1 | #| |
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2 | Library for logical analysis of the network structure of |
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3 | signal transduction networks |
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4 | |
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5 | Authors: Julio Saez-Rodriguez, Martin Ginkel, Rebecca Hemenway |
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6 | $Id$ |
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7 | |# |
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8 | |
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9 | (add-icon-dir "promot:kb;SignalTransd;libraries;") |
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10 | (add-icon-dir "promot:kb;SignalTransd;structure;") |
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11 | (add-mdl-dir "promot:kb;SignalTransd;structure;") |
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12 | |
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13 | |
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14 | (define-module |
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15 | :class "struct-library" |
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16 | :super-classes ("module")) |
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17 | |
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18 | (define-terminal |
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19 | :class "term-struct" |
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20 | :super-classes ("terminal") |
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21 | :geometry-width "13" |
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22 | :geometry-height "13" |
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23 | :link-color "blue" |
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24 | :variables |
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25 | (("a" |
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26 | :system-theoretic "state" |
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27 | :value "1"))) |
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28 | |
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29 | #| |
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30 | (define-variable |
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31 | :class "var-real-parameter" |
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32 | :super-classes ("variable") |
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33 | :system-theoretic "real-parameter") |
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34 | |
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35 | |
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36 | (define-variable |
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37 | :class "var-integer-parameter" |
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38 | :super-classes ("variable") |
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39 | :system-theoretic "integer-parameter") |
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40 | |# |
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41 | |
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42 | (define-terminal |
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43 | :class "term-struct-compound" |
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44 | :super-classes ("term-struct") |
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45 | :properties |
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46 | (("abstract" :value "no")) |
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47 | :icon "icons/struct/term-compound") |
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48 | |
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49 | |
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50 | (define-terminal |
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51 | :class "term-struct-gate" |
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52 | :super-classes ("term-struct")) |
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53 | |
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54 | |
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55 | (define-terminal |
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56 | :class "term-struct-input" |
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57 | :super-classes ("term-struct-gate") |
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58 | :properties |
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59 | (("abstract" :value "no")) |
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60 | :icon "icons/struct/term-input" |
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61 | :parameters |
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62 | (("a" |
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63 | :system-theoretic "input" |
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64 | :value "1"))) |
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65 | |
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66 | |
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67 | (define-terminal |
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68 | :class "term-struct-output" |
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69 | :super-classes ("term-struct-gate") |
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70 | :properties |
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71 | (("abstract" :value "no")) |
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72 | :icon "icons/struct/term-output" |
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73 | :parameters |
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74 | (("a" |
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75 | :system-theoretic "output" |
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76 | :value "1"))) |
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77 | |
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78 | |
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79 | (define-module |
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80 | :class "struct-adapter" |
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81 | :super-classes ("struct-library") |
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82 | :icon "icons/struct/struct-adapt" |
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83 | :terminals |
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84 | (("input" |
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85 | :is-a "term-struct" |
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86 | :geometry-side "top" |
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87 | :geometry-position "0.5") |
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88 | ("output" |
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89 | :is-a "term-struct" |
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90 | :geometry-side "bottom" |
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91 | :geometry-position "0.5"))) |
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92 | |
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93 | |
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94 | (define-module |
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95 | :class "struct-adapter-compound" |
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96 | :super-classes ("struct-adapter") |
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97 | :properties |
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98 | (("abstract" :value "no")) |
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99 | :icon "icons/struct/struct-adapt" |
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100 | :terminals |
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101 | (("input" |
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102 | :is-a "term-struct-compound") |
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103 | ("output" |
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104 | :is-a "term-struct-compound"))) |
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105 | |
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106 | |
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107 | (define-module |
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108 | :class "struct-adapter-gate" |
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109 | :super-classes ("struct-adapter") |
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110 | :icon "icons/struct/struct-adapt" |
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111 | :properties |
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112 | (("abstract" :value "no")) |
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113 | :terminals |
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114 | (("input" |
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115 | :is-a "term-struct-input") |
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116 | ("output" |
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117 | :is-a "term-struct-output"))) |
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118 | |
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119 | |
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120 | (define-module |
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121 | :class "gate" |
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122 | :super-classes ("struct-library") |
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123 | :variables |
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124 | (("conf" |
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125 | :system-theoretic "real-parameter" |
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126 | :documentation "confidency level of this element: 1-most established (values between 0 and 1)" |
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127 | :value "1") |
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128 | ("defval" |
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129 | :system-theoretic "integer-parameter" |
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130 | :documentation "Default value of the logical state of the reaction. empty = undefined") |
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131 | ("time" |
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132 | :system-theoretic "real-parameter" |
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133 | :documentation "parameter determining the time-scale, 1 being the fastest" |
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134 | :value "1") |
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135 | ("logexcl" |
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136 | :system-theoretic "integer-parameter" |
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137 | :documentation "parameter defining the gate to be excluded from logical |
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138 | analysis. Allowed Values 0 (included) or 1 (excluded), default 0." |
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139 | :value "0") |
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140 | ("ignore_in_export" |
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141 | :system-theoretic "integer-parameter" |
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142 | :documentation "parameter determining whether the gate is exported to the |
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143 | CellNetAnalyzer. Allowed Values 0 (exported) or 1 (ignored in export), default |
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144 | 0." |
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145 | :value "0") |
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146 | ("monotone" |
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147 | :system-theoretic "real-parameter" |
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148 | :documentation "parameter defining the gate to be monotone. Allowed Values 0 (non monotone) or 1 (monotone), default 0." |
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149 | :value "0.01") |
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150 | ("map_number" |
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151 | :system-theoretic "integer-parameter" |
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152 | :documentation "parameter determining the map in CellNetAnalyzer. Should be a positive int, default is 1." |
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153 | :value "1") |
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154 | ("textbox_type" |
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155 | :system-theoretic "integer-parameter" |
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156 | :documentation "parameter determining if the textbox in CellNetAnalyzer is editable (1), not-editable (2) or non-visible (3). The default value is 1." |
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157 | :value "1") |
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158 | )) |
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159 | |
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160 | |
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161 | (define-module |
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162 | :class "gate-2" |
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163 | :super-classes ("gate") |
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164 | :terminals |
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165 | (("input1" |
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166 | :is-a "term-struct-input" |
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167 | :geometry-side "top" |
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168 | :geometry-position "0.1") |
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169 | ("input2" |
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170 | :is-a "term-struct-input" |
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171 | :geometry-side "top" |
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172 | :geometry-position "0.9") |
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173 | ("output" |
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174 | :is-a "term-struct-output" |
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175 | :geometry-side "bottom" |
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176 | :geometry-position "0.5"))) |
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177 | |
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178 | |
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179 | (define-module |
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180 | :class "gate-2-lr" |
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181 | :super-classes ("gate-2") |
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182 | :terminals |
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183 | (("input1" |
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184 | :geometry-side "left") |
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185 | ("input2" |
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186 | :geometry-side "left") |
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187 | ("output" |
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188 | :geometry-side "right"))) |
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189 | |
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190 | (define-module |
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191 | :class "gate-2-rl" |
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192 | :super-classes ("gate-2") |
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193 | :terminals |
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194 | (("input1" |
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195 | :geometry-side "right") |
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196 | ("input2" |
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197 | :geometry-side "right") |
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198 | ("output" |
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199 | :geometry-side "left"))) |
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200 | |
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201 | (define-module |
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202 | :class "gate-2-du" |
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203 | :super-classes ("gate-2") |
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204 | :terminals |
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205 | (("input1" |
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206 | :geometry-side "bottom") |
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207 | ("input2" |
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208 | :geometry-side "bottom") |
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209 | ("output" |
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210 | :geometry-side "top"))) |
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211 | |
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212 | (define-module |
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213 | :class "gate-2-2" |
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214 | :super-classes ("gate-2") |
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215 | :terminals |
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216 | (("input1" |
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217 | :is-eq-to "gate_2.input1" |
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218 | :geometry-side "TOP" |
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219 | :geometry-position "0.1") |
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220 | ("input2" |
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221 | :is-eq-to "struct_adapter.input" |
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222 | :geometry-side "TOP" |
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223 | :geometry-position "0.5") |
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224 | ("input3" |
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225 | :is-eq-to "gate_2b.input2" |
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226 | :geometry-side "TOP" |
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227 | :geometry-position "0.9") |
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228 | ("output" |
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229 | :is-eq-to "struct_adapterb.output" |
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230 | :geometry-side "BOTTOM" |
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231 | :geometry-position "0.5")) |
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232 | :modules |
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233 | (("gate_2" |
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234 | :is-a "gate-2" |
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235 | :geometry-x "48" |
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236 | :geometry-y "147") |
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237 | ("gate_2b" |
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238 | :is-a "gate-2" |
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239 | :geometry-x "228" |
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240 | :geometry-y "147") |
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241 | ("struct_adapter" |
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242 | :is-a "struct-adapter-gate" |
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243 | :geometry-x "137" |
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244 | :geometry-y "82") |
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245 | ("struct_adapterb" |
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246 | :is-a "struct-adapter-gate" |
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247 | :geometry-x "138" |
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248 | :geometry-y "209")) |
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249 | :links |
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250 | (("struct_adapterbinput_gate_2output" |
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251 | :terminals ("struct_adapterb.input" "gate_2.output" "gate_2b.output") |
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252 | :nodes (("138" "158")) |
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253 | :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil))) |
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254 | ("struct_adapteroutput_gate_2input2" |
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255 | :terminals ("struct_adapter.output" "gate_2.input2" "gate_2b.input1") |
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256 | :nodes (("138" "136")) |
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257 | :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil)))) |
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258 | :variables |
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259 | (("visibility" |
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260 | :value "1")) |
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261 | :parameters( |
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262 | ("gate_2.ignore_in_export" |
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263 | :value "parent.ignore_in_export") |
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264 | ("gate_2b.ignore_in_export" |
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265 | :value "parent.ignore_in_export") |
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266 | ("struct_adapter.ignore_in_export" |
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267 | :value "parent.ignore_in_export") |
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268 | ("struct_adapterb.ignore_in_export" |
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269 | :value "parent.ignore_in_export"))) |
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270 | |
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271 | |
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272 | (define-module |
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273 | :class "gate-3" |
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274 | :super-classes ("gate") |
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275 | :terminals |
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276 | (("input1" |
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277 | :is-a "term-struct-input" |
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278 | :geometry-side "top" |
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279 | :geometry-position "0.1") |
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280 | ("input2" |
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281 | :is-a "term-struct-input" |
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282 | :geometry-side "top" |
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283 | :geometry-position "0.5") |
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284 | ("input3" |
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285 | :is-a "term-struct-input" |
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286 | :geometry-side "top" |
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287 | :geometry-position "0.9") |
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288 | ("output" |
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289 | :is-a "term-struct-output" |
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290 | :geometry-side "bottom" |
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291 | :geometry-position "0.5"))) |
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292 | |
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293 | (define-module |
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294 | :class "gate-3-lr" |
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295 | :super-classes ("gate-3") |
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296 | :terminals |
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297 | (("input1" |
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298 | :geometry-side "left") |
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299 | ("input2" |
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300 | :geometry-side "left") |
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301 | ("input3" |
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302 | :geometry-side "left") |
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303 | ("output" |
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304 | :geometry-side "right"))) |
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305 | |
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306 | (define-module |
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307 | :class "gate-3-rl" |
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308 | :super-classes ("gate-3") |
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309 | :terminals |
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310 | (("input1" |
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311 | :geometry-side "right") |
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312 | ("input2" |
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313 | :geometry-side "right") |
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314 | ("input3" |
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315 | :geometry-side "right") |
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316 | ("output" |
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317 | :geometry-side "left"))) |
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318 | |
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319 | (define-module |
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320 | :class "gate-3-du" |
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321 | :super-classes ("gate-3") |
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322 | :terminals |
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323 | (("input1" |
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324 | :geometry-side "bottom") |
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325 | ("input2" |
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326 | :geometry-side "bottom") |
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327 | ("input3" |
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328 | :geometry-side "bottom") |
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329 | ("output" |
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330 | :geometry-side "top"))) |
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331 | |
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332 | (define-module |
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333 | :class "gate-4" |
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334 | :super-classes ("gate") |
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335 | :terminals |
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336 | (("input1" |
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337 | :is-a "term-struct-input" |
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338 | :geometry-side "left" |
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339 | :geometry-position "0.5") |
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340 | ("input2" |
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341 | :is-a "term-struct-input" |
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342 | :geometry-side "top" |
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343 | :geometry-position "0.25") |
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344 | ("input3" |
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345 | :is-a "term-struct-input" |
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346 | :geometry-side "top" |
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347 | :geometry-position "0.77") |
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348 | ("input4" |
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349 | :is-a "term-struct-input" |
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350 | :geometry-side "right" |
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351 | :geometry-position "0.5") |
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352 | ("output" |
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353 | :is-a "term-struct-output" |
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354 | :geometry-side "bottom" |
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355 | :geometry-position "0.5"))) |
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356 | |
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357 | |
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358 | (define-module |
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359 | :class "gate-5" |
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360 | :super-classes ("gate") |
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361 | :terminals |
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362 | (("input1" |
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363 | :is-a "term-struct-input" |
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364 | :geometry-side "left" |
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365 | :geometry-position "0.9") |
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366 | ("input2" |
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367 | :is-a "term-struct-input" |
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368 | :geometry-side "left" |
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369 | :geometry-position "0.1") |
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370 | ("input3" |
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371 | :is-a "term-struct-input" |
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372 | :geometry-side "top" |
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373 | :geometry-position "0.5") |
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374 | ("input4" |
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375 | :is-a "term-struct-input" |
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376 | :geometry-side "right" |
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377 | :geometry-position "0.1") |
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378 | ("input5" |
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379 | :is-a "term-struct-input" |
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380 | :geometry-side "right" |
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381 | :geometry-position "0.9") |
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382 | ("output" |
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383 | :is-a "term-struct-output" |
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384 | :geometry-side "bottom" |
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385 | :geometry-position "0.5"))) |
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386 | |
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387 | (define-module |
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388 | :class "gate-6" |
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389 | :super-classes ("gate") |
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390 | :terminals |
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391 | (("input1" |
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392 | :is-a "term-struct-input" |
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393 | :geometry-side "left" |
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394 | :geometry-position "0.9") |
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395 | ("input2" |
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396 | :is-a "term-struct-input" |
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397 | :geometry-side "left" |
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398 | :geometry-position "0.1") |
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399 | ("input3" |
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400 | :is-a "term-struct-input" |
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401 | :geometry-side "top" |
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402 | :geometry-position "0.5") |
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403 | ("input4" |
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404 | :is-a "term-struct-input" |
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405 | :geometry-side "right" |
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406 | :geometry-position "0.1") |
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407 | ("input5" |
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408 | :is-a "term-struct-input" |
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409 | :geometry-side "right" |
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410 | :geometry-position "0.5") |
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411 | ("input6" |
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412 | :is-a "term-struct-input" |
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413 | :geometry-side "right" |
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414 | :geometry-position "0.9") |
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415 | ("output" |
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416 | :is-a "term-struct-output" |
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417 | :geometry-side "bottom" |
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418 | :geometry-position "0.5"))) |
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419 | |
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420 | (define-module |
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421 | :class "activ" |
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422 | :super-classes ("gate") |
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423 | :icon "icons/struct/activ" |
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424 | :terminals |
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425 | (("input1" |
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426 | :is-a "term-struct-input" |
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427 | :geometry-side "top" |
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428 | :geometry-position "0.5") |
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429 | ("output" |
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430 | :is-a "term-struct-output" |
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431 | :geometry-side "bottom" |
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432 | :geometry-position "0.5"))) |
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433 | |
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434 | (define-module |
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435 | :class "activ-ud" |
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436 | :super-classes ("activ") |
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437 | :properties |
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438 | (("abstract" :value "no"))) |
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439 | |
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440 | (define-module |
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441 | :class "activ-du" |
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442 | :super-classes ("activ") |
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443 | :properties |
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444 | (("abstract" :value "no")) |
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445 | :icon "icons/struct/activ-du" |
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446 | :terminals |
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447 | (("input1" |
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448 | :geometry-side "bottom") |
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449 | ("output" |
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450 | :geometry-side "top"))) |
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451 | |
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452 | (define-module |
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453 | :class "activ-lr" |
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454 | :super-classes ("activ") |
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455 | :properties |
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456 | (("abstract" :value "no")) |
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457 | :icon "icons/struct/activ-lr" |
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458 | :terminals |
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459 | (("input1" |
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460 | :geometry-side "left") |
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461 | ("output" |
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462 | :geometry-side "right"))) |
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463 | |
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464 | (define-module |
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465 | :class "activ-rl" |
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466 | :super-classes ("activ") |
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467 | :properties |
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468 | (("abstract" :value "no")) |
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469 | :icon "icons/struct/activ-rl" |
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470 | :terminals |
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471 | (("input1" |
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472 | :geometry-side "right") |
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473 | ("output" |
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474 | :geometry-side "left"))) |
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475 | |
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476 | (define-module |
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477 | :class "and" |
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478 | :super-classes ("gate") |
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479 | :icon "icons/struct/and") |
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480 | |
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481 | (define-module |
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482 | :class "and-2" |
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483 | :super-classes ("and" "gate-2")) |
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484 | |
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485 | (define-module |
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486 | :class "and-2-ud" |
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487 | :super-classes ("and-2") |
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488 | :properties |
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489 | (("abstract" :value "no"))) |
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490 | |
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491 | (define-module |
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492 | :class "and-2-lr" |
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493 | :super-classes ("and-2" "gate-2-lr") |
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494 | :properties |
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495 | (("abstract" :value "no"))) |
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496 | |
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497 | (define-module |
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498 | :class "and-2-rl" |
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499 | :super-classes ("and-2" "gate-2-rl") |
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500 | :properties |
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501 | (("abstract" :value "no"))) |
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502 | |
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503 | (define-module |
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504 | :class "and-2-du" |
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505 | :super-classes ("and-2" "gate-2-du") |
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506 | :properties |
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507 | (("abstract" :value "no"))) |
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508 | |
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509 | (define-module |
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510 | :class "and-2-2" |
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511 | :super-classes ("and" "gate-2-2") |
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512 | :properties |
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513 | (("abstract" :value "no")) |
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514 | :modules |
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515 | (("gate_2" |
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516 | :is-a "and-2") |
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517 | ("gate_2b" |
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518 | :is-a "and-2")) |
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519 | :parameters( |
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520 | ("gate_2.ignore_in_export" |
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521 | :value "parent.ignore_in_export") |
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522 | ("gate_2b.ignore_in_export" |
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523 | :value "parent.ignore_in_export")) |
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524 | ) |
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525 | |
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526 | (define-module |
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527 | :class "and-3" |
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528 | :super-classes ("and" "gate-3") |
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529 | :properties |
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530 | (("abstract" :value "no"))) |
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531 | |
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532 | |
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533 | (define-module |
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534 | :class "and-4" |
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535 | :super-classes ("and" "gate-4") |
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536 | :properties (("abstract" :value "no"))) |
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537 | |
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538 | |
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539 | (define-module |
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540 | :class "and-5" |
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541 | :super-classes ("and" "gate-5") |
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542 | :properties |
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543 | (("abstract" :value "no"))) |
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544 | |
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545 | |
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546 | (define-module |
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547 | :class "and-6" |
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548 | :super-classes ("and" "gate-6") |
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549 | :properties |
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550 | (("abstract" :value "no"))) |
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551 | |
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552 | (define-module |
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553 | :class "compound" |
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554 | :super-classes ("struct-library") |
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555 | :icon "icons/struct/comp" |
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556 | :parameters |
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557 | (("input.a" |
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558 | :system-theoretic "real-parameter")) |
---|
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