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PT.aisc

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Last change on this file was 13191, checked in by westram, 9 years ago
reintegrates 'slv' into 'trunk' performs #624 adds: log:branches/slv@13152:13190
Property svn:eol-style set to `native` Property svn:keywords set to `Author Date Id Revision`
File size: 21.8 KB

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1	PROJECT pb_com
2	OBJECT_KEY PT, # MAIN PREFIX
3	MAX_KEY 37, # 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_tprobes, TPROBE, 9, (~the probe we want to test~), {
55	@TYPE, @IDENT, @REF, @ACC, @KEY, @KEYC, @INIT, @DOCU;
56	dllh, mh, t, , (~~), 0, , (~Header~);
57	aisc_string,sequence, t, r, SEQUENCE, 8, , (~The Sequence to check~);
58	int, seq_len, t, , , , , (~The len of the sequence~);
59	double, sum_bonds, t, , , , , (~The sum of all bonds~);
60	double, quality, t, r, QUALITY, 9, , (~The quality of the probe = GROUPSIZE*dT~);
61	int, groupsize, t, r, GROUPSIZE, 10, , (~The Size of the group~);
62	int, hairpin, t, r, HAIRPIN, 11, , (~How many hairpin bonds~);
63	double, whairpin, t, r, WHAIRPIN, 12, , (~Weighted Hairpins~);
64	int, perc, vt, r, PERC, 13, , (~Result: How many non group hits per centigrade~), SIZE PERC_SIZE;
65	double, temp, t, r, TEMPERATURE, 14, , (~The temperature of the probe~);
66	int, mishits, t, r, MISHIT, 15, , (~How many outgroup members hit~);
67	int, apos, t, , APOS, 16, , (~The absolute position of probe~);
68	int, get_r_pos, t, , ECOLI_POS, 17, , (~The ecoli based position of probe~);
69	aisc_string,get_design_info, %, r, INFO, 19, , (~the info text for each of the designed probes~);
70	};
71
72	PT_bond, , , (~the definition of a bond~), {
73	@TYPE, @IDENT, @REF, @ACC, @KEY, @KEYC, @INIT, @DOCU;
74	double, val, t, , VAL, 0, 0.0, (~how strong is that bond~);
75	};
76
77	PT_sequence, SEQUENCE, 8, (~the additional sequences~), {
78	@TYPE, @IDENT, @REF, @ACC, @KEY, @KEYC, @INIT, @DOCU;
79	dllh, mh, t, , (~~), 0, , (~Header~);
80	bytestring,seq, t, , SEQUENCE, 8, , (~The Sequence~);
81	};
82
83	PT_pdc, PDC, 7, (~probe design~), {
84	@TYPE, @IDENT, @REF, @ACC, @KEY, @KEYC, @INIT, @DOCU;
85	dllh, mh, t, , (~~), 0, , (~Header~);
86	double, dte, t, , DTEDGE, 9, 50.0, (~The Temperature drop per percent mismatch on the edge of the probe~);
87	double, dt, t, , DT, 10, 50.0, (~The temperature drop per percent mismatch~);
88	int, looplen, t, , LOOPLEN, 14, 4, (~The Loop Length of a probe~);
89	int, min_probelen, t, , MIN_PROBELEN, 15, 18, (~the minimum length of the designed probes~);
90	double, mintemp, t, , MINTEMP, 16, 30.0, (~minimum temperature~);
91	double, maxtemp, t, , MAXTEMP, 17, 100.0, (~maximum temperature~);
92	double, min_gc, t, , MINGC, 18, .3, (~the minimum GC content~);
93	double, max_gc, t, , MAXGC, 19, 1.0, (~the maximum GC content~);
94	double, maxbonds, t, , MAXBOND, 20, 4.0, (~The maximum of hairpin bonds~);
95	int, min_ecolipos, t, , MIN_ECOLIPOS, 21, -1, (~the minimum ecoli position [1..N]. -1 means 'no restriction'~);
96	int, max_ecolipos, t, , MAX_ECOLIPOS, 22, -1, (~the maximum ecoli position [1..N]. -1 means 'no restriction'~);
97	double, min_coverage, t, , MINTARGETS, 23, .7, (~the minimum coverage for the targetted group of species~);
98	int, max_mishits, t, , MISHIT, 24, 0, (~the maximum mishits~);
99	int, clipresult, t, , CLIPRESULT, 25, 40, (~Clip the Result list~);
100	int, pos_groups, vt, , , , , (~Position of Groups~), SIZE ALPHA_SIZE;
101	bytestring, checksums, t, w, CHECKSUMS, 26, , (~a list of sequence checksums separated by '#' is optional~);
102	bytestring, names, t, w, NAMES, 27, , (~a list of names separated by '#' is expected~);
103	bytestring, PT_unknown_names, %, r, UNKNOWN_NAMES, 28, , (~List of unknown names~);
104	PT_sequence, sequences, d, , SEQUENCE, 29, , (~Additional Sequences~);
105	int, PT_start_design, %, w, GO, 31, , (~Start the design procedure~);
106	PT_tprobes, tprobes, d, r, TPROBE, 32, , (~The result~);
107	double, max_rj_coverage, t, r, MAX_RJ_TARGETS, 34, 0.0, (~the maximum rejected coverage for the targetted group of species~);
108	int, min_rj_mishits, t, r, MIN_RJ_MISHIT, 35, INT_MAX, (~the minimum rejected mishits~);
109	aisc_string, get_design_hinfo, %, r, INFO_HEADER, 36, , (~the result info header of this probe design~);
110	int, max_probelen, t, , MAX_PROBELEN, 37, -1, (~the maximum length of the designed probes (or -1 to use MIN_PROBELEN~);
111	};
112
113	# function to iterate through all probes existing in PT-Server
114
115	PT_exProb, PEP, 6, (~iterate all existing probes~), {
116	@TYPE, @IDENT, @REF, @ACC, @KEY, @KEYC, @INIT, @DOCU;
117	dllh, mh, t, , (~~), 0, , (~Header~);
118	int, plength, t, , PLENGTH, 8, 20, (~Length of searched probes~);
119	int, numget, t, , NUMGET, 9, 200, (~Number of searched probes~);
120	int, readable, t, , READABLE, 14, 0, (~Return readable probes~);
121	int, separator, t, , SEPARATOR, 15, 59, (~Separator for result (';') ~);
122	int, tu, t, , TU, 16, 84, (~Char used for T/U ('T') ~);
123	int, restart, t, , RESTART, 10, 1, (~1 => start from beginning~);
124	bytestring, next_probe, t, , NEXT_PROBE, 11, , (~next probe to look for (internal)~);
125	int, PT_find_exProb, %, w, FIND_PROBES,12, , (~search probes (result=separated by SEPARATOR )~);
126	aisc_string, result, t, r, RESULT, 13, , (~The result~);
127	};
128
129	# get next relatives (used by AWTC and NALIGNER)
130
131	PT_family_list, FAMILYLIST, 5, (~the family list~), {
132	@TYPE, @IDENT, @REF, @ACC, @SAVE, @KEY, @KEYC, @INIT, @DOCU;
133	dllh, mh, t, , , (~~), 0, , (~Header~);
134	aisc_string, name, t, r, , NAME, 8, , (~name of species~);
135	int, matches, t, r, , MATCHES, 9, , (~number of matches~);
136	double, rel_matches, t, r, , REL_MATCHES, 10, , (~MATCHES / (SEQ_LEN - PROBE_LEN + 1)~);
137	};
138
139	PT_family, FAMILYFINDER, 12, (~next relative search~), {
140	@TYPE, @IDENT, @REF, @ACC, @SAVE, @KEY, @KEYC, @INIT, @DOCU;
141	dllh, mh, t, , , (~~), 0, , (~Header~);
142	bytestring, find_family, %, w, , FIND_FAMILY, 8, , (~Searches the family~);
143	int, pr_len, t, rw, , PROBE_LEN, 9, 12, (~Length of probes~);
144	int, mis_nr, t, rw, , MISMATCH_NUMBER, 10, 0, (~Number of mismatches~);
145	int, only_A_probes, t, rw, , FIND_TYPE, 11, 0, (~Type of search: 0 = search all, 1 = only a*~);
146	int, complement, t, rw, , COMPLEMENT, 12, 1, (~Search for complement? (see FF_complement)~);
147	PT_family_list, fl, d, r, , FAMILY_LIST, 13, , (~Sorted List of family~); # note: This uses 13 AND 14!
148	int, list_size, t, r, , FAMILY_LIST_SIZE, 15, , (~size of result list~);
149	int, sort_type, t, rw, , SORT_TYPE, 16, 0, (~Type of sorting 0 = MATCHES, 1 = REL_MATCHES~);
150	int, sort_max, t, rw, , SORT_MAX, 17, 0, (~Sort only the SORT_MAX best hits~);
151	int, range_start, t, rw, , RANGE_STARTPOS, 18, -1, (~if != -1 -> ignore matches starting left of that position [0..N-1]~);
152	int, range_end, t, rw, , RANGE_ENDPOS, 19, -1, (~if != -1 -> ignore matches ending right of that position [0..N-1]~);
153	double, min_score, t, rw, , MIN_SCORE, 20, 0, (~Skip results with rel or abs score below MIN_SCORE (affects reported FAMILY_LIST_SIZE)~);
154	int, rel_scoring, t, rw, , REL_SCORING, 21, 0, (~relative scoring scaling mode (see RelativeScoreScaling)~);
155	aisc_string, ff_error, t, r, , ERROR, 22, "", (~the error text~);
156	};
157
158	# used below in LOCS/MATCH_STRING
159
160	PT_probematch, MATCHLIST, 4, (~the probe match list~), {
161	@TYPE, @IDENT, @REF, @ACC, @SAVE, @KEY, @KEYC, @INIT, @DOCU;
162	dllh, mh, t, , , (~~), 0, , (~Header~);
163	int, name, t, r, , ID, 8, , (~id of species~);
164	aisc_string, virt_name, %, r, , NAME, 9, , (~name of species~);
165	int, b_pos, t, r, , POS, 10, , (~pos of probe~);
166	int, g_pos, t, r, , GPOS, 11, , (~pos of probe (gene relative)~);
167	int, rpos, t, r, , , , , (~relative pos of probe~);
168	int, mismatches, t, r, , MISMATCHES, 12, , (~number of mismatches~);
169	aisc_string, virt_fullname, %, r, , FULLNAME, 13, , (~fullname of species (or genename if it's a gene pt server)~);
170	double, wmismatches, t, r, , WMISMATCHES, 14, , (~number of weighted mismatches~);
171	int, N_mismatches, t, r, , N_MISMATCHES, 15, , (~number of 'N' mismatches~);
172	double, dt, t, r, , DT, 16, , (~the dt of a probe~);
173	char, sequence, l, r, , SEQUENCE, 17, , (~path of probe~);
174	int, reversed, t, r, , REVERSED, 18, , (~reversed probe matches~);
175	aisc_string, get_match_overlay, %, r, , OVERLAY, 19, , (~ascii visualization of match~);
176	aisc_string, get_match_acc, %, r, , FIELD_ACC, 20, , (~get db field acc~);
177	int, get_match_start, %, r, , FIELD_START, 21, , (~get db field start~);
178	int, get_match_stop, %, r, , FIELD_STOP, 22, , (~get db field stop~);
179	};
180
181	# used below in MAIN/SPECIESLIST
182
183	PT_species_list, SPECIESLIST, 3, (~the species list~), {
184	@TYPE, @IDENT, @REF, @ACC, @SAVE, @KEY, @KEYC, @INIT, @DOCU;
185	dllh, mh, t, , , (~~), 0, , (~Header~);
186	int, member, t, rw, , MEMBER, 8, , (~species member of group~);
187	};
188
189	# global interface
190
191	PT_local, LOCS, 2, (~local communication buffer~), {
192	@TYPE, @IDENT, @REF, @ACC, @SAVE, @KEY, @KEYC, @INIT, @DOCU;
193	dllh, mh, t, , , (~~), 0, , (~Header~);
194	int, socket, t, , , , , pt_init_socket(THIS), (~the callback~), DESTROY pt_destroy_socket(THIS);
195
196	aisc_string, probe_match, %, w, , SEARCHMATCH, 8, , (~Searches all species where probe matches~);
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_hits, t, rw, , MATCH_MAX_HITS, 12, 1000000, (~max number of hits reported (0=unlimited)~);
203	int, sort_by, t, rw, , MATCH_SORT_BY, 13, , (~0 == mismatches 1 == weighted mismatches 2 == weighted mismatches with pos and strength~);
204	int, pm_nmatches_ignored, t, rw, , MATCH_N_ACCEPT, 14, 1, (~max. of accepted matches vs N~);
205	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 ~);
206	PT_probematch, pm, d, r, , MATCH_LIST, 15, , (~result: List of species where probe matches~);
207	int, matches_truncated, t, r, , MATCHES_TRUNCATED, 17, , (~result: whether MATCH_LIST was truncated~);
208	bytestring, match_string, %, r, , MATCH_STRING, 18, , (~result: List of species where probe matches~);
209
210	bytestring, MP_match_string, %, r, , MP_MATCH_STRING, 19, , (~result: List of species where probe matches (each entry is followed by: number of mismatches and weighted mismatches)~);
211	bytestring, MP_all_species_string,%, r, , MP_ALL_SPECIES_STRING,20, , (~result: List of all species in Database~);
212	int, MP_count_all_species, %, r, , MP_COUNT_ALL_SPECIES, 21, , (~result: Number of all species in Database~);
213
214	aisc_string, ls_error, t, r, , ERROR, 22, "", (~the error text~);
215
216	int, group_count, t, r, , PROBE_NGROUP, 23, , (~result: Number of selected species~);
217
218	PT_pdc, pdc, d, , , PROBE_DESIGN_CONFIG, 24, , (~The new probe design~);
219	PT_exProb, ep, d, , , PROBE_FIND_CONFIG, 26, , (~Find all existing probes~);
220
221	PT_family, ffinder, d, , , FFINDER, 28, , (~next relative search~);
222
223	aisc_string, user, t, rw, , USER, 30, "unknown", (~the username~);
224	aisc_string, address, t, rw, , ADDRESS, 31, "unknown", (~the useraddress~);
225	aisc_string, login, t, rw, , LOGINTIME, 32, "notime", (~the date the user logged in~);
226
227	PT_bond, bond, siv, , , BOND, 34, , (~The bond matrix~), SIZE (4*4);
228	int, dummy, t, , , , , init_bond_matrix(THIS), (~init bond matrix~);
229	double, split, t, , , SPLIT, 35, .5, (~Split the domains if bond value is less the average bond value - split~);
230	};
231
232	PT_main, MAIN, 1, (~global data~), {
233	@TYPE, @IDENT, @REF, @ACC, @SAVE, @KEY, @KEYC, @INIT, @DOCU;
234	t_key, key, t, n, , , , , (~the KEY~);
235	PT_local, loc_st, d, , , LOCS, 1, , (~the parameters~);
236	aisc_string, server_shutdown,%, w, , SHUTDOWN, 3, , (~shut down~);
237	int, who, t, rw, , STARTER, 4, , (~who started this server~);
238	int, m_type, t, , , MESSAGE_TYPE, 5, 0, (~the message type~);
239	aisc_string, m_text, t, , , MESSAGE, 6, "NO_MSG", (~the message text~);
240	int, broadcast, %, w, , BROADCAST, 7, , (~broadcast func~);
241	PT_species_list,sl, d, r, , SPECIESLIST, 8, , (~list of species~);
242	aisc_string, dumpname, t, rw, , DUMP_NAME, 10, "", (~filename used for DUMP_INDEX~);
243	int, PT_index_dump, %, r, , DUMP_INDEX, 11, , (~dump index (=postree) to file~);
244	};
245
246	};

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