NCL: nxsassumptionsblock.h Source File

00001 //  Copyright (C) 1999-2003 Paul O. Lewis
00002 //
00003 //  This file is part of NCL (Nexus Class Library) version 2.0.
00004 //
00005 //  NCL is free software; you can redistribute it and/or modify
00006 //  it under the terms of the GNU General Public License as published by
00007 //  the Free Software Foundation; either version 2 of the License, or
00008 //  (at your option) any later version.
00009 //
00010 //  NCL is distributed in the hope that it will be useful,
00011 //  but WITHOUT ANY WARRANTY; without even the implied warranty of
00012 //  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
00013 //  GNU General Public License for more details.
00014 //
00015 //  You should have received a copy of the GNU General Public License
00016 //  along with NCL; if not, write to the Free Software Foundation, Inc.,
00017 //  59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
00018 //
00019 
00020 #ifndef NCL_ASSUMPTIONSBLOCK_H
00021 #define NCL_ASSUMPTIONSBLOCK_H
00022 
00023 #include <vector>
00024 
00025 #include "ncl/nxsdefs.h"
00026 #include "ncl/nxsblock.h"
00027 #include "ncl/nxstreesblock.h"
00028 #include "ncl/nxscharactersblock.h"
00029 #include "ncl/nxstaxablock.h"
00030 
00031 class NxsCharactersBlockAPI;
00032 class NxsTaxaBlockAPI;
00033 
00034 using std::vector;
00035 
00036 class NxsAssumptionsBlockAPI
00037   : public NxsBlock
00038     {
00039     public:
00040         virtual void    SetCallback(NxsCharactersBlockAPI *p) = 0;
00041 
00042 
00043 
00044         virtual void SetCharBlockPtr(NxsCharactersBlockAPI * c, NxsBlockLinkStatus s) = 0;
00045         virtual void SetTaxaBlockPtr(NxsTaxaBlockAPI *, NxsBlockLinkStatus s) = 0;
00046         virtual void SetTreesBlockPtr(NxsTreesBlockAPI *, NxsBlockLinkStatus s) = 0;
00047 
00048         virtual NxsCharactersBlockAPI * GetCharBlockPtr(int *status=NULL) = 0; /*v2.1to2.2 13 */
00049         virtual NxsTaxaBlockAPI * GetTaxaBlockPtr(int *status=NULL) = 0; /*v2.1to2.2 13 */
00050         virtual NxsTreesBlockAPI * GetTreesBlockPtr(int *status=NULL) = 0; /*v2.1to2.2 13 */
00051 
00052         /* i14 */ /*v2.1to2.2 14 */
00053         /* i15 */ /*v2.1to2.2 15 */
00054         /* i16 */ /*v2.1to2.2 16 */
00055 
00056         virtual void AddCharPartition(const std::string & name, const NxsPartition &) = 0;
00057         virtual void AddTaxPartition(const std::string & name, const NxsPartition &) = 0;
00058         virtual void AddTreePartition(const std::string & name, const NxsPartition &) = 0;
00059         virtual void AddCodeSet(const std::string & name, const NxsPartition &, bool asterisked) = 0;
00060         virtual void AddCodonPosSet(const std::string & name, const NxsPartition &, bool asterisked) = 0;
00061 
00062         virtual void FlagCharBlockAsUsed() = 0;
00063         virtual void FlagTaxaBlockAsUsed() = 0;
00064         virtual void FlagTreesBlockAsUsed() = 0;
00065 
00066         virtual void ReadCharsetDef(NxsString charset_name, NxsToken &token, bool asterisked) = 0;
00067         virtual void ReadExsetDef(NxsString charset_name, NxsToken &token, bool asterisked) = 0;
00068         virtual void ReadTaxsetDef(NxsString set_name, NxsToken &token, bool asterisked) = 0;
00069         virtual void ReadTreesetDef(NxsString set_name, NxsToken &token, bool asterisked) = 0;
00070 
00071         virtual NxsTransformationManager & GetNxsTransformationManagerRef() = 0;
00072         virtual NxsGeneticCodesManager & GetNxsGeneticCodesManagerRef() = 0;
00073         virtual void SetGapsAsNewstate(bool v) = 0;
00074     };
00075 
00088 class NxsAssumptionsBlock
00089   : public NxsAssumptionsBlockAPI
00090     {
00091     enum NameOfAssumpBlockAsRead
00092         {
00093         UNREAD_OR_GENERATED_BLOCK,
00094         ASSUMPTIONS_BLOCK_READ,
00095         SETS_BLOCK_READ,
00096         CODONS_BLOCK_READ
00097         };
00098 
00099 
00100     public:
00101                             NxsAssumptionsBlock(NxsTaxaBlockAPI *t);
00102         virtual             ~NxsAssumptionsBlock();
00103 
00104         virtual bool        CanReadBlockType(const NxsToken & token);
00105 
00106         void                ReplaceTaxaBlockPtr(NxsTaxaBlockAPI *tb);
00107         void                SetCallback(NxsCharactersBlockAPI *p);
00108 
00109         int                 GetNumCharSets() const;
00110         /* i17 */ /*v2.1to2.2 17 */
00111         void                GetCharSetNames(NxsStringVector &names) const; /*v2.1to2.2 3 */
00112         const NxsUnsignedSet *GetCharSet(NxsString nm) const; /*v2.1to2.2 4 */
00113 
00114         int                 GetNumCharPartitions(); /*v2.1to2.2 6 */
00115         void                GetCharPartitionNames(vector<std::string> &names); /*v2.1to2.2 6 */
00116         const NxsPartition      *GetCharPartition(std::string nm) const;
00117 
00118         int                 GetNumTaxSets(); /*v2.1to2.2 6 */
00119         void                GetTaxSetNames(NxsStringVector &names); /*v2.1to2.2 3 */ /*v2.1to2.2 6 */
00120         NxsUnsignedSet &    GetTaxSet(NxsString nm); /*v2.1to2.2 6 */ /*v2.1to2.2 8 */ /*v2.1to2.2 4 */
00121 
00122         int                 GetNumExSets();/*v2.1to2.2 6 */
00123         void                GetExSetNames(NxsStringVector &names); /*v2.1to2.2 3 */ /*v2.1to2.2 6 */
00124         NxsUnsignedSet &    GetExSet(NxsString nm); /*v2.1to2.2 6 */ /*v2.1to2.2 8 */ /*v2.1to2.2 4 */
00125         NxsString           GetDefExSetName(); /*v2.1to2.2 6 */ /*v2.1to2.2 4 */
00126         void                ApplyExset(NxsString nm); /*v2.1to2.2 4 */
00127 
00128         virtual void        Read(NxsToken& token);
00129         virtual void        Report(std::ostream& out) NCL_COULD_BE_CONST ; /*v2.1to2.2 1 */
00130         virtual void        Reset();
00131         virtual void        WriteAsNexus(std::ostream &out) const;
00132 
00133         /*only used it the linkAPI is enabled*/
00134         virtual void        HandleLinkCommand(NxsToken & );
00135         virtual void        WriteLinkCommand(std::ostream &out) const;
00136 
00137         virtual VecBlockPtr     GetImpliedBlocks()
00138             {
00139             return GetCreatedTaxaBlocks();
00140             }
00141 
00142         int                 GetCharLinkStatus() {return charLinkStatus;}
00143         int                 GetTaxaLinkStatus() {return taxaLinkStatus;}
00144         int                 GetTreesLinkStatus() {return treesLinkStatus;}
00145 
00146         void                FlagCharBlockAsUsed() {charLinkStatus |= NxsBlock::BLOCK_LINK_USED;}
00147         void                FlagTaxaBlockAsUsed() {taxaLinkStatus |= NxsBlock::BLOCK_LINK_USED;}
00148         void                FlagTreesBlockAsUsed() {treesLinkStatus |= NxsBlock::BLOCK_LINK_USED;}
00149 
00150         void                SetCharLinkStatus(NxsBlockLinkStatus s);
00151         void                SetTaxaLinkStatus(NxsBlockLinkStatus s);
00152         void                SetTreesLinkStatus(NxsBlockLinkStatus s);
00153 
00154         void                SetCharBlockPtr(NxsCharactersBlockAPI * c, NxsBlockLinkStatus s);
00155         void                SetTaxaBlockPtr(NxsTaxaBlockAPI *, NxsBlockLinkStatus s);
00156         void                SetTreesBlockPtr(NxsTreesBlockAPI *, NxsBlockLinkStatus s);
00157         NxsCharactersBlockAPI * GetCharBlockPtr(int *status=NULL); /*v2.1to2.2 13 */
00158         NxsTaxaBlockAPI *   GetTaxaBlockPtr(int *status=NULL); /*v2.1to2.2 13 */
00159         NxsTreesBlockAPI *  GetTreesBlockPtr(int *status=NULL); /*v2.1to2.2 13 */
00160 
00161         NxsTransformationManager & GetNxsTransformationManagerRef()
00162             {
00163             return transfMgr;
00164             }
00165         NxsGeneticCodesManager & GetNxsGeneticCodesManagerRef()
00166             {
00167             return codesMgr;
00168             }
00169         virtual void AddCharPartition(const std::string & name, const NxsPartition &);
00170         virtual void AddTaxPartition(const std::string & name, const NxsPartition &);
00171         virtual void AddTreePartition(const std::string & name, const NxsPartition &);
00172         virtual void AddCodeSet(const std::string & name, const NxsPartition &, bool asterisked);
00173         virtual void AddCodonPosSet(const std::string & name, const NxsPartition &, bool asterisked);
00174 
00175         /*---------------------------------------------------------------------------------------
00176         | Results in aliasing of the taxa, trees, and characters blocks!
00177         */
00178         NxsAssumptionsBlock &operator=(const NxsAssumptionsBlock &other)
00179             {
00180             CopyBaseBlockContents(static_cast<const NxsBlock &>(other));
00181             CopyAssumptionsContents(other);
00182             return *this;
00183             }
00184 
00185         /*---------------------------------------------------------------------------------------
00186         | Results in aliasing of the taxa, trees, and characters blocks!
00187         |
00188         | passedRefOfOwnedBlock is set to this->true to avoid double deletion (other
00189         |   retains ownership of these blocks
00190         */
00191         virtual void CopyAssumptionsContents(const NxsAssumptionsBlock &other)
00192             {
00193             taxa = other.taxa;
00194             charBlockPtr = other.charBlockPtr;
00195             treesBlockPtr = other.treesBlockPtr;
00196             charsets = other.charsets;
00197             taxsets = other.taxsets;
00198             treesets = other.treesets;
00199             exsets = other.exsets;
00200             charPartitions = other.charPartitions;
00201             taxPartitions = other.taxPartitions;
00202             treePartitions = other.treePartitions;
00203             def_exset = other.def_exset;
00204             charLinkStatus = other.charLinkStatus;
00205             taxaLinkStatus = other.taxaLinkStatus;
00206             treesLinkStatus = other.treesLinkStatus;
00207             passedRefOfOwnedBlock = true;
00208             readAs = other.readAs;
00209             transfMgr = other.transfMgr;
00210             codesMgr = other.codesMgr;
00211             createdSubBlocks = other.createdSubBlocks;
00212             polyTCountValue = other.polyTCountValue;
00213             gapsAsNewstate = other.gapsAsNewstate;
00214             codonPosSets = other.codonPosSets;
00215             def_codonPosSet = other.def_codonPosSet;
00216             codeSets = other.codeSets;
00217             def_codeSet = other.def_codeSet;
00218             }
00219 
00220         virtual NxsAssumptionsBlock * Clone() const
00221             {
00222             NxsAssumptionsBlock * a = new NxsAssumptionsBlock(taxa);
00223             *a = *this;
00224             return a;
00225             }
00226         virtual void SetGapsAsNewstate(bool v)
00227             {
00228             gapsAsNewstate = v;
00229             }
00230 
00231 
00232     protected:
00233         typedef std::vector<NxsAssumptionsBlockAPI *> VecAssumpBlockPtr;
00234 
00235         virtual void        ReadCharsetDef(NxsString charset_name, NxsToken &token, bool asterisked);
00236         virtual void        ReadExsetDef(NxsString charset_name, NxsToken &token, bool asterisked);
00237         virtual void        ReadTreesetDef(NxsString set_name, NxsToken &token, bool asterisked);
00238         virtual void        ReadTaxsetDef(NxsString set_name, NxsToken &token, bool asterisked);
00239 
00240 
00241         VecBlockPtr         GetCreatedTaxaBlocks();
00242         virtual unsigned    TaxonLabelToNumber(NxsString s) const; /*v2.1to2.2 4 */
00243 
00244         void                HandleCharPartition(NxsToken& token);
00245         void                HandleCharSet(NxsToken& token);
00246         void                HandleCodeSet(NxsToken& token);
00247         void                HandleCodonPosSet(NxsToken& token);
00248         void                HandleExSet(NxsToken& token);
00249         void                HandleOptions(NxsToken & token);
00250         void                HandleTaxPartition(NxsToken& token);
00251         void                HandleTaxSet(NxsToken& token);
00252         void                HandleTreePartition(NxsToken& token);
00253         void                HandleTreeSet(NxsToken& token);
00254         void                HandleTypeSet(NxsToken& token);
00255         void                HandleUserType(NxsToken& token);
00256         void                HandleWeightSet(NxsToken& token);
00257 
00258         void                WriteCharSet(std::ostream &out) const
00259             {
00260             NxsWriteSetCommand("CHARSET", charsets, out);
00261             }
00262         void                WriteCharPartition(std::ostream &out) const
00263             {
00264             NxsWritePartitionCommand("CharPartition", charPartitions, out);
00265             }
00266         void                WriteExSet(std::ostream &out) const
00267             {
00268             NxsWriteSetCommand("EXSET", exsets, out, def_exset.c_str());
00269             }
00270         void                WriteOptions(std::ostream &out) const;
00271         void                WriteTaxPartition(std::ostream &out) const
00272             {
00273             NxsWritePartitionCommand("TaxPartition", taxPartitions, out);
00274             }
00275         void                WriteTaxSet(std::ostream &out) const
00276             {
00277             NxsWriteSetCommand("TAXSET", taxsets, out);
00278             }
00279         void                WriteTreePartition(std::ostream &out) const
00280             {
00281             NxsWritePartitionCommand("TreePartition", treePartitions, out);
00282             }
00283         void                WriteTreeSet(std::ostream &out) const
00284             {
00285             NxsWriteSetCommand("TREESET", treesets, out);
00286             }
00287         void WriteCodeSet(std::ostream &out) const
00288             {
00289             NxsWritePartitionCommand("CodeSet", codeSets, out, def_codeSet.c_str());
00290             }
00291         void WriteCodonPosSet(std::ostream &out) const
00292             {
00293             NxsWritePartitionCommand("CodonPosSet", codonPosSets, out, def_codonPosSet.c_str());
00294             }
00295         NameOfAssumpBlockAsRead GetIDOfBlockTypeIDFromParse() const
00296             {
00297             return readAs;
00298             }
00299     private:
00300         NxsAssumptionsBlockAPI  *GetAssumptionsBlockForCharTitle(const char *title, NxsToken &token, const char *cmd);
00301         NxsAssumptionsBlockAPI  *GetAssumptionsBlockForTaxaTitle(const char *title, NxsToken &token, const char *cmd);
00302         NxsAssumptionsBlockAPI  *GetAssumptionsBlockForTreesTitle(const char *title, NxsToken &token, const char *cmd);
00303 
00304         NxsAssumptionsBlockAPI  *GetAssumptionsBlockForCharBlock(NxsCharactersBlockAPI *, NxsBlockLinkStatus, NxsToken &token);
00305         NxsAssumptionsBlockAPI  *GetAssumptionsBlockForTaxaBlock(NxsTaxaBlockAPI *, NxsBlockLinkStatus, NxsToken &token);
00306         NxsAssumptionsBlockAPI  *GetAssumptionsBlockForTreesBlock(NxsTreesBlockAPI *, NxsBlockLinkStatus, NxsToken &token);
00307 
00308         NxsAssumptionsBlockAPI  *CreateNewAssumptionsBlock(NxsToken &token);
00309         NxsAssumptionsBlockAPI *DealWithPossibleParensInCharDependentCmd(NxsToken &token, const char *cmd, const std::vector<std::string> *unsupported = NULL, bool * isVect = false);
00310         bool                    HasAssumptionsBlockCommands() const;
00311         bool                    HasSetsBlockCommands() const;
00312         bool                    HasCodonsBlockCommands() const;
00313 
00314 
00315         NxsTaxaBlockAPI         *taxa;              /* pointer to the NxsTaxaBlockAPI object */
00316         NxsCharactersBlockAPI   *charBlockPtr;      /* pointer to the NxsCharactersBlockAPI-derived object to be notified in the event of exset changes */
00317         NxsTreesBlockAPI        *treesBlockPtr;     /* pointer to the NxsTreesBlockAPI-derived object to be notified in the event of exset changes */
00318 
00319 
00320 
00321         NxsUnsignedSetMap   charsets;
00322         NxsUnsignedSetMap   taxsets;
00323         NxsUnsignedSetMap   treesets;
00324         NxsUnsignedSetMap   exsets;
00325 
00326         NxsPartitionsByName charPartitions;
00327         NxsPartitionsByName taxPartitions;
00328         NxsPartitionsByName treePartitions;
00329 
00330         NxsString           def_exset;          /* the default exset */
00331 
00332         NxsPartitionsByName codonPosSets;
00333         NxsString           def_codonPosSet;    /* the default codonPosSet */
00334         NxsPartitionsByName codeSets;
00335         NxsString           def_codeSet;        /* the default codeSet */
00336 
00337         int                 charLinkStatus;
00338         int                 taxaLinkStatus;
00339         int                 treesLinkStatus;
00340         bool                passedRefOfOwnedBlock;
00341         NameOfAssumpBlockAsRead readAs;
00342         NxsTransformationManager transfMgr;
00343         NxsGeneticCodesManager  codesMgr;
00344 
00345         std::vector<NxsAssumptionsBlockAPI *> createdSubBlocks;
00346         enum PolyTCountValue
00347             {
00348             POLY_T_COUNT_UNKNOWN,
00349             POLY_T_COUNT_MIN,
00350             POLY_T_COUNT_MAX
00351             };
00352         PolyTCountValue     polyTCountValue;
00353         bool                gapsAsNewstate;
00354 
00355         friend class NxsAssumptionsBlockFactory;
00356         friend class PublicNexusReader;
00357     };
00358 
00359 class NxsAssumptionsBlockFactory
00360     :public NxsBlockFactory
00361     {
00362     public:
00363         virtual NxsAssumptionsBlock * GetBlockReaderForID(const std::string & id, NxsReader *reader, NxsToken *token);
00364     };
00365 
00366 typedef NxsAssumptionsBlock AssumptionsBlock;   // for backward compatibility
00367 
00368 #endif
00369