a default tree using an asterisk in the NEXUS data file */
virtual void Read(NxsToken &token);
void HandleTreeDescription(NxsToken &token, bool utree);
};
typedef NxsTreesBlock TreesBlock;
#endif
|
