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tree.h

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Last change on this file was 10416, checked in by aboeckma, 11 years ago
Added mr bayes (no menu yet)
File size: 5.4 KB

Line
1	#define TREEBUFINCREASE 200
2
3	/* tree utility functions */
4	int AddToTreeList (TreeList treeList, Tree tree);
5	Tree *AllocateTree (int numTaxa);
6	Tree *AllocateFixedTree (int numTaxa, int isRooted);
7	int AllocateTreePartitions (Tree *t);
8	PolyTree *AllocatePolyTree (int numTaxa);
9	int AllocatePolyTreePartitions (PolyTree *pt);
10	int AllocatePolyTreeRelClockParams (PolyTree *pt, int nBSets, int nESets);
11	int AreTopologiesSame(Tree t1, Tree t2);
12	int AreTreesSame (Tree t1, Tree t2);
13	int BuildConstraintTree (Tree t, PolyTree pt, char **localTaxonNames);
14	int BuildRandomRTopology (Tree t, SafeLong seed);
15	int BuildRandomUTopology (Tree t, SafeLong seed);
16	int CheckConstraints (Tree *t);
17	int CheckSetConstraints (Tree *t);
18	void ColorClusters (TreeNode p, int index);
19	void CopySubtreeToTree (Tree subtree, Tree t);
20	int CopyToPolyTreeFromPolyTree (PolyTree to, PolyTree from);
21	int CopyToSpeciesTreeFromPolyTree (Tree to, PolyTree from);
22	int CopyToTreeFromPolyTree (Tree to, PolyTree from);
23	void CopyPolyNodes (PolyNode p, PolyNode q, int nLongsNeeded);
24	int CopyToTreeFromTree (Tree to, Tree from);
25	void CopyTreeNodes (TreeNode p, TreeNode q, int nLongsNeeded);
26	void CopyTreeToSubtree (Tree t, Tree subtree);
27	int Deroot(PolyTree *pt);
28	void EraseTreeList (TreeList *treeList);
29	void findAllowedClockrate (Tree t, MrBFlt minClockRate, MrBFlt *maxClockRate );
30	void FreePolyTree (PolyTree *pt);
31	void FreePolyTreePartitions (PolyTree *pt);
32	void FreePolyTreePopSizeParams (PolyTree *pt);
33	void FreePolyTreeRelClockParams (PolyTree *pt);
34	void FreeTree (Tree *t);
35	void FreeTreePartitions (Tree *pt);
36	void GetDatedNodeDepths (TreeNode p, MrBFlt nodeDepths);
37	void GetDatedNodes (TreeNode p, TreeNode *datedNodes);
38	void GetDownPass (Tree *t);
39	void GetNodeDownPass (Tree t, TreeNode p, int i, int j);
40	void GetPolyAges (PolyTree *t);
41	void GetPolyDepths (PolyTree *t);
42	void GetPolyDownPass (PolyTree *t);
43	void GetPolyNodeDownPass (PolyTree t, PolyNode p, int i, int j);
44	int GetRandomEmbeddedSubtree (Tree t, int nTerminals, SafeLong seed, int *nEmbeddedTrees);
45	int GetFromTreeList (TreeList treeList, Tree tree);
46	int InitBrlens (Tree *t, MrBFlt v);
47	int InitCalibratedBrlens (Tree t, MrBFlt minLength, SafeLong seed);
48	int InitClockBrlens (Tree *t);
49	int IsCalibratedClockSatisfied (Tree t,MrBFlt minClockRate,MrBFlt *maxClockRate , MrBFlt tol);
50	int IsClockSatisfied (Tree *t, MrBFlt tol);
51	int IsTreeConsistent (Param *param, int chain, int state);
52	int LabelTree (Tree t, char *taxonNames);
53	void Mark (TreeNode *p);
54	void MarkDatedSubtree (TreeNode *p);
55	int MoveCalculationRoot (Tree *t, int outgroup);
56	int MovePolyCalculationRoot (PolyTree *t, int outgroup);
57	int NumConstrainedTips (TreeNode *p);
58	int NumDatedTips (TreeNode *p);
59	void OrderTips (PolyTree *t);
60	void PrintNewick (char *s, int len, Tree *t);
61	void PrintNodes (Tree *t);
62	void PrintPolyNodes (PolyTree *pt);
63	int PrunePolyTree (PolyTree *pt);
64	int RandPerturb (Tree t, int nPert, SafeLong seed);
65	int RandResolve (Tree tt, PolyTree t, SafeLong *seed, int destinationIsRooted);
66	int ResetBrlensFromTree (Tree tree, Tree vTree);
67	void ResetIntNodeIndices(PolyTree *t);
68	void ResetPolyTree (PolyTree *t);
69	void ResetPolyTreePartitions (PolyTree *pt);
70	void ResetPolyTreeRelClockParams (PolyTree *pt);
71	int ResetRootHeight (Tree *t, MrBFlt rootHeight);
72	void ResetTipIndices (PolyTree *pt);
73	int ResetTopology (Tree t, char s);
74	int ResetTopologyFromTree (Tree tree, Tree top);
75	int ResetTopologyFromPolyTree (Tree tree, PolyTree top);
76	void ResetTreePartitions (Tree *t);
77	int RetrieveRTopology (Tree t, int order);
78	int RetrieveRTree (Tree t, int order, MrBFlt *brlens);
79	int RetrieveRTreeWithIndices (Tree t, int order, MrBFlt *brlens);
80	int RetrieveUTopology (Tree t, int order);
81	int RetrieveUTree (Tree t, int order, MrBFlt *brlens);
82	void SetDatedNodeAges(Param* param, int chain, int state);
83	void SetNodeDepths (Tree *t);
84	int SetTreeNodeAges (Param *param, int chain, int state);
85	int ShowPolyNodes (PolyTree *pt);
86	int ShowTree (Tree *t);
87	int StoreRPolyTopology (PolyTree t, int order);
88	int StoreRPolyTree (PolyTree t, int order, MrBFlt *brlens);
89	int StoreRTopology (Tree t, int order);
90	int StoreRTree (Tree t, int order, MrBFlt *brlens);
91	int StoreRTreeWithIndices (Tree t, int order, MrBFlt *brlens);
92	int StoreUPolyTopology (PolyTree t, int order);
93	int StoreUPolyTree (PolyTree t, int order, MrBFlt *brlens);
94	int StoreUTopology (Tree t, int order);
95	int StoreUTree (Tree t, int order, MrBFlt *brlens);
96	MrBFlt TreeLen (Tree *t);
97	void Unmark (TreeNode *p);
98	void UpdateTreeWithClockrate (Tree *t, MrBFlt clockRate);
99	void WriteEventTree (TreeNode p, int chain, Param param);
100	void WriteEventTreeToPrintString (TreeNode p, int chain, Param param, int printAll);
101	void WriteEvolTree (TreeNode p, int chain, Param param);
102	void WriteTopologyToFile (FILE fp, TreeNode p, int isRooted);
103	void WriteTreeToPrintString (Param param, int chain, TreeNode p, int showBrlens, int isRooted);

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source: branches/items/GDE/MrBAYES/mrbayes_3.2.1/tree.h

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