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Last change on this file was 7986, checked in by westram, 14 years ago
PT-SERVER allow to specify amount+limit where N is accept moved hardcoded PT_MAX_MATCHES into AISC interface as parameter (with same limit) added links to information related to MAGIC_NUMBER maintain a list of previously used MAGIC_NUMBERs AISC parameters removed unused parameter MATCH_MAX_SPECIES added new parameters MATCH_MAX_HITS, MATCH_N_ACCEPT, MATCH_N_LIMIT defaulted them to previously hardcoded limits parametrized set_table_for_PT_N_mis() using MATCH_N_ACCEPT + MATCH_N_LIMIT protect vs illegal index into psg.N_mismatches arb_probe fixed commandline parser (no longer modifies passed argv) added new parameters matchacceptN, matchlimitN + matchmaxresults added some unit tests testing N-matches (in match-string and/or seqdata) testing truncation of results
Property svn:eol-style set to `native` Property svn:keywords set to `Author Date Id Revision`
File size: 21.4 KB

Line
1	PROJECT pb_com
2	OBJECT_KEY PT, # MAIN PREFIX
3	MAX_KEY 33, # MAX NUMBER OF AN ATTRIBUTE
4	MAX_OBJECT 12, # MAX DIFFERENT USER STRUCTURES
5	MAX_STRING_LEN 1024,
6	MAX_PAR_CNT 16,
7	MAGIC_NUMBER 0x615054, # MAGIC_NUMBER 6 HEX DIGITS (see AISC/magic.lst@PTSERVER)
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, 52, (~26 BIG, 26 small 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, , , (~parent of dll (=DoubledLinkedList)~), {
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, (~link header (should be head of each function)~), {
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, 11, (~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, 8, , (~==1 -> split domains; ==0 -> don't split domains~);
68	double, ll, t, , LLEFT, 9, , (~the bond value of the character left of the left~);
69	double, l, t, , LEFT, 10, , (~The bond value left character~);
70	double, c, t, , CENTER, 11, , (~The center character~);
71	double, r, t, , RIGHT, 12, , (~...~);
72	double, rr, t, , RRIGHT, 13, , (~...~);
73	};
74
75	PT_tprobes, TPROBE, 9, (~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, 8, , (~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, 9, , (~The quality of the probe = GROUPSIZE*dT~);
82	int, groupsize, t, r, GROUPSIZE, 10, , (~The Size of the group~);
83	int, hairpin, t, r, HAIRPIN, 11, , (~How many hairpin bonds~);
84	double, whairpin, t, r, WHAIRPIN, 12, , (~Weighted Hairpins~);
85	int, perc, vt, r, PERC, 13, , (~Result: How many non group hits per centigrade~), SIZE PERC_SIZE;
86	double, temp, t, r, TEMPERATURE, 14, , (~The temperature of the probe~);
87	int, mishit, t, r, MISHIT, 15, , (~How many non group members hit~);
88	int, apos, t, , APOS, 16, , (~The absolute position of probe~);
89	int, get_r_pos, t, , ECOLI_POS, 17, , (~The ecoli based position of probe~);
90	aisc_string,get_design_hinfo,%, r, INFO_HEADER, 18, , (~the combined info text of a probe design~);
91	aisc_string,get_design_info, %, r, INFO, 19, , (~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, 8, (~the additional sequences~), {
100	@TYPE, @IDENT, @REF, @ACC, @KEY, @KEYC, @INIT, @DOCU;
101	dllh, mh, t, , (~~), 0, , (~Header~);
102	bytestring,seq, t, , SEQUENCE, 8, , (~The Sequence~);
103	};
104
105	PT_pdc, PDC, 7, (~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, 8, , (~The bond matrix~), SIZE (4*4);
111	int, dummy, t, , , , init_bond_matrix(THIS), (~init bond matrix~);
112	double, dte, t, , DTEDGE, 9, 50.0, (~The Temperature drop per percent mismatch on the edge of the probe~);
113	double, dt, t, , DT, 10, 50.0, (~The temperature drop per percent mismatch~);
114	double, split, t, , SPLIT, 11, .5, (~Split the domains if bond value is less the average bond value - split~);
115	PT_pdc_specials,specials, d, , SPECIALS, 12, , (~Exceptions of splitting domains~);
116	int, looplen, t, , LOOPLEN, 14, 4, (~The Loop Length of a probe~);
117	int, probelen, t, , PROBELENGTH, 15, 18, (~the length of the probe~);
118	double, mintemp, t, , MINTEMP, 16, 30.0, (~minimum temperature~);
119	double, maxtemp, t, , MAXTEMP, 17, 100.0, (~maximum temperature~);
120	double, min_gc, t, , MINGC, 18, .3, (~the minimum GC content~);
121	double, max_gc, t, , MAXGC, 19, 1.0, (~the maximum GC content~);
122	double, maxbonds, t, , MAXBOND, 20, 4.0, (~The maximum of hairpin bonds~);
123	int, min_ecolipos, t, , MIN_ECOLIPOS, 21, -1, (~the minimum ecoli position [1..N]. -1 means 'no restriction'~);
124	int, max_ecolipos, t, , MAX_ECOLIPOS, 22, -1, (~the maximum ecoli position [1..N]. -1 means 'no restriction'~);
125	double, mintarget, t, , MINTARGETS, 23, .7, (~the minimum targets for a group of species~);
126	int, mishit, t, , MISHIT, 24, 0, (~the maximum mis hits~);
127	int, clipresult, t, , CLIPRESULT, 25, 40, (~Clip the Result list~);
128	int, pos_groups, vt, , , , , (~Position of Groups~), SIZE ALPHA_SIZE;
129	bytestring, checksums, t, w, CHECKSUMS, 26, , (~a list of sequence checksums separated by '#' is optional~);
130	bytestring, names, t, w, NAMES, 27, , (~a list of names separated by '#' is expected~);
131	bytestring, PT_unknown_names,%, r, UNKNOWN_NAMES, 28, , (~List of unknown names~);
132	PT_sequence, sequences, d, , SEQUENCE, 29, , (~Additional Sequences~);
133	int, PT_start_design,%, w, GO, 31, , (~Start the design procedure~);
134	PT_tprobes, tprobes, d, r, TPROBE, 32, , (~The result~);
135	};
136
137	# function to iterate through all probes existing in PT-Server
138
139	PT_exProb, PEP, 6, (~iterate all existing probes~), {
140	@TYPE, @IDENT, @REF, @ACC, @KEY, @KEYC, @INIT, @DOCU;
141	dllh, mh, t, , (~~), 0, , (~Header~);
142	int, plength, t, , PLENGTH, 8, 20, (~Length of searched probes~);
143	int, numget, t, , NUMGET, 9, 200, (~Number of searched probes~);
144	int, restart, t, , RESTART, 10, 1, (~1 => start from beginning~);
145	bytestring, next_probe, t, , NEXT_PROBE, 11, , (~next probe to look for (internal)~);
146	int, PT_find_exProb, %, w, FIND_PROBES,12, , (~search probes (result=separated by ','s )~);
147	aisc_string, result, t, r, RESULT, 13, , (~The result~);
148	};
149
150	# get next relatives (used by AWTC and NALIGNER)
151
152	PT_family_list, FAMILYLIST, 5, (~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, 8, , (~name of species~);
156	int, matches, t, r, , MATCHES, 9, , (~number of matches~);
157	double, rel_matches, t, r, , REL_MATCHES, 10, , (~MATCHES / (SEQ_LEN - PROBE_LEN + 1)~);
158	};
159
160	PT_family, FAMILYFINDER, 12, (~next relative search~), {
161	@TYPE, @IDENT, @REF, @ACC, @SAVE, @KEY, @KEYC, @INIT, @DOCU;
162	dllh, mh, t, , , (~~), 0, , (~Header~);
163	bytestring, find_family, %, w, , FIND_FAMILY, 8, , (~Searches the family~);
164	int, pr_len, t, rw, , PROBE_LEN, 9, 12, (~Length of probes~);
165	int, mis_nr, t, rw, , MISMATCH_NUMBER, 10, 0, (~Number of mismatches~);
166	int, find_type, t, rw, , FIND_TYPE, 11, 0, (~Type of find 0 = search all, 1 = a*~);
167	int, complement, t, rw, , COMPLEMENT, 12, 1, (~Search for complement? (combination of: fwd=1, rev=2, rev.compl=4, compl=8)~);
168	PT_family_list, fl, d, r, , FAMILY_LIST, 13, , (~Sorted List of family~); # note: This uses 80 AND 81!
169	int, list_size, t, r, , FAMILY_LIST_SIZE, 15, , (~size of result list~);
170	int, sort_type, t, rw, , SORT_TYPE, 16, 0, (~Type of sorting 0 = MATCHES, 1 = REL_MATCHES~);
171	int, sort_max, t, rw, , SORT_MAX, 17, 0, (~Sort only best FF_SORT_MAX sequences~);
172	int, range_start, t, rw, , RANGE_STARTPOS, 18, -1, (~if != -1 -> ignore matches starting left of that position [0..N-1]~);
173	int, range_end, t, rw, , RANGE_ENDPOS, 19, -1, (~if != -1 -> ignore matches ending right of that position [0..N-1]~);
174	};
175
176	# used below in LOCS/MATCH_STRING
177
178	PT_probematch, MATCHLIST, 4, (~the probe match list~), {
179	@TYPE, @IDENT, @REF, @ACC, @SAVE, @KEY, @KEYC, @INIT, @DOCU;
180	dllh, mh, t, , , (~~), 0, , (~Header~);
181	int, name, t, r, , ID, 8, , (~id of species~);
182	aisc_string, virt_name, %, r, , NAME, 9, , (~name of species~);
183	int, b_pos, t, r, , POS, 10, , (~pos of probe~);
184	int, g_pos, t, r, , GPOS, 11, , (~pos of probe (gene relative)~);
185	int, rpos, t, r, , , , , (~relative pos of probe~);
186	int, mismatches, t, r, , MISMATCHES, 12, , (~number of mismatches~);
187	aisc_string, virt_fullname, %, r, , FULLNAME, 13, , (~fullname of species (or genename if it's a gene pt server)~);
188	double, wmismatches, t, r, , WMISMATCHES, 14, , (~number of weighted mismatches~);
189	int, N_mismatches, t, r, , N_MISMATCHES, 15, , (~number of 'N' mismatches~);
190	double, dt, t, r, , DT, 16, , (~the dt of a probe~);
191	char, sequence, l, r, , SEQUENCE, 17, , (~path of probe~);
192	int, reversed, t, r, , REVERSED, 18, , (~reversed probe matches~);
193	aisc_string, get_match_overlay, %, r, , OVERLAY, 19, , (~ascii visualization of match~);
194	};
195
196	# used below in MAIN/SPECIESLIST
197
198	PT_species_list, SPECIESLIST, 3, (~the species list~), {
199	@TYPE, @IDENT, @REF, @ACC, @SAVE, @KEY, @KEYC, @INIT, @DOCU;
200	dllh, mh, t, , , (~~), 0, , (~Header~);
201	int, member, t, rw, , MEMBER, 8, , (~species member of group~);
202	};
203
204	# global interface
205
206	PT_local, LOCS, 2, (~local communication buffer~), {
207	@TYPE, @IDENT, @REF, @ACC, @SAVE, @KEY, @KEYC, @INIT, @DOCU;
208	dllh, mh, t, , , (~~), 0, , (~Header~);
209	int, socket, t, , , , , pt_init_socket(THIS), (~the callback~), DESTROY pt_destroy_socket(THIS);
210
211	aisc_string, probe_match, %, w, , SEARCHMATCH, 8, , (~Searches all species where probe matches~);
212	aisc_string, pm_sequence, t, , , , , , (~the sequence~);
213	aisc_string, pm_csequence, t, , , , , , (~the complement sequence~);
214	int, pm_reversed, t, rw, , MATCH_REVERSED, 9, 1, (~reverse probe~);
215	int, pm_complement, t, rw, , MATCH_COMPLEMENT, 10, , (~complement probe~);
216	int, pm_max, t, rw, , MATCH_MAX_MISMATCHES, 11, , (~max mismatches~);
217	int, pm_max_hits, t, rw, , MATCH_MAX_HITS, 12, 1000000, (~max number of hits reported (0=unlimited)~);
218	int, sort_by, t, rw, , MATCH_SORT_BY, 13, , (~0 == mismatches 1 == weighted mismatches 2 == weighted mismatches with pos and strength~);
219	int, pm_nmatches_ignored, t, rw, , MATCH_N_ACCEPT, 14, 1, (~max. of accepted matches vs N~);
220	int, pm_nmatches_limit, t, rw, , MATCH_N_LIMIT, 33, 4, (~N-matches are only accepted, if less than NMATCHES_LIMIT occur, otherwise no N-matches are accepted ~);
221	PT_probematch, pm, d, r, , MATCH_LIST, 15, , (~result: List of species where probe matches~);
222	int, matches_truncated, t, r, , MATCHES_TRUNCATED, 17, , (~result: whether MATCH_LIST was truncated~);
223	bytestring, match_string, %, r, , MATCH_STRING, 18, , (~result: List of species where probe matches~);
224
225	bytestring, MP_match_string, %, r, , MP_MATCH_STRING, 19, , (~result: List of species where probe matches and #mismatches~);
226	bytestring, MP_all_species_string,%, r, , MP_ALL_SPECIES_STRING,20, , (~result: List of all species in Database~);
227	int, MP_count_all_species, %, r, , MP_COUNT_ALL_SPECIES, 21, , (~result: Number of all species in Database~);
228
229	aisc_string, ls_error, t, r, , ERROR, 22, "", (~the error text~);
230
231	int, group_count, t, r, , PROBE_NGROUP, 23, , (~result: Number of selected species~);
232
233	PT_pdc, pdc, d, , , PROBE_DESIGN_CONFIG, 24, , (~The new probe design~);
234	PT_exProb, ep, d, , , PROBE_FIND_CONFIG, 26, , (~Find all existing probes~);
235
236	PT_family, ffinder, d, , , FFINDER, 28, , (~next relative search~);
237
238	aisc_string, user, t, rw, , USER, 30, "unknown", (~the username~);
239	aisc_string, address, t, rw, , ADDRESS, 31, "unknown", (~the useraddress~);
240	aisc_string, login, t, rw, , LOGINTIME, 32, "notime", (~the date the user logged in~);
241	};
242
243	PT_main, MAIN, 1, (~global data~), {
244	@TYPE, @IDENT, @REF, @ACC, @SAVE, @KEY, @KEYC, @INIT, @DOCU;
245	t_key, key, t, n, , , , , (~the KEY~);
246	PT_local, loc_st, d, , , LOCS, 1, , (~the parameters~);
247	aisc_string, server_shutdown,%, w, , SHUTDOWN, 3, , (~shut down~);
248	int, who, t, rw, , STARTER, 4, , (~who started this server~);
249	int, m_type, t, , , MESSAGE_TYPE, 5, 0, (~the message type~);
250	aisc_string, m_text, t, , , MESSAGE, 6, "NO_MSG", (~the message text~);
251	int, broadcast, %, w, , BROADCAST, 7, , (~broadcast func~);
252	PT_species_list,sl, d, r, , SPECIESLIST, 8, , (~list of species~);
253	};
254
255	};

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