toxtree 0.0.1

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  1. checksums.yaml +7 -0
  2. data/Toxtree-v2.6.13/LICENSE.txt +6 -0
  3. data/Toxtree-v2.6.13/README.txt +813 -0
  4. data/Toxtree-v2.6.13/Toxtree/Toxtree-2.6.13.jar +0 -0
  5. data/Toxtree-v2.6.13/Toxtree/example.java +41 -0
  6. data/Toxtree-v2.6.13/Toxtree/ext/toxtree-ames-2.6.13.jar +0 -0
  7. data/Toxtree-v2.6.13/Toxtree/ext/toxtree-biodegradation-2.6.13.jar +0 -0
  8. data/Toxtree-v2.6.13/Toxtree/ext/toxtree-cramer-2.6.13-tests.jar +0 -0
  9. data/Toxtree-v2.6.13/Toxtree/ext/toxtree-cramer-2.6.13.jar +0 -0
  10. data/Toxtree-v2.6.13/Toxtree/ext/toxtree-cramer2-2.6.13.jar +0 -0
  11. data/Toxtree-v2.6.13/Toxtree/ext/toxtree-dnabinding-2.6.13.jar +0 -0
  12. data/Toxtree-v2.6.13/Toxtree/ext/toxtree-eye-2.6.13.jar +0 -0
  13. data/Toxtree-v2.6.13/Toxtree/ext/toxtree-functional_groups-2.6.13.jar +0 -0
  14. data/Toxtree-v2.6.13/Toxtree/ext/toxtree-kroes-2.6.13.jar +0 -0
  15. data/Toxtree-v2.6.13/Toxtree/ext/toxtree-mic-2.6.13.jar +0 -0
  16. data/Toxtree-v2.6.13/Toxtree/ext/toxtree-michaelacceptors-2.6.13.jar +0 -0
  17. data/Toxtree-v2.6.13/Toxtree/ext/toxtree-mutant-2.6.13.jar +0 -0
  18. data/Toxtree-v2.6.13/Toxtree/ext/toxtree-proteinbinding-2.6.13.jar +0 -0
  19. data/Toxtree-v2.6.13/Toxtree/ext/toxtree-sicret-2.6.13.jar +0 -0
  20. data/Toxtree-v2.6.13/Toxtree/ext/toxtree-skinsensitisation-2.6.13.jar +0 -0
  21. data/Toxtree-v2.6.13/Toxtree/ext/toxtree-smartcyp-2.6.13.jar +0 -0
  22. data/Toxtree-v2.6.13/Toxtree/ext/toxtree-verhaar-2.6.13.jar +0 -0
  23. data/Toxtree-v2.6.13/Toxtree/ext/toxtree-verhaar2-2.6.13.jar +0 -0
  24. data/Toxtree-v2.6.13/Toxtree/input.txt +4 -0
  25. data/Toxtree-v2.6.13/Toxtree/result.txt +2 -0
  26. data/Toxtree-v2.6.13/Toxtree/toxtree-plugins.properties +24 -0
  27. data/Toxtree-v2.6.13/doc/Toxtree_BenigniBossaRulebase_manual.pdf +0 -0
  28. data/Toxtree-v2.6.13/doc/Toxtree_CramerExtensions_manual.pdf +0 -0
  29. data/Toxtree-v2.6.13/doc/Toxtree_START_manual.pdf +0 -0
  30. data/Toxtree-v2.6.13/doc/Toxtree_ToxMic_manual.pdf +0 -0
  31. data/Toxtree-v2.6.13/doc/Toxtree_installation_manual.pdf +0 -0
  32. data/Toxtree-v2.6.13/doc/Toxtree_user_manual.pdf +0 -0
  33. data/Toxtree-v2.6.13/doc/src/toxtree-2.6.13-javadoc.jar +0 -0
  34. data/Toxtree-v2.6.13/lib/javacpl.exe +0 -0
  35. data/Toxtree-v2.6.13/src/META-INF/MANIFEST.MF +6 -0
  36. data/Toxtree-v2.6.13/src/bodymol.inchi +398 -0
  37. data/Toxtree-v2.6.13/src/bodymol.sdf +34220 -0
  38. data/Toxtree-v2.6.13/src/com/molecularnetworks/start/BiodgeradationRules.java +205 -0
  39. data/Toxtree-v2.6.13/src/com/molecularnetworks/start/BiodgeradationRules.properties +7 -0
  40. data/Toxtree-v2.6.13/src/com/molecularnetworks/start/categories/CategoryBiodegradable.java +62 -0
  41. data/Toxtree-v2.6.13/src/com/molecularnetworks/start/categories/CategoryPersistent.java +63 -0
  42. data/Toxtree-v2.6.13/src/com/molecularnetworks/start/categories/CategoryUnknown.java +55 -0
  43. data/Toxtree-v2.6.13/src/com/molecularnetworks/start/positive_examples.sml +32 -0
  44. data/Toxtree-v2.6.13/src/com/molecularnetworks/start/rules/RuleAlcohols.java +68 -0
  45. data/Toxtree-v2.6.13/src/com/molecularnetworks/start/rules/RuleAldehyde.java +68 -0
  46. data/Toxtree-v2.6.13/src/com/molecularnetworks/start/rules/RuleAliphaticCyclicNoBranches.java +70 -0
  47. data/Toxtree-v2.6.13/src/com/molecularnetworks/start/rules/RuleAliphaticEther.java +67 -0
  48. data/Toxtree-v2.6.13/src/com/molecularnetworks/start/rules/RuleAliphaticFusedRingsNonBranched.java +79 -0
  49. data/Toxtree-v2.6.13/src/com/molecularnetworks/start/rules/RuleAlyphaticSulphonicAcids.java +73 -0
  50. data/Toxtree-v2.6.13/src/com/molecularnetworks/start/rules/RuleAminoAcids.java +70 -0
  51. data/Toxtree-v2.6.13/src/com/molecularnetworks/start/rules/RuleAromaticHalogen.java +76 -0
  52. data/Toxtree-v2.6.13/src/com/molecularnetworks/start/rules/RuleAromaticNGroups.java +72 -0
  53. data/Toxtree-v2.6.13/src/com/molecularnetworks/start/rules/RuleAromaticSulphonicAcid.java +70 -0
  54. data/Toxtree-v2.6.13/src/com/molecularnetworks/start/rules/RuleAzoGroup.java +68 -0
  55. data/Toxtree-v2.6.13/src/com/molecularnetworks/start/rules/RuleCyanoGroupOnMoreThanEightAtomsChain.java +70 -0
  56. data/Toxtree-v2.6.13/src/com/molecularnetworks/start/rules/RuleEpoxide.java +68 -0
  57. data/Toxtree-v2.6.13/src/com/molecularnetworks/start/rules/RuleEsters.java +67 -0
  58. data/Toxtree-v2.6.13/src/com/molecularnetworks/start/rules/RuleFormaldehyde.java +67 -0
  59. data/Toxtree-v2.6.13/src/com/molecularnetworks/start/rules/RuleHalogenSubstitutedBranched.java +71 -0
  60. data/Toxtree-v2.6.13/src/com/molecularnetworks/start/rules/RuleKetone.java +67 -0
  61. data/Toxtree-v2.6.13/src/com/molecularnetworks/start/rules/RuleMoreThanTwoHydroxyOnAromaticRing.java +133 -0
  62. data/Toxtree-v2.6.13/src/com/molecularnetworks/start/rules/RuleNNitroso.java +75 -0
  63. data/Toxtree-v2.6.13/src/com/molecularnetworks/start/rules/RuleNitrile.java +68 -0
  64. data/Toxtree-v2.6.13/src/com/molecularnetworks/start/rules/RuleOneHalogenOnUnbranched.java +135 -0
  65. data/Toxtree-v2.6.13/src/com/molecularnetworks/start/rules/RulePhosphateEsters.java +71 -0
  66. data/Toxtree-v2.6.13/src/com/molecularnetworks/start/rules/RulePyridineRing.java +67 -0
  67. data/Toxtree-v2.6.13/src/com/molecularnetworks/start/rules/RuleTerminalIsopropylNonCyclic.java +132 -0
  68. data/Toxtree-v2.6.13/src/com/molecularnetworks/start/rules/RuleTerminalTertButyl.java +68 -0
  69. data/Toxtree-v2.6.13/src/com/molecularnetworks/start/rules/RuleTertiaryAmine.java +67 -0
  70. data/Toxtree-v2.6.13/src/com/molecularnetworks/start/rules/RuleTriazineRing.java +68 -0
  71. data/Toxtree-v2.6.13/src/com/molecularnetworks/start/rules/RuleTrifluoromethyl.java +69 -0
  72. data/Toxtree-v2.6.13/src/com/molecularnetworks/start/rules/RuleTwoHalogensOnUnbranchedNonCyclic.java +137 -0
  73. data/Toxtree-v2.6.13/src/com/molecularnetworks/start/rules/RuleTwoOrMoreRings.java +99 -0
  74. data/Toxtree-v2.6.13/src/com/molecularnetworks/start/rules/RuleTwoTerminalDiaminoGroupsOnNonCyclic.java +132 -0
  75. data/Toxtree-v2.6.13/src/com/molecularnetworks/start/rules/RuleTwoTerminalDoubleBondsOnUnbranched.java +132 -0
  76. data/Toxtree-v2.6.13/src/cramer2/CramerRulesWithExtensions.java +283 -0
  77. data/Toxtree-v2.6.13/src/cramer2/CramerRulesWithExtensions.properties +10 -0
  78. data/Toxtree-v2.6.13/src/cramer2/MANIFEST.plugin +10 -0
  79. data/Toxtree-v2.6.13/src/cramer2/categories/CramerClass1.java +51 -0
  80. data/Toxtree-v2.6.13/src/cramer2/categories/CramerClass2.java +55 -0
  81. data/Toxtree-v2.6.13/src/cramer2/categories/CramerClass3.java +53 -0
  82. data/Toxtree-v2.6.13/src/cramer2/categories/CramerTreeResult.java +80 -0
  83. data/Toxtree-v2.6.13/src/cramer2/package.html +17 -0
  84. data/Toxtree-v2.6.13/src/cramer2/rules/RuleBenzeneAnalogues.java +58 -0
  85. data/Toxtree-v2.6.13/src/cramer2/rules/RuleDivalentSulphur.java +57 -0
  86. data/Toxtree-v2.6.13/src/cramer2/rules/RuleFreeABUnsaturatedHetero.java +52 -0
  87. data/Toxtree-v2.6.13/src/cramer2/rules/RuleHasOnlySaltSulphonateSulphate.java +279 -0
  88. data/Toxtree-v2.6.13/src/cramer2/rules/RuleNormalBodyConstituent.java +75 -0
  89. data/Toxtree-v2.6.13/src/cramer2/rules/RuleReadilyHydrolysedPO4.java +106 -0
  90. data/Toxtree-v2.6.13/src/cramer2/rules/RuleUnchargedOrganophosphates.java +53 -0
  91. data/Toxtree-v2.6.13/src/cramer2/rules/RuleUnchargedOrganophosphates_wrong.txt +207 -0
  92. data/Toxtree-v2.6.13/src/eye/EyeIrritationRules.java +356 -0
  93. data/Toxtree-v2.6.13/src/eye/EyeIrritationRules.properties +7 -0
  94. data/Toxtree-v2.6.13/src/eye/MANIFEST.plugin +11 -0
  95. data/Toxtree-v2.6.13/src/eye/categories/CategoryCorrosiveEye.java +45 -0
  96. data/Toxtree-v2.6.13/src/eye/categories/CategoryCorrosiveSkin.java +42 -0
  97. data/Toxtree-v2.6.13/src/eye/categories/CategoryModerateIrritation2Eye.java +42 -0
  98. data/Toxtree-v2.6.13/src/eye/categories/CategoryNotCorrosive2Eye.java +46 -0
  99. data/Toxtree-v2.6.13/src/eye/categories/CategoryNotCorrosive2Skin.java +46 -0
  100. data/Toxtree-v2.6.13/src/eye/categories/CategoryNotCorrosive2SkinAndIrritating2Eye.java +42 -0
  101. data/Toxtree-v2.6.13/src/eye/categories/CategoryNotCorrosive2SkinEye.java +45 -0
  102. data/Toxtree-v2.6.13/src/eye/categories/CategoryNotCorrosive2SkinOrIrritating2Eye.java +42 -0
  103. data/Toxtree-v2.6.13/src/eye/categories/CategoryNotIrritating2Eye.java +50 -0
  104. data/Toxtree-v2.6.13/src/eye/categories/CategoryNotIrritatingOrCorrosive2Eye.java +49 -0
  105. data/Toxtree-v2.6.13/src/eye/categories/CategoryUnknown.java +61 -0
  106. data/Toxtree-v2.6.13/src/eye/categories/package.html +77 -0
  107. data/Toxtree-v2.6.13/src/eye/package.html +17 -0
  108. data/Toxtree-v2.6.13/src/eye/rules/Rule1.java +41 -0
  109. data/Toxtree-v2.6.13/src/eye/rules/Rule13_AliphaticMonoalcohols.java +158 -0
  110. data/Toxtree-v2.6.13/src/eye/rules/Rule14Aliphatic_glycerol_monoethers.java +52 -0
  111. data/Toxtree-v2.6.13/src/eye/rules/Rule15.java +61 -0
  112. data/Toxtree-v2.6.13/src/eye/rules/Rule16.java +69 -0
  113. data/Toxtree-v2.6.13/src/eye/rules/Rule17.java +55 -0
  114. data/Toxtree-v2.6.13/src/eye/rules/Rule18.java +54 -0
  115. data/Toxtree-v2.6.13/src/eye/rules/Rule19.java +59 -0
  116. data/Toxtree-v2.6.13/src/eye/rules/Rule20.java +53 -0
  117. data/Toxtree-v2.6.13/src/eye/rules/Rule21.java +56 -0
  118. data/Toxtree-v2.6.13/src/eye/rules/Rule22.java +57 -0
  119. data/Toxtree-v2.6.13/src/eye/rules/Rule23.java +61 -0
  120. data/Toxtree-v2.6.13/src/eye/rules/Rule24.java +128 -0
  121. data/Toxtree-v2.6.13/src/eye/rules/Rule25.java +52 -0
  122. data/Toxtree-v2.6.13/src/eye/rules/Rule26.java +57 -0
  123. data/Toxtree-v2.6.13/src/eye/rules/Rule27.java +52 -0
  124. data/Toxtree-v2.6.13/src/eye/rules/Rule28.java +53 -0
  125. data/Toxtree-v2.6.13/src/eye/rules/Rule29.java +52 -0
  126. data/Toxtree-v2.6.13/src/eye/rules/Rule30.java +60 -0
  127. data/Toxtree-v2.6.13/src/eye/rules/Rule31.java +57 -0
  128. data/Toxtree-v2.6.13/src/eye/rules/Rule32.java +56 -0
  129. data/Toxtree-v2.6.13/src/eye/rules/Rule33.java +84 -0
  130. data/Toxtree-v2.6.13/src/eye/rules/Rule34.java +58 -0
  131. data/Toxtree-v2.6.13/src/eye/rules/Rule35.java +61 -0
  132. data/Toxtree-v2.6.13/src/eye/rules/Rule36.java +56 -0
  133. data/Toxtree-v2.6.13/src/eye/rules/Rule37.java +56 -0
  134. data/Toxtree-v2.6.13/src/eye/rules/Rule38.java +156 -0
  135. data/Toxtree-v2.6.13/src/eye/rules/Rule39.java +60 -0
  136. data/Toxtree-v2.6.13/src/eye/rules/RuleAqueousSolubility.java +48 -0
  137. data/Toxtree-v2.6.13/src/eye/rules/RuleAqueousSolubility1.java +47 -0
  138. data/Toxtree-v2.6.13/src/eye/rules/RuleAqueousSolubility_10_2.java +67 -0
  139. data/Toxtree-v2.6.13/src/eye/rules/RuleAqueousSolubility_10_5.java +51 -0
  140. data/Toxtree-v2.6.13/src/eye/rules/RuleAqueousSolubility_11_7.java +49 -0
  141. data/Toxtree-v2.6.13/src/eye/rules/RuleAqueousSolubility_8_3.java +50 -0
  142. data/Toxtree-v2.6.13/src/eye/rules/RuleAqueousSolubility_8_4.java +48 -0
  143. data/Toxtree-v2.6.13/src/eye/rules/RuleAqueousSolubility_9_3.java +51 -0
  144. data/Toxtree-v2.6.13/src/eye/rules/RuleHasOnlyC_H_O.java +36 -0
  145. data/Toxtree-v2.6.13/src/eye/rules/RuleHasOnlyC_H_O_Halogen.java +44 -0
  146. data/Toxtree-v2.6.13/src/eye/rules/RuleHasOnlyC_H_O_N.java +45 -0
  147. data/Toxtree-v2.6.13/src/eye/rules/RuleHasOnlyC_H_O_N_Halogen.java +40 -0
  148. data/Toxtree-v2.6.13/src/eye/rules/RuleHasOnlyC_H_O_N_S.java +51 -0
  149. data/Toxtree-v2.6.13/src/eye/rules/RuleLipidSolubility.java +47 -0
  150. data/Toxtree-v2.6.13/src/eye/rules/RuleLipidSolubility_10_4.java +50 -0
  151. data/Toxtree-v2.6.13/src/eye/rules/RuleLipidSolubility_9_1.java +50 -0
  152. data/Toxtree-v2.6.13/src/eye/rules/RuleLogP.java +52 -0
  153. data/Toxtree-v2.6.13/src/eye/rules/RuleLogP1.java +49 -0
  154. data/Toxtree-v2.6.13/src/eye/rules/RuleLogP_10_1.java +48 -0
  155. data/Toxtree-v2.6.13/src/eye/rules/RuleLogP_11_4.java +43 -0
  156. data/Toxtree-v2.6.13/src/eye/rules/RuleLogP_11_5.java +47 -0
  157. data/Toxtree-v2.6.13/src/eye/rules/RuleLogP_11_6.java +45 -0
  158. data/Toxtree-v2.6.13/src/eye/rules/RuleLogP_12_4.java +41 -0
  159. data/Toxtree-v2.6.13/src/eye/rules/RuleLogP_9_4.java +47 -0
  160. data/Toxtree-v2.6.13/src/eye/rules/RuleMeltingPoint_11_2.java +44 -0
  161. data/Toxtree-v2.6.13/src/eye/rules/RuleMeltingPoint_12_3.java +48 -0
  162. data/Toxtree-v2.6.13/src/eye/rules/RuleMeltingPoint_8_1.java +49 -0
  163. data/Toxtree-v2.6.13/src/eye/rules/RuleMelting_Point_11_3.java +45 -0
  164. data/Toxtree-v2.6.13/src/eye/rules/RuleMolWeight.java +53 -0
  165. data/Toxtree-v2.6.13/src/eye/rules/RuleMolWeight_10_3.java +46 -0
  166. data/Toxtree-v2.6.13/src/eye/rules/RuleMolWeight_11_1.java +45 -0
  167. data/Toxtree-v2.6.13/src/eye/rules/RuleMolWeight_12_2.java +65 -0
  168. data/Toxtree-v2.6.13/src/eye/rules/RuleMolWeight_8_2.java +46 -0
  169. data/Toxtree-v2.6.13/src/eye/rules/RuleMolWeight_9_2.java +54 -0
  170. data/Toxtree-v2.6.13/src/eye/rules/RuleMolweight_12_1.java +49 -0
  171. data/Toxtree-v2.6.13/src/eye/rules/package.html +15 -0
  172. data/Toxtree-v2.6.13/src/foodmol.inchi +104 -0
  173. data/Toxtree-v2.6.13/src/foodmol.sdf +6200 -0
  174. data/Toxtree-v2.6.13/src/kroes/KroesFig1Q1.sdf +110 -0
  175. data/Toxtree-v2.6.13/src/mic/MICRules.java +260 -0
  176. data/Toxtree-v2.6.13/src/mic/MICRules.properties +5 -0
  177. data/Toxtree-v2.6.13/src/mic/categories/micronucleusClass1.java +53 -0
  178. data/Toxtree-v2.6.13/src/mic/categories/micronucleusClass2.java +53 -0
  179. data/Toxtree-v2.6.13/src/mic/rules/MICTreeResult.java +158 -0
  180. data/Toxtree-v2.6.13/src/mic/rules/PB29.java +67 -0
  181. data/Toxtree-v2.6.13/src/mic/rules/PB30.java +68 -0
  182. data/Toxtree-v2.6.13/src/mic/rules/RuleAlertsForMIC.java +47 -0
  183. data/Toxtree-v2.6.13/src/mic/rules/SA1.java +59 -0
  184. data/Toxtree-v2.6.13/src/mic/rules/SA10.java +128 -0
  185. data/Toxtree-v2.6.13/src/mic/rules/SA11.java +76 -0
  186. data/Toxtree-v2.6.13/src/mic/rules/SA12.java +71 -0
  187. data/Toxtree-v2.6.13/src/mic/rules/SA13.java +70 -0
  188. data/Toxtree-v2.6.13/src/mic/rules/SA14.java +64 -0
  189. data/Toxtree-v2.6.13/src/mic/rules/SA15.java +59 -0
  190. data/Toxtree-v2.6.13/src/mic/rules/SA16.java +61 -0
  191. data/Toxtree-v2.6.13/src/mic/rules/SA18.java +211 -0
  192. data/Toxtree-v2.6.13/src/mic/rules/SA19.java +87 -0
  193. data/Toxtree-v2.6.13/src/mic/rules/SA2.java +184 -0
  194. data/Toxtree-v2.6.13/src/mic/rules/SA21.java +66 -0
  195. data/Toxtree-v2.6.13/src/mic/rules/SA22.java +70 -0
  196. data/Toxtree-v2.6.13/src/mic/rules/SA23.java +67 -0
  197. data/Toxtree-v2.6.13/src/mic/rules/SA24.java +65 -0
  198. data/Toxtree-v2.6.13/src/mic/rules/SA25.java +110 -0
  199. data/Toxtree-v2.6.13/src/mic/rules/SA26.java +93 -0
  200. data/Toxtree-v2.6.13/src/mic/rules/SA27.java +146 -0
  201. data/Toxtree-v2.6.13/src/mic/rules/SA28.java +204 -0
  202. data/Toxtree-v2.6.13/src/mic/rules/SA28bis.java +108 -0
  203. data/Toxtree-v2.6.13/src/mic/rules/SA28ter.java +94 -0
  204. data/Toxtree-v2.6.13/src/mic/rules/SA29.java +83 -0
  205. data/Toxtree-v2.6.13/src/mic/rules/SA3.java +65 -0
  206. data/Toxtree-v2.6.13/src/mic/rules/SA30.java +63 -0
  207. data/Toxtree-v2.6.13/src/mic/rules/SA32.java +67 -0
  208. data/Toxtree-v2.6.13/src/mic/rules/SA33.java +67 -0
  209. data/Toxtree-v2.6.13/src/mic/rules/SA34.java +76 -0
  210. data/Toxtree-v2.6.13/src/mic/rules/SA35.java +67 -0
  211. data/Toxtree-v2.6.13/src/mic/rules/SA36.java +68 -0
  212. data/Toxtree-v2.6.13/src/mic/rules/SA4.java +68 -0
  213. data/Toxtree-v2.6.13/src/mic/rules/SA5.java +61 -0
  214. data/Toxtree-v2.6.13/src/mic/rules/SA6.java +64 -0
  215. data/Toxtree-v2.6.13/src/mic/rules/SA7.java +60 -0
  216. data/Toxtree-v2.6.13/src/mic/rules/SA8.java +128 -0
  217. data/Toxtree-v2.6.13/src/mic/rules/SA9.java +60 -0
  218. data/Toxtree-v2.6.13/src/michaelacceptors/MATreeResult.java +34 -0
  219. data/Toxtree-v2.6.13/src/michaelacceptors/MichaelAcceptorRules.java +186 -0
  220. data/Toxtree-v2.6.13/src/michaelacceptors/MichaelAcceptorRules.properties +6 -0
  221. data/Toxtree-v2.6.13/src/michaelacceptors/categories/CategoryMichaelAcceptor.java +43 -0
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  870. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG16.java +55 -0
  871. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG17.java +59 -0
  872. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG18.java +59 -0
  873. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG19.java +60 -0
  874. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG2.java +53 -0
  875. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG20.java +51 -0
  876. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG21.java +59 -0
  877. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG22.java +58 -0
  878. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG23_1.java +59 -0
  879. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG23_2.java +58 -0
  880. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG23_3.java +59 -0
  881. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG23_4.java +58 -0
  882. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG23_5.java +58 -0
  883. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG23_6.java +58 -0
  884. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG23_7.java +59 -0
  885. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG23_8.java +59 -0
  886. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG23_LS.java +59 -0
  887. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG24_1.java +59 -0
  888. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG24_2.java +58 -0
  889. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG24_3.java +58 -0
  890. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG24_LS.java +59 -0
  891. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG25.java +59 -0
  892. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG26.java +59 -0
  893. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG27.java +59 -0
  894. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG28.java +59 -0
  895. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG29.java +59 -0
  896. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG30.java +59 -0
  897. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG31_1.java +59 -0
  898. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG31_2.java +58 -0
  899. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG31_3.java +59 -0
  900. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG31_4.java +58 -0
  901. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG31_5.java +58 -0
  902. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG31_6.java +58 -0
  903. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG31_7.java +59 -0
  904. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG31_8.java +59 -0
  905. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG31_9.java +59 -0
  906. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG31_LS.java +59 -0
  907. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG32.java +59 -0
  908. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG33_1.java +59 -0
  909. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG33_2.java +58 -0
  910. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG33_3.java +59 -0
  911. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG33_4.java +58 -0
  912. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG33_5.java +58 -0
  913. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG33_6.java +58 -0
  914. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG33_7.java +59 -0
  915. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG33_8.java +59 -0
  916. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG33_LS.java +59 -0
  917. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG34_1.java +59 -0
  918. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG34_2.java +58 -0
  919. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG34_LS.java +59 -0
  920. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG35_1.java +59 -0
  921. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG35_10.java +59 -0
  922. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG35_11.java +59 -0
  923. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG35_12.java +59 -0
  924. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG35_13.java +59 -0
  925. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG35_2.java +59 -0
  926. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG35_3.java +59 -0
  927. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG35_4.java +59 -0
  928. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG35_5.java +59 -0
  929. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG35_6.java +59 -0
  930. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG35_7.java +59 -0
  931. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG35_8.java +59 -0
  932. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG35_9.java +59 -0
  933. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG35_LS.java +59 -0
  934. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG36.java +59 -0
  935. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG37_1.java +59 -0
  936. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG37_2.java +59 -0
  937. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG37_3.java +59 -0
  938. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG37_4.java +59 -0
  939. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG37_LS.java +59 -0
  940. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG38.java +59 -0
  941. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG39.java +59 -0
  942. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG3_1.java +58 -0
  943. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG3_2.java +58 -0
  944. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG3_LS.java +58 -0
  945. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG4.java +60 -0
  946. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG40.java +59 -0
  947. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG41_1.java +59 -0
  948. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG41_2.java +59 -0
  949. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG41_3.java +59 -0
  950. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG41_4.java +59 -0
  951. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG41_5.java +59 -0
  952. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG41_LS.java +59 -0
  953. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG42.java +59 -0
  954. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG43.java +59 -0
  955. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG44.java +59 -0
  956. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG45.java +59 -0
  957. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG46_1.java +59 -0
  958. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG46_2.java +59 -0
  959. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG46_LS.java +59 -0
  960. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG47.java +59 -0
  961. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG48_1.java +59 -0
  962. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG48_2.java +59 -0
  963. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG48_LS.java +59 -0
  964. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG49.java +59 -0
  965. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG4_1.java +58 -0
  966. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG4_2.java +58 -0
  967. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG4_LS.java +59 -0
  968. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG5.java +58 -0
  969. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG50_1.java +59 -0
  970. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG50_2.java +59 -0
  971. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG50_3.java +59 -0
  972. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG50_LS.java +59 -0
  973. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG51_1.java +59 -0
  974. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG51_2.java +59 -0
  975. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG51_3.java +59 -0
  976. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG51_LS.java +59 -0
  977. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG52_1.java +59 -0
  978. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG52_2.java +59 -0
  979. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG52_3.java +59 -0
  980. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG52_LS.java +59 -0
  981. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG53_1.java +59 -0
  982. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG53_2.java +59 -0
  983. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG53_3.java +59 -0
  984. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG53_LS.java +59 -0
  985. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG54.java +59 -0
  986. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG55.java +59 -0
  987. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG56.java +59 -0
  988. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG57.java +59 -0
  989. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG58.java +59 -0
  990. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG59.java +59 -0
  991. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG6.java +59 -0
  992. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG60.java +59 -0
  993. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG61.java +59 -0
  994. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG62.java +59 -0
  995. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG63.java +59 -0
  996. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG64.java +59 -0
  997. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG65.java +59 -0
  998. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG66.java +59 -0
  999. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG67.java +59 -0
  1000. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG68.java +59 -0
  1001. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG69.java +59 -0
  1002. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG7.java +51 -0
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  1004. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG71.java +59 -0
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  1006. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG73.java +59 -0
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  1033. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG80_1.java +59 -0
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  1059. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG9.java +59 -0
  1060. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FG90.java +59 -0
  1061. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/FuncTreeResult.java +154 -0
  1062. data/Toxtree-v2.6.13/src/toxtree/plugins/func/rules/RuleAlertsForFunc.java +47 -0
  1063. data/Toxtree-v2.6.13/src/toxtree/plugins/kroes/Kroes1Tree.java +151 -0
  1064. data/Toxtree-v2.6.13/src/toxtree/plugins/kroes/Kroes1Tree.properties +5 -0
  1065. data/Toxtree-v2.6.13/src/toxtree/plugins/kroes/categories/NegligibleRisk.java +18 -0
  1066. data/Toxtree-v2.6.13/src/toxtree/plugins/kroes/categories/NotASafetyConcern.java +27 -0
  1067. data/Toxtree-v2.6.13/src/toxtree/plugins/kroes/categories/RequireCompoundSpecificToxicityData.java +25 -0
  1068. data/Toxtree-v2.6.13/src/toxtree/plugins/kroes/rules/KroesRule10.java +25 -0
  1069. data/Toxtree-v2.6.13/src/toxtree/plugins/kroes/rules/KroesRule11.java +24 -0
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  1264. data/Toxtree-v2.6.13/src/toxtree/ui/tree/actions/EditDecisionMethodAction.java +97 -0
  1265. data/Toxtree-v2.6.13/src/toxtree/ui/tree/actions/EditRuleAction.java +90 -0
  1266. data/Toxtree-v2.6.13/src/toxtree/ui/tree/actions/EditTreeExplanation.java +149 -0
  1267. data/Toxtree-v2.6.13/src/toxtree/ui/tree/actions/ICategoryAction.java +31 -0
  1268. data/Toxtree-v2.6.13/src/toxtree/ui/tree/actions/INodeAction.java +36 -0
  1269. data/Toxtree-v2.6.13/src/toxtree/ui/tree/actions/IRuleAction.java +31 -0
  1270. data/Toxtree-v2.6.13/src/toxtree/ui/tree/actions/ITreeAction.java +32 -0
  1271. data/Toxtree-v2.6.13/src/toxtree/ui/tree/actions/LiadMethodsListAction.java +101 -0
  1272. data/Toxtree-v2.6.13/src/toxtree/ui/tree/actions/LoadAndEditTreeAction.java +121 -0
  1273. data/Toxtree-v2.6.13/src/toxtree/ui/tree/actions/LoadTreeAction.java +154 -0
  1274. data/Toxtree-v2.6.13/src/toxtree/ui/tree/actions/NewRuleAction.java +184 -0
  1275. data/Toxtree-v2.6.13/src/toxtree/ui/tree/actions/NewTreeAction.java +89 -0
  1276. data/Toxtree-v2.6.13/src/toxtree/ui/tree/actions/SaveMethodsListAction.java +118 -0
  1277. data/Toxtree-v2.6.13/src/toxtree/ui/tree/actions/SaveTreeAction.java +168 -0
  1278. data/Toxtree-v2.6.13/src/toxtree/ui/tree/actions/SelectAndEditTreeAction.java +116 -0
  1279. data/Toxtree-v2.6.13/src/toxtree/ui/tree/actions/SelectCategoryFromListAction.java +88 -0
  1280. data/Toxtree-v2.6.13/src/toxtree/ui/tree/actions/SelectNewTreeAction.java +80 -0
  1281. data/Toxtree-v2.6.13/src/toxtree/ui/tree/actions/SelectTreeAction.java +88 -0
  1282. data/Toxtree-v2.6.13/src/toxtree/ui/tree/actions/SetBranchAction.java +175 -0
  1283. data/Toxtree-v2.6.13/src/toxtree/ui/tree/actions/SubstructureFromListAction.java +99 -0
  1284. data/Toxtree-v2.6.13/src/toxtree/ui/tree/actions/SubstructuresFromFileAction.java +113 -0
  1285. data/Toxtree-v2.6.13/src/toxtree/ui/tree/actions/TreeOptionsAction.java +74 -0
  1286. data/Toxtree-v2.6.13/src/toxtree/ui/tree/actions/VerifyUnreachableRulesAction.java +101 -0
  1287. data/Toxtree-v2.6.13/src/toxtree/ui/tree/actions/VerifyUnusedCategories.java +78 -0
  1288. data/Toxtree-v2.6.13/src/toxtree/ui/tree/actions/ViewTreeAction.java +86 -0
  1289. data/Toxtree-v2.6.13/src/toxtree/ui/tree/actions/package.html +16 -0
  1290. data/Toxtree-v2.6.13/src/toxtree/ui/tree/categories/CategoriesPanel.java +154 -0
  1291. data/Toxtree-v2.6.13/src/toxtree/ui/tree/categories/CategoriesTableModel.java +132 -0
  1292. data/Toxtree-v2.6.13/src/toxtree/ui/tree/categories/CategoryPanel.java +130 -0
  1293. data/Toxtree-v2.6.13/src/toxtree/ui/tree/categories/package.html +15 -0
  1294. data/Toxtree-v2.6.13/src/toxtree/ui/tree/molecule/CompoundPanel.java +215 -0
  1295. data/Toxtree-v2.6.13/src/toxtree/ui/tree/package.html +15 -0
  1296. data/Toxtree-v2.6.13/src/toxtree/ui/tree/qsar/DescriptorOptions.java +106 -0
  1297. data/Toxtree-v2.6.13/src/toxtree/ui/tree/qsar/OptionsPanel.java +181 -0
  1298. data/Toxtree-v2.6.13/src/toxtree/ui/tree/qsar/QSARModelEditor.java +140 -0
  1299. data/Toxtree-v2.6.13/src/toxtree/ui/tree/qsar/RuleQSARModelEditor.java +49 -0
  1300. data/Toxtree-v2.6.13/src/toxtree/ui/tree/rules/DecisionNodesListTableModel.java +80 -0
  1301. data/Toxtree-v2.6.13/src/toxtree/ui/tree/rules/RuleDeleteSubstructureAction.java +67 -0
  1302. data/Toxtree-v2.6.13/src/toxtree/ui/tree/rules/RuleEditor.java +114 -0
  1303. data/Toxtree-v2.6.13/src/toxtree/ui/tree/rules/RuleExampleEditAction.java +124 -0
  1304. data/Toxtree-v2.6.13/src/toxtree/ui/tree/rules/RuleMoleculeEditAction.java +84 -0
  1305. data/Toxtree-v2.6.13/src/toxtree/ui/tree/rules/RulePanel.java +284 -0
  1306. data/Toxtree-v2.6.13/src/toxtree/ui/tree/rules/RulePropertyEditor.java +127 -0
  1307. data/Toxtree-v2.6.13/src/toxtree/ui/tree/rules/RuleRangeEditor.java +138 -0
  1308. data/Toxtree-v2.6.13/src/toxtree/ui/tree/rules/RuleStructuresPanel.java +122 -0
  1309. data/Toxtree-v2.6.13/src/toxtree/ui/tree/rules/RuleSubstructuresEditAction.java +131 -0
  1310. data/Toxtree-v2.6.13/src/toxtree/ui/tree/rules/SMARTSRuleEditor.java +272 -0
  1311. data/Toxtree-v2.6.13/src/toxtree/ui/tree/rules/SmartsPanelEditor.java +367 -0
  1312. data/Toxtree-v2.6.13/src/toxtree/ui/tree/rules/SubstructureRulePanel.java +206 -0
  1313. data/Toxtree-v2.6.13/src/toxtree/ui/wizard/DecisionNodeWizard.java +531 -0
  1314. data/Toxtree-v2.6.13/src/toxtree/ui/wizard/DecisionTreeWizard.java +49 -0
  1315. data/Toxtree-v2.6.13/src/toxtree/ui/wizard/EditorPanel.java +65 -0
  1316. data/Toxtree-v2.6.13/src/toxtree/ui/wizard/ListPanelDescriptor.java +39 -0
  1317. data/Toxtree-v2.6.13/src/toxtree/ui/wizard/RadioBoxPanel.java +131 -0
  1318. data/Toxtree-v2.6.13/src/toxtree/ui/wizard/ToxTreeWizardPanelDescriptor.java +113 -0
  1319. data/Toxtree-v2.6.13/src/toxtree/ui/wizard/WizardWrapper.java +63 -0
  1320. data/Toxtree-v2.6.13/src/toxtree/ui/wizard/package.html +19 -0
  1321. data/Toxtree-v2.6.13/src/verhaar/VerhaarScheme.java +260 -0
  1322. data/Toxtree-v2.6.13/src/verhaar/VerhaarScheme.properties +7 -0
  1323. data/Toxtree-v2.6.13/src/verhaar/categories/Class1BaselineToxicity.java +42 -0
  1324. data/Toxtree-v2.6.13/src/verhaar/categories/Class2LessInertCompounds.java +42 -0
  1325. data/Toxtree-v2.6.13/src/verhaar/categories/Class3UnspecificReactivity.java +55 -0
  1326. data/Toxtree-v2.6.13/src/verhaar/categories/Class4SpecificMechanism.java +67 -0
  1327. data/Toxtree-v2.6.13/src/verhaar/categories/Class5Unknown.java +66 -0
  1328. data/Toxtree-v2.6.13/src/verhaar/categories/package.html +16 -0
  1329. data/Toxtree-v2.6.13/src/verhaar/package.html +20 -0
  1330. data/Toxtree-v2.6.13/src/verhaar/query/AromaticQueryBond.java +63 -0
  1331. data/Toxtree-v2.6.13/src/verhaar/query/FunctionalGroups.java +429 -0
  1332. data/Toxtree-v2.6.13/src/verhaar/query/OrderQueryBondAromatic.java +53 -0
  1333. data/Toxtree-v2.6.13/src/verhaar/query/QueryAssociationBond.java +88 -0
  1334. data/Toxtree-v2.6.13/src/verhaar/query/QueryUnsaturatedBond.java +100 -0
  1335. data/Toxtree-v2.6.13/src/verhaar/rules/Rule01.java +58 -0
  1336. data/Toxtree-v2.6.13/src/verhaar/rules/Rule03.java +80 -0
  1337. data/Toxtree-v2.6.13/src/verhaar/rules/Rule11.java +66 -0
  1338. data/Toxtree-v2.6.13/src/verhaar/rules/Rule13.java +52 -0
  1339. data/Toxtree-v2.6.13/src/verhaar/rules/Rule14.java +56 -0
  1340. data/Toxtree-v2.6.13/src/verhaar/rules/Rule141.java +85 -0
  1341. data/Toxtree-v2.6.13/src/verhaar/rules/Rule142.java +96 -0
  1342. data/Toxtree-v2.6.13/src/verhaar/rules/Rule143.java +123 -0
  1343. data/Toxtree-v2.6.13/src/verhaar/rules/Rule144.java +80 -0
  1344. data/Toxtree-v2.6.13/src/verhaar/rules/Rule15.java +53 -0
  1345. data/Toxtree-v2.6.13/src/verhaar/rules/Rule151.java +66 -0
  1346. data/Toxtree-v2.6.13/src/verhaar/rules/Rule152.java +109 -0
  1347. data/Toxtree-v2.6.13/src/verhaar/rules/Rule153.java +74 -0
  1348. data/Toxtree-v2.6.13/src/verhaar/rules/Rule154.java +66 -0
  1349. data/Toxtree-v2.6.13/src/verhaar/rules/Rule16.java +53 -0
  1350. data/Toxtree-v2.6.13/src/verhaar/rules/Rule161.java +75 -0
  1351. data/Toxtree-v2.6.13/src/verhaar/rules/Rule17.java +57 -0
  1352. data/Toxtree-v2.6.13/src/verhaar/rules/Rule171.java +77 -0
  1353. data/Toxtree-v2.6.13/src/verhaar/rules/Rule21.java +211 -0
  1354. data/Toxtree-v2.6.13/src/verhaar/rules/Rule22.java +56 -0
  1355. data/Toxtree-v2.6.13/src/verhaar/rules/Rule23.java +78 -0
  1356. data/Toxtree-v2.6.13/src/verhaar/rules/Rule24.java +95 -0
  1357. data/Toxtree-v2.6.13/src/verhaar/rules/Rule25.java +63 -0
  1358. data/Toxtree-v2.6.13/src/verhaar/rules/Rule31.java +82 -0
  1359. data/Toxtree-v2.6.13/src/verhaar/rules/Rule32.java +77 -0
  1360. data/Toxtree-v2.6.13/src/verhaar/rules/Rule33.java +71 -0
  1361. data/Toxtree-v2.6.13/src/verhaar/rules/Rule34.java +69 -0
  1362. data/Toxtree-v2.6.13/src/verhaar/rules/Rule35.java +69 -0
  1363. data/Toxtree-v2.6.13/src/verhaar/rules/Rule36.java +73 -0
  1364. data/Toxtree-v2.6.13/src/verhaar/rules/Rule37.java +72 -0
  1365. data/Toxtree-v2.6.13/src/verhaar/rules/Rule38.java +121 -0
  1366. data/Toxtree-v2.6.13/src/verhaar/rules/Rule4.java +97 -0
  1367. data/Toxtree-v2.6.13/src/verhaar/rules/RuleAlertsClass1.java +47 -0
  1368. data/Toxtree-v2.6.13/src/verhaar/rules/RuleAlertsClass2.java +47 -0
  1369. data/Toxtree-v2.6.13/src/verhaar/rules/RuleAlertsClass3.java +47 -0
  1370. data/Toxtree-v2.6.13/src/verhaar/rules/RuleIonicGroups.java +84 -0
  1371. data/Toxtree-v2.6.13/src/verhaar/rules/RuleLogPRange.java +96 -0
  1372. data/Toxtree-v2.6.13/src/verhaar/rules/RuleRingMainStrucSubstituents.java +38 -0
  1373. data/Toxtree-v2.6.13/src/verhaar/rules/RuleVerifyClass1Alerts.java +16 -0
  1374. data/Toxtree-v2.6.13/src/verhaar/rules/RuleVerifyClass2Alerts.java +16 -0
  1375. data/Toxtree-v2.6.13/src/verhaar/rules/RuleVerifyClass3Alerts.java +17 -0
  1376. data/Toxtree-v2.6.13/src/verhaar/rules/VerhaarTreeResult.java +57 -0
  1377. data/Toxtree-v2.6.13/src/verhaar/rules/helper/RuleAnySubstructureCounter.java +45 -0
  1378. data/Toxtree-v2.6.13/src/verhaar/rules/helper/RuleElementsCounter.java +44 -0
  1379. data/Toxtree-v2.6.13/src/verhaar/rules/helper/RuleOnlyAllowedSubstructuresCounter.java +44 -0
  1380. data/Toxtree-v2.6.13/src/verhaar/rules/package.html +15 -0
  1381. data/ext/toxtree/extconf.rb +21 -0
  1382. data/lib/toxtree.rb +91 -0
  1383. data/test/toxtree.rb +26 -0
  1384. metadata +1427 -0
@@ -0,0 +1,83 @@
1
+ /*
2
+ Copyright Ideaconsult Ltd. (C) 2005-2007
3
+
4
+ Contact: nina@acad.bg
5
+
6
+ This program is free software; you can redistribute it and/or
7
+ modify it under the terms of the GNU General Public License
8
+ as published by the Free Software Foundation; either version 2
9
+ of the License, or (at your option) any later version.
10
+ All we ask is that proper credit is given for our work, which includes
11
+ - but is not limited to - adding the above copyright notice to the beginning
12
+ of your source code files, and to any copyright notice that you may distribute
13
+ with programs based on this work.
14
+
15
+ This program is distributed in the hope that it will be useful,
16
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
17
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
18
+ GNU General Public License for more details.
19
+
20
+ You should have received a copy of the GNU General Public License
21
+ along with this program; if not, write to the Free Software
22
+ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
23
+
24
+ */
25
+ package toxTree.io.batch;
26
+
27
+ /**
28
+ * An {@link java.lang.Exception} to be used in {@link toxTree.io.batch.IBatchProcessing}
29
+ * @author Nina Jeliazkova
30
+ * <b>Modified</b> 2005-9-4
31
+ */
32
+ public class BatchProcessingException extends Exception {
33
+ protected IBatchProcessing batch = null;
34
+
35
+ /**
36
+ * Comment for <code>serialVersionUID</code>
37
+ */
38
+ private static final long serialVersionUID = 6837815972092687580L;
39
+
40
+ /**
41
+ *
42
+ */
43
+ public BatchProcessingException() {
44
+ super();
45
+ // TODO Auto-generated constructor stub
46
+ }
47
+
48
+ /**
49
+ * @param message
50
+ */
51
+ public BatchProcessingException(String message) {
52
+ super(message);
53
+ // TODO Auto-generated constructor stub
54
+ }
55
+ public BatchProcessingException(String message, IBatchProcessing batch) {
56
+ super(message);
57
+ this.batch = batch;
58
+ }
59
+ public BatchProcessingException(Throwable cause, IBatchProcessing batch) {
60
+ super(cause);
61
+ this.batch = batch;
62
+ }
63
+ /**
64
+ * @param cause
65
+ */
66
+ public BatchProcessingException(Throwable cause) {
67
+ super(cause);
68
+ // TODO Auto-generated constructor stub
69
+ }
70
+
71
+ /**
72
+ * @param message
73
+ * @param cause
74
+ */
75
+ public BatchProcessingException(String message, Throwable cause) {
76
+ super(message, cause);
77
+ }
78
+ public BatchProcessingException(String message, Throwable cause, IBatchProcessing batch) {
79
+ super(message, cause);
80
+ this.batch = batch;
81
+ }
82
+
83
+ }
@@ -0,0 +1,281 @@
1
+ /*
2
+ Copyright Ideaconsult Ltd. (C) 2005-2007
3
+
4
+ Contact: nina@acad.bg
5
+
6
+ This program is free software; you can redistribute it and/or
7
+ modify it under the terms of the GNU General Public License
8
+ as published by the Free Software Foundation; either version 2
9
+ of the License, or (at your option) any later version.
10
+ All we ask is that proper credit is given for our work, which includes
11
+ - but is not limited to - adding the above copyright notice to the beginning
12
+ of your source code files, and to any copyright notice that you may distribute
13
+ with programs based on this work.
14
+
15
+ This program is distributed in the hope that it will be useful,
16
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
17
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
18
+ GNU General Public License for more details.
19
+
20
+ You should have received a copy of the GNU General Public License
21
+ along with this program; if not, write to the Free Software
22
+ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
23
+
24
+ */
25
+ package toxTree.io.batch;
26
+
27
+ import java.io.File;
28
+ import java.io.FileInputStream;
29
+ import java.io.FileNotFoundException;
30
+ import java.io.FileOutputStream;
31
+ import java.io.IOException;
32
+ import java.io.UnsupportedEncodingException;
33
+ import java.util.logging.Level;
34
+
35
+ import javax.swing.ProgressMonitorInputStream;
36
+
37
+ import org.openscience.cdk.exception.CDKException;
38
+ import org.openscience.cdk.interfaces.IChemObject;
39
+ import org.openscience.cdk.io.IChemObjectWriter;
40
+ import org.openscience.cdk.io.iterator.IIteratingChemObjectReader;
41
+ import org.openscience.cdk.io.iterator.IteratingSMILESReader;
42
+ import org.openscience.cdk.silent.SilentChemObjectBuilder;
43
+
44
+ import ambit2.core.io.DelimitedFileFormat;
45
+ import ambit2.core.io.DelimitedFileWriter;
46
+ import ambit2.core.io.IteratingDelimitedFileReader;
47
+ import ambit2.core.io.MDLWriter;
48
+ import ambit2.core.io.MyIteratingMDLReader;
49
+
50
+
51
+ /**
52
+ * Implements batch processing of chemical files
53
+ * @author Nina Jeliazkova
54
+ * <b>Modified</b> 2005-9-4
55
+ */
56
+ public class ChemObjectBatchProcessing extends BatchProcessing {
57
+ protected transient IIteratingChemObjectReader reader;
58
+ protected transient IChemObjectWriter writer;
59
+ protected transient IChemObject chemObject;
60
+
61
+ public transient static final String[] extensions = {".sdf",".csv",".smi",".txt"};
62
+ public transient static final String[] extensions_descr = {"SDF files (*.sdf)",
63
+ "Comma delimited (*.csv)","SMILES (*.smi)","Text files (*.txt)"};
64
+ protected transient static int SDF_INDEX = 0;
65
+ protected transient static int CSV_INDEX = 1;
66
+ protected transient static int SMI_INDEX = 2;
67
+ protected transient static int TXT_INDEX = 3;
68
+
69
+ /**
70
+ * Comment for <code>serialVersionUID</code>
71
+ */
72
+ private static final long serialVersionUID = -7112745841569991346L;
73
+
74
+ /**
75
+ *
76
+ */
77
+ public ChemObjectBatchProcessing() {
78
+ super();
79
+ }
80
+
81
+ /**
82
+ * @param input Input file name
83
+ * @param output Output file name
84
+ * @throws BatchProcessingException
85
+ */
86
+ public ChemObjectBatchProcessing(String input, String output)
87
+ throws BatchProcessingException {
88
+ super(input, output);
89
+
90
+ }
91
+ /**
92
+ *
93
+ * @param input Input File
94
+ * @param output Output File
95
+ * @throws BatchProcessingException
96
+ */
97
+ public ChemObjectBatchProcessing(File input, File output) throws BatchProcessingException {
98
+ super(input, output);
99
+ }
100
+ protected org.openscience.cdk.io.iterator.IIteratingChemObjectReader getReader(FileState file,boolean monitor) throws BatchProcessingException {
101
+ try {
102
+ String fname = file.filename.toLowerCase();
103
+ if (fname.endsWith(extensions[SDF_INDEX]))
104
+ if (monitor)
105
+ return new MyIteratingMDLReader(new ProgressMonitorInputStream(
106
+ null,
107
+ "Reading " + file.getFile().getName(),
108
+ new FileInputStream(file.getFile())),SilentChemObjectBuilder.getInstance());
109
+ else
110
+ return new MyIteratingMDLReader(new FileInputStream(file.getFile()),SilentChemObjectBuilder.getInstance());
111
+ else if (fname.endsWith(extensions[SMI_INDEX]))
112
+ return new IteratingSMILESReader(new FileInputStream(file.getFile()));
113
+ else if (fname.endsWith(extensions[CSV_INDEX]))
114
+ return new IteratingDelimitedFileReader(new FileInputStream(file.getFile()));
115
+ else if (fname.endsWith(extensions[TXT_INDEX]))
116
+ return new IteratingDelimitedFileReader(new FileInputStream(file.getFile()),
117
+ new DelimitedFileFormat(" \t",'"'));
118
+ else throw new BatchProcessingException(MSG_UNSUPPORTEDFORMAT+file.filename,this);
119
+ } catch (CDKException x) {
120
+ logger.log(Level.SEVERE,x.getMessage(),x);
121
+ throw new BatchProcessingException(x,this);
122
+ } catch (UnsupportedEncodingException x) {
123
+ logger.log(Level.SEVERE,x.getMessage(),x);
124
+ throw new BatchProcessingException(x,this);
125
+ } catch (FileNotFoundException x) {
126
+ logger.log(Level.SEVERE,x.getMessage(),x);
127
+ throw new BatchProcessingException(x,this);
128
+ }
129
+ }
130
+ /**
131
+ * Opens the input file as set by constructor and creates {@link IteratingChemObjectReader}
132
+ */
133
+ @Override
134
+ public void openInputFile() throws BatchProcessingException {
135
+ super.openInputFile();
136
+ reader = null;
137
+ try {
138
+ logger.fine(MSG_OPEN+inputFile.filename);
139
+ reader = getReader(inputFile,false);
140
+ if ((reader != null) && (inputFile.currentRecord>0)) {
141
+ logger.fine("Have to skip\t"+Long.toString(inputFile.currentRecord)+"\trecords");
142
+ int count = 0;
143
+ while (reader.hasNext() && (count < inputFile.currentRecord)) {
144
+ reader.next();
145
+ count++;
146
+ }
147
+ if (count == inputFile.currentRecord)
148
+ logger.info(Long.toString(inputFile.currentRecord)+"\trecords skipped.");
149
+ else {
150
+ /*
151
+ logger.error("Input file is expected to have at least\t",Long.toString(inputFile.currentRecord),
152
+ "\trecords, but only \t",Long.toString(count),"\t have been found!");
153
+ */
154
+ throw new BatchProcessingException("Input file "+ inputFile.getFilename()+
155
+ "is expected to have at least\t"+Long.toString(inputFile.currentRecord)+
156
+ "\trecords, but only \t"+Long.toString(count)+"\t have been found!",this);
157
+ }
158
+ }
159
+ } catch (Exception x) {
160
+ logger.log(Level.SEVERE,x.getMessage(),x);
161
+ throw new BatchProcessingException(x);
162
+ }
163
+ }
164
+ /**
165
+ * Creates {@link ChemObjectWriter}
166
+ */
167
+ @Override
168
+ public void createOutputFile() throws BatchProcessingException {
169
+ super.createOutputFile();
170
+ String fname = outputFile.filename.toLowerCase();
171
+ boolean append = outputFile.currentRecord>0;
172
+ try {
173
+ if (fname.endsWith(extensions[SDF_INDEX])) {
174
+ writer = new MDLWriter(new FileOutputStream(outputFile.getFile(),append));
175
+ ((MDLWriter) writer).dontWriteAromatic();
176
+ } else if (fname.endsWith(extensions[CSV_INDEX]))
177
+ writer = new DelimitedFileWriter(new FileOutputStream(outputFile.getFile(),append));
178
+ else if ((fname.endsWith(extensions[TXT_INDEX])))
179
+ writer = new DelimitedFileWriter(new FileOutputStream(outputFile.getFile(),append),
180
+ new DelimitedFileFormat(" \t",'"'));
181
+ else throw new BatchProcessingException(MSG_UNSUPPORTEDFORMAT+outputFile.filename,this);
182
+ } catch (Exception x) {
183
+ logger.log(Level.SEVERE,MSG_ERRORSAVE+outputFile.filename,x);
184
+ throw new BatchProcessingException(x);
185
+ }
186
+ if ((writer != null) && append) {
187
+ /*TODO
188
+ int count = 0;
189
+ try {
190
+ IteratingChemObjectReader r = getReader(outputFile,true);
191
+
192
+ while (r.hasNext()) {
193
+ r.next();
194
+ count ++;
195
+ }
196
+ r.close();
197
+ } catch (Exception x) {
198
+ logger.error(MSG_ERRORCOUNTING,outputFile.filename);
199
+ throw new BatchProcessingException(MSG_ERRORCOUNTING+outputFile.filename,this);
200
+ }
201
+ if (count == outputFile.getCurrentRecord())
202
+ logger.info("Verifying if the file has indeed \t",Long.toString(outputFile.currentRecord),"\trecords\tYES");
203
+ else {
204
+ logger.info("Verifying if the file has indeed \t",Long.toString(outputFile.currentRecord),"\trecords\tNO");
205
+ throw new BatchProcessingException("Output file "+
206
+ outputFile.getFilename() +
207
+ " is expected to have exactly \t"+Long.toString(inputFile.currentRecord)+
208
+ "\t records, but \t"+Long.toString(count)+"\t records have been found!",this);
209
+
210
+ }
211
+ */
212
+
213
+ }
214
+
215
+ }
216
+ /* (non-Javadoc)
217
+ * @see toxTree.io.BatchProcessing#start()
218
+ */
219
+ @Override
220
+ public void start() throws BatchProcessingException {
221
+ super.start();
222
+ }
223
+ /* (non-Javadoc)
224
+ * @see toxTree.io.IBatchProcessing#closeInputFile()
225
+ */
226
+ public void closeInputFile() throws BatchProcessingException {
227
+ try {
228
+ if (reader != null)
229
+ reader.close();
230
+ reader = null;
231
+ } catch (IOException x) {
232
+ throw new BatchProcessingException(x,this);
233
+ }
234
+ }
235
+ /* (non-Javadoc)
236
+ * @see toxTree.io.IBatchProcessing#closeOutputFile()
237
+ */
238
+ public void closeOutputFile() throws BatchProcessingException {
239
+ try {
240
+ if (writer != null)
241
+ writer.close();
242
+ writer = null;
243
+ } catch (IOException x) {
244
+ throw new BatchProcessingException(x,this);
245
+ }
246
+ }
247
+ /* (non-Javadoc)
248
+ * @see toxTree.io.IBatchProcessing#processRecord()
249
+ */
250
+ public void processRecord() throws BatchProcessingException {
251
+ //do something with chemObject
252
+
253
+ }
254
+
255
+ /* (non-Javadoc)
256
+ * @see toxTree.io.IBatchProcessing#readRecord()
257
+ */
258
+ public void readRecord() throws BatchProcessingException {
259
+ chemObject = (IChemObject) reader.next();
260
+ }
261
+
262
+ /* (non-Javadoc)
263
+ * @see toxTree.io.IBatchProcessing#writeRecord()
264
+ */
265
+ public void writeRecord() throws BatchProcessingException {
266
+ try {
267
+ writer.write(chemObject);
268
+ } catch (CDKException x) {
269
+ throw new BatchProcessingException("Error on writing record\t",x,this);
270
+ }
271
+
272
+ }
273
+
274
+ /* (non-Javadoc)
275
+ * @see toxTree.io.IBatchProcessing#hasNextRecord()
276
+ */
277
+ public boolean hasNextRecord() {
278
+ return reader.hasNext();
279
+ }
280
+
281
+ }
@@ -0,0 +1,232 @@
1
+ /*
2
+ Copyright Ideaconsult Ltd. (C) 2005-2007
3
+
4
+ Contact: nina@acad.bg
5
+
6
+ This program is free software; you can redistribute it and/or
7
+ modify it under the terms of the GNU General Public License
8
+ as published by the Free Software Foundation; either version 2
9
+ of the License, or (at your option) any later version.
10
+ All we ask is that proper credit is given for our work, which includes
11
+ - but is not limited to - adding the above copyright notice to the beginning
12
+ of your source code files, and to any copyright notice that you may distribute
13
+ with programs based on this work.
14
+
15
+ This program is distributed in the hope that it will be useful,
16
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
17
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
18
+ GNU General Public License for more details.
19
+
20
+ You should have received a copy of the GNU General Public License
21
+ along with this program; if not, write to the Free Software
22
+ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
23
+
24
+ */
25
+ package toxTree.io.batch;
26
+
27
+ import java.io.File;
28
+ import java.io.IOException;
29
+ import java.io.ObjectInputStream;
30
+ import java.io.ObjectOutputStream;
31
+ import java.io.Serializable;
32
+
33
+
34
+ /**
35
+ * This is to be able to verify if a file has changed since it has been last processed by BatchProcessing
36
+ * @author Nina Jeliazkova
37
+ * <b>Modified</b> 2005-9-4
38
+ */
39
+ public class FileState implements Serializable {
40
+ /**
41
+ * Comment for <code>serialVersionUID</code>
42
+ */
43
+ private static final long serialVersionUID = -9098389880881547516L;
44
+ protected String filename=null;
45
+ protected long length=0;
46
+ protected long lastModified=0;
47
+ protected int hashCode=0;
48
+ protected transient File file = null;
49
+ protected long offset = 0;
50
+ protected long currentRecord = 0;
51
+ /**
52
+ *
53
+ */
54
+ public FileState() {
55
+ super();
56
+ }
57
+ public FileState(String filename) {
58
+ this(new File(filename));
59
+ }
60
+ public FileState(File file) {
61
+ this();
62
+ setFile(file);
63
+
64
+ }
65
+ /* (non-Javadoc)
66
+ * @see java.lang.Object#equals(java.lang.Object)
67
+ */
68
+ @Override
69
+ public boolean equals(Object obj) {
70
+ FileState fs = (FileState) obj;
71
+ return filename.equals(fs.getFilename()) &&
72
+ (length == fs.length) &&
73
+ (lastModified == fs.lastModified) &&
74
+ (hashCode == fs.hashCode) &&
75
+ (currentRecord == fs.currentRecord) &&
76
+ (offset == fs.offset)
77
+ ;
78
+
79
+ }
80
+
81
+ /**
82
+ * @return Returns the filename.
83
+ */
84
+ public synchronized String getFilename() {
85
+ return filename;
86
+ }
87
+ /**
88
+ * @param filename The filename to set.
89
+ */
90
+ public synchronized void setFilename(String filename) {
91
+ this.filename = filename;
92
+ }
93
+ /**
94
+ * @return Returns the hashCode.
95
+ */
96
+ public synchronized int getHashCode() {
97
+ return hashCode;
98
+ }
99
+ /**
100
+ * @param hashCode The hashCode to set.
101
+ */
102
+ public synchronized void setHashCode(int hashCode) {
103
+ this.hashCode = hashCode;
104
+ }
105
+ /**
106
+ * @return Returns the lastModified.
107
+ */
108
+ public synchronized long getLastModified() {
109
+ return lastModified;
110
+ }
111
+ /**
112
+ * @param lastModified The lastModified to set.
113
+ */
114
+ public synchronized void setLastModified(long lastModified) {
115
+ this.lastModified = lastModified;
116
+ }
117
+ /**
118
+ * @return Returns the length.
119
+ */
120
+ public synchronized long getLength() {
121
+ return length;
122
+ }
123
+ /**
124
+ * @param length The length to set.
125
+ */
126
+ public synchronized void setLength(long length) {
127
+ this.length = length;
128
+ }
129
+ /*
130
+ private void writeObject(java.io.ObjectOutputStream out)
131
+ throws IOException {
132
+
133
+ }
134
+ private void readObject(java.io.ObjectInputStream in)
135
+ throws IOException, ClassNotFoundException {
136
+
137
+ }
138
+ */
139
+
140
+ /**
141
+ * @return Returns the file.
142
+ */
143
+ public synchronized File getFile() {
144
+ return file;
145
+ }
146
+ /**
147
+ * @param file The file to set.
148
+ */
149
+ public synchronized void setFile(File file) {
150
+ this.file = file;
151
+ filename = file.getAbsolutePath();
152
+ length = file.length();
153
+ lastModified = file.lastModified();
154
+ hashCode = file.hashCode();
155
+ this.file = file;
156
+ currentRecord = 0;
157
+ offset = 0;
158
+ }
159
+ /**
160
+ * @return Returns the currentRecord.
161
+ */
162
+ public synchronized long getCurrentRecord() {
163
+ return currentRecord;
164
+ }
165
+ /**
166
+ * @param currentRecord The currentRecord to set.
167
+ */
168
+ public synchronized void setCurrentRecord(long currentRecord) {
169
+ this.currentRecord = currentRecord;
170
+ }
171
+ /**
172
+ * @return Returns the offset.
173
+ */
174
+ public synchronized long getOffset() {
175
+ return offset;
176
+ }
177
+ /**
178
+ * @param offset The offset to set.
179
+ */
180
+ public synchronized void setOffset(long offset) {
181
+ this.offset = offset;
182
+ }
183
+ public boolean match() throws BatchProcessingException {
184
+ return match(createFile());
185
+ }
186
+ public boolean match(File file) {
187
+
188
+ return filename.equals(file.getAbsolutePath()) &&
189
+ (length == file.length()) &&
190
+ (lastModified == file.lastModified())
191
+ //&& (hashCode == file.hashCode())
192
+ ;
193
+
194
+ }
195
+ public File createFile() throws BatchProcessingException {
196
+ try {
197
+ return new File(filename);
198
+ } catch (Exception x) {
199
+ throw new BatchProcessingException(x);
200
+ }
201
+ }
202
+ @Override
203
+ public String toString() {
204
+ StringBuffer b = new StringBuffer();
205
+ b.append(" [");
206
+ b.append((currentRecord+1));
207
+ b.append(" ] ");
208
+ b.append(filename);
209
+ return b.toString();
210
+ }
211
+ private void writeObject(ObjectOutputStream out) throws IOException {
212
+ out.writeLong(serialVersionUID);
213
+ out.writeObject(filename);
214
+ out.writeLong(length);
215
+ out.writeLong(lastModified);
216
+ out.writeInt(hashCode);
217
+ out.writeLong(offset);
218
+ out.writeLong(currentRecord);
219
+ }
220
+
221
+
222
+ private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
223
+ if (in.readLong() != serialVersionUID) throw new ClassNotFoundException();
224
+ filename =in.readObject().toString();
225
+ length =in.readLong();
226
+ lastModified = in.readLong();
227
+ hashCode = in.readInt();
228
+ offset = in.readLong();
229
+ currentRecord = in.readLong();
230
+ file = new File(filename);
231
+ }
232
+ }