# -*- encoding: utf-8 -*-
# stub: mspire 0.4.5 ruby lib

Gem::Specification.new do |s|
  s.name = "mspire".freeze
  s.version = "0.4.5".freeze

  s.required_rubygems_version = Gem::Requirement.new(">= 0".freeze) if s.respond_to? :required_rubygems_version=
  s.require_paths = ["lib".freeze]
  s.authors = ["John Prince".freeze]
  s.date = "2008-09-25"
  s.description = "mspire is for working with mass spectrometry proteomics data".freeze
  s.email = "jprince@icmb.utexas.edu".freeze
  s.executables = ["gi2annot.rb".freeze, "protxml2prots_peps.rb".freeze, "filter_and_validate.rb".freeze, "raw_to_mzXML.rb".freeze, "run_percolator.rb".freeze, "srf_to_sqt.rb".freeze, "prob_validate.rb".freeze, "srf_group.rb".freeze, "ms_to_lmat.rb".freeze, "protein_summary.rb".freeze, "bioworks_to_pepxml_gui.rb".freeze, "id_class_anal.rb".freeze, "id_precision.rb".freeze, "sqt_group.rb".freeze, "aafreqs.rb".freeze, "pepproph_filter.rb".freeze, "bioworks2excel.rb".freeze, "bioworks_to_pepxml.rb".freeze, "fasta_shaker.rb".freeze]
  s.extra_rdoc_files = ["README.rdoc".freeze]
  s.files = ["INSTALL".freeze, "LICENSE".freeze, "README".freeze, "README.rdoc".freeze, "Rakefile".freeze, "bin/aafreqs.rb".freeze, "bin/bioworks2excel.rb".freeze, "bin/bioworks_to_pepxml.rb".freeze, "bin/bioworks_to_pepxml_gui.rb".freeze, "bin/fasta_shaker.rb".freeze, "bin/filter_and_validate.rb".freeze, "bin/gi2annot.rb".freeze, "bin/id_class_anal.rb".freeze, "bin/id_precision.rb".freeze, "bin/ms_to_lmat.rb".freeze, "bin/pepproph_filter.rb".freeze, "bin/prob_validate.rb".freeze, "bin/protein_summary.rb".freeze, "bin/protxml2prots_peps.rb".freeze, "bin/raw_to_mzXML.rb".freeze, "bin/run_percolator.rb".freeze, "bin/sqt_group.rb".freeze, "bin/srf_group.rb".freeze, "bin/srf_to_sqt.rb".freeze, "changelog.txt".freeze, "lib/align".freeze, "lib/align.rb".freeze, "lib/align/chams.rb".freeze, "lib/archive".freeze, "lib/archive/targz.rb".freeze, "lib/bsearch.rb".freeze, "lib/core_extensions.rb".freeze, "lib/fasta.rb".freeze, "lib/gi.rb".freeze, "lib/group_by.rb".freeze, "lib/index_by.rb".freeze, "lib/merge_deep.rb".freeze, "lib/ms".freeze, "lib/ms.rb".freeze, "lib/ms/converter".freeze, "lib/ms/converter/mzxml.rb".freeze, "lib/ms/gradient_program.rb".freeze, "lib/ms/msrun.rb".freeze, "lib/ms/msrun_index.rb".freeze, "lib/ms/parser".freeze, "lib/ms/parser.rb".freeze, "lib/ms/parser/mzdata".freeze, "lib/ms/parser/mzdata.rb".freeze, "lib/ms/parser/mzdata/axml.rb".freeze, "lib/ms/parser/mzdata/dom.rb".freeze, "lib/ms/parser/mzdata/libxml.rb".freeze, "lib/ms/parser/mzxml".freeze, "lib/ms/parser/mzxml.rb".freeze, "lib/ms/parser/mzxml/axml.rb".freeze, "lib/ms/parser/mzxml/dom.rb".freeze, "lib/ms/parser/mzxml/hpricot.rb".freeze, "lib/ms/parser/mzxml/libxml.rb".freeze, "lib/ms/parser/mzxml/regexp.rb".freeze, "lib/ms/parser/mzxml/rexml.rb".freeze, "lib/ms/parser/mzxml/xmlparser.rb".freeze, "lib/ms/precursor.rb".freeze, "lib/ms/scan.rb".freeze, "lib/ms/spectrum.rb".freeze, "lib/mspire.rb".freeze, "lib/pi_zero.rb".freeze, "lib/qvalue.rb".freeze, "lib/roc.rb".freeze, "lib/sample_enzyme.rb".freeze, "lib/scan_i.rb".freeze, "lib/spec_id".freeze, "lib/spec_id.rb".freeze, "lib/spec_id/aa_freqs.rb".freeze, "lib/spec_id/bioworks.rb".freeze, "lib/spec_id/digestor.rb".freeze, "lib/spec_id/mass.rb".freeze, "lib/spec_id/parser".freeze, "lib/spec_id/parser/proph.rb".freeze, "lib/spec_id/precision".freeze, "lib/spec_id/precision/filter".freeze, "lib/spec_id/precision/filter.rb".freeze, "lib/spec_id/precision/filter/cmdline.rb".freeze, "lib/spec_id/precision/filter/interactive.rb".freeze, "lib/spec_id/precision/filter/output.rb".freeze, "lib/spec_id/precision/output.rb".freeze, "lib/spec_id/precision/prob".freeze, "lib/spec_id/precision/prob.rb".freeze, "lib/spec_id/precision/prob/cmdline.rb".freeze, "lib/spec_id/precision/prob/output.rb".freeze, "lib/spec_id/proph".freeze, "lib/spec_id/proph.rb".freeze, "lib/spec_id/proph/pep_summary.rb".freeze, "lib/spec_id/proph/prot_summary.rb".freeze, "lib/spec_id/protein_summary.rb".freeze, "lib/spec_id/sequest".freeze, "lib/spec_id/sequest.rb".freeze, "lib/spec_id/sequest/params.rb".freeze, "lib/spec_id/sequest/pepxml.rb".freeze, "lib/spec_id/sqt.rb".freeze, "lib/spec_id/srf.rb".freeze, "lib/spec_id_xml.rb".freeze, "lib/transmem".freeze, "lib/transmem.rb".freeze, "lib/transmem/phobius.rb".freeze, "lib/transmem/toppred.rb".freeze, "lib/validator".freeze, "lib/validator.rb".freeze, "lib/validator/aa.rb".freeze, "lib/validator/aa_est.rb".freeze, "lib/validator/background.rb".freeze, "lib/validator/bias.rb".freeze, "lib/validator/cmdline.rb".freeze, "lib/validator/decoy.rb".freeze, "lib/validator/digestion_based.rb".freeze, "lib/validator/probability.rb".freeze, "lib/validator/prot_from_pep.rb".freeze, "lib/validator/q_value.rb".freeze, "lib/validator/transmem.rb".freeze, "lib/validator/true_pos.rb".freeze, "lib/xml.rb".freeze, "lib/xml_style_parser.rb".freeze, "lib/xmlparser_wrapper.rb".freeze, "release_notes.txt".freeze, "script/compile_and_plot_smriti_final.rb".freeze, "script/create_little_pepxml.rb".freeze, "script/degenerate_peptides.rb".freeze, "script/estimate_fpr_by_cysteine.rb".freeze, "script/extract_gradient_programs.rb".freeze, "script/find_cysteine_background.rb".freeze, "script/genuine_tps_and_probs.rb".freeze, "script/get_apex_values_rexml.rb".freeze, "script/histogram_probs.rb".freeze, "script/mascot_fix_pepxml.rb".freeze, "script/msvis.rb".freeze, "script/mzXML2timeIndex.rb".freeze, "script/peps_per_bin.rb".freeze, "script/prep_dir.rb".freeze, "script/simple_protein_digestion.rb".freeze, "script/smriti_final_analysis.rb".freeze, "script/sqt_to_meta.rb".freeze, "script/top_hit_per_scan.rb".freeze, "script/toppred_to_yaml.rb".freeze, "script/tpp_installer.rb".freeze, "specs/align_spec.rb".freeze, "specs/bin".freeze, "specs/bin/bioworks_to_pepxml_spec.rb".freeze, "specs/bin/fasta_shaker_spec.rb".freeze, "specs/bin/filter_and_validate__multiple_vals_helper.yaml".freeze, "specs/bin/filter_and_validate_spec.rb".freeze, "specs/bin/ms_to_lmat_spec.rb".freeze, "specs/bin/prob_validate_spec.rb".freeze, "specs/bin/protein_summary_spec.rb".freeze, "specs/fasta_spec.rb".freeze, "specs/gi_spec.rb".freeze, "specs/load_bin_path.rb".freeze, "specs/merge_deep_spec.rb".freeze, "specs/ms".freeze, "specs/ms/gradient_program_spec.rb".freeze, "specs/ms/msrun_spec.rb".freeze, "specs/ms/parser_spec.rb".freeze, "specs/ms/spectrum_spec.rb".freeze, "specs/pi_zero_spec.rb".freeze, "specs/qvalue_spec.rb".freeze, "specs/roc_spec.rb".freeze, "specs/rspec_autotest.rb".freeze, "specs/sample_enzyme_spec.rb".freeze, "specs/spec_helper.rb".freeze, "specs/spec_id".freeze, "specs/spec_id/aa_freqs_spec.rb".freeze, "specs/spec_id/bioworks_spec.rb".freeze, "specs/spec_id/digestor_spec.rb".freeze, "specs/spec_id/precision".freeze, "specs/spec_id/precision/filter".freeze, "specs/spec_id/precision/filter/cmdline_spec.rb".freeze, "specs/spec_id/precision/filter/output_spec.rb".freeze, "specs/spec_id/precision/filter_spec.rb".freeze, "specs/spec_id/precision/prob_spec.rb".freeze, "specs/spec_id/precision/prob_spec_helper.rb".freeze, "specs/spec_id/proph".freeze, "specs/spec_id/proph/pep_summary_spec.rb".freeze, "specs/spec_id/proph/prot_summary_spec.rb".freeze, "specs/spec_id/protein_summary_spec.rb".freeze, "specs/spec_id/sequest".freeze, "specs/spec_id/sequest/params_spec.rb".freeze, "specs/spec_id/sequest/pepxml_spec.rb".freeze, "specs/spec_id/sequest_spec.rb".freeze, "specs/spec_id/sqt_spec.rb".freeze, "specs/spec_id/srf_spec.rb".freeze, "specs/spec_id/srf_spec_helper.rb".freeze, "specs/spec_id_helper.rb".freeze, "specs/spec_id_spec.rb".freeze, "specs/spec_id_xml_spec.rb".freeze, "specs/transmem".freeze, "specs/transmem/phobius_spec.rb".freeze, "specs/transmem/toppred_spec.rb".freeze, "specs/transmem_spec.rb".freeze, "specs/transmem_spec_shared.rb".freeze, "specs/validator".freeze, "specs/validator/aa_est_spec.rb".freeze, "specs/validator/aa_spec.rb".freeze, "specs/validator/background_spec.rb".freeze, "specs/validator/bias_spec.rb".freeze, "specs/validator/decoy_spec.rb".freeze, "specs/validator/fasta_helper.rb".freeze, "specs/validator/prot_from_pep_spec.rb".freeze, "specs/validator/transmem_spec.rb".freeze, "specs/validator/true_pos_spec.rb".freeze, "specs/validator_helper.rb".freeze, "specs/xml_spec.rb".freeze, "test_files/000_pepxml18_small.xml".freeze, "test_files/020a.mzXML.timeIndex".freeze, "test_files/4-03-03_mzXML".freeze, "test_files/4-03-03_mzXML/000.mzXML.timeIndex".freeze, "test_files/4-03-03_mzXML/020.mzXML.timeIndex".freeze, "test_files/4-03-03_small-prot.xml".freeze, "test_files/4-03-03_small.xml".freeze, "test_files/7MIX_STD_110802_1.sequest_params_fragment.srf".freeze, "test_files/bioworks-3.3_10prots.xml".freeze, "test_files/bioworks31.params".freeze, "test_files/bioworks32.params".freeze, "test_files/bioworks33.params".freeze, "test_files/bioworks_single_run_small.xml".freeze, "test_files/bioworks_small.fasta".freeze, "test_files/bioworks_small.params".freeze, "test_files/bioworks_small.phobius".freeze, "test_files/bioworks_small.toppred.out".freeze, "test_files/bioworks_small.xml".freeze, "test_files/bioworks_with_INV_small.xml".freeze, "test_files/bioworks_with_SHUFF_small.xml".freeze, "test_files/corrupted_900.srf".freeze, "test_files/head_of_7MIX.srf".freeze, "test_files/interact-opd1_mods_small-prot.xml".freeze, "test_files/messups.fasta".freeze, "test_files/opd1".freeze, "test_files/opd1/000.my_answer.100lines.xml".freeze, "test_files/opd1/000.tpp_1.2.3.first10.xml".freeze, "test_files/opd1/000.tpp_2.9.2.first10.xml".freeze, "test_files/opd1/000.v2.1.mzXML.timeIndex".freeze, "test_files/opd1/000_020-prot.png".freeze, "test_files/opd1/000_020_3prots-prot.mod_initprob.xml".freeze, "test_files/opd1/000_020_3prots-prot.xml".freeze, "test_files/opd1/opd1_cat_inv_small-prot.xml".freeze, "test_files/opd1/sequest.3.1.params".freeze, "test_files/opd1/sequest.3.2.params".freeze, "test_files/opd1/twenty_scans.mzXML".freeze, "test_files/opd1/twenty_scans.v2.1.mzXML".freeze, "test_files/opd1/twenty_scans_answ.lmat".freeze, "test_files/opd1/twenty_scans_answ.lmata".freeze, "test_files/opd1_020_beginning.RAW".freeze, "test_files/opd1_2runs_2mods".freeze, "test_files/opd1_2runs_2mods/data".freeze, "test_files/opd1_2runs_2mods/data/020.mzData.xml".freeze, "test_files/opd1_2runs_2mods/data/020.readw.mzXML".freeze, "test_files/opd1_2runs_2mods/data/040.mzData.xml".freeze, "test_files/opd1_2runs_2mods/data/040.readw.mzXML".freeze, "test_files/opd1_2runs_2mods/data/README.txt".freeze, "test_files/opd1_2runs_2mods/interact-opd1_mods__small.xml".freeze, "test_files/orbitrap_mzData".freeze, "test_files/orbitrap_mzData/000_cut.xml".freeze, "test_files/pepproph_small.xml".freeze, "test_files/phobius.small.noheader.txt".freeze, "test_files/phobius.small.small.txt".freeze, "test_files/s01_anC1_ld020mM.key.txt".freeze, "test_files/s01_anC1_ld020mM.meth".freeze, "test_files/small.fasta".freeze, "test_files/small.sqt".freeze, "test_files/smallraw.RAW".freeze, "test_files/tf_bioworks2excel.bioXML".freeze, "test_files/tf_bioworks2excel.txt.actual".freeze, "test_files/toppred.small.out".freeze, "test_files/toppred.xml.out".freeze, "test_files/validator_hits_separate".freeze, "test_files/validator_hits_separate/bias_bioworks_small_HS.fasta".freeze, "test_files/validator_hits_separate/bioworks_small_HS.xml".freeze, "test_files/yeast_gly_small-prot.xml".freeze, "test_files/yeast_gly_small.1.0_1.0_1.0.parentTimes".freeze, "test_files/yeast_gly_small.xml".freeze, "test_files/yeast_gly_small2.parentTimes".freeze]
  s.homepage = "http://mspire.rubyforge.org".freeze
  s.rdoc_options = ["--main".freeze, "README.rdoc".freeze, "--title".freeze, "mspire".freeze]
  s.requirements = ["\"libxml\" is the prefered xml parser right now.  libxml, xmlparser, REXML and regular expressions are used as fallback in some routines.".freeze, "some plotting functions will not be available without the \"gnuplot\" gem (and underlying gnuplot binary)".freeze, "the \"t2x\" binary (in archive) or readw.exe is required to convert .RAW files to mzXML in some applications".freeze, "\"rake\" is useful for development".freeze, "\"webgen (with gems redcloth and bluecloth) is necessary to build web pages".freeze]
  s.rubygems_version = "3.5.10".freeze
  s.summary = "Mass Spectrometry Proteomics Objects, Scripts, and Executables".freeze
  s.test_files = ["specs/ms/gradient_program_spec.rb".freeze, "specs/ms/parser_spec.rb".freeze, "specs/ms/spectrum_spec.rb".freeze, "specs/ms/msrun_spec.rb".freeze, "specs/merge_deep_spec.rb".freeze, "specs/qvalue_spec.rb".freeze, "specs/fasta_spec.rb".freeze, "specs/transmem/phobius_spec.rb".freeze, "specs/transmem/toppred_spec.rb".freeze, "specs/align_spec.rb".freeze, "specs/transmem_spec.rb".freeze, "specs/spec_id/protein_summary_spec.rb".freeze, "specs/spec_id/bioworks_spec.rb".freeze, "specs/spec_id/sqt_spec.rb".freeze, "specs/spec_id/sequest/pepxml_spec.rb".freeze, "specs/spec_id/sequest/params_spec.rb".freeze, "specs/spec_id/precision/filter_spec.rb".freeze, "specs/spec_id/precision/prob_spec.rb".freeze, "specs/spec_id/precision/filter/cmdline_spec.rb".freeze, "specs/spec_id/precision/filter/output_spec.rb".freeze, "specs/spec_id/proph/prot_summary_spec.rb".freeze, "specs/spec_id/proph/pep_summary_spec.rb".freeze, "specs/spec_id/srf_spec.rb".freeze, "specs/spec_id/sequest_spec.rb".freeze, "specs/spec_id/digestor_spec.rb".freeze, "specs/spec_id/aa_freqs_spec.rb".freeze, "specs/pi_zero_spec.rb".freeze, "specs/xml_spec.rb".freeze, "specs/sample_enzyme_spec.rb".freeze, "specs/gi_spec.rb".freeze, "specs/spec_id_spec.rb".freeze, "specs/validator/true_pos_spec.rb".freeze, "specs/validator/aa_est_spec.rb".freeze, "specs/validator/background_spec.rb".freeze, "specs/validator/bias_spec.rb".freeze, "specs/validator/transmem_spec.rb".freeze, "specs/validator/prot_from_pep_spec.rb".freeze, "specs/validator/decoy_spec.rb".freeze, "specs/validator/aa_spec.rb".freeze, "specs/bin/protein_summary_spec.rb".freeze, "specs/bin/filter_and_validate_spec.rb".freeze, "specs/bin/ms_to_lmat_spec.rb".freeze, "specs/bin/fasta_shaker_spec.rb".freeze, "specs/bin/bioworks_to_pepxml_spec.rb".freeze, "specs/bin/prob_validate_spec.rb".freeze, "specs/roc_spec.rb".freeze, "specs/spec_id_xml_spec.rb".freeze]

  s.specification_version = 2

  s.add_runtime_dependency(%q<libjtp>.freeze, ["~> 0.2.14".freeze])
  s.add_runtime_dependency(%q<axml>.freeze, ["~> 0.0.0".freeze])
  s.add_runtime_dependency(%q<arrayclass>.freeze, ["~> 0.1.0".freeze])
end