mspire 0.8.1 → 0.8.2

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Files changed (29) hide show
  1. data/VERSION +1 -1
  2. data/lib/mspire/cv/paramable.rb +25 -4
  3. data/lib/mspire/digester.rb +0 -16
  4. data/lib/mspire/imzml/writer.rb +1 -1
  5. data/lib/mspire/mzml/activation.rb +4 -0
  6. data/lib/mspire/mzml/chromatogram.rb +7 -3
  7. data/lib/mspire/mzml/component.rb +3 -1
  8. data/lib/mspire/mzml/data_array.rb +77 -87
  9. data/lib/mspire/mzml/data_array_container_like.rb +3 -8
  10. data/lib/mspire/mzml/isolation_window.rb +4 -0
  11. data/lib/mspire/mzml/precursor.rb +1 -1
  12. data/lib/mspire/mzml/reader.rb +3 -0
  13. data/lib/mspire/mzml/scan_window.rb +7 -0
  14. data/lib/mspire/mzml/selected_ion.rb +4 -0
  15. data/lib/mspire/mzml/spectrum.rb +18 -3
  16. data/lib/mspire/mzml.rb +2 -0
  17. data/lib/mspire/user_param.rb +13 -0
  18. data/spec/mspire/imzml/writer_spec.rb +17 -21
  19. data/spec/mspire/mzml/data_array_spec.rb +0 -5
  20. data/spec/mspire/mzml_spec.rb +56 -13
  21. data/spec/spec_helper.rb +22 -0
  22. data/spec/testfiles/mspire/{mzml → imzml}/1_BB7_SIM_478.5.CHECK.ibd +0 -0
  23. data/spec/testfiles/mspire/{mzml → imzml}/1_BB7_SIM_478.5.CHECK.imzML +144 -432
  24. data/spec/testfiles/mspire/imzml/{continuous_binary_check.ibd → continuous_binary.CHECK.ibd} +0 -0
  25. data/spec/testfiles/mspire/imzml/{processed_binary_check.ibd → processed_binary.CHECK.ibd} +0 -0
  26. data/spec/testfiles/mspire/mzml/j24z.idx_comp.3.NORMALIZED.CHECK.mzML +257 -0
  27. data/spec/testfiles/mspire/mzml/j24z.idx_comp.3.ROUNDTRIP.CHECK.mzML +257 -0
  28. data/spec/testfiles/mspire/mzml/{mspire_simulated.MSn.check.mzML → mspire_simulated.MSn.CHECK.mzML} +8 -6
  29. metadata +10 -8
data/spec/testfiles/mspire/mzml/{mspire_simulated.MSn.check.mzML → mspire_simulated.MSn.CHECK.mzML} RENAMED
@@ -1,5 +1,5 @@
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  <?xml version="1.0" encoding="UTF-8"?>
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- <mzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xsd="http://www.w3.org/2001/XMLSchema" version="1.1.0" id="ms1_and_ms2">
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+ <mzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xsd="http://www.w3.org/2001/XMLSchema" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0.xsd" version="1.1.0" id="ms1_and_ms2">
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  <cvList count="3">
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  <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo" version="3.29.0"/>
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  <cv id="UO" fullName="Unit Ontology" URI="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo" version="12:10:2011"/>
@@ -30,7 +30,7 @@
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  </dataProcessingList>
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  <run id="little_run" defaultInstrumentConfigurationRef="IC">
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  <spectrumList count="2" defaultDataProcessingRef="did_nothing">
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- <spectrum id="scan=1" index="0" defaultArrayLength="3">
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+ <spectrum index="0" id="scan=1" defaultArrayLength="3">
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  <cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum"/>
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  <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1"/>
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  <scanList count="1">
@@ -53,7 +53,7 @@
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  </binaryDataArray>
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  </binaryDataArrayList>
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  </spectrum>
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- <spectrum id="scan=2" index="1" defaultArrayLength="3">
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+ <spectrum index="1" id="scan=2" defaultArrayLength="3">
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  <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum"/>
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  <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="2"/>
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  <cvParam cvRef="MS" accession="MS:1000580" name="MSn spectrum"/>
@@ -65,9 +65,11 @@
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  <precursorList count="1">
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  <precursor spectrumRef="scan=1">
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  <selectedIonList count="1">
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- <cvParam cvRef="MS" accession="MS:1000744" name="selected ion m/z" value="2.0"/>
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- <cvParam cvRef="MS" accession="MS:1000041" name="charge state" value="2"/>
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- <cvParam cvRef="MS" accession="MS:1000042" name="peak intensity" value="5.0"/>
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+ <selectedIon>
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+ <cvParam cvRef="MS" accession="MS:1000744" name="selected ion m/z" value="2.0"/>
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+ <cvParam cvRef="MS" accession="MS:1000041" name="charge state" value="2"/>
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+ <cvParam cvRef="MS" accession="MS:1000042" name="peak intensity" value="5.0"/>
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+ </selectedIon>
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  </selectedIonList>
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  </precursor>
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  </precursorList>
metadata CHANGED
@@ -1,7 +1,7 @@
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  --- !ruby/object:Gem::Specification
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  name: mspire
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  version: !ruby/object:Gem::Version
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- version: 0.8.1
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+ version: 0.8.2
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  prerelease:
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  platform: ruby
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  authors:
@@ -10,7 +10,7 @@ authors:
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  autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2012-07-25 00:00:00.000000000 Z
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+ date: 2012-07-27 00:00:00.000000000 Z
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  dependencies:
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  - !ruby/object:Gem::Dependency
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  name: nokogiri
@@ -350,13 +350,15 @@ files:
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  - spec/testfiles/continuous_binary.tmp.ibd
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  - spec/testfiles/mspire/ident/peptide/db/uni_11_sp_tr.fasta
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  - spec/testfiles/mspire/ident/peptide/db/uni_11_sp_tr.msd_clvg2.min_aaseq4.yml
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- - spec/testfiles/mspire/imzml/continuous_binary_check.ibd
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- - spec/testfiles/mspire/imzml/processed_binary_check.ibd
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- - spec/testfiles/mspire/mzml/1_BB7_SIM_478.5.CHECK.ibd
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- - spec/testfiles/mspire/mzml/1_BB7_SIM_478.5.CHECK.imzML
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+ - spec/testfiles/mspire/imzml/1_BB7_SIM_478.5.CHECK.ibd
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+ - spec/testfiles/mspire/imzml/1_BB7_SIM_478.5.CHECK.imzML
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+ - spec/testfiles/mspire/imzml/continuous_binary.CHECK.ibd
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+ - spec/testfiles/mspire/imzml/processed_binary.CHECK.ibd
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  - spec/testfiles/mspire/mzml/1_BB7_SIM_478.5.mzML
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+ - spec/testfiles/mspire/mzml/j24z.idx_comp.3.NORMALIZED.CHECK.mzML
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+ - spec/testfiles/mspire/mzml/j24z.idx_comp.3.ROUNDTRIP.CHECK.mzML
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  - spec/testfiles/mspire/mzml/j24z.idx_comp.3.mzML
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- - spec/testfiles/mspire/mzml/mspire_simulated.MSn.check.mzML
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+ - spec/testfiles/mspire/mzml/mspire_simulated.MSn.CHECK.mzML
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  - spec/testfiles/mspire/mzml/openms.noidx_nocomp.12.mzML
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  - spec/testfiles/mspire/quant/kill_extra_tabs.rb
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  - spec/testfiles/mspire/quant/max_quant_output.provenance.txt
@@ -400,7 +402,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
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  version: '0'
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  requirements: []
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  rubyforge_project:
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- rubygems_version: 1.8.24
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+ rubygems_version: 1.8.18
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  signing_key:
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  specification_version: 3
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  summary: mass spectrometry proteomics, lipidomics, and tools