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