bio-svgenes 0.3.1 → 0.3.2

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Files changed (144) hide show
  1. data/README.md +88 -0
  2. data/VERSION +1 -1
  3. data/bio-svgenes.gemspec +131 -8
  4. data/doc/classes/Bio.html +131 -0
  5. data/doc/classes/Bio/Graphics.html +142 -0
  6. data/doc/classes/Bio/Graphics/Glyph.html +987 -0
  7. data/doc/classes/Bio/Graphics/Glyph.src/M000001.html +26 -0
  8. data/doc/classes/Bio/Graphics/Glyph.src/M000002.html +27 -0
  9. data/doc/classes/Bio/Graphics/Glyph.src/M000003.html +32 -0
  10. data/doc/classes/Bio/Graphics/Glyph.src/M000004.html +27 -0
  11. data/doc/classes/Bio/Graphics/Glyph.src/M000005.html +25 -0
  12. data/doc/classes/Bio/Graphics/Glyph.src/M000006.html +29 -0
  13. data/doc/classes/Bio/Graphics/Glyph.src/M000007.html +107 -0
  14. data/doc/classes/Bio/Graphics/Glyph.src/M000008.html +51 -0
  15. data/doc/classes/Bio/Graphics/Glyph.src/M000009.html +23 -0
  16. data/doc/classes/Bio/Graphics/Glyph.src/M000010.html +18 -0
  17. data/doc/classes/Bio/Graphics/Glyph.src/M000011.html +75 -0
  18. data/doc/classes/Bio/Graphics/Glyph.src/M000012.html +51 -0
  19. data/doc/classes/Bio/Graphics/Glyph.src/M000013.html +23 -0
  20. data/doc/classes/Bio/Graphics/Glyph.src/M000014.html +26 -0
  21. data/doc/classes/Bio/Graphics/Glyph.src/M000015.html +27 -0
  22. data/doc/classes/Bio/Graphics/Glyph.src/M000016.html +32 -0
  23. data/doc/classes/Bio/Graphics/Glyph.src/M000017.html +27 -0
  24. data/doc/classes/Bio/Graphics/Glyph.src/M000018.html +25 -0
  25. data/doc/classes/Bio/Graphics/Glyph.src/M000019.html +29 -0
  26. data/doc/classes/Bio/Graphics/Glyph.src/M000020.html +107 -0
  27. data/doc/classes/Bio/Graphics/Glyph.src/M000021.html +51 -0
  28. data/doc/classes/Bio/Graphics/Glyph.src/M000022.html +23 -0
  29. data/doc/classes/Bio/Graphics/Glyph.src/M000023.html +18 -0
  30. data/doc/classes/Bio/Graphics/Glyph.src/M000024.html +75 -0
  31. data/doc/classes/Bio/Graphics/MiniFeature.html +243 -0
  32. data/doc/classes/Bio/Graphics/MiniFeature.src/M000001.html +25 -0
  33. data/doc/classes/Bio/Graphics/MiniFeature.src/M000003.html +25 -0
  34. data/doc/classes/Bio/Graphics/MiniFeature.src/M000024.html +25 -0
  35. data/doc/classes/Bio/Graphics/Page.html +705 -0
  36. data/doc/classes/Bio/Graphics/Page.src/M000010.html +35 -0
  37. data/doc/classes/Bio/Graphics/Page.src/M000011.html +83 -0
  38. data/doc/classes/Bio/Graphics/Page.src/M000012.html +24 -0
  39. data/doc/classes/Bio/Graphics/Page.src/M000013.html +29 -0
  40. data/doc/classes/Bio/Graphics/Page.src/M000014.html +24 -0
  41. data/doc/classes/Bio/Graphics/Page.src/M000015.html +20 -0
  42. data/doc/classes/Bio/Graphics/Page.src/M000016.html +20 -0
  43. data/doc/classes/Bio/Graphics/Page.src/M000017.html +18 -0
  44. data/doc/classes/Bio/Graphics/Page.src/M000018.html +18 -0
  45. data/doc/classes/Bio/Graphics/Page.src/M000019.html +18 -0
  46. data/doc/classes/Bio/Graphics/Page.src/M000020.html +18 -0
  47. data/doc/classes/Bio/Graphics/Page.src/M000021.html +18 -0
  48. data/doc/classes/Bio/Graphics/Page.src/M000022.html +18 -0
  49. data/doc/classes/Bio/Graphics/Page.src/M000023.html +18 -0
  50. data/doc/classes/Bio/Graphics/Page.src/M000024.html +18 -0
  51. data/doc/classes/Bio/Graphics/Page.src/M000025.html +35 -0
  52. data/doc/classes/Bio/Graphics/Page.src/M000026.html +83 -0
  53. data/doc/classes/Bio/Graphics/Page.src/M000027.html +24 -0
  54. data/doc/classes/Bio/Graphics/Page.src/M000028.html +29 -0
  55. data/doc/classes/Bio/Graphics/Page.src/M000029.html +24 -0
  56. data/doc/classes/Bio/Graphics/Page.src/M000030.html +20 -0
  57. data/doc/classes/Bio/Graphics/Page.src/M000031.html +20 -0
  58. data/doc/classes/Bio/Graphics/Page.src/M000032.html +18 -0
  59. data/doc/classes/Bio/Graphics/Page.src/M000033.html +18 -0
  60. data/doc/classes/Bio/Graphics/Page.src/M000034.html +18 -0
  61. data/doc/classes/Bio/Graphics/Page.src/M000035.html +18 -0
  62. data/doc/classes/Bio/Graphics/Page.src/M000036.html +18 -0
  63. data/doc/classes/Bio/Graphics/Page.src/M000037.html +18 -0
  64. data/doc/classes/Bio/Graphics/Page.src/M000038.html +18 -0
  65. data/doc/classes/Bio/Graphics/Page.src/M000039.html +18 -0
  66. data/doc/classes/Bio/Graphics/Page.src/M000040.html +107 -0
  67. data/doc/classes/Bio/Graphics/Page.src/M000041.html +18 -0
  68. data/doc/classes/Bio/Graphics/Page.src/M000042.html +23 -0
  69. data/doc/classes/Bio/Graphics/Page.src/M000043.html +18 -0
  70. data/doc/classes/Bio/Graphics/Page.src/M000044.html +18 -0
  71. data/doc/classes/Bio/Graphics/Primitive.html +204 -0
  72. data/doc/classes/Bio/Graphics/Primitive.src/M000001.html +21 -0
  73. data/doc/classes/Bio/Graphics/Primitive.src/M000002.html +20 -0
  74. data/doc/classes/Bio/Graphics/Primitive.src/M000008.html +21 -0
  75. data/doc/classes/Bio/Graphics/Primitive.src/M000009.html +20 -0
  76. data/doc/classes/Bio/Graphics/Primitive.src/M000022.html +21 -0
  77. data/doc/classes/Bio/Graphics/Primitive.src/M000023.html +20 -0
  78. data/doc/classes/Bio/Graphics/SVGEE.html +290 -0
  79. data/doc/classes/Bio/Graphics/SVGEE.src/M000002.html +24 -0
  80. data/doc/classes/Bio/Graphics/SVGEE.src/M000003.html +18 -0
  81. data/doc/classes/Bio/Graphics/SVGEE.src/M000004.html +24 -0
  82. data/doc/classes/Bio/Graphics/SVGEE.src/M000005.html +18 -0
  83. data/doc/classes/Bio/Graphics/SVGEE.src/M000006.html +18 -0
  84. data/doc/classes/Bio/Graphics/SVGEE.src/M000007.html +21 -0
  85. data/doc/classes/Bio/Graphics/SVGEE.src/M000008.html +27 -0
  86. data/doc/classes/Bio/Graphics/SVGEE.src/M000009.html +23 -0
  87. data/doc/classes/Bio/Graphics/SVGEE.src/M000016.html +24 -0
  88. data/doc/classes/Bio/Graphics/SVGEE.src/M000017.html +18 -0
  89. data/doc/classes/Bio/Graphics/SVGEE.src/M000018.html +18 -0
  90. data/doc/classes/Bio/Graphics/SVGEE.src/M000019.html +21 -0
  91. data/doc/classes/Bio/Graphics/SVGEE.src/M000020.html +27 -0
  92. data/doc/classes/Bio/Graphics/SVGEE.src/M000021.html +23 -0
  93. data/doc/classes/Bio/Graphics/Track.html +473 -0
  94. data/doc/classes/Bio/Graphics/Track.src/M000001.html +35 -0
  95. data/doc/classes/Bio/Graphics/Track.src/M000002.html +18 -0
  96. data/doc/classes/Bio/Graphics/Track.src/M000003.html +28 -0
  97. data/doc/classes/Bio/Graphics/Track.src/M000004.html +18 -0
  98. data/doc/classes/Bio/Graphics/Track.src/M000010.html +35 -0
  99. data/doc/classes/Bio/Graphics/Track.src/M000011.html +18 -0
  100. data/doc/classes/Bio/Graphics/Track.src/M000012.html +28 -0
  101. data/doc/classes/Bio/Graphics/Track.src/M000013.html +18 -0
  102. data/doc/created.rid +1 -9
  103. data/doc/files/lib/bio-svgenes_rb.html +131 -0
  104. data/doc/files/lib/bio/graphics/glyph_rb.html +101 -0
  105. data/doc/files/lib/bio/graphics/mini_feature_rb.html +101 -0
  106. data/doc/files/lib/bio/graphics/page_rb.html +111 -0
  107. data/doc/files/lib/bio/graphics/primitive_rb.html +101 -0
  108. data/doc/files/lib/bio/graphics/svgee_rb.html +101 -0
  109. data/doc/files/lib/bio/graphics/track_rb.html +101 -0
  110. data/doc/fr_class_index.html +34 -0
  111. data/doc/fr_file_index.html +33 -0
  112. data/doc/fr_method_index.html +70 -0
  113. data/doc/index.html +21 -91
  114. data/doc/manual/bootstrap/css/bootstrap-responsive.css +1109 -0
  115. data/doc/manual/bootstrap/css/bootstrap-responsive.min.css +9 -0
  116. data/doc/manual/bootstrap/css/bootstrap.css +6158 -0
  117. data/doc/manual/bootstrap/css/bootstrap.min.css +9 -0
  118. data/doc/manual/bootstrap/img/glyphicons-halflings-white.png +0 -0
  119. data/doc/manual/bootstrap/img/glyphicons-halflings.png +0 -0
  120. data/doc/manual/bootstrap/js/bootstrap.js +2276 -0
  121. data/doc/manual/bootstrap/js/bootstrap.min.js +6 -0
  122. data/doc/manual/img/circle.png +0 -0
  123. data/doc/manual/img/directed.png +0 -0
  124. data/doc/manual/img/down_triangle.png +0 -0
  125. data/doc/manual/img/histogram.png +0 -0
  126. data/doc/manual/img/span.png +0 -0
  127. data/doc/manual/img/transcript.png +0 -0
  128. data/doc/manual/img/up_triangle.png +0 -0
  129. data/doc/manual/manual.html +360 -0
  130. data/doc/manual/manual.md +307 -0
  131. data/doc/rdoc-style.css +208 -0
  132. data/examples/example.rb +12 -8
  133. data/examples/{make_example.rb → example2.rb} +5 -16
  134. data/lib/bio/graphics/glyph.rb +293 -126
  135. data/lib/bio/graphics/mini_feature.rb +24 -17
  136. data/lib/bio/graphics/page.rb +112 -54
  137. data/lib/bio/graphics/primitive.rb +12 -9
  138. data/lib/bio/graphics/svgee.rb +9 -11
  139. data/lib/bio/graphics/track.rb +92 -10
  140. metadata +132 -9
  141. data/README.rdoc +0 -19
  142. data/examples/annotate_snps.rb +0 -86
  143. data/examples/eg2.rb +0 -40
  144. data/examples/get_coverage_in_windows.rb +0 -176

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