libncl-dev 2.1.18+dfsg-2 / usr / include / ncl / nxstaxablock.h

//	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_NXSTAXABLOCK_H
#define NCL_NXSTAXABLOCK_H

#include "ncl/nxsdefs.h"
#include "ncl/nxsblock.h"

/*! This abstract class describes the interface that every block that wants to serve
	as a reader of NEXUS TAXA blocks should fulfill.

	A parsed taxa block in NEXUS is essentially a list of unique taxon labels.

	When compared the label comparison is not case-sensitive.

	The taxon can be referred to in NEXUS files by its number (numbering starting at 1), or its label.
*/
class NxsTaxaBlockAPI
  : public NxsBlock, public NxsLabelToIndicesMapper
  {
  public:
		/*! Adds taxon label 's' to end of list of taxon labels and increments dimNTax by 1.

			\returns the (0-based) index of taxon label just added.
		*/
		virtual unsigned			AddTaxonLabel(const std::string & s) = 0;
		/*! Changes the label for taxon `i` to `s`
			The index `i` should be 0-based.
			\throws NxsNCLAPIException if `i` is out of range.
			\throws DuplicatedLabelNxsException if the label is already in the block
			\throws NxsException if the label is not a legal taxon name (eg. it is a punctation character).
		*/
		virtual void  				ChangeTaxonLabel(unsigned i, NxsString s) = 0;  /*v2.1to2.2 4 */
		/*! \returns the 0-based index of taxon named 's' in taxonLabels list.

			\throws NxsX_NoSuchTaxon exception if taxon named 's' cannot be found.

			\warning {This function does NOT implement the interpret-label-as-a-number functionality}
		*/
		virtual unsigned			FindTaxon(const NxsString & label) const  = 0;  /*v2.1to2.2 4 */
		/*! \returns true if the label `label` already a taxon label (not case sensitive)
		*/
		virtual bool  				IsAlreadyDefined(const std::string & label) = 0;
		/*! \returns the length of the longest label.

			\note {The label length, does not include any extra characters (such as quotes) that may be needed to write the file
			out to NEXUS format}
		*/
		virtual unsigned			GetMaxTaxonLabelLength() = 0;
		/*! \returns the number of taxon labels (should be the same as GetNTax after a valid parse).
		*/
		virtual unsigned			GetNumTaxonLabels() const = 0;
		/*! \returns the number of taxa
		*/
		virtual unsigned			GetNTax() const = 0;
		/*! \returns the number of taxa
			The prescence of this function and GetNTax is a historical artifact.  They have the same behavior.
		*/
		virtual unsigned			GetNTaxTotal() const = 0;
		/*! \returns the label for taxon with (0-based) index of `i`

			\throws NxsNCLAPIException if `i` is out of range.
			\warning{Can return a 1-based number if the taxon lacks a name (in NEXUS parsing "1" refers to the first taxon).}
		*/
		virtual NxsString 			GetTaxonLabel(unsigned i) const = 0;  /*v2.1to2.2 4 */

		/*! \returns a vector of all of the taxon labels */
		virtual std::vector<std::string> GetAllLabels() const;

		/*! \returns a 1-based number of the taxon with label of `label` (not case-sensitive).
			This is a low-level function not intended for widespread use (it is faster way to
			query the label list because it does not throw exceptions or do the numeric interpretation
			of labels).

			\warning{does NOT apply the numeric interpretation of the label.}

			\warning{ 1-based numbering}
		*/
		virtual unsigned			TaxLabelToNumber(const std::string &label) const = 0;

		/*! hook called during NxsTaxaBlock::Read() when the TaxLabels command is encountered */
		virtual void 				HandleTaxLabels(NxsToken &token) = 0;
		/*! writes the taxon labes as NEXUS to `out` */
		virtual void 				WriteTaxLabelsCommand(std::ostream &out) const = 0;
		/*! Sets the number of taxa to be included in the block

			\warning{This can cause the cropping of labels.}
		*/
		virtual void 				SetNtax(unsigned n) = 0;

		/*! \returns the number of taxa that have not been inactivated by calling InactivateTaxa
		*/
		virtual unsigned		 	GetNumActiveTaxa() const = 0;
		/*! \returns true if the taxon (denoted by a 0-based index) is in range and not inactivated

			\note{Works, but is not currently used by the library added for planned delete/restor functionality}
		*/
		virtual bool		 		IsActiveTaxon(unsigned i) const = 0;
		/*! flags a set of taxa as inactive. Takes a set of 0-based indices.

			\note{Works, but is not currently used by the library added for planned delete/restor functionality}
		*/
		virtual unsigned		 	InactivateTaxa(const std::set<unsigned> &s) = 0;
		/*! flags a set of taxa as active. Takes a set of 0-based indices.

			\note{Works, but is not currently used by the library added for planned delete/restor functionality}
		*/
		virtual unsigned		 	ActivateTaxa(const std::set<unsigned> &) = 0;
		/*! flags a taxon as active. Takes a  0-based index.

			\note{Works, but is not currently used by the library added for planned delete/restor functionality}
		*/
		virtual unsigned		 	InactivateTaxon(unsigned ) = 0;
		/*! flags a taxon as active. Takes a  0-based index.

			\note{Works, but is not currently used by the library added for planned delete/restor functionality}
		*/
		virtual unsigned		 	ActivateTaxon(unsigned ) = 0;

  };

/*! The default implementation of the NxsTaxaBlockAPI that is used to parse TAXA blocks into a list of
	unique (case-insensitive) labels.

*/
class NxsTaxaBlock
  : public NxsTaxaBlockAPI
	{
	friend class NxsDataBlock;
	friend class NxsAllelesBlock;
	friend class NxsCharactersBlock;
	friend class NxsDistancesBlock;

	public:
							NxsTaxaBlock();
		virtual				~NxsTaxaBlock();

		virtual unsigned	AddTaxonLabel(const std::string & s);
		void  				ChangeTaxonLabel(unsigned i, NxsString s); /*v2.1to2.2 4 */
		unsigned			TaxLabelToNumber(const std::string &label) const;
		unsigned			FindTaxon(const NxsString & label) const;  /*v2.1to2.2 4 */
		bool  				IsAlreadyDefined(const std::string &label);
		unsigned GetIndexSet(const std::string &label, NxsUnsignedSet * toFill) const
			{
			return NxsLabelToIndicesMapper::GetIndicesFromSets(label, toFill, taxSets);
			}
		unsigned			GetMaxTaxonLabelLength();
		unsigned			GetNTax() const;
		unsigned			GetNTaxTotal() const;
		unsigned			GetNumTaxonLabels() const;
		NxsString 			GetTaxonLabel(unsigned i) const;  /*v2.1to2.2 4 */
		void 				HandleTaxLabels(NxsToken &token);
		bool 				NeedsQuotes(unsigned i);
		virtual void		Report(std::ostream &out) NCL_COULD_BE_CONST ; /*v2.1to2.2 1 */
		virtual void 		Reset();
		void 				SetNtax(unsigned n);
		void				WriteAsNexus(std::ostream &out) const;


		virtual unsigned		 	GetNumActiveTaxa() const;
		virtual bool		 		IsActiveTaxon(unsigned i) const;
		virtual unsigned		 	InactivateTaxa(const std::set<unsigned> &);
		virtual unsigned		 	ActivateTaxa(const std::set<unsigned> &);
		virtual unsigned		 	InactivateTaxon(unsigned );
		virtual unsigned		 	ActivateTaxon(unsigned );

		class NxsX_NoSuchTaxon {};	/* thrown if FindTaxon cannot locate a supplied taxon label in the taxLabels vector */

		void 				WriteTaxLabelsCommand(std::ostream &out) const;

		unsigned GetMaxIndex() const;
		unsigned GetNumLabelsCurrentlyStored() const;
		unsigned GetIndicesForLabel(const std::string &label, NxsUnsignedSet *inds) const;
		bool AddNewIndexSet(const std::string &label, const NxsUnsignedSet & inds);
		bool AddNewPartition(const std::string &label, const NxsPartition & inds);

		/*----------------------------------------------------------------------
		| AppendNewLabel should not be called in most client code.  It is only
		| 	added because some blocks create their own taxa block on-the-fly.
		*/
		virtual unsigned AppendNewLabel(std::string &label)
			{
			while (dimNTax <= taxLabels.size())
				dimNTax++;
			return AddTaxonLabel(label);
			}

		NxsTaxaBlock &operator=(const NxsTaxaBlock &other)
			{
			Reset();
			CopyBaseBlockContents(static_cast<const NxsBlock &>(other));
			CopyTaxaContents(other);
			return *this;
			}

		void CopyTaxaContents(const NxsTaxaBlock &other)
			{
			taxLabels = other.taxLabels;
			labelToIndex = other.labelToIndex;
			dimNTax = other.dimNTax;
			taxSets = taxSets;
			taxPartitions = other.taxPartitions;
			inactiveTaxa = other.inactiveTaxa;
			}
		NxsTaxaBlock * Clone() const
			{
			NxsTaxaBlock *taxa = new NxsTaxaBlock();
			*taxa = *this;
			return taxa;
			}
	protected:
		NxsStringVector	taxLabels;	/* storage for list of taxon labels */
		std::map<std::string, unsigned> labelToIndex;
		unsigned		dimNTax;
		NxsUnsignedSetMap taxSets;
		NxsPartitionsByName taxPartitions;
		std::set<unsigned> inactiveTaxa;

		virtual void 	Read(NxsToken &token);
		void CheckCapitalizedTaxonLabel(const std::string &s) const;
		unsigned CapitalizedTaxLabelToNumber(const std::string & s) const;
		void 			RemoveTaxonLabel(unsigned taxInd);
	};


/*! This class is the base class for blocks that can (in a pinch) serve as
a TAXA block reader(NxsCharactersBlock, NxsTreesBlock, NxsUnalignedBlock, and NxsDistancesBlock)

	Client code rarely needs to call the special functionality of this class.

	In broad terms, this class delegates calls to the taxa block if there is an
		external taxa block.
	If no external taxa block has been associated with the NxsTaxaBlockSurrogate, then
		will create one (which will later be returned to the NxsReader as an
		implied block)
*/
class NxsTaxaBlockSurrogate
	{
	public:
		void SetCreateImpliedBlock(bool v)
        	{
        	createImpliedBlock = v;
        	}

		/*! \returns an integer that will be a facet of NxsBlockLinkStatus which reflects how the taxa block was determined.*/
		int GetTaxaLinkStatus() const
			{
			return taxaLinkStatus;
			}

		void SetTaxaLinkStatus(NxsBlock::NxsBlockLinkStatus s);
		NxsTaxaBlockAPI * GetTaxaBlockPtr(int *status) const;
		NxsTaxaBlockAPI * GetTaxaBlockPtr() {return GetTaxaBlockPtr(0L);}

		virtual const std::string & GetBlockName() const = 0;

		virtual unsigned			GetNTax() const;
		virtual unsigned			GetNTaxTotal() const;
		virtual unsigned			GetNumActiveTaxa() const;
		virtual bool				IsActiveTaxon(unsigned i) const;
		virtual unsigned			InactivateTaxa(const std::set<unsigned> &);
		virtual unsigned			ActivateTaxa(const std::set<unsigned> &);
		virtual unsigned			InactivateTaxon(unsigned );
		virtual unsigned			ActivateTaxon(unsigned );

		NxsTaxaBlockSurrogate &operator=(const NxsTaxaBlockSurrogate &other)
			{
			ResetSurrogate();
			CopyTaxaBlockSurrogateContents(other);
			return *this;
			}

		/*
		|  Aliases the same taxa block as `other`, but `other` retains ownership!!
		*/
		virtual void CopyTaxaBlockSurrogateContents(const NxsTaxaBlockSurrogate &other)
			{
			ResetSurrogate();
			taxa = other.taxa;
			taxaLinkStatus = other.taxaLinkStatus;
			newtaxa = other.newtaxa;
			ownsTaxaBlock = false;
			passedRefOfOwnedBlock = other.passedRefOfOwnedBlock;
			createImpliedBlock = other.createImpliedBlock;
			nxsReader = other.nxsReader;
			}

	protected:
		NxsTaxaBlockSurrogate(NxsTaxaBlockAPI *tb, NxsReader * reader)
			:taxa(tb),
			newtaxa(false),
			ownsTaxaBlock(false),
			passedRefOfOwnedBlock(false),
			createImpliedBlock(false),
			nxsReader(reader)
			{
			taxaLinkStatus = (tb == NULL ? NxsBlock::BLOCK_LINK_UNINITIALIZED : NxsBlock::BLOCK_LINK_TO_ONLY_CHOICE);
			}
		virtual ~NxsTaxaBlockSurrogate()
			{
			ResetSurrogate();
			}

		void SetTaxaBlockPtr(NxsTaxaBlockAPI *c, NxsBlock::NxsBlockLinkStatus s);

		VecBlockPtr GetCreatedTaxaBlocks();
		void FlagTaxaBlockAsUsed()
			{
			taxaLinkStatus |= NxsBlock::BLOCK_LINK_USED;
			}

		void AssureTaxaBlock(bool allocBlock, NxsToken &, const char *cmd);
		void ResetSurrogate();
		void SetNexusReader(NxsReader *nxsptr)
			{
			nxsReader = nxsptr;
			}
		virtual void 			HandleTaxLabels(NxsToken & token);
		virtual void			HandleLinkTaxaCommand(NxsToken & );
		virtual void			WriteLinkTaxaCommand(std::ostream &out) const;
		bool					SurrogateSwapEquivalentTaxaBlock(NxsTaxaBlockAPI * tb);

		NxsTaxaBlockAPI			*taxa;				/* pointer to the TAXA block in which taxon labels are stored */
		int						taxaLinkStatus;
		bool					newtaxa;
		bool					ownsTaxaBlock;
		bool					passedRefOfOwnedBlock;
		bool					createImpliedBlock; /*if true and NEWTAXA is read in the DIMENSIONS command, then a new TaxaBlock will be allocated (instead of resetting the TAXA block). false by default.*/
		NxsReader 				*nxsReader;
	};
// The following typedef maintains compatibility with existing code.
// The TaxaBlock class name is deprecated; please use NxsTaxaBlock instead.
//
typedef NxsTaxaBlock TaxaBlock;
class NxsTaxaBlockFactory
	:public NxsBlockFactory
	{
	public:
		virtual NxsTaxaBlock  *	GetBlockReaderForID(const std::string & NCL_BLOCKTYPE_ATTR_NAME, NxsReader *reader, NxsToken *token);
	};

inline unsigned NxsTaxaBlock::GetNTax() const
	{
	return dimNTax;
	}

inline unsigned NxsTaxaBlock::GetNTaxTotal() const
	{
	return dimNTax;
	}

/*!	\returns a 1-based number of the taxon with label of `r` OR returns 0 to indicate that the label was not found.
	Not for public usage

	\warning{`r` must be capitalized for this function to work.}

	\warning{does NOT apply the numeric interpretation of the label.}

	\warning{ 1-based numbering}
*/
inline unsigned NxsTaxaBlock::CapitalizedTaxLabelToNumber(const std::string &r) const
	{
	std::map<std::string, unsigned>::const_iterator rIt = labelToIndex.find(r);
	if (rIt == labelToIndex.end())
		return 0;
	return rIt->second + 1;
	}


/*!
	Returns true if taxon `i' is active. If taxon `i' has been deleted, returns false. Assumes `i' is in the range
	[0..`ntax').
*/
inline bool NxsTaxaBlockSurrogate::IsActiveTaxon(
  unsigned taxInd) const	/* the taxon in question, in the range [0..`ntax') */
	{
	if (!taxa)
	    throw NxsNCLAPIException("Calling IsActiveTaxon on uninitialized block");
	return taxa->IsActiveTaxon(taxInd);
	}
inline unsigned NxsTaxaBlockSurrogate::GetNumActiveTaxa() const
	{
	if (!taxa)
	    throw NxsNCLAPIException("Calling GetNumActiveTaxa on uninitialized block");
	return taxa->GetNumActiveTaxa();
	}
inline unsigned NxsTaxaBlockSurrogate::InactivateTaxa(const std::set<unsigned> &s)
	{
	if (!taxa)
	    throw NxsNCLAPIException("Calling InactivateTaxa on uninitialized block");
	return taxa->InactivateTaxa(s);
	}
inline unsigned NxsTaxaBlockSurrogate::ActivateTaxa(const std::set<unsigned> &s)
	{
	if (!taxa)
	    throw NxsNCLAPIException("Calling ActivateTaxa on uninitialized block");
	return taxa->ActivateTaxa(s);
	}

inline unsigned NxsTaxaBlockSurrogate::InactivateTaxon(unsigned i)
	{
	if (!taxa)
	    throw NxsNCLAPIException("Calling InactivateTaxon on uninitialized block");
	return taxa->InactivateTaxon(i);
	}

inline unsigned NxsTaxaBlockSurrogate::ActivateTaxon(unsigned i)
	{
	if (!taxa)
	    throw NxsNCLAPIException("Calling ActivateTaxon on uninitialized block");
	return taxa->ActivateTaxon(i);
	}

inline unsigned NxsTaxaBlockSurrogate::GetNTax() const
	{
	if (!taxa)
	    throw NxsNCLAPIException("Calling GetNTax on uninitialized block");
	return taxa->GetNTax();
	}

inline unsigned NxsTaxaBlockSurrogate::GetNTaxTotal() const
	{
	if (!taxa)
	    throw NxsNCLAPIException("Calling GetNTaxTotal on uninitialized block");
	return taxa->GetNTaxTotal();
	}


inline unsigned NxsTaxaBlock::GetNumActiveTaxa() const
	{
	return GetNTax() - (unsigned)inactiveTaxa.size();
	}

inline bool NxsTaxaBlock::IsActiveTaxon(unsigned i) const
	{
	return i < GetNTax() && (inactiveTaxa.count(i) == 0);
	}

inline unsigned NxsTaxaBlock::InactivateTaxa(const std::set<unsigned> &s)
	{
	for (std::set<unsigned>::const_iterator sIt = s.begin(); sIt != s.end(); ++sIt)
		InactivateTaxon(*sIt);
	return GetNumActiveTaxa();
	}

inline unsigned NxsTaxaBlock::ActivateTaxa(const std::set<unsigned> &s)
	{
	for (std::set<unsigned>::const_iterator sIt = s.begin(); sIt != s.end(); ++sIt)
		ActivateTaxon(*sIt);
	return GetNumActiveTaxa();
	}
inline unsigned NxsTaxaBlock::InactivateTaxon(unsigned i)
	{
	if (i > GetNTax())
		throw NxsNCLAPIException("Taxon index out of range in InactivateTaxon");
	inactiveTaxa.insert(i);
	return GetNumActiveTaxa();
	}
inline unsigned NxsTaxaBlock::ActivateTaxon(unsigned i)
	{
	if (i > GetNTax())
		throw NxsNCLAPIException("Taxon index out of range in InactivateTaxon");
	inactiveTaxa.erase(i);
	return GetNumActiveTaxa();
	}


#endif