mspire 0.6.26 → 0.7.2

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Files changed (132) hide show
  1. data/VERSION +1 -1
  2. data/lib/mspire.rb +1 -1
  3. data/lib/{ms → mspire}/cv.rb +1 -1
  4. data/lib/{ms → mspire}/cv/param.rb +5 -5
  5. data/lib/{ms → mspire}/cv/paramable.rb +5 -5
  6. data/lib/{ms → mspire}/digester.rb +2 -2
  7. data/lib/{ms → mspire}/error_rate/decoy.rb +1 -1
  8. data/lib/{ms → mspire}/error_rate/qvalue.rb +4 -4
  9. data/lib/{ms → mspire}/fasta.rb +5 -5
  10. data/lib/{ms → mspire}/ident.rb +10 -10
  11. data/lib/{ms → mspire}/ident/peptide.rb +3 -3
  12. data/lib/{ms → mspire}/ident/peptide/db.rb +12 -12
  13. data/lib/{ms → mspire}/ident/peptide_hit.rb +6 -6
  14. data/lib/{ms → mspire}/ident/peptide_hit/qvalue.rb +7 -7
  15. data/lib/{ms → mspire}/ident/pepxml.rb +7 -7
  16. data/lib/{ms → mspire}/ident/pepxml/modifications.rb +7 -7
  17. data/lib/{ms → mspire}/ident/pepxml/msms_pipeline_analysis.rb +6 -6
  18. data/lib/{ms → mspire}/ident/pepxml/msms_run_summary.rb +9 -9
  19. data/lib/{ms → mspire}/ident/pepxml/parameters.rb +1 -1
  20. data/lib/{ms → mspire}/ident/pepxml/sample_enzyme.rb +4 -4
  21. data/lib/{ms → mspire}/ident/pepxml/search_database.rb +5 -5
  22. data/lib/{ms → mspire}/ident/pepxml/search_hit.rb +4 -4
  23. data/lib/{ms → mspire}/ident/pepxml/search_hit/modification_info.rb +7 -7
  24. data/lib/{ms → mspire}/ident/pepxml/search_result.rb +5 -5
  25. data/lib/{ms → mspire}/ident/pepxml/search_summary.rb +12 -12
  26. data/lib/{ms → mspire}/ident/pepxml/spectrum_query.rb +7 -7
  27. data/lib/{ms → mspire}/ident/protein.rb +2 -2
  28. data/lib/{ms → mspire}/ident/protein_group.rb +2 -2
  29. data/lib/{ms → mspire}/ident/search.rb +1 -1
  30. data/lib/{ms → mspire}/isotope.rb +3 -3
  31. data/lib/{ms → mspire}/isotope/aa.rb +1 -1
  32. data/lib/{ms → mspire}/isotope/distribution.rb +17 -17
  33. data/lib/{ms → mspire}/isotope/nist_isotope_info.yml +0 -0
  34. data/lib/{ms → mspire}/mascot.rb +1 -1
  35. data/lib/{ms → mspire}/mass.rb +7 -7
  36. data/lib/{ms → mspire}/mass/aa.rb +6 -6
  37. data/lib/{ms → mspire}/molecular_formula.rb +7 -7
  38. data/lib/{ms → mspire}/mzml.rb +55 -55
  39. data/lib/{ms → mspire}/mzml/activation.rb +3 -3
  40. data/lib/{ms → mspire}/mzml/chromatogram.rb +3 -3
  41. data/lib/{ms → mspire}/mzml/chromatogram_list.rb +1 -1
  42. data/lib/{ms → mspire}/mzml/component.rb +5 -5
  43. data/lib/{ms → mspire}/mzml/contact.rb +3 -3
  44. data/lib/{ms → mspire}/mzml/cv.rb +1 -1
  45. data/lib/{ms → mspire}/mzml/data_array.rb +12 -12
  46. data/lib/{ms → mspire}/mzml/data_array_container_like.rb +7 -7
  47. data/lib/{ms → mspire}/mzml/data_processing.rb +3 -3
  48. data/lib/{ms → mspire}/mzml/file_content.rb +3 -3
  49. data/lib/{ms → mspire}/mzml/file_description.rb +4 -4
  50. data/lib/{ms → mspire}/mzml/index_list.rb +2 -2
  51. data/lib/{ms → mspire}/mzml/instrument_configuration.rb +7 -7
  52. data/lib/{ms → mspire}/mzml/isolation_window.rb +3 -3
  53. data/lib/{ms → mspire}/mzml/list.rb +1 -1
  54. data/lib/{ms → mspire}/mzml/plms1.rb +3 -3
  55. data/lib/{ms → mspire}/mzml/precursor.rb +6 -6
  56. data/lib/{ms → mspire}/mzml/processing_method.rb +3 -3
  57. data/lib/{ms → mspire}/mzml/product.rb +3 -3
  58. data/lib/{ms → mspire}/mzml/referenceable_param_group.rb +4 -4
  59. data/lib/{ms → mspire}/mzml/run.rb +3 -3
  60. data/lib/{ms → mspire}/mzml/sample.rb +5 -5
  61. data/lib/{ms → mspire}/mzml/scan.rb +4 -4
  62. data/lib/{ms → mspire}/mzml/scan_list.rb +3 -3
  63. data/lib/{ms → mspire}/mzml/scan_settings.rb +5 -5
  64. data/lib/{ms → mspire}/mzml/selected_ion.rb +5 -5
  65. data/lib/{ms → mspire}/mzml/software.rb +5 -5
  66. data/lib/{ms → mspire}/mzml/source_file.rb +5 -5
  67. data/lib/{ms → mspire}/mzml/spectrum.rb +33 -20
  68. data/lib/{ms → mspire}/mzml/spectrum_list.rb +4 -4
  69. data/lib/{ms → mspire}/obo.rb +1 -1
  70. data/lib/{ms → mspire}/peak.rb +3 -3
  71. data/lib/{ms → mspire}/peak/point.rb +1 -1
  72. data/lib/{ms → mspire}/plms1.rb +4 -4
  73. data/lib/{ms → mspire}/quant/qspec.rb +4 -4
  74. data/lib/{ms → mspire}/quant/qspec/protein_group_comparison.rb +4 -4
  75. data/lib/{ms → mspire}/spectrum.rb +6 -6
  76. data/lib/{ms → mspire}/spectrum/centroid.rb +1 -1
  77. data/lib/{ms → mspire}/spectrum_like.rb +5 -5
  78. data/lib/{ms → mspire}/user_param.rb +2 -2
  79. data/script/mzml_read_binary.rb +1 -1
  80. data/spec/{ms → mspire}/cv/param_spec.rb +6 -6
  81. data/spec/{ms → mspire}/digester_spec.rb +10 -10
  82. data/spec/{ms → mspire}/error_rate/qvalue_spec.rb +3 -3
  83. data/spec/{ms → mspire}/fasta_spec.rb +10 -10
  84. data/spec/{ms → mspire}/ident/peptide/db_spec.rb +9 -9
  85. data/spec/{ms → mspire}/ident/pepxml/sample_enzyme_spec.rb +10 -10
  86. data/spec/{ms → mspire}/ident/pepxml/search_hit/modification_info_spec.rb +4 -4
  87. data/spec/{ms → mspire}/ident/pepxml_spec.rb +22 -22
  88. data/spec/{ms → mspire}/ident/protein_group_spec.rb +4 -4
  89. data/spec/{ms → mspire}/isotope/aa_spec.rb +3 -3
  90. data/spec/{ms → mspire}/isotope/distribution_spec.rb +4 -4
  91. data/spec/{ms → mspire}/isotope_spec.rb +9 -9
  92. data/spec/{ms → mspire}/mass_spec.rb +8 -8
  93. data/spec/{ms → mspire}/molecular_formula_spec.rb +4 -4
  94. data/spec/{ms → mspire}/mzml/cv_spec.rb +4 -4
  95. data/spec/{ms → mspire}/mzml/data_array_spec.rb +7 -7
  96. data/spec/{ms → mspire}/mzml/file_content_spec.rb +4 -4
  97. data/spec/{ms → mspire}/mzml/file_description_spec.rb +4 -4
  98. data/spec/{ms → mspire}/mzml/index_list_spec.rb +13 -13
  99. data/spec/{ms → mspire}/mzml/plms1_spec.rb +8 -8
  100. data/spec/{ms → mspire}/mzml/referenceable_param_group_spec.rb +6 -6
  101. data/spec/{ms → mspire}/mzml_spec.rb +30 -30
  102. data/spec/{ms → mspire}/peak_spec.rb +10 -10
  103. data/spec/{ms → mspire}/plms1_spec.rb +7 -7
  104. data/spec/{ms → mspire}/quant/qspec_spec.rb +2 -2
  105. data/spec/{ms → mspire}/spectrum_spec.rb +8 -8
  106. data/spec/{ms → mspire}/user_param_spec.rb +8 -8
  107. data/spec/testfiles/{ms → mspire}/ident/peptide/db/uni_11_sp_tr.fasta +0 -0
  108. data/spec/testfiles/{ms → mspire}/ident/peptide/db/uni_11_sp_tr.msd_clvg2.min_aaseq4.yml +0 -0
  109. data/spec/testfiles/{ms → mspire}/mzml/j24z.idx_comp.3.mzML +0 -0
  110. data/spec/testfiles/{ms → mspire}/mzml/mspire_simulated.MSn.check.mzML +0 -0
  111. data/spec/testfiles/{ms → mspire}/mzml/openms.noidx_nocomp.12.mzML +0 -0
  112. data/spec/testfiles/{ms → mspire}/quant/kill_extra_tabs.rb +0 -0
  113. data/spec/testfiles/{ms → mspire}/quant/max_quant_output.provenance.txt +0 -0
  114. data/spec/testfiles/{ms → mspire}/quant/max_quant_output.txt +0 -0
  115. data/spec/testfiles/{ms → mspire}/quant/pdcd5_final.killedextratabs.tsv +0 -0
  116. data/spec/testfiles/{ms → mspire}/quant/pdcd5_final.killedextratabs.tsv_qspecgp +0 -0
  117. data/spec/testfiles/{ms → mspire}/quant/pdcd5_final.killedextratabs.tsv_qspecgp.csv +0 -0
  118. data/spec/testfiles/{ms → mspire}/quant/pdcd5_final.txt +0 -0
  119. data/spec/testfiles/{ms → mspire}/quant/pdcd5_final.txt_qspecgp +0 -0
  120. data/spec/testfiles/{ms → mspire}/quant/pdcd5_lfq_qspec.CSV.csv +0 -0
  121. data/spec/testfiles/{ms → mspire}/quant/pdcd5_lfq_qspec.csv +0 -0
  122. data/spec/testfiles/{ms → mspire}/quant/pdcd5_lfq_qspec.oneprot.csv +0 -0
  123. data/spec/testfiles/{ms → mspire}/quant/pdcd5_lfq_qspec.oneprot.tsv +0 -0
  124. data/spec/testfiles/{ms → mspire}/quant/pdcd5_lfq_qspec.oneprot.tsv_qspecgp +0 -0
  125. data/spec/testfiles/{ms → mspire}/quant/pdcd5_lfq_qspec.oneprot.tsv_qspecgp.csv +0 -0
  126. data/spec/testfiles/{ms → mspire}/quant/pdcd5_lfq_qspec.txt +0 -0
  127. data/spec/testfiles/{ms → mspire}/quant/pdcd5_lfq_tabdel.txt +0 -0
  128. data/spec/testfiles/{ms → mspire}/quant/pdcd5_lfq_tabdel.txt_qspecgp +0 -0
  129. data/spec/testfiles/{ms → mspire}/quant/remove_rest_of_proteins.rb +0 -0
  130. data/spec/testfiles/{ms → mspire}/quant/unlog_transform.rb +0 -0
  131. metadata +148 -194
  132. data/lib/ms.rb +0 -3
data/lib/ms.rb DELETED
@@ -1,3 +0,0 @@
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-
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- module MS
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- end