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#define TREEBUFINCREASE 200
/* tree utility functions */
int AddToTreeList (TreeList *treeList, Tree *tree);
Tree *AllocateTree (int numTaxa);
Tree *AllocateFixedTree (int numTaxa, int isRooted);
int AllocateTreePartitions (Tree *t);
PolyTree *AllocatePolyTree (int numTaxa);
int AllocatePolyTreePartitions (PolyTree *pt);
int AllocatePolyTreeRelClockParams (PolyTree *pt, int nBSets, int nESets);
int AreTopologiesSame(Tree *t1, Tree *t2);
int AreTreesSame (Tree *t1, Tree *t2);
int BuildConstraintTree (Tree *t, PolyTree *pt, char **localTaxonNames);
int BuildRandomRTopology (Tree *t, SafeLong *seed);
int BuildRandomUTopology (Tree *t, SafeLong *seed);
int CheckConstraints (Tree *t);
int CheckSetConstraints (Tree *t);
void ColorClusters (TreeNode *p, int *index);
void CopySubtreeToTree (Tree *subtree, Tree *t);
int CopyToPolyTreeFromPolyTree (PolyTree *to, PolyTree *from);
int CopyToSpeciesTreeFromPolyTree (Tree *to, PolyTree *from);
int CopyToTreeFromPolyTree (Tree *to, PolyTree *from);
void CopyPolyNodes (PolyNode *p, PolyNode *q, int nLongsNeeded);
int CopyToTreeFromTree (Tree *to, Tree *from);
void CopyTreeNodes (TreeNode *p, TreeNode *q, int nLongsNeeded);
void CopyTreeToSubtree (Tree *t, Tree *subtree);
int Deroot(PolyTree *pt);
void EraseTreeList (TreeList *treeList);
void findAllowedClockrate (Tree *t, MrBFlt *minClockRate, MrBFlt *maxClockRate );
void FreePolyTree (PolyTree *pt);
void FreePolyTreePartitions (PolyTree *pt);
void FreePolyTreePopSizeParams (PolyTree *pt);
void FreePolyTreeRelClockParams (PolyTree *pt);
void FreeTree (Tree *t);
void FreeTreePartitions (Tree *pt);
void GetDatedNodeDepths (TreeNode *p, MrBFlt *nodeDepths);
void GetDatedNodes (TreeNode *p, TreeNode **datedNodes);
void GetDownPass (Tree *t);
void GetNodeDownPass (Tree *t, TreeNode *p, int *i, int *j);
void GetPolyAges (PolyTree *t);
void GetPolyDepths (PolyTree *t);
void GetPolyDownPass (PolyTree *t);
void GetPolyNodeDownPass (PolyTree *t, PolyNode *p, int *i, int *j);
int GetRandomEmbeddedSubtree (Tree *t, int nTerminals, SafeLong *seed, int *nEmbeddedTrees);
int GetFromTreeList (TreeList *treeList, Tree *tree);
int InitBrlens (Tree *t, MrBFlt v);
int InitCalibratedBrlens (Tree *t, MrBFlt minLength, SafeLong *seed);
int InitClockBrlens (Tree *t);
int IsCalibratedClockSatisfied (Tree *t,MrBFlt *minClockRate,MrBFlt *maxClockRate , MrBFlt tol);
int IsClockSatisfied (Tree *t, MrBFlt tol);
int IsTreeConsistent (Param *param, int chain, int state);
int LabelTree (Tree *t, char **taxonNames);
void Mark (TreeNode *p);
void MarkDatedSubtree (TreeNode *p);
int MoveCalculationRoot (Tree *t, int outgroup);
int MovePolyCalculationRoot (PolyTree *t, int outgroup);
int NumConstrainedTips (TreeNode *p);
int NumDatedTips (TreeNode *p);
void OrderTips (PolyTree *t);
void PrintNewick (char **s, int *len, Tree *t);
void PrintNodes (Tree *t);
void PrintPolyNodes (PolyTree *pt);
int PrunePolyTree (PolyTree *pt);
int RandPerturb (Tree *t, int nPert, SafeLong *seed);
int RandResolve (Tree *tt, PolyTree *t, SafeLong *seed, int destinationIsRooted);
int ResetBrlensFromTree (Tree *tree, Tree *vTree);
void ResetIntNodeIndices(PolyTree *t);
void ResetPolyTree (PolyTree *t);
void ResetPolyTreePartitions (PolyTree *pt);
void ResetPolyTreeRelClockParams (PolyTree *pt);
int ResetRootHeight (Tree *t, MrBFlt rootHeight);
void ResetTipIndices (PolyTree *pt);
int ResetTopology (Tree *t, char *s);
int ResetTopologyFromTree (Tree *tree, Tree *top);
int ResetTopologyFromPolyTree (Tree *tree, PolyTree *top);
void ResetTreePartitions (Tree *t);
int RetrieveRTopology (Tree *t, int *order);
int RetrieveRTree (Tree *t, int *order, MrBFlt *brlens);
int RetrieveRTreeWithIndices (Tree *t, int *order, MrBFlt *brlens);
int RetrieveUTopology (Tree *t, int *order);
int RetrieveUTree (Tree *t, int *order, MrBFlt *brlens);
void SetDatedNodeAges(Param* param, int chain, int state);
void SetNodeDepths (Tree *t);
int SetTreeNodeAges (Param *param, int chain, int state);
int ShowPolyNodes (PolyTree *pt);
int ShowTree (Tree *t);
int StoreRPolyTopology (PolyTree *t, int *order);
int StoreRPolyTree (PolyTree *t, int *order, MrBFlt *brlens);
int StoreRTopology (Tree *t, int *order);
int StoreRTree (Tree *t, int *order, MrBFlt *brlens);
int StoreRTreeWithIndices (Tree *t, int *order, MrBFlt *brlens);
int StoreUPolyTopology (PolyTree *t, int *order);
int StoreUPolyTree (PolyTree *t, int *order, MrBFlt *brlens);
int StoreUTopology (Tree *t, int *order);
int StoreUTree (Tree *t, int *order, MrBFlt *brlens);
MrBFlt TreeLen (Tree *t);
void Unmark (TreeNode *p);
void UpdateTreeWithClockrate (Tree *t, MrBFlt clockRate);
void WriteEventTree (TreeNode *p, int chain, Param *param);
void WriteEventTreeToPrintString (TreeNode *p, int chain, Param *param, int printAll);
void WriteEvolTree (TreeNode *p, int chain, Param *param);
void WriteTopologyToFile (FILE *fp, TreeNode *p, int isRooted);
void WriteTreeToPrintString (Param *param, int chain, TreeNode *p, int showBrlens, int isRooted);
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