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Last change on this file was 5876, checked in by westram, 15 years ago
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1	PROJECT pb_com
2	OBJECT_KEY PT, # MAIN PREFIX
3	MAX_KEY 100, # MAX NUMBER OF AN ATTRIBUTE
4	MAX_OBJECT 20, # MAX DIFFERENT STRUCTURES
5	MAX_STRING_LEN 1024,
6	MAX_PAR_CNT 16,
7	MAGIC_NUMBER 0x471100, # MAGIC_NUMBER 6 HEX DIGITS
8
9	SERVER_INCLUDES (~
10	#include <stdio.h>
11	#include "PT_server.h"
12	#include "PT_com.h"~)
13	INCLUDE_INCLUDES (~$$(#FILE aisc_include.header)~)
14
15	DATA {
16
17	# ******************************* USER DATA *****************************************
18
19	@CONST, @VALUE, @DOCU;
20	LIST_SIZE, 20, (~Size of I_STR Buffer~);
21	PERC_SIZE, 20, (~How many centigrades to look~);
22	ALPHA_SIZE, 24, (~24 letters~);
23	DOMAIN_MIN_LENGTH, 8, (~Minimum length of a domain~);
24	PT_PART_DEEP, 2, (~The Deep of the Partitions~);
25
26
27	# ***************************** PRIVAT STRUCTURES: DO NOT CHANGE *******************************
28
29	@STRUCT, @SKEY, @SKEYC, @SDOCU;
30
31	dll_public, , , (~Vater einer DoubledLinkedList dll~), {
32	@TYPE, @IDENT, @REF, @ACC, @SAVE, @KEY, @KEYC, @INIT, @DOCU;
33	t_key, key, t, r, , , , , (~ The key~);
34	int, cnt, t, r, , CNT, 0, , (~ Number of elements~);
35	long, hash, t, , , , , , (~ Hash Table~);
36	dllheader_ext, parent, flt, r, , PARENT, 1, , (~ My Owner~);
37	dllheader_ext, last, flt, r, , LAST, 2, , (~ Pointer to the last element~);
38	};
39
40
41	dll_header, COMMON, 0, (~Der Link Header (sollte Kopf jeder Funktion sein)~), {
42	@TYPE, @IDENT, @REF, @ACC, @SAVE, @KEY, @KEYC, @INIT, @DOCU;
43	t_key, key, t, r, , KEY, 0, , (~ The Key~);
44	aisc_string, aisc_get_keystring,%,r, , KEYSTRING,1, , (~ THE STRING of the KEY ~);
45	dll_public, parent, ls, r, , (~~), 2, , (~ Pointer to dll_public~);
46	aisc_string, ident, t, , 1, IDENT, 5, , (~ The ident [not necessary]~);
47	};
48
49
50	# ******************************* USER STRUCTURES *****************************************
51
52	# new probe design/match:
53
54	PT_probeparts, TPROBEPARTS, 9, (~a part of a probe to search in the Prefix tree~), {
55	@TYPE, @IDENT, @REF, @ACC, @KEY, @KEYC, @INIT, @DOCU;
56	dllh, mh, t, , (~~), 0, , (~Header~);
57	aisc_string,sequence, t, , , , , (~ The Sequence to check ~);
58	PT_tprobes, source, fl, , , , , (~ A pointer to the source ~);
59	int, start, t, , , , , (~ The number of characters cut off at the start of the tprobe~);
60	double, dt, t, , , , , (~ Add this temperature to the result ~);
61	double, sum_bonds,t, , , , , (~ The sum of bonds of the longest non mismatch string ~);
62	};
63
64	PT_pdc_specials, SPECIALS, 10, (~ non standard substrings of a probe ~), {
65	@TYPE, @IDENT, @REF, @ACC, @KEY, @KEYC, @INIT, @DOCU;
66	dllh, mh, t, , (~~), 0, , (~Header~);
67	int, mode, t, , MODE, 9, , (~ ==1 -> split domains; ==0 -> dont split domains ~);
68	double, ll, t, , LLEFT, 10, , (~ the bond value of the character left of the left ~);
69	double, l, t, , LEFT, 11, , (~ The bond value left character ~);
70	double, c, t, , CENTER, 12, , (~ The center character~);
71	double, r, t, , RIGHT, 13, , (~...~);
72	double, rr, t, , RRIGHT, 14, , (~...~);
73	};
74
75	PT_tprobes, TPROBE, 11, (~ The probe we want to test ~), {
76	@TYPE, @IDENT, @REF, @ACC, @KEY, @KEYC, @INIT, @DOCU;
77	dllh, mh, t, , (~~), 0, , (~Header~);
78	aisc_string,sequence, t, r, SEQUENCE, 10, , (~ The Sequence to check ~);
79	int, seq_len, t, , , , , (~ The len of the sequence ~);
80	double, sum_bonds, t, , , , , (~ The sum of all bonds ~);
81	double, quality, t, r, QUALITY, 11, , (~ The quality of the probe = GROUPSIZE*dT ~);
82	int, groupsize, t, r, GROUPSIZE, 15, , (~ The Size of the group ~);
83	int, hairpin, t, r, HAIRPIN, 16, , (~ How many hairpin bonds ~);
84	double, whairpin, t, r, WHAIRPIN, 17, , (~ Weighted Hairpins ~);
85	int, perc, vt, r, PERC, 18, , (~ Result: How many non group hits per centigrade ~), SIZE PERC_SIZE;
86	double, temp, t, r, TEMPERATURE, 20, , (~ The temperature of the probe ~);
87	int, mishit, t, r, MISHIT, 25, , (~ How many non group members hit ~);
88	int, apos, t, , APOS, 26, , (~ The absolute position of probe ~);
89	int, get_r_pos, t, , ECOLI_POS, 27, , (~ The ecoli based position of probe ~);
90	aisc_string,get_design_hinfo,%, r, INFO_HEADER, 30, , (~the combined info text of a probe design~);
91	aisc_string,get_design_info, %, r, INFO, 31, , (~the combined info text of a probe design~);
92	};
93
94	PT_bond, , , (~ The definition of a bond ~), {
95	@TYPE, @IDENT, @REF, @ACC, @KEY, @KEYC, @INIT, @DOCU;
96	double, val, t, , VAL, 0, 0.0, (~ how strong is that bond ~);
97	};
98
99	PT_sequence, SEQUENCE, 13, (~ The additional sequences ~), {
100	@TYPE, @IDENT, @REF, @ACC, @KEY, @KEYC, @INIT, @DOCU;
101	dllh, mh, t, , (~~), 0, , (~Header~);
102	bytestring,seq, t, , SEQUENCE, 10, , (~The Sequence~);
103	};
104
105	PT_pdc, PDC, 12, (~ The new probe design ~), {
106	@TYPE, @IDENT, @REF, @ACC, @KEY, @KEYC, @INIT, @DOCU;
107	dllh, mh, t, , (~~), 0, , (~Header~);
108	PT_probeparts, parts, d, , , , , (~ The parts of the probes ~);
109	PT_probeparts, dparts, d, , , , , (~ The duplicated parts of the probes ~);
110	PT_bond, bond, siv, , BOND, 10, , (~The bond matrix~), SIZE (4*4);
111	int, dummy, t, , , , init_bond_matrix(THIS), (~ init bond matrix ~);
112	double, dte, t, , DTEDGE, 12, 50.0, (~ The Temperature drop per percent mismatch on the edge of the probe ~);
113	double, dt, t, , DT, 13, 50.0, (~ The temperature drop per percent mismatch ~);
114	double, split, t, , SPLIT, 14, .5, (~ Split the domains if bond value is less the average bond value - split ~);
115	PT_pdc_specials,specials, d, , SPECIALS, 15, , (~ Exceptions of splitting domains~);
116	int, looplen, t, , LOOPLEN, 17, 4, (~ The Loop Length of a probe ~);
117	int, probelen, t, , PROBELENGTH, 20, 18, (~the length of the probe~);
118	double, mintemp, t, , MINTEMP, 22, 30.0, (~minimum temperuture~);
119	double, maxtemp, t, , MAXTEMP, 23, 100.0, (~maximum temperature~);
120	double, min_gc, t, , MINGC, 25, .3, (~the minimum GC content~);
121	double, max_gc, t, , MAXGC, 26, 1.0, (~the maximum GC content~);
122	double, maxbonds, t, , MAXBOND, 27, 4.0, (~The maximum of hairpin bonds~);
123	int, minpos, t, , MINPOS, 30, 0, (~the minimum position~);
124	int, maxpos, t, , MAXPOS, 31, 100000, (~the maximum position~);
125	double, mintarget, t, , MINTARGETS, 35, .7, (~the minimum targets for a group of species~);
126	int, mishit, t, , MISHIT, 36, 0, (~the maximum mis hits~);
127	int, clipresult, t, , CLIPRESULT, 40, 40, (~Clip the Result list~);
128	int, pos_groups, vt, , , , , (~Position of Groups~), SIZE ALPHA_SIZE;
129	bytestring, checksums, t, w, CHECKSUMS, 44, , (~a list of sequence checksums seperated by '#' is optional~);
130	bytestring, names, t, w, NAMES, 45, , (~a list of names seperated by '#' is expected~);
131	bytestring, PT_unknown_names,%, r, UNKNOWN_NAMES, 46, , (~List of unknown names~);
132	PT_sequence, sequences, d, , SEQUENCE, 47, , (~Additional Sequences~);
133	int, PT_start_design,%, w, GO, 50, , (~Start the design procedure~);
134	PT_tprobes, tprobes, d, r, TPROBE, 60, , (~ The result ~);
135	};
136
137	# function to iterate through all probes existing in PT-Server
138
139	PT_exProb, PEP, 14, (~ Get all existing probes ~), {
140	@TYPE, @IDENT, @REF, @ACC, @KEY, @KEYC, @INIT, @DOCU;
141	dllh, mh, t, , (~~), 0, , (~ Header ~);
142	int, plength, t, , PLENGTH, 10, 20, (~ Length of searched probes ~);
143	int, numget, t, , NUMGET, 11, 200, (~ Number of searched probes ~);
144	int, restart, t, , RESTART, 12, 1, (~ 1 => start from beginning ~);
145	bytestring, next_probe, t, , NEXT_PROBE, 13, , (~ next probe to look for (internal) ~);
146	int, PT_find_exProb, %, w, FIND_PROBES,14, , (~ search probes (result=separated by ','s ) ~);
147	aisc_string, result, t, r, RESULT, 15, , (~ The result ~);
148	};
149
150	# get next relatives (used by AWTC and NALIGNER)
151
152	PT_family_list, FAMILYLIST, 8, (~the family list~), {
153	@TYPE, @IDENT, @REF, @ACC, @SAVE, @KEY, @KEYC, @INIT, @DOCU;
154	dllh, mh, t, , , (~~), 0, , (~Header~);
155	aisc_string, name, t, r, , NAME, 11, , (~name of species~);
156	int, matches, t, r, , MATCHES, 13, , (~number of matches~);
157	double, rel_matches, t, r, , REL_MATCHES, 14, , (~MATCHES / (SEQ_LEN - PROBE_LEN + 1) ~);
158	};
159
160	# used below in LOCS/MATCH_STRING
161
162	PT_probematch, MATCHLIST, 1, (~the PROBEMATCH list~), {
163	@TYPE, @IDENT, @REF, @ACC, @SAVE, @KEY, @KEYC, @INIT, @DOCU;
164	dllh, mh, t, , , (~~), 0, , (~Header~);
165	int, name, t, r, , ID, 10, , (~id of species~);
166	aisc_string,virt_name, %, r, , NAME, 11, , (~name of species~);
167	int, b_pos, t, r, , POS, 12, , (~pos of probe~);
168	int, g_pos, t, r, , GPOS, 13, , (~pos of probe (gene relative)~);
169	int, rpos, t, r, , , , , (~relative pos of probe~);
170	int, mismatches, t, r, , MISMATCHES, 14, , (~number of mismatches~);
171	aisc_string,virt_fullname, %, r, , FULLNAME, 15, , (~fullname of species (or genename if it's a gene pt server)~);
172	double, wmismatches, t, r, , WMISMATCHES, 16, , (~number of weighted mismatches~);
173	int, N_mismatches, t, r, , N_MISMATCHES, 17, , (~number of 'N' mismatches~);
174	int, is_member, t, r, , IS_MEMBER, 18, , (~member of group~);
175	double, dt, t, r, , DT, 19, , (~the dt of a probe~);
176	char, sequence, l, r, , SEQUENCE, 22, , (~path of probe~);
177	int, reversed, t, r, , REVERSED, 25, , (~reversed probe matches~);
178	# aisc_string,get_match_hinfo,%, r, , INFO_HEADER, 26, , (~the combined info text of _one_ probe match (header)~);
179	# aisc_string,get_match_info, %, r, , INFO, 27, , (~the combined info text of _one_ probe match~);
180	};
181
182	# used below in MAIN/SPECIESLIST
183
184	PT_species_list, SPECIESLIST, 5, (~the species list~), {
185	@TYPE, @IDENT, @REF, @ACC, @SAVE, @KEY, @KEYC, @INIT, @DOCU;
186	dllh, mh, t, , , (~~), 0, , (~Header~);
187	int, member, t, rw, , MEMBER, 12, , (~species member of group~);
188	};
189
190	# global interface
191
192	PT_local, LOCS, 6, (~local communication buffer~), {
193	@TYPE, @IDENT, @REF, @ACC, @SAVE, @KEY, @KEYC, @INIT, @DOCU;
194	dllh, mh, t, , , (~~), 0, , (~Header~);
195	int, socket, t, , , , , pt_init_socket(THIS), (~the callback~), DESTROY pt_destroy_socket(THIS);
196	aisc_string, probe_match, %, w, , SEARCHMATCH, 8, , (~ Searches all species where probe maches ~);
197	aisc_string, pm_sequence, t, , , , , , (~ the sequence ~);
198	aisc_string, pm_csequence, t, , , , , , (~ the complement sequence ~);
199	int, pm_reversed, t, rw, , MATCH_REVERSED, 9, 1, (~ reverse probe ~);
200	int, pm_complement, t, rw, , MATCH_COMPLEMENT, 10, , (~ complement probe ~);
201	int, pm_max, t, rw, , MATCH_MAX_MISMATCHES, 11, , (~ max mismatches ~);
202	int, pm_max_spec, t, rw, , MATCH_MAX_SPECIES, 12, , (~ max number of species matching ~);
203	int, sort_by, t, rw, , MATCH_SORT_BY, 13, , (~ 0 == mismatches 1 == weighted mismatches 2 == weighted mismatches with pos and strength~);
204	PT_probematch, pm, d, r, , MATCH_LIST, 15, , (~ result: List of species where probe maches ~);
205	int, matches_truncated, t, r, , MATCHES_TRUNCATED, 17, , (~ result: whether MATCH_LIST was truncated ~);
206	bytestring, match_string, %, r, , MATCH_STRING, 18, , (~ result: List of species where probe maches ~);
207	bytestring, MP_match_string, %, r, , MP_MATCH_STRING, 19, , (~ result: List of species where probe maches and #mismatches ~);
208	bytestring, MP_all_species_string,%, r, , MP_ALL_SPECIES_STRING,20, , (~ result: List of all species in Database ~);
209	int, MP_count_all_species, %, r, , MP_COUNT_ALL_SPECIES, 21, , (~ result: Number of all species in Database ~);
210	aisc_string, ls_error, t, r, , ERROR, 23, "", (~ the error text ~);
211
212	int, group_count, t, r, , PROBE_NGROUP, 34, , (~ result: Number of selected species~);
213
214	PT_pdc, pdc, d, , , PROBE_DESIGN_CONFIG, 40, , (~The new probe design~);
215	PT_exProb, ep, d, , , PROBE_FIND_CONFIG, 42, , (~Find all existing probes~);
216
217	# com-codes 50-59 were used by find-family, dont re-use for some time (ralf 10/2008)
218
219	aisc_string, user, t, rw, , USER, 60, "unknown", (~the username~);
220	aisc_string, address, t, rw, , ADDRESS, 61, "unknown", (~the useraddress~);
221	aisc_string, login, t, rw, , LOGINTIME, 62, "notime", (~the date the user logged in~);
222
223	bytestring, ff_find_family, %, w, , FF_FIND_FAMILY, 70, , (~ Searches the family ~);
224	int, ff_pr_len, t, rw, , FF_PROBE_LEN, 71, 12, (~ Length of probes ~);
225	int, ff_mis_nr, t, rw, , FF_MISMATCH_NUMBER, 72, 0, (~ Number of mismatches ~);
226	int, ff_find_type, t, rw, , FF_FIND_TYPE, 73, 0, (~ Type of find 0 = search all, 1 = a* ~);
227	int, ff_compl, t, rw, , FF_COMPLEMENT, 74, 1, (~ Search for complement? (combination of: fwd=1, rev=2, rev.compl=4, compl=8) ~);
228	PT_family_list, ff_fl, d, r, , FF_FAMILY_LIST, 80, , (~ Sorted List of family ~); # note: This uses 80 AND 81!
229	int, ff_list_size, t, r, , FF_FAMILY_LIST_SIZE, 82, , (~ size of result list ~);
230	int, ff_sort_type, t, rw, , FF_SORT_TYPE, 83, 0, (~ Type of sorting 0 = MATCHES, 1 = REL_MATCHES ~);
231	int, ff_sort_max, t, rw, , FF_SORT_MAX, 84, 0, (~ Sort only best FF_SORT_MAX sequences ~);
232	};
233
234	PT_main, MAIN, 7, (~Die globalen Daten~), {
235	@TYPE, @IDENT, @REF, @ACC, @SAVE, @KEY, @KEYC, @INIT, @DOCU;
236	t_key, key, t, n, , , , , (~Der KEY~);
237	PT_local, loc_st, d, , , LOCS, 10, , (~Die Parameter~);
238	aisc_string, server_shutdown,%, w, , SHUTDOWN, 20, , (~shut down~);
239	int, who, t, rw, , STARTER, 21, , (~who started this server~);
240	int, m_type, t, , , MESSAGE_TYPE, 31, 0, (~the message type ~);
241	aisc_string, m_text, t, , , MESSAGE, 32, "NO_MSG", (~ the message text ~);
242	int, broadcast, %, w, , BROADCAST, 33, , (~ broadcast func ~);
243	PT_species_list,sl, d, r, , SPECIESLIST, 50, , (~list of species~);
244	};
245
246	};

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