pyopenms 2.3.0__zip

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (166) hide show
  1. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/License.txt +52 -0
  2. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/__init__.py +54 -0
  3. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/__init__.pyc +0 -0
  4. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/all_modules.py +4 -0
  5. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/all_modules.pyc +0 -0
  6. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/docompile.py +35 -0
  7. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/docompile.pyc +0 -0
  8. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/libOpenMS.so +0 -0
  9. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/libOpenSwathAlgo.so +0 -0
  10. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/libSuperHirn.so +0 -0
  11. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/pyopenms_1.so +0 -0
  12. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/pyopenms_2.so +0 -0
  13. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/pyopenms_3.so +0 -0
  14. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/pyopenms_4.so +0 -0
  15. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/python_extras.py +22 -0
  16. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/python_extras.pyc +0 -0
  17. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/qt_version_info.py +2 -0
  18. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/qt_version_info.pyc +0 -0
  19. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/CHEMISTRY/Elements.xml +1221 -0
  20. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/CHEMISTRY/Enzymes.xml +269 -0
  21. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/CHEMISTRY/HMDBMappingFile.tsv +10104 -0
  22. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/CHEMISTRY/MetaboliteIsoModel.scale +6 -0
  23. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/CHEMISTRY/MetaboliteIsoModel.svm +626 -0
  24. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/CHEMISTRY/MetaboliteIsoModelNoised2.scale +4 -0
  25. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/CHEMISTRY/MetaboliteIsoModelNoised2.svm +559 -0
  26. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/CHEMISTRY/MetaboliteIsoModelNoised5.scale +4 -0
  27. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/CHEMISTRY/MetaboliteIsoModelNoised5.svm +1010 -0
  28. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/CHEMISTRY/MissedCleavage.model +229 -0
  29. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/CHEMISTRY/NegativeAdducts.tsv +15 -0
  30. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/CHEMISTRY/OMSSA_modification_mapping +158 -0
  31. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/CHEMISTRY/PSI-MOD.obo +23804 -0
  32. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/CHEMISTRY/PositiveAdducts.tsv +33 -0
  33. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/CHEMISTRY/Residues.xml +470 -0
  34. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/CHEMISTRY/XLMOD.obo +623 -0
  35. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/CHEMISTRY/XTandem_default_input.xml +181 -0
  36. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/CHEMISTRY/unimod.xml +38885 -0
  37. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/CV/brenda.obo +22923 -0
  38. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/CV/goslim_goa.obo +823 -0
  39. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/CV/psi-ms.obo +17899 -0
  40. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/CV/psi-mzdata.obo +2920 -0
  41. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/CV/qc-cv.obo +471 -0
  42. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/CV/quality.obo +12581 -0
  43. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/CV/unimod.obo +13214 -0
  44. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/CV/unit.obo +2585 -0
  45. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/DESKTOP/TOPPAS.appdata.xml +33 -0
  46. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/DESKTOP/TOPPAS.desktop +10 -0
  47. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/DESKTOP/TOPPView.appdata.xml +35 -0
  48. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/DESKTOP/TOPPView.desktop +11 -0
  49. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/DESKTOP/readme.txt +5 -0
  50. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/GUISTYLE/qtStyleSheet.qss +9 -0
  51. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/IDPool/IDPool.txt +0 -0
  52. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/IDPool/README +29 -0
  53. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/MAPPING/TraML-mapping.xml +171 -0
  54. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/MAPPING/ms-mapping.xml +187 -0
  55. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/MAPPING/mzIdentML-mapping.xml +221 -0
  56. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/MAPPING/mzdata-mapping.xml +158 -0
  57. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/PIP/codebooks.data +2 -0
  58. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/PIP/linearMapping.data +2 -0
  59. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/CTD_0_3.xsd +168 -0
  60. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/ConsensusXML_1_0.xsd +376 -0
  61. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/ConsensusXML_1_1.xsd +381 -0
  62. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/ConsensusXML_1_2.xsd +202 -0
  63. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/ConsensusXML_1_3.xsd +686 -0
  64. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/ConsensusXML_1_4.xsd +694 -0
  65. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/ConsensusXML_1_5.xsd +698 -0
  66. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/ConsensusXML_1_6.xsd +613 -0
  67. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/ConsensusXML_1_7.xsd +618 -0
  68. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/CvMapping.xsd +157 -0
  69. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/FeatureXML_1_0.xsd +737 -0
  70. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/FeatureXML_1_1.xsd +770 -0
  71. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/FeatureXML_1_2.xsd +770 -0
  72. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/FeatureXML_1_3.xsd +660 -0
  73. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/FeatureXML_1_4.xsd +660 -0
  74. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/FeatureXML_1_5.xsd +670 -0
  75. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/FeatureXML_1_6.xsd +674 -0
  76. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/FeatureXML_1_7.xsd +679 -0
  77. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/FeatureXML_1_8.xsd +587 -0
  78. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/FeatureXML_1_9.xsd +592 -0
  79. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/FuGElightv1.0.0.xsd +1118 -0
  80. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/IdXML_1_0.xsd +340 -0
  81. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/IdXML_1_1.xsd +345 -0
  82. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/IdXML_1_2.xsd +354 -0
  83. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/IdXML_1_3.xsd +367 -0
  84. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/IdXML_1_4.xsd +371 -0
  85. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/IdXML_1_5.xsd +371 -0
  86. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/Param_1_0.xsd +91 -0
  87. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/Param_1_1.xsd +101 -0
  88. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/Param_1_2.xsd +168 -0
  89. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/Param_1_3.xsd +173 -0
  90. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/Param_1_4.xsd +149 -0
  91. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/Param_1_6_2.xsd +99 -0
  92. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/ToolDescriptor_1_0.xsd +232 -0
  93. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/TraML0.9.3.xsd +552 -0
  94. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/TraML1.0.0.xsd +622 -0
  95. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/TrafoXML_1_0.xsd +102 -0
  96. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/general_types_1.0.xsd +17 -0
  97. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/mzData_1_05.xsd +631 -0
  98. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/mzIdentML1.0.0.xsd +1339 -0
  99. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/mzIdentML1.1.0.xsd +1845 -0
  100. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/mzML_1_00.xsd +921 -0
  101. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/mzML_1_10.xsd +1119 -0
  102. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/mzML_idx_1_00.xsd +992 -0
  103. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/mzML_idx_1_10.xsd +1201 -0
  104. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/mzQCML_0_0_5.xsd +220 -0
  105. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/mzQuantML_1_0_0-rc2.xsd +1557 -0
  106. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/mzXML_2_1.xsd +1 -1
  107. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/mzXML_3.1.xsd +1 -1
  108. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/mzXML_3.1_mod.xsd +686 -0
  109. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/mzXML_idx_3.1.xsd +60 -0
  110. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/pepXML_v114.xsd +1448 -0
  111. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/protXML_v6.xsd +935 -0
  112. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/qcML_0.0.7.xsd +235 -0
  113. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/separation_technique_1.0.xsd +10 -0
  114. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCHEMAS/xQuest_1_0.xsd +210 -0
  115. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCRIPTS/InternalCalibration_Models.R +40 -0
  116. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCRIPTS/InternalCalibration_Residuals.R +57 -0
  117. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCRIPTS/ProduceQCFigures_acc.R +28 -0
  118. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCRIPTS/ProduceQCFigures_idmap.R +39 -0
  119. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCRIPTS/ProduceQCFigures_inj.R +27 -0
  120. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCRIPTS/ProduceQCFigures_rt_acc.R +31 -0
  121. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCRIPTS/ProduceQCFigures_setid.R +27 -0
  122. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCRIPTS/ProduceQCFigures_tic.R +23 -0
  123. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCRIPTS/Rscript_generic_example.R +88 -0
  124. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCRIPTS/mzTab2tsv_PEP.R +47 -0
  125. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCRIPTS/mzTab2tsv_PRT.R +104 -0
  126. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCRIPTS/mzTab2tsv_PSM.R +80 -0
  127. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/SCRIPTS/plot_trafo.R +126 -0
  128. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/THIRDPARTY/ReadMe.txt +9 -0
  129. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/TOOLS/EXTERNAL/Hardkloer.ttd +109 -0
  130. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/TOOLS/EXTERNAL/LINUX/TPP_ProteinProphet.ttd +46 -0
  131. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/TOOLS/EXTERNAL/LINUX/mail.ttd +22 -0
  132. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/TOOLS/EXTERNAL/MSGFtoPercolator.ttd +30 -0
  133. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/TOOLS/EXTERNAL/MascotPercolator.ttd +42 -0
  134. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/TOOLS/EXTERNAL/Percolator.ttd +29 -0
  135. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/TOOLS/EXTERNAL/QCExporter.ttd +51 -0
  136. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/TOOLS/EXTERNAL/RawDirConvert.ttd +25 -0
  137. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/TOOLS/EXTERNAL/ReadMe.txt +72 -0
  138. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/TOOLS/EXTERNAL/Rscript_generic.ttd +42 -0
  139. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/TOOLS/EXTERNAL/Rscript_mzTab2tsv_PEP.ttd +26 -0
  140. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/TOOLS/EXTERNAL/Rscript_mzTab2tsv_PRT.ttd +26 -0
  141. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/TOOLS/EXTERNAL/Rscript_mzTab2tsv_PSM.ttd +26 -0
  142. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/TOOLS/EXTERNAL/Rscript_qcfigures_acc.ttd +30 -0
  143. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/TOOLS/EXTERNAL/Rscript_qcfigures_idmap.ttd +33 -0
  144. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/TOOLS/EXTERNAL/Rscript_qcfigures_rt_acc.ttd +30 -0
  145. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/TOOLS/EXTERNAL/Rscript_qcfigures_setid.ttd +30 -0
  146. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/TOOLS/EXTERNAL/Rscript_qcfigures_tic.ttd +30 -0
  147. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/TOOLS/EXTERNAL/Rscript_qcfigures_trapfill.ttd +30 -0
  148. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/TOOLS/EXTERNAL/TEMPLATE.ttd_ +52 -0
  149. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/TOOLS/EXTERNAL/TPP_RefreshParser.ttd +28 -0
  150. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/TOOLS/EXTERNAL/WINDOWS/TPP_ProteinProphet.ttd +46 -0
  151. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/TOOLS/EXTERNAL/XTandemToPercolator.ttd +30 -0
  152. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/TOOLS/EXTERNAL/msconvert.ttd +25 -0
  153. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/XSL/APML_to_CSV.xsl +43 -0
  154. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/XSL/ConsensusXML.xsl +76 -0
  155. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/XSL/IdXML.xsl +210 -0
  156. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/XSL/QcML_report_sheet.xsl +548 -0
  157. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/XSL/index.html +97 -0
  158. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/sysinfo.py +47 -0
  159. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/sysinfo.pyc +0 -0
  160. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/version.py +1 -0
  161. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/version.pyc +0 -0
  162. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms-2.3.0-py2.7.egg-info/PKG-INFO +108 -0
  163. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms-2.3.0-py2.7.egg-info/SOURCES.txt +158 -0
  164. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms-2.3.0-py2.7.egg-info/dependency_links.txt +1 -0
  165. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms-2.3.0-py2.7.egg-info/not-zip-safe +1 -0
  166. media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms-2.3.0-py2.7.egg-info/top_level.txt +5 -0
media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/XSL/QcML_report_sheet.xsl ADDED
@@ -0,0 +1,548 @@
1
+ <?xml version="1.0" encoding="UTF-8"?>
2
+ <xsl:stylesheet id="openms-qc-stylesheet" version="1.1" xmlns:xsl="http://www.w3.org/1999/XSL/Transform" xmlns:ns="https://github.com/qcML/qcml" xmlns="">
3
+ <xsl:template match="/">
4
+ <html>
5
+ <head>
6
+ <script type="text/javascript" src="http://d3js.org/d3.v3.min.js"></script>
7
+ <style>
8
+ <!-- css settings for div elements -->
9
+ H1 {
10
+ font-family:Arial; font-size:20pt
11
+ }
12
+
13
+ div.rahmen {
14
+ background: #FFFAF0;
15
+ border: 1px solid;
16
+ padding: 5px;
17
+ margin: 40px;
18
+ }
19
+
20
+ div.thickline {
21
+ border-width: 2px;
22
+ border-style: solid;
23
+ }
24
+
25
+ path { 4
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+ stroke: steelblue;
27
+ stroke-width: 2;
28
+ fill: none;
29
+ }
30
+
31
+ .axis path,
32
+ .axis line {
33
+ fill: none;
34
+ stroke: #000;
35
+ shape-rendering: crispEdges;
36
+ }
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+
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+ .line {
39
+ fill: none;
40
+ stroke: steelblue;
41
+ stroke-width: 1.5px;
42
+ }
43
+
44
+ .grid .tick {
45
+ stroke: lightgrey;
46
+ opacity: 0.7;
47
+ }
48
+
49
+ .grid path {
50
+ stroke-width: 0;
51
+ }
52
+
53
+ .dot {
54
+ stroke: #000;
55
+ stroke-width: 2;
56
+ radius: 5;
57
+ }
58
+
59
+ div.tooltip {
60
+ position: absolute;
61
+ text-align: center;
62
+ width: 80px;
63
+ height: 40px;
64
+ padding: 2px;
65
+ font: 12px sans-serif;
66
+ background: #eee;
67
+ border: 1px solid #ccc;
68
+ border-radius: 8px;
69
+ }
70
+ </style>
71
+ </head>
72
+ <body>
73
+ <!-- Document caption-->
74
+ <xsl:choose>
75
+ <xsl:when test="ns:qcML/ns:setQuality">
76
+ <center><H1>Set Quality Report</H1></center>
77
+ </xsl:when>
78
+ <xsl:otherwise>
79
+ <center><H1>Run Quality Report</H1></center>
80
+ </xsl:otherwise>
81
+ </xsl:choose>
82
+
83
+ <!-- MetaData Box-->
84
+ <p style="border-color:#000000; border-width:2px; border-style:solid; padding:4px">
85
+ Metadata
86
+ <xsl:for-each select="ns:qcML/ns:runQuality">
87
+ <center><table border="1" rules="none" color="black">
88
+ <tr>
89
+ <td>Filename</td>
90
+ <td>
91
+ <xsl:apply-templates select="ns:qualityParameter[@accession = 'MS:1000577']"/>
92
+ </td>
93
+ </tr>
94
+ <tr>
95
+ <td>Instrument</td>
96
+ <td>
97
+ <xsl:apply-templates select="ns:qualityParameter[@accession = 'MS:1000031']"/>
98
+ </td>
99
+ </tr>
100
+ <tr>
101
+ <td>Date</td>
102
+ <td>
103
+ <xsl:apply-templates select="ns:qualityParameter[@accession = 'MS:1000747']"/>
104
+ </td>
105
+ </tr>
106
+ </table></center>
107
+ <br/>
108
+ </xsl:for-each>
109
+ </p>
110
+
111
+ <!-- Overview Box-->
112
+ <xsl:choose>
113
+ <xsl:when test="ns:qcML/ns:setQuality">
114
+ <xsl:variable name="set_setting" select="true()"/>
115
+ <p style="border-color:#000000; border-width:2px; border-style:solid; padding:4px">
116
+ Control charts
117
+ </p>
118
+ <div id="control-chart"></div>
119
+
120
+ <script>
121
+ var data_control_chart = [<xsl:for-each select="ns:qcML/ns:runQuality">
122
+ {
123
+ idx: "<xsl:value-of select="position()" />" ,
124
+ MS1count: "<xsl:value-of select="ns:qualityParameter[@accession = 'QC:0000006']/@value"/>" ,
125
+ MS2count: "<xsl:value-of select="ns:qualityParameter[@accession = 'QC:0000007']/@value"/>" ,
126
+ PSMcount: "<xsl:value-of select="ns:qualityParameter[@accession = 'QC:0000029']/@value"/>" ,
127
+ FEATUREcount: "<xsl:value-of select="ns:qualityParameter[@accession = 'QC:0000046']/@value"/>" ,
128
+ idFEATUREcount: "<xsl:value-of select="ns:qualityParameter[@accession = 'QC:0000058']/@value"/>" ,
129
+ },
130
+ </xsl:for-each>];
131
+ </script>
132
+ <script>
133
+ var margin = {top: 20, right: 100, bottom: 30, left: 100},
134
+ width = 960 - margin.left - margin.right,
135
+ height = 500 - margin.top - margin.bottom;
136
+
137
+ var color = d3.scale.category10();
138
+
139
+ data_control_chart.forEach( function(d) {
140
+ console.log(d);
141
+ color.domain(d3.keys(d).filter(function(key) { return key !== "idx"; }));
142
+ });
143
+ console.log(data_control_chart);
144
+ console.log(color.domain());
145
+
146
+ var svg = d3.select("#control-chart").append("svg")
147
+ .attr("width", width + margin.left + margin.right)
148
+ .attr("height", height + margin.top + margin.bottom)
149
+ .append("g")
150
+ .attr("transform", "translate(" + margin.left + "," + margin.top + ")");
151
+
152
+ var div = d3.select("#control-chart").append("div").attr("class", "tooltip")
153
+ .style("opacity", 0);
154
+
155
+ var control_values = color.domain().map(function(name) {
156
+ return {
157
+ name: name,
158
+ values: data_control_chart.map(function(d) {
159
+ return {idx: d.idx, vals: +d[name]};
160
+ })
161
+ };
162
+ });
163
+ console.log(control_values);
164
+
165
+ var line = d3.svg.line()
166
+ //.interpolate("basis")
167
+ .x(function(d) { return x(d.idx); })
168
+ .y(function(d) { return y(d.vals); });
169
+
170
+ var x = d3.scale.linear()
171
+ .range([0, width]);
172
+
173
+ var y = d3.scale.linear()
174
+ .range([height, 0]);
175
+
176
+ function xAxis() {
177
+ return d3.svg.axis()
178
+ .scale(x)
179
+ .ticks(data_control_chart.length)
180
+ .tickSubdivide(0)
181
+ .orient("bottom")
182
+ }
183
+
184
+ function yAxis() {
185
+ return d3.svg.axis()
186
+ .scale(y)
187
+ .orient("left")
188
+ }
189
+
190
+ x.domain(d3.extent(data_control_chart, function(d) { return d.idx; }));
191
+
192
+ y.domain([
193
+ d3.min(control_values, function(c) { return d3.min(c.values, function(v) { return v.vals; }); }),
194
+ d3.max(control_values, function(c) { return d3.max(c.values, function(v) { return v.vals; }); })
195
+ ]);
196
+
197
+ svg.append("g")
198
+ .attr("class", "grid")
199
+ .attr("transform", "translate(0," + height + ")")
200
+ .call(xAxis()
201
+ .tickSize(-height, 0, 0)
202
+ .tickFormat("")
203
+ );
204
+
205
+ svg.append("g")
206
+ .attr("class", "x axis")
207
+ .attr("transform", "translate(0," + height + ")")
208
+ .call(xAxis() )
209
+ .append("text")
210
+ .attr("transform", "translate(" + width +",0)")
211
+ .attr("y", -6)
212
+ .attr("x", -6)
213
+ .attr("dx", ".71em")
214
+ .style("text-anchor", "end")
215
+ .text("runs");
216
+
217
+ svg.append("g")
218
+ .attr("class", "y axis")
219
+ .call(yAxis())
220
+ .append("text")
221
+ .attr("transform", "rotate(-90)")
222
+ .attr("y", 6)
223
+ .attr("dy", ".71em")
224
+ .style("text-anchor", "end")
225
+ .text("counts");
226
+
227
+ var control_metric = svg.selectAll(".control_metric")
228
+ .data(control_values)
229
+ .enter().append("g")
230
+ .attr("class", "control_metric");
231
+
232
+ control_metric.append("path")
233
+ .attr("class", "line")
234
+ .attr("d", function(d) { return line(d.values); })
235
+ .style("stroke", function(d) { return color(d.name); });
236
+
237
+ control_metric.append("text")
238
+ .datum(function(d) { return {name: d.name, value: d.values[d.values.length - 1]}; })
239
+ .attr("transform", function(d) { return "translate(" + x(d.value.idx) + "," + y(d.value.vals) + ")"; })
240
+ .attr("x", 3)
241
+ .attr("dy", ".35em")
242
+ .text(function(d) { return d.name; });
243
+
244
+ control_metric.append("g").selectAll(".dot")
245
+ .data(function (d) { return d.values })
246
+ .enter().append("circle")
247
+ .attr("stroke", function (d) { return color(this.parentNode.__data__.name) })
248
+ .attr("cx", function (d) { return x(d.idx); })
249
+ .attr("cy", function (d) { return y(d.vals); })
250
+ .attr("r", 2)
251
+ .attr("fill", "white").attr("fill-opacity", .5)
252
+ .attr("stroke-width", 2)
253
+ .on("mouseover", function (d) {
254
+ div.transition()
255
+ .duration(200)
256
+ .style("opacity", .9);
257
+ div.html(
258
+ this.parentNode.__data__.name + "&lt;br&gt;" + d.vals + "&lt;br&gt;" + "&lt;a href='#" + d.idx + "'&gt; run " +d.idx + "&lt;/a&gt;")
259
+ .style("left", (d3.event.pageX + 18) + "px").style("top", (d3.event.pageY - 18) + "px").attr('r', 8);
260
+ d3.select(this).attr('r', 4)
261
+ })
262
+ .on("mouseout", function (d) {
263
+ div.transition().duration(2200).style("opacity", 0)
264
+ d3.select(this).attr('r', 2);
265
+ });
266
+ </script>
267
+
268
+
269
+ </xsl:when>
270
+ <xsl:otherwise>
271
+ <xsl:variable name="set_setting" select="false()"/>
272
+ <p style="border-color:#000000; border-width:2px; border-style:solid; padding:4px">
273
+ Overview Plots
274
+ <table border="1">
275
+ <tr>
276
+ <td>
277
+ TIC
278
+ <xsl:for-each select="ns:qcML/ns:runQuality">
279
+ <xsl:apply-templates select="ns:attachment[@accession = 'MS:1000235']"/>
280
+ </xsl:for-each>
281
+ </td>
282
+ <td>
283
+ Map overview
284
+ <xsl:for-each select="ns:qcML/ns:runQuality">
285
+ <xsl:apply-templates select="ns:attachment[@accession = 'QC:0000055']"/>
286
+ </xsl:for-each>
287
+ </td>
288
+ <td>
289
+ Mass accuracy
290
+ <xsl:for-each select="ns:qcML/ns:runQuality">
291
+ <xsl:apply-templates select="ns:attachment[@accession = 'QC:0000053']"/>
292
+ </xsl:for-each>
293
+ </td>
294
+ </tr>
295
+ </table>
296
+ </p>
297
+ </xsl:otherwise>
298
+ </xsl:choose>
299
+
300
+
301
+
302
+ <!-- Details Box-->
303
+ <xsl:for-each select="ns:qcML/ns:runQuality">
304
+ <p style="border-color:#000000; border-width:2px; border-style:solid; padding:4px">
305
+ <a name="{position()}"> Details <xsl:value-of select="@ID"/> </a>
306
+
307
+ <table>
308
+ <tr>
309
+ <td rowspan="3" width="200" height="20">Aquisition details</td> <td width="400" height="20">Name</td> <td width="400" height="20">Value</td>
310
+ </tr>
311
+ <tr>
312
+ <xsl:apply-templates select="ns:qualityParameter[@accession = 'QC:0000006']"/>
313
+ </tr>
314
+ <tr>
315
+ <xsl:apply-templates select="ns:qualityParameter[@accession = 'QC:0000007']"/>
316
+ </tr>
317
+ </table>
318
+ <br/>
319
+
320
+ <table>
321
+ <tr>
322
+ <td rowspan="3" width="200" height="20">Aquisition ranges</td> <td width="400" height="20"></td> <td width="400" height="20">Minimum</td> <td width="400" height="20">Maximum</td>
323
+ </tr>
324
+ <tr>
325
+ <td>RT [s] </td>
326
+ <xsl:apply-templates select="ns:attachment[@accession = 'QC:0000012']"/>
327
+ </tr>
328
+ <tr>
329
+ <td>MZ [amu] </td>
330
+ <xsl:apply-templates select="ns:attachment[@accession = 'QC:0000009']"/>
331
+ </tr>
332
+ </table>
333
+ <br/>
334
+
335
+ <table>
336
+ <tr>
337
+ <td rowspan="7" width="200" height="20">Identification details</td> <td width="400" height="20">Name</td> <td width="400" height="20">Value</td>
338
+ </tr>
339
+ <tr>
340
+ <xsl:apply-templates select="ns:qualityParameter[@accession = 'QC:0000029']"/>
341
+ </tr>
342
+ <tr>
343
+ <xsl:apply-templates select="ns:qualityParameter[@accession = 'QC:0000030']"/>
344
+ </tr>
345
+ <tr>
346
+ <xsl:apply-templates select="ns:qualityParameter[@accession = 'QC:0000031']"/>
347
+ </tr>
348
+ <tr>
349
+ <xsl:apply-templates select="ns:qualityParameter[@accession = 'QC:0000032']"/>
350
+ </tr>
351
+ <tr>
352
+ <xsl:apply-templates select="ns:qualityParameter[@accession = 'QC:0000033']"/>
353
+ </tr>
354
+ <tr>
355
+ <xsl:apply-templates select="ns:qualityParameter[@accession = 'QC:0000037']"/>
356
+ </tr>
357
+ </table>
358
+ <br/>
359
+
360
+ <table>
361
+ <tr>
362
+ <td rowspan="1" width="200" height="30">Database</td>
363
+ <td>
364
+ <xsl:apply-templates select="ns:attachment[@accession = 'QC:0000026']"/>
365
+ </td>
366
+ </tr>
367
+ </table>
368
+ <br/>
369
+
370
+ <table>
371
+ <tr>
372
+ <td rowspan="3" width="200" height="20">Feature Finding</td>
373
+ <td width="400" height="30">Name</td>
374
+ <td width="400" height="30">Value</td>
375
+ </tr>
376
+ <tr>
377
+ <xsl:apply-templates select="ns:qualityParameter[@accession = 'QC:0000046']"/>
378
+ </tr>
379
+ <tr>
380
+ <xsl:apply-templates select="ns:qualityParameter[@accession = 'QC:0000058']"/>
381
+ </tr>
382
+ </table>
383
+ </p>
384
+
385
+ <p style="border-color:#000000; border-width:2px; border-style:solid; padding:4px">
386
+ Metric plots <xsl:value-of select="@ID"/>
387
+ <br/>
388
+
389
+ <xsl:if test="ns:qcML/ns:setQuality">
390
+ <table border="1">
391
+ <tr>
392
+ <td>
393
+ TIC
394
+ <xsl:apply-templates select="ns:attachment[@accession = 'MS:1000235']"/>
395
+ </td>
396
+ <td>
397
+ Map overview
398
+ <xsl:apply-templates select="ns:attachment[@accession = 'QC:0000055']"/>
399
+ </td>
400
+ <td>
401
+ Mass accuracy
402
+ <xsl:apply-templates select="ns:attachment[@accession = 'QC:0000053']"/>
403
+ </td>
404
+ </tr>
405
+ </table>
406
+ </xsl:if>
407
+
408
+ <table>
409
+ <xsl:apply-templates select="ns:attachment[
410
+ not(@accession = 'QC:0000055') and not(@accession = 'QC:0000053') and not(@accession = 'MS:1000235') and
411
+ not(@accession = 'QC:0000026') and not(@accession = 'QC:0000009') and not(@accession = 'QC:0000012') and
412
+ not(@accession = 'QC:0000044') and not(@accession = 'QC:0000022') and not(@accession = 'QC:0000038') and
413
+ not(@accession = 'QC:0000047') and not(@accession = 'QC:0000018')]"/>
414
+ </table>
415
+ </p>
416
+ </xsl:for-each>
417
+ <!--
418
+ <xsl:for-each select="ns:qcML/ns:setQuality">
419
+ <xsl:apply-templates/>
420
+ </xsl:for-each>
421
+ -->
422
+
423
+ </body>
424
+ </html>
425
+ </xsl:template>
426
+
427
+ <!-- for MetaData Box qp template-->
428
+ <xsl:template match="ns:qualityParameter[(@accession = 'MS:1000577') or (@accession = 'MS:1000031') or (@accession = 'MS:1000747' )]">
429
+ <b><xsl:value-of select="@value"/></b>
430
+ </xsl:template>
431
+ <!-- for further detail Box qp template-->
432
+ <xsl:template match="ns:qualityParameter[not(@accession = 'MS:1000577') and not(@accession = 'MS:1000031') and not(@accession = 'MS:1000747' ) and @value]">
433
+ <td><xsl:value-of select="@name"/></td>
434
+ <td><xsl:value-of select="@value"/></td>
435
+ </xsl:template>
436
+ <!-- for generic qp name + attachment output if no value in qp-->
437
+ <xsl:template match="ns:qualityParameter[not(@value)]">
438
+ <td><xsl:value-of select="@name"/></td>
439
+ <td><xsl:call-template name="qp-attachments">
440
+ <xsl:with-param name="qpref" select="@ID"/>
441
+ </xsl:call-template></td>
442
+ </xsl:template>
443
+ <!-- called from generic qp template -->
444
+ <xsl:template name="qp-attachments">
445
+ <xsl:param name="qpref"/>
446
+ <xsl:for-each select="../ns:attachment[@qualityParameterRef=$qpref]"> <xsl:value-of select="@name"/><br/>
447
+ <xsl:choose>
448
+ <xsl:when test="ns:binary">
449
+ <img>
450
+ <xsl:attribute name="src"> data:image/png;base64,<xsl:value-of select="ns:binary"/>
451
+ </xsl:attribute>
452
+ </img>
453
+ <br/>
454
+ </xsl:when>
455
+ <xsl:otherwise>
456
+ <table border="0">
457
+ <tr bgcolor="#B2CCFF">
458
+ <xsl:call-template name="output-header">
459
+ <xsl:with-param name="list"><xsl:value-of select="ns:table/ns:tableColumnTypes"/></xsl:with-param>
460
+ </xsl:call-template>
461
+ </tr>
462
+ <xsl:for-each select="ns:table/ns:tableRowValues">
463
+ <tr>
464
+ <xsl:call-template name="output-row">
465
+ <xsl:with-param name="list"><xsl:value-of select="." /></xsl:with-param>
466
+ </xsl:call-template>
467
+ </tr>
468
+ </xsl:for-each>
469
+ </table><br/>
470
+ </xsl:otherwise>
471
+ </xsl:choose>
472
+ </xsl:for-each>
473
+ </xsl:template>
474
+ <!-- for Overview plots Box template-->
475
+ <xsl:template match="ns:attachment[(@accession = 'MS:1000235') or (@accession = 'QC:0000055') or (@accession = 'QC:0000053' )]">
476
+ <xsl:choose>
477
+ <xsl:when test="ns:binary">
478
+ <img style="width: 100%" alt="?missing?">
479
+ <xsl:attribute name="src"> data:image/png;base64,<xsl:value-of select="ns:binary"/>
480
+ </xsl:attribute>
481
+ </img>
482
+ </xsl:when>
483
+ <xsl:otherwise>
484
+ <xsl:for-each select="ns:table/ns:tableRowValues">
485
+ <xsl:call-template name="output-row">
486
+ <xsl:with-param name="list"><xsl:value-of select="." /></xsl:with-param>
487
+ </xsl:call-template>
488
+ </xsl:for-each>
489
+ </xsl:otherwise>
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+ </xsl:choose>
491
+ </xsl:template>
492
+ <!-- for Details Box aquisition range template-->
493
+ <xsl:template match="ns:attachment[(@accession = 'QC:0000009') or (@accession = 'QC:0000012' ) or (@accession = 'QC:0000026' )]">
494
+ <xsl:for-each select="ns:table/ns:tableRowValues">
495
+ <xsl:call-template name="output-row">
496
+ <xsl:with-param name="list"><xsl:value-of select="." /></xsl:with-param>
497
+ </xsl:call-template>
498
+ </xsl:for-each>
499
+ </xsl:template>
500
+ <!-- generic attachment template for att as table row-->
501
+ <xsl:template match="ns:attachment">
502
+ <tr>
503
+ <td><xsl:value-of select="@name"/></td>
504
+ <td>
505
+ <xsl:choose>
506
+ <xsl:when test="ns:binary">
507
+ <img>
508
+ <xsl:attribute name="src"> data:image/png;base64,<xsl:value-of select="ns:binary"/>
509
+ </xsl:attribute>
510
+ </img>
511
+ </xsl:when>
512
+ <xsl:otherwise> subtable </xsl:otherwise>
513
+ </xsl:choose>
514
+ </td>
515
+ </tr>
516
+ </xsl:template>
517
+ <!-- generic output table header-->
518
+ <xsl:template name="output-header">
519
+ <xsl:param name="list"/>
520
+ <xsl:variable name="newlist" select="concat(normalize-space($list), ' ')"/>
521
+ <xsl:variable name="first" select="substring-before($newlist, ' ')"/>
522
+ <xsl:variable name="remaining" select="substring-after($newlist, ' ')"/>
523
+ <th>
524
+ <xsl:value-of select="$first"/>
525
+ </th>
526
+ <xsl:if test="$remaining">
527
+ <xsl:call-template name="output-header">
528
+ <xsl:with-param name="list" select="$remaining"/>
529
+ </xsl:call-template>
530
+ </xsl:if>
531
+ </xsl:template>
532
+ <!-- generic output table row-->
533
+ <xsl:template name="output-row">
534
+ <xsl:param name="list"/>
535
+ <xsl:variable name="newlist" select="concat(normalize-space($list), ' ')"/>
536
+ <xsl:variable name="first" select="substring-before($newlist, ' ')"/>
537
+ <xsl:variable name="remaining" select="substring-after($newlist, ' ')"/>
538
+ <td>
539
+ <xsl:value-of select="$first"/>
540
+ </td>
541
+ <xsl:if test="$remaining">
542
+ <xsl:call-template name="output-row">
543
+ <xsl:with-param name="list" select="$remaining"/>
544
+ </xsl:call-template>
545
+ </xsl:if>
546
+ </xsl:template>
547
+
548
+ </xsl:stylesheet>
media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/XSL/index.html ADDED
@@ -0,0 +1,97 @@
1
+ <html>
2
+ <body>
3
+
4
+ <div>
5
+
6
+ This script allows you to apply an XSL-Transformation to an XML-File, without manually entering the XSL definition into the XML-File.
7
+ <br>
8
+ With new browser generations this script works only when used on a webserver. Using it locally from your harddrive will NOT work, since the browser will not allow it for security reasons (there is workaround for Chrome though).
9
+ <p></p>
10
+
11
+ <script type="text/javascript">
12
+
13
+ function reformat()
14
+ {
15
+
16
+ xmlfile = document.getElementById ('xmlfile').value;
17
+ xsltfile = document.getElementById ('xslfile').value;
18
+
19
+ document.getElementById('status').innerHTML = "parsing ... please wait..";
20
+ // allow the above message to be displayed by delaying the transformation
21
+ setTimeout('rf(xmlfile,xsltfile)',100);
22
+ }
23
+
24
+ function rf (xmlfile, xsltfile)
25
+ {
26
+ var xslStylesheet;
27
+ var xsltProcessor = new XSLTProcessor();
28
+ var myDOM;
29
+
30
+ var xmlDoc;
31
+
32
+ try
33
+ {
34
+ // load the xslt file
35
+ var myXMLHTTPRequest = new XMLHttpRequest();
36
+ myXMLHTTPRequest.open("GET", xsltfile, false);
37
+ myXMLHTTPRequest.send(null);
38
+
39
+ xslStylesheet = myXMLHTTPRequest.responseXML;
40
+ xsltProcessor.importStylesheet(xslStylesheet);
41
+
42
+ // load the xml file, example1.xml
43
+ myXMLHTTPRequest = new XMLHttpRequest();
44
+ myXMLHTTPRequest.open("GET", xmlfile, false);
45
+ myXMLHTTPRequest.send(null);
46
+
47
+ textDoc = myXMLHTTPRequest.responseText;
48
+ // the APML file has a nasty <apml ...> tag whose xmlns-attribute leads to a parsing error -- remove it!
49
+ textDoc = textDoc.replace(/<apml.*>/g,'<apml>')
50
+
51
+ var xmlobject = (new DOMParser()).parseFromString(textDoc, "text/xml");
52
+ textDoc = null;
53
+ var fragment = xsltProcessor.transformToFragment(xmlobject, document);
54
+ //var fragment = xsltProcessor.transformToDocument(xmlobject);
55
+
56
+ //document.getElementById("data").appendChild(fragment);
57
+ newWindow=window.open('','output',
58
+ 'width=1024,height=550'
59
+ +',menubar=0'
60
+ +',toolbar=1'
61
+ +',status=0'
62
+ +',scrollbars=1'
63
+ +',resizable=1');
64
+ newWindow.document.writeln('<html><body><div id="data"></div></body></html>');
65
+ newWindow.document.getElementById("data").appendChild(fragment);
66
+ newWindow.document.close();
67
+ //newWindow.document = fragment;
68
+ }
69
+ catch (e)
70
+ {
71
+ alert('An error occured during the transformation' + e);
72
+ }
73
+
74
+
75
+ document.getElementById('status').innerHTML = "done!";
76
+
77
+ }
78
+
79
+
80
+ </script>
81
+
82
+ <form action="javascript:reformat()">
83
+
84
+ <label>XML file</label><input id="xmlfile" type="file" size=40 value=""/><br>
85
+ <label>XSLT file</label><input id="xslfile" type="file" size=40 value=""/><br>
86
+
87
+ <input type="submit">
88
+
89
+ </form>
90
+
91
+ </div>
92
+
93
+ <div id="status">
94
+ </div>
95
+
96
+ </body>
97
+ </html>