source: branches/profile/EDIT4/ed4_awars.hxx

Last change on this file was 11154, checked in by westram, 6 years ago
  • remove AWAR_MIN_MISMATCHES
    • no such functionality provided by ptserver (maybe it was planned but not implemented?)
    • use local awar following common naming scheme in EDIT4
  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 11.4 KB
Line 
1// ================================================================= //
2//                                                                   //
3//   File      : ed4_awars.hxx                                       //
4//   Purpose   : edit4 awars                                         //
5//                                                                   //
6//   Institute of Microbiology (Technical University Munich)         //
7//   http://www.arb-home.de/                                         //
8//                                                                   //
9// ================================================================= //
10
11#ifndef ED4_AWARS_HXX
12#define ED4_AWARS_HXX
13
14#define ED4_TEMP_AWAR        "/tmp/edit4/" // path for temporary awars
15#define ED4_SEARCH_SAVE_BASE ED4_TEMP_AWAR "srchpara"
16
17//      Level 1 Options
18
19#define ED4_AWAR_SEQUENCE_INFO_WIDTH "sequence_info/width"
20#define ED4_AWAR_TREE_WIDTH          "tree/width"
21
22#define ED4_AWAR_COMPRESS_SEQUENCE_TYPE    "sequence/compression_type"
23#define ED4_AWAR_COMPRESS_SEQUENCE_GAPS    "sequence/compression_type_gaps"
24#define ED4_AWAR_COMPRESS_SEQUENCE_HIDE    "sequence/compression_type_hide"
25#define ED4_AWAR_COMPRESS_SEQUENCE_PERCENT "sequence/compression_type_hide_percent"
26
27#define ED4_AWAR_DIGITS_AS_REPEAT "edit/digits_as_repeat"
28#define ED4_AWAR_FAST_CURSOR_JUMP "edit/fast_cursor_jump"
29#define ED4_AWAR_CURSOR_TYPE      "edit/cursor_type"
30
31#define ED4_AWAR_SCROLL_SPEED_X "scrolling/speed_x"
32#define ED4_AWAR_SCROLL_SPEED_Y "scrolling/speed_y"
33#define ED4_AWAR_SCROLL_MARGIN  "scrolling/margin"
34
35#define ED4_AWAR_GAP_CHARS                 "sequence/gap_chars"
36#define ED4_AWAR_ANNOUNCE_CHECKSUM_CHANGES "sequence/announce_checksum_changes"
37
38//      Expert Options
39
40#define ED4_AWAR_GROUP_INDENT "group/indent" // Width of Group Bracket
41#define ED4_AWAR_GROUP_COLOR  "group/color" // Color Nr for Brackets
42
43//      consensus definition
44
45#define ED4_AWAR_CONSENSUS_COUNTGAPS   "con/countgaps"
46#define ED4_AWAR_CONSENSUS_GAPBOUND    "con/gapbound"
47#define ED4_AWAR_CONSENSUS_GROUP       "con/group"
48#define ED4_AWAR_CONSENSUS_CONSIDBOUND "con/considbound"
49#define ED4_AWAR_CONSENSUS_UPPER       "con/upper"
50#define ED4_AWAR_CONSENSUS_LOWER       "con/lower"
51#define ED4_AWAR_CONSENSUS_SHOW        "con/show"
52
53//      create species from consensus
54
55#define ED4_AWAR_CREATE_FROM_CONS_REPL_EQUAL    "concreate/repl_equal"
56#define ED4_AWAR_CREATE_FROM_CONS_REPL_POINT    "concreate/repl_point"
57#define ED4_AWAR_CREATE_FROM_CONS_CREATE_POINTS "concreate/create_points"
58#define ED4_AWAR_CREATE_FROM_CONS_ALL_UPPER     "concreate/all_upper"
59#define ED4_AWAR_CREATE_FROM_CONS_DATA_SOURCE   "concreate/data_source"
60
61//      Replace awars
62
63#define ED4_AWAR_REP_SEARCH_PATTERN  "replace/spat"
64#define ED4_AWAR_REP_REPLACE_PATTERN "replace/rpat"
65
66//      NDS awars
67
68#define ED4_AWAR_NDS_SELECT               "nds/select"
69#define ED4_AWAR_NDS_SELECT_TEMPLATE      "nds/pat_%i/select"
70#define ED4_AWAR_NDS_DESCRIPTION_TEMPLATE "nds/pat_%i/description"
71#define ED4_AWAR_NDS_ACI_TEMPLATE         "nds/pat_%i/aci"
72#define ED4_AWAR_NDS_WIDTH_TEMPLATE       "nds/pat_%i/width"
73#define ED4_AWAR_NDS_BRACKETS             "nds/brackets"
74#define ED4_AWAR_NDS_INFO_WIDTH           "nds/infowidth"
75#define ED4_AWAR_NDS_ECOLI_NAME           "nds/ecoliname"
76
77//      Search awars
78
79#define ED4_AWAR_USER1_SEARCH_PATTERN        "search/user1/pattern"
80#define ED4_AWAR_USER1_SEARCH_MIN_MISMATCHES "search/user1/min_mismatches"
81#define ED4_AWAR_USER1_SEARCH_MAX_MISMATCHES "search/user1/max_mismatches"
82#define ED4_AWAR_USER1_SEARCH_CASE           "search/user1/case"
83#define ED4_AWAR_USER1_SEARCH_TU             "search/user1/tu"
84#define ED4_AWAR_USER1_SEARCH_PAT_GAPS       "search/user1/pat_gaps"
85#define ED4_AWAR_USER1_SEARCH_SEQ_GAPS       "search/user1/seq_gaps"
86#define ED4_AWAR_USER1_SEARCH_SHOW           "search/user1/show"
87#define ED4_AWAR_USER1_SEARCH_OPEN_FOLDED    "search/user1/open_folded"
88#define ED4_AWAR_USER1_SEARCH_AUTO_JUMP      "search/user1/autoJump"
89#define ED4_AWAR_USER1_SEARCH_REVERSE        "search/user1/reverse"
90#define ED4_AWAR_USER1_SEARCH_COMPLEMENT     "search/user1/complement"
91#define ED4_AWAR_USER1_SEARCH_EXACT          "search/user1/exact"
92
93#define ED4_AWAR_USER2_SEARCH_PATTERN        "search/user2/pattern"
94#define ED4_AWAR_USER2_SEARCH_MIN_MISMATCHES "search/user2/min_mismatches"
95#define ED4_AWAR_USER2_SEARCH_MAX_MISMATCHES "search/user2/max_mismatches"
96#define ED4_AWAR_USER2_SEARCH_CASE           "search/user2/case"
97#define ED4_AWAR_USER2_SEARCH_TU             "search/user2/tu"
98#define ED4_AWAR_USER2_SEARCH_PAT_GAPS       "search/user2/pat_gaps"
99#define ED4_AWAR_USER2_SEARCH_SEQ_GAPS       "search/user2/seq_gaps"
100#define ED4_AWAR_USER2_SEARCH_SHOW           "search/user2/show"
101#define ED4_AWAR_USER2_SEARCH_OPEN_FOLDED    "search/user2/open_folded"
102#define ED4_AWAR_USER2_SEARCH_AUTO_JUMP      "search/user2/autoJump"
103#define ED4_AWAR_USER2_SEARCH_REVERSE        "search/user2/reverse"
104#define ED4_AWAR_USER2_SEARCH_COMPLEMENT     "search/user2/complement"
105#define ED4_AWAR_USER2_SEARCH_EXACT          "search/user2/exact"
106
107#define ED4_AWAR_PROBE_SEARCH_PATTERN        AWAR_TARGET_STRING // s.a.: PROBE_DESIGN/probe_design.cxx
108#define ED4_AWAR_PROBE_SEARCH_MIN_MISMATCHES "search/probe/min_mismatches"
109#define ED4_AWAR_PROBE_SEARCH_MAX_MISMATCHES AWAR_MAX_MISMATCHES
110#define ED4_AWAR_PROBE_SEARCH_CASE           "search/probe/case"
111#define ED4_AWAR_PROBE_SEARCH_TU             "search/probe/tu"
112#define ED4_AWAR_PROBE_SEARCH_PAT_GAPS       "search/probe/pat_gaps"
113#define ED4_AWAR_PROBE_SEARCH_SEQ_GAPS       "search/probe/seq_gaps"
114#define ED4_AWAR_PROBE_SEARCH_SHOW           "search/probe/show"
115#define ED4_AWAR_PROBE_SEARCH_OPEN_FOLDED    "search/probe/open_folded"
116#define ED4_AWAR_PROBE_SEARCH_AUTO_JUMP      "search/probe/autoJump"
117#define ED4_AWAR_PROBE_SEARCH_REVERSE        "search/probe/reverse"
118#define ED4_AWAR_PROBE_SEARCH_COMPLEMENT     "search/probe/complement"
119#define ED4_AWAR_PROBE_SEARCH_EXACT          "search/probe/exact"
120
121#define ED4_AWAR_PRIMER1_SEARCH_PATTERN        AWAR_PRIMER_TARGET_STRING
122#define ED4_AWAR_PRIMER1_SEARCH_MIN_MISMATCHES "search/primer1/min_mismatches"
123#define ED4_AWAR_PRIMER1_SEARCH_MAX_MISMATCHES "search/primer1/max_mismatches"
124#define ED4_AWAR_PRIMER1_SEARCH_CASE           "search/primer1/case"
125#define ED4_AWAR_PRIMER1_SEARCH_TU             "search/primer1/tu"
126#define ED4_AWAR_PRIMER1_SEARCH_PAT_GAPS       "search/primer1/pat_gaps"
127#define ED4_AWAR_PRIMER1_SEARCH_SEQ_GAPS       "search/primer1/seq_gaps"
128#define ED4_AWAR_PRIMER1_SEARCH_SHOW           "search/primer1/show"
129#define ED4_AWAR_PRIMER1_SEARCH_OPEN_FOLDED    "search/primer1/open_folded"
130#define ED4_AWAR_PRIMER1_SEARCH_AUTO_JUMP      "search/primer1/autoJump"
131#define ED4_AWAR_PRIMER1_SEARCH_REVERSE        "search/primer1/reverse"
132#define ED4_AWAR_PRIMER1_SEARCH_COMPLEMENT     "search/primer1/complement"
133#define ED4_AWAR_PRIMER1_SEARCH_EXACT          "search/primer1/exact"
134
135#define ED4_AWAR_PRIMER2_SEARCH_PATTERN        "search/primer2/pattern"
136#define ED4_AWAR_PRIMER2_SEARCH_MIN_MISMATCHES "search/primer2/min_mismatches"
137#define ED4_AWAR_PRIMER2_SEARCH_MAX_MISMATCHES "search/primer2/max_mismatches"
138#define ED4_AWAR_PRIMER2_SEARCH_CASE           "search/primer2/case"
139#define ED4_AWAR_PRIMER2_SEARCH_TU             "search/primer2/tu"
140#define ED4_AWAR_PRIMER2_SEARCH_PAT_GAPS       "search/primer2/pat_gaps"
141#define ED4_AWAR_PRIMER2_SEARCH_SEQ_GAPS       "search/primer2/seq_gaps"
142#define ED4_AWAR_PRIMER2_SEARCH_SHOW           "search/primer2/show"
143#define ED4_AWAR_PRIMER2_SEARCH_OPEN_FOLDED    "search/primer2/open_folded"
144#define ED4_AWAR_PRIMER2_SEARCH_AUTO_JUMP      "search/primer2/autoJump"
145#define ED4_AWAR_PRIMER2_SEARCH_REVERSE        "search/primer2/reverse"
146#define ED4_AWAR_PRIMER2_SEARCH_COMPLEMENT     "search/primer2/complement"
147#define ED4_AWAR_PRIMER2_SEARCH_EXACT          "search/primer2/exact"
148
149#define ED4_AWAR_PRIMER3_SEARCH_PATTERN        "search/primer3/pattern"
150#define ED4_AWAR_PRIMER3_SEARCH_MIN_MISMATCHES "search/primer3/min_mismatches"
151#define ED4_AWAR_PRIMER3_SEARCH_MAX_MISMATCHES "search/primer3/max_mismatches"
152#define ED4_AWAR_PRIMER3_SEARCH_CASE           "search/primer3/case"
153#define ED4_AWAR_PRIMER3_SEARCH_TU             "search/primer3/tu"
154#define ED4_AWAR_PRIMER3_SEARCH_PAT_GAPS       "search/primer3/pat_gaps"
155#define ED4_AWAR_PRIMER3_SEARCH_SEQ_GAPS       "search/primer3/seq_gaps"
156#define ED4_AWAR_PRIMER3_SEARCH_SHOW           "search/primer3/show"
157#define ED4_AWAR_PRIMER3_SEARCH_OPEN_FOLDED    "search/primer3/open_folded"
158#define ED4_AWAR_PRIMER3_SEARCH_AUTO_JUMP      "search/primer3/autoJump"
159#define ED4_AWAR_PRIMER3_SEARCH_REVERSE        "search/primer3/reverse"
160#define ED4_AWAR_PRIMER3_SEARCH_COMPLEMENT     "search/primer3/complement"
161#define ED4_AWAR_PRIMER3_SEARCH_EXACT          "search/primer3/exact"
162
163#define ED4_AWAR_SIG1_SEARCH_PATTERN        AWAR_GENE_CONTENT
164#define ED4_AWAR_SIG1_SEARCH_MIN_MISMATCHES "search/sig1/min_mismatches"
165#define ED4_AWAR_SIG1_SEARCH_MAX_MISMATCHES "search/sig1/max_mismatches"
166#define ED4_AWAR_SIG1_SEARCH_CASE           "search/sig1/case"
167#define ED4_AWAR_SIG1_SEARCH_TU             "search/sig1/tu"
168#define ED4_AWAR_SIG1_SEARCH_PAT_GAPS       "search/sig1/pat_gaps"
169#define ED4_AWAR_SIG1_SEARCH_SEQ_GAPS       "search/sig1/seq_gaps"
170#define ED4_AWAR_SIG1_SEARCH_SHOW           "search/sig1/show"
171#define ED4_AWAR_SIG1_SEARCH_OPEN_FOLDED    "search/sig1/open_folded"
172#define ED4_AWAR_SIG1_SEARCH_AUTO_JUMP      "search/sig1/autoJump"
173#define ED4_AWAR_SIG1_SEARCH_REVERSE        "search/sig1/reverse"
174#define ED4_AWAR_SIG1_SEARCH_COMPLEMENT     "search/sig1/complement"
175#define ED4_AWAR_SIG1_SEARCH_EXACT          "search/sig1/exact"
176
177#define ED4_AWAR_SIG2_SEARCH_PATTERN        "search/sig2/pattern"
178#define ED4_AWAR_SIG2_SEARCH_MIN_MISMATCHES "search/sig2/min_mismatches"
179#define ED4_AWAR_SIG2_SEARCH_MAX_MISMATCHES "search/sig2/max_mismatches"
180#define ED4_AWAR_SIG2_SEARCH_CASE           "search/sig2/case"
181#define ED4_AWAR_SIG2_SEARCH_TU             "search/sig2/tu"
182#define ED4_AWAR_SIG2_SEARCH_PAT_GAPS       "search/sig2/pat_gaps"
183#define ED4_AWAR_SIG2_SEARCH_SEQ_GAPS       "search/sig2/seq_gaps"
184#define ED4_AWAR_SIG2_SEARCH_SHOW           "search/sig2/show"
185#define ED4_AWAR_SIG2_SEARCH_OPEN_FOLDED    "search/sig2/open_folded"
186#define ED4_AWAR_SIG2_SEARCH_AUTO_JUMP      "search/sig2/autoJump"
187#define ED4_AWAR_SIG2_SEARCH_REVERSE        "search/sig2/reverse"
188#define ED4_AWAR_SIG2_SEARCH_COMPLEMENT     "search/sig2/complement"
189#define ED4_AWAR_SIG2_SEARCH_EXACT          "search/sig2/exact"
190
191#define ED4_AWAR_SIG3_SEARCH_PATTERN        "search/sig3/pattern"
192#define ED4_AWAR_SIG3_SEARCH_MIN_MISMATCHES "search/sig3/min_mismatches"
193#define ED4_AWAR_SIG3_SEARCH_MAX_MISMATCHES "search/sig3/max_mismatches"
194#define ED4_AWAR_SIG3_SEARCH_CASE           "search/sig3/case"
195#define ED4_AWAR_SIG3_SEARCH_TU             "search/sig3/tu"
196#define ED4_AWAR_SIG3_SEARCH_PAT_GAPS       "search/sig3/pat_gaps"
197#define ED4_AWAR_SIG3_SEARCH_SEQ_GAPS       "search/sig3/seq_gaps"
198#define ED4_AWAR_SIG3_SEARCH_SHOW           "search/sig3/show"
199#define ED4_AWAR_SIG3_SEARCH_OPEN_FOLDED    "search/sig3/open_folded"
200#define ED4_AWAR_SIG3_SEARCH_AUTO_JUMP      "search/sig3/autoJump"
201#define ED4_AWAR_SIG3_SEARCH_REVERSE        "search/sig3/reverse"
202#define ED4_AWAR_SIG3_SEARCH_COMPLEMENT     "search/sig3/complement"
203#define ED4_AWAR_SIG3_SEARCH_EXACT          "search/sig3/exact"
204
205//      Other internal awars
206
207#define ED4_AWAR_SPECIES_TO_CREATE ED4_TEMP_AWAR "species_to_create"
208
209#else
210#error ed4_awars.hxx included twice
211#endif
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