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1 %!PS-Adobe-3.0 EPSF-3.0
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2 %%Title: Sequence Logo : {$TITLE}
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3 %%Creator: {$CREATOR}
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4 %%CreationDate: {$CREATIONDATE}
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5 %%BoundingBox: 0 0 {$LOGOWIDTHPOINTS} {$LOGOHEIGHTPOINTS}
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6 %%Pages: 0
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7 %%DocumentFonts:
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8 %%EndComments
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9
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10 {$DESC}
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11
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12
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13 % ---- CONSTANTS ----
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14 /cmfactor 72 2.54 div def % defines points -> cm conversion
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15 /cm {cmfactor mul} bind def % defines centimeters
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16
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17
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18 % ---- VARIABLES ----
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19
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20 {$COLORDEF}
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21
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22 /logoWidth {$LOGOWIDTH} cm def
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23 /logoHeight {$LOGOLINEHEIGHT} cm def
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24 /logoTitle ({$TITLE}) def
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25
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26 /yaxis {$YAXIS} def
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27 /yaxisLabel ({$YAXIS_LABEL}) def
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28 /yaxisBits {$BARBITS} def % bits
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29 /yaxisTicBits {$TICBITS} def
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30
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31
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32 /xaxis {$NUMBERING} def
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33 /xaxisLabel ({$XAXIS_LABEL}) def
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34 /showEnds ({$SHOWENDS}) def % d: DNA, p: PROTEIN, -: none
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35
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36 /showFineprint true def
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37 /fineprint ({$FINEPRINT}) def
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38
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39 /charsPerLine {$CHARSPERLINE} def
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40 /logoLines {$LOGOLINES} def
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41
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42 /showingBox ({$SHOWINGBOX}) def %n s f
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43 /shrinking {$SHRINKBOOLEAN} def
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44 /shrink {$SHRINKFACTOR} def
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45 /outline {$OUTLINE} def
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46
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47 /IbeamFraction {$ERRORBARFRACTION} def
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48 /IbeamGray 0.50 def
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49 /IbeamLineWidth 0.5 def
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50
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51 /fontsize 12 def
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52 /titleFontsize 14 def
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53 /smallFontsize 6 def
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54
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55 /defaultColor {$DEFAULT_COLOR} def
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56
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57 {$COLORDICT}
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58
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59 % Standard DNA/RNA color scheme
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60 % /colorDict <<
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61 % (G) orange
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62 % (T) red
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63 % (C) blue
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64 % (A) green
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65 % (U) red
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66 % >> def
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67
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68 % Standard Amino Acid colors
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69 %/colorDict <<
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70 % (G) green
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71 % (S) green
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72 % (T) green
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73 % (Y) green
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74 % (C) green
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75 % (N) purple
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76 % (Q) purple
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77 % (K) blue
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78 % (R) blue
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79 % (H) blue
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80 % (D) red
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81 % (E) red
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82 % (P) black
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83 % (A) black
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84 % (W) black
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85 % (F) black
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86 % (L) black
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87 % (I) black
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88 % (M) black
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89 % (V) black
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90 %>> def
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91
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92
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93
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94 % ---- DERIVED PARAMETERS ----
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95
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96 /leftMargin
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97 fontsize 3.5 mul
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98
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99 def
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100
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101 /bottomMargin
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102 fontsize 0.75 mul
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103
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104 % Add extra room for axis
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105 xaxis {fontsize 1.75 mul add } if
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106 xaxisLabel () eq {} {fontsize 0.75 mul add} ifelse
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107 def
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108
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109
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110 /topMargin
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111 logoTitle () eq { 10 }{titleFontsize 4 add} ifelse
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112 def
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113
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114 /rightMargin
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115 %Add extra room if showing ends
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116 showEnds (-) eq { fontsize}{fontsize 1.5 mul} ifelse
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117 def
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118
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119 /yaxisHeight
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120 logoHeight
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121 bottomMargin sub
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122 topMargin sub
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123 def
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124
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125 /ticWidth fontsize 2 div def
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126
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127 /pointsPerBit yaxisHeight yaxisBits div def
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128
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129 /isBoxed
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130 showingBox (s) eq
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131 showingBox (f) eq or {
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132 true
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133 } {
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134 false
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135 } ifelse
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136 def
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137
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138 /stackMargin 1 def
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139
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140 % Do not add space aroung characters if characters are boxed
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141 /charRightMargin
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142 isBoxed { 0.0 } {stackMargin} ifelse
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143 def
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144
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145 /charTopMargin
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146 isBoxed { 0.0 } {stackMargin} ifelse
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147 def
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148
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149 /charWidth
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150 logoWidth
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151 leftMargin sub
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152 rightMargin sub
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153 charsPerLine div
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154 charRightMargin sub
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155 def
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156
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157 /charWidth4 charWidth 4 div def
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158 /charWidth2 charWidth 2 div def
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159
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160 /stackWidth
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161 charWidth charRightMargin add
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162 def
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163
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164 /numberFontsize
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165 fontsize charWidth lt {fontsize}{charWidth} ifelse
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166 def
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167
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168 % movements to place 5'/N and 3'/C symbols
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169 /leftEndDeltaX fontsize neg def
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170 /leftEndDeltaY fontsize 1.5 mul neg def
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171 /rightEndDeltaX fontsize 0.25 mul def
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172 /rightEndDeltaY leftEndDeltaY def
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173
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174 % Outline width is proporional to charWidth,
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175 % but no less that 1 point
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176 /outlinewidth
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177 charWidth 32 div dup 1 gt {}{pop 1} ifelse
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178 def
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179
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180
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181 % ---- PROCEDURES ----
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182
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183 /StartLogo {
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184 % Save state
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185 save
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186 gsave
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187
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188 % Print Logo Title, top center
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189 gsave
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190 SetTitleFont
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191
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192 logoWidth 2 div
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193 logoTitle
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194 stringwidth pop 2 div sub
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195 logoHeight logoLines mul
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196 titleFontsize sub
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197 moveto
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198
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199 logoTitle
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200 show
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201 grestore
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202
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203 % Print X-axis label, bottom center
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204 gsave
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205 SetStringFont
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206
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207 logoWidth 2 div
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208 xaxisLabel stringwidth pop 2 div sub
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209 fontsize 3 div
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210 moveto
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211
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212 xaxisLabel
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213 show
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214 grestore
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215
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216 % Show Fine Print
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217 showFineprint {
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218 gsave
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219 SetSmallFont
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220 logoWidth
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221 fineprint stringwidth pop sub
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222 smallFontsize sub
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223 smallFontsize 3 div
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224 moveto
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225
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226 fineprint show
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227 grestore
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228 } if
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229
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230 % Move to lower left corner of last line, first stack
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231 leftMargin bottomMargin translate
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232
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233 % Move above first line ready for StartLine
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234 0 logoLines logoHeight mul translate
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235
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236 SetLogoFont
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237 } bind def
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238
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239 /EndLogo {
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240 grestore
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241 showpage
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242 restore
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243 } bind def
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244
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245
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246 /StartLine{
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247 % move down to the bottom of the line:
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248 0 logoHeight neg translate
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249
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250 gsave
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251 yaxis { MakeYaxis } if
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252 xaxis { ShowLeftEnd } if
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253 } bind def
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254
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255 /EndLine{
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256 xaxis { ShowRightEnd } if
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257 grestore
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258 } bind def
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259
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260
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261 /MakeYaxis {
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262 gsave
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263 stackMargin neg 0 translate
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264 ShowYaxisBar
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265 ShowYaxisLabel
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266 grestore
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267 } bind def
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268
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269
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270 /ShowYaxisBar {
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271 gsave
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272 SetStringFont
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273
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274 /str 10 string def % string to hold number
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275 /smallgap stackMargin 2 div def
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276
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277 % Draw first tic and bar
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278 gsave
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279 ticWidth neg 0 moveto
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280 ticWidth 0 rlineto
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281 0 yaxisHeight rlineto
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282 stroke
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283 grestore
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284
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285
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286 % Draw the tics
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287 % initial increment limit proc for
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288 0 yaxisTicBits yaxisBits abs %cvi
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289 {/loopnumber exch def
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290
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291 % convert the number coming from the loop to a string
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292 % and find its width
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293 loopnumber 10 str cvrs
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294 /stringnumber exch def % string representing the number
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295
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296 stringnumber stringwidth pop
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297 /numberwidth exch def % width of number to show
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298
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299 /halfnumberheight
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300 stringnumber CharBoxHeight 2 div
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301 def
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302
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303 numberwidth % move back width of number
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304 neg loopnumber pointsPerBit mul % shift on y axis
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305 halfnumberheight sub % down half the digit
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306
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307 moveto % move back the width of the string
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308
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309 ticWidth neg smallgap sub % Move back a bit more
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310 0 rmoveto % move back the width of the tic
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311
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312 stringnumber show
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313 smallgap 0 rmoveto % Make a small gap
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314
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315 % now show the tic mark
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316 0 halfnumberheight rmoveto % shift up again
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317 ticWidth 0 rlineto
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318 stroke
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319 } for
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320 grestore
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321 } bind def
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322
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323 /ShowYaxisLabel {
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324 gsave
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325 SetStringFont
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326
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327 % How far we move left depends on the size of
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328 % the tic labels.
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329 /str 10 string def % string to hold number
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330 yaxisBits yaxisTicBits div cvi yaxisTicBits mul
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331 str cvs stringwidth pop
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332 ticWidth 1.5 mul add neg
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333
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334
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335 yaxisHeight
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336 yaxisLabel stringwidth pop
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337 sub 2 div
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338
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339 translate
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340 90 rotate
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341 0 0 moveto
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342 yaxisLabel show
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343 grestore
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344 } bind def
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345
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346
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347 /StartStack { % <stackNumber> startstack
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348 xaxis {MakeNumber}{pop} ifelse
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349 gsave
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350 } bind def
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351
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352 /EndStack {
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353 grestore
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354 stackWidth 0 translate
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355 } bind def
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356
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357
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358 % Draw a character whose height is proportional to symbol bits
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359 /MakeSymbol{ % charbits character MakeSymbol
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360 gsave
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361 /char exch def
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362 /bits exch def
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363
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364 /bitsHeight
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365 bits pointsPerBit mul
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366 def
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367
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368 /charHeight
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369 bitsHeight charTopMargin sub
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370 dup
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371 0.0 gt {}{pop 0.0} ifelse % if neg replace with zero
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372 def
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373
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374 charHeight 0.0 gt {
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375 char SetColor
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376 charWidth charHeight char ShowChar
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377
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378 showingBox (s) eq { % Unfilled box
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379 0 0 charWidth charHeight false ShowBox
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380 } if
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381
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382 showingBox (f) eq { % Filled box
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383 0 0 charWidth charHeight true ShowBox
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384 } if
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385
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386 } if
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387
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388 grestore
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389
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390 0 bitsHeight translate
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391 } bind def
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392
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393
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394 /ShowChar { % <width> <height> <char> ShowChar
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395 gsave
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396 /tc exch def % The character
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397 /ysize exch def % the y size of the character
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398 /xsize exch def % the x size of the character
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399
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400 /xmulfactor 1 def
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401 /ymulfactor 1 def
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402
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403
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404 % if ysize is negative, make everything upside down!
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405 ysize 0 lt {
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406 % put ysize normal in this orientation
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407 /ysize ysize abs def
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408 xsize ysize translate
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409 180 rotate
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410 } if
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411
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412 shrinking {
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413 xsize 1 shrink sub 2 div mul
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414 ysize 1 shrink sub 2 div mul translate
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415
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416 shrink shrink scale
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417 } if
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418
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419 % Calculate the font scaling factors
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420 % Loop twice to catch small correction due to first scaling
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421 2 {
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422 gsave
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423 xmulfactor ymulfactor scale
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424
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425 ysize % desired size of character in points
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426 tc CharBoxHeight
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427 dup 0.0 ne {
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428 div % factor by which to scale up the character
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429 /ymulfactor exch def
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430 } % end if
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431 {pop pop}
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432 ifelse
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433
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434 xsize % desired size of character in points
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435 tc CharBoxWidth
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436 dup 0.0 ne {
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437 div % factor by which to scale up the character
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438 /xmulfactor exch def
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439 } % end if
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440 {pop pop}
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441 ifelse
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442 grestore
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443 } repeat
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444
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445 % Adjust horizontal position if the symbol is an I
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446 tc (I) eq {
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447 charWidth 2 div % half of requested character width
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448 tc CharBoxWidth 2 div % half of the actual character
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449 sub 0 translate
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450 % Avoid x scaling for I
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451 /xmulfactor 1 def
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452 } if
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453
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454
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455 % ---- Finally, draw the character
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456
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457 newpath
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458 xmulfactor ymulfactor scale
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459
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460 % Move lower left corner of character to start point
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461 tc CharBox pop pop % llx lly : Lower left corner
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462 exch neg exch neg
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463 moveto
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464
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465 outline { % outline characters:
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466 outlinewidth setlinewidth
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467 tc true charpath
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468 gsave 1 setgray fill grestore
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469 clip stroke
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470 } { % regular characters
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471 tc show
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472 } ifelse
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473
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474 grestore
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475 } bind def
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476
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477
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478 /ShowBox { % x1 y1 x2 y2 filled ShowBox
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479 gsave
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480 /filled exch def
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481 /y2 exch def
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482 /x2 exch def
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483 /y1 exch def
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484 /x1 exch def
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485 newpath
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486 x1 y1 moveto
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487 x2 y1 lineto
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488 x2 y2 lineto
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489 x1 y2 lineto
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490 closepath
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491
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492 clip
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493
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494 filled {
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495 fill
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496 }{
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497 0 setgray stroke
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498 } ifelse
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499
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500 grestore
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501 } bind def
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502
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503
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504 /MakeNumber { % number MakeNumber
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505 gsave
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506 SetNumberFont
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507 stackWidth 0 translate
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508 90 rotate % rotate so the number fits
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509 dup stringwidth pop % find the length of the number
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510 neg % prepare for move
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511 stackMargin sub % Move back a bit
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512 charWidth (0) CharBoxHeight % height of numbers
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513 sub 2 div %
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514 moveto % move back to provide space
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515 show
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516 grestore
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517 } bind def
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518
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519
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520 /Ibeam{ % heightInBits Ibeam
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521 gsave
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522 % Make an Ibeam of twice the given height in bits
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523 /height exch pointsPerBit mul def
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524 /heightDRAW height IbeamFraction mul def
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525
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526 IbeamLineWidth setlinewidth
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527 IbeamGray setgray
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528
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529 charWidth2 height neg translate
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530 ShowIbar
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531 newpath
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532 0 0 moveto
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533 0 heightDRAW rlineto
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534 stroke
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535 newpath
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536 0 height moveto
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537 0 height rmoveto
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538 currentpoint translate
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539 ShowIbar
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540 newpath
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541 0 0 moveto
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542 0 heightDRAW neg rlineto
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543 currentpoint translate
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544 stroke
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545 grestore
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546 } bind def
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547
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548
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549 /ShowIbar { % make a horizontal bar
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550 gsave
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551 newpath
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552 charWidth4 neg 0 moveto
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553 charWidth4 0 lineto
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554 stroke
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555 grestore
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556 } bind def
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557
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558
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559 /ShowLeftEnd {
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560 gsave
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561 SetStringFont
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562 leftEndDeltaX leftEndDeltaY moveto
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563 showEnds (d) eq {(5) show ShowPrime} if
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564 showEnds (p) eq {(N) show} if
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565 grestore
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566 } bind def
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567
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568
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569 /ShowRightEnd {
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570 gsave
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571 SetStringFont
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572 rightEndDeltaX rightEndDeltaY moveto
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573 showEnds (d) eq {(3) show ShowPrime} if
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574 showEnds (p) eq {(C) show} if
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575 grestore
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576 } bind def
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577
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578
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579 /ShowPrime {
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580 gsave
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581 SetPrimeFont
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582 (\242) show
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583 grestore
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584 } bind def
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585
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586
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587 /SetColor{ % <char> SetColor
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588 dup colorDict exch known {
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589 colorDict exch get aload pop setrgbcolor
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590 } {
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591 pop
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592 defaultColor aload pop setrgbcolor
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593 } ifelse
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594 } bind def
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595
|
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596 % define fonts
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|
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597 /SetTitleFont {/Times-Bold findfont titleFontsize scalefont setfont} bind def
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|
598 /SetLogoFont {/Helvetica-Narrow-Bold findfont charWidth scalefont setfont} bind def
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|
|
599 /SetStringFont{/Helvetica-Bold findfont fontsize scalefont setfont} bind def
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600 /SetPrimeFont {/Symbol findfont fontsize scalefont setfont} bind def
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|
601 /SetSmallFont {/Helvetica findfont smallFontsize scalefont setfont} bind def
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602
|
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603 /SetNumberFont {
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604 /Helvetica-Bold findfont
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605 numberFontsize
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|
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606 scalefont
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607 setfont
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608 } bind def
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609
|
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610 %Take a single character and return the bounding box
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611 /CharBox { % <char> CharBox <lx> <ly> <ux> <uy>
|
|
|
612 gsave
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613 newpath
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614 0 0 moveto
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|
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615 % take the character off the stack and use it here:
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|
|
616 true charpath
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617 flattenpath
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618 pathbbox % compute bounding box of 1 pt. char => lx ly ux uy
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|
|
619 % the path is here, but toss it away ...
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|
|
620 grestore
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621 } bind def
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622
|
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|
623
|
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|
624 % The height of a characters bounding box
|
|
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625 /CharBoxHeight { % <char> CharBoxHeight <num>
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626 CharBox
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|
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627 exch pop sub neg exch pop
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|
628 } bind def
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|
|
629
|
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630
|
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|
631 % The width of a characters bounding box
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|
|
632 /CharBoxWidth { % <char> CharBoxHeight <num>
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|
|
633 CharBox
|
|
|
634 pop exch pop sub neg
|
|
|
635 } bind def
|
|
|
636
|
|
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637
|
|
|
638 % Deprecated names
|
|
|
639 /startstack {StartStack} bind def
|
|
|
640 /endstack {EndStack} bind def
|
|
|
641 /makenumber {MakeNumber} bind def
|
|
|
642 /numchar { MakeSymbol } bind def
|
|
|
643
|
|
|
644 %%EndProlog
|
|
|
645
|
|
|
646 %%Page: 1 1
|
|
|
647 StartLogo
|
|
|
648 StartLine % line number 1
|
|
|
649
|
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|
650 {$DATA}
|
|
|
651
|
|
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652 EndLine
|
|
|
653 EndLogo
|
|
|
654
|
|
|
655 %%EOF
|
|
|
656
|
|
|
657
|
|
|
658
|
|
|
659
|
|
|
660
|
|
|
661
|
|
|
662
|
|
|
663
|
|
|
664
|
|
|
665
|
|
|
666
|
|
|
667
|
|
|
668
|
|
|
669
|
|
|
670
|
|
|
671
|
|
|
672
|
|
|
673
|
|
|
674
|
