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discrete.h

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Last change on this file was 2175, checked in by westram, 21 years ago
upgrade to PHYLIP 3.6
Property svn:eol-style set to `native` Property svn:keywords set to `Author Date Id Revision`
File size: 5.4 KB

Line
1
2	/* version 3.6. (c) Copyright 1993-2000 by the University of Washington.
3	Written by Joseph Felsenstein, Akiko Fuseki, Sean Lamont, and Andrew Keeffe.
4	Permission is granted to copy and use this program provided no fee is
5	charged for it and provided that this copyright notice is not removed. */
6
7	/*
8	discrete.h: included in pars
9	*/
10
11	typedef struct gbases {
12	discbaseptr discbase;
13	struct gbases *next;
14	} gbases;
15
16	struct LOC_hyptrav {
17	boolean bottom;
18	node *r;
19	discbaseptr hypset;
20	boolean maybe, nonzero;
21	unsigned char tempset, anc;
22	} ;
23
24
25	extern long nonodes, endsite, outgrno, nextree, which;
26	extern boolean interleaved, printdata, outgropt, treeprint, dotdiff;
27	extern steptr weight, category, alias, location, ally;
28	extern sequence y, convtab;
29
30	#ifndef OLDC
31	/function prototypes/
32	void inputdata(long);
33	void alloctree(pointarray *, long, boolean);
34	void setuptree(pointarray, long, boolean);
35	void alloctip(node , long , unsigned char *);
36	void sitesort(long, steptr);
37	void sitecombine(long);
38	void sitescrunch(long);
39
40	void makevalues(pointarray, long , unsigned char , boolean);
41	void fillin(node , node , node *);
42	long getlargest(long *);
43	void multifillin(node , node , long);
44	void sumnsteps(node , node , node *, long, long);
45	void sumnsteps2(node , node , node , long, long, long );
46	void multisumnsteps(node , node , long, long, long *);
47	void multisumnsteps2(node *);
48	void findoutgroup(node , boolean );
49	boolean alltips(node , node );
50
51	void gdispose(node , node *, pointarray);
52	void preorder(node , node , node , node , node , node , long );
53	void updatenumdesc(node , node , long);
54	void add(node , node , node , node *, boolean, pointarray,
55	node *, long , unsigned char *);
56	void findbelow(node *, node , node *);
57	void re_move(node , node , node *, boolean, pointarray,
58	node *, long , unsigned char *);
59	void postorder(node *);
60	void getnufork(node , node , pointarray, long , unsigned char );
61	void reroot(node , node );
62	void reroot2(node , node );
63
64	void reroot3(node , node , node , node , node **);
65	void savetraverse(node *);
66	void newindex(long, node *);
67	void flipindexes(long, pointarray);
68	boolean parentinmulti(node *);
69	long sibsvisited(node , long );
70	long smallest(node , long );
71	void bintomulti(node , node , node *, long , unsigned char *);
72	void backtobinary(node *, node , node **);
73	boolean outgrin(node , node );
74
75	void flipnodes(node , node );
76	void moveleft(node , node , node **);
77	void savetree(node , long , pointarray, node *, long ,
78	unsigned char *);
79	void addnsave(node , node , node , node , node *, boolean multf,
80	pointarray , long , long , unsigned char *);
81	void addbestever(long , long , long, boolean, long , bestelm );
82	void addtiedtree(long, long , long, boolean, long , bestelm *);
83	void clearcollapse(pointarray);
84	void clearbottom(pointarray);
85	void collabranch(node ,node ,node *);
86	boolean allcommonbases(node , node , boolean *);
87
88	void findbottom(node , node *);
89	boolean moresteps(node , node );
90	boolean passdown(node , node , node , node , node , node , node *,
91	node , node , boolean);
92	boolean trycollapdesc(node , node , node , node , node , node ,
93	node , node , node , boolean ,long , unsigned char *);
94	void setbottom(node *);
95	boolean zeroinsubtree(node , node , node , node , node , node ,
96	node , node , boolean , node , long , unsigned char *);
97	boolean collapsible(node , node , node , node , node , node , node *,
98	node , boolean , node , long , unsigned char , pointarray);
99	void replaceback(node *,node ,node ,node ,long ,unsigned char *);
100	void putback(node , node , node , node *);
101	void savelocrearr(node , node , node , node , node , node ,
102	node , node , node , node , long, long , boolean, boolean,
103	boolean , long , bestelm , pointarray, node , long ,
104	unsigned char *);
105
106	void clearvisited(pointarray);
107	void hyprint(long,long,struct LOC_hyptrav *, pointarray);
108	void gnubase(gbases , gbases , long);
109	void chuckbase(gbases , gbases *);
110	void hyptrav(node *, discbaseptr, long, long, boolean, pointarray,
111	gbases **);
112	void hypstates(long, node , pointarray, gbases *);
113	void initbranchlen(node *);
114	void initmin(node *, long, boolean);
115	void initbase(node *, long);
116	void inittreetrav(node *, long);
117
118	void compmin(node , node );
119	void minpostorder(node *, pointarray);
120	void branchlength(node , node , double *, pointarray);
121	void printbranchlengths(node *);
122	void branchlentrav(node , node , long, long, double *, pointarray);
123	void treelength(node *, long, pointarray);
124	void coordinates(node , long , double , long *);
125	void drawline(long, double, node *);
126	void printree(node *, double);
127	void writesteps(long, boolean, steptr, node *);
128
129	void treeout(node , long, long , node *);
130	void drawline3(long, double, node *);
131	void standev(long, long, long, double, double , long *, longer);
132	void freetip(node *);
133	void freenontip(node *);
134	void freenodes(long, pointarray);
135	void freenode(node **);
136	void freetree(long, pointarray);
137	void freegarbage(gbases **);
138	void freegrbg(node **);
139	void treeout3(node p, long nextree, long col, node *root);
140	/function prototypes/
141	#endif

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source: trunk/GDE/PHYLIP/discrete.h

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