msf 0.1.0
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- data/.document +5 -0
- data/.rspec +1 -0
- data/Gemfile +24 -0
- data/Gemfile.lock +67 -0
- data/LICENSE.txt +20 -0
- data/README.md +45 -0
- data/Rakefile +43 -0
- data/VERSION +1 -0
- data/bin/ibspectra +43 -0
- data/erd/config.png +0 -0
- data/erd/empty.png +0 -0
- data/erd/erd.png +0 -0
- data/erd/msf.xcdatamodeld/.xccurrentversion +8 -0
- data/erd/msf.xcdatamodeld/msf.xcdatamodel/contents +330 -0
- data/erd/schema.txt +666 -0
- data/lib/msf.rb +2 -0
- data/lib/msf/models.rb +4 -0
- data/lib/msf/models/amino_acid.rb +50 -0
- data/lib/msf/models/amino_acid_modification.rb +55 -0
- data/lib/msf/models/amino_acid_modification_neutral_loss.rb +31 -0
- data/lib/msf/models/amino_acid_modifications_amino_acid_nls.rb +23 -0
- data/lib/msf/models/amino_acid_modifications_amino_acids.rb +27 -0
- data/lib/msf/models/annotation_data_version.rb +20 -0
- data/lib/msf/models/annotation_dataset.rb +29 -0
- data/lib/msf/models/annotation_group.rb +38 -0
- data/lib/msf/models/annotation_type.rb +23 -0
- data/lib/msf/models/chromatogram.rb +26 -0
- data/lib/msf/models/custom_data_field.rb +56 -0
- data/lib/msf/models/custom_data_peptide.rb +25 -0
- data/lib/msf/models/custom_data_processing_node.rb +25 -0
- data/lib/msf/models/custom_data_protein.rb +25 -0
- data/lib/msf/models/custom_data_spectrum.rb +25 -0
- data/lib/msf/models/enzyme.rb +32 -0
- data/lib/msf/models/fasta_file.rb +50 -0
- data/lib/msf/models/file_info.rb +41 -0
- data/lib/msf/models/mass_peak.rb +36 -0
- data/lib/msf/models/peptide.rb +118 -0
- data/lib/msf/models/peptide_score.rb +34 -0
- data/lib/msf/models/peptide_score_decoy.rb +34 -0
- data/lib/msf/models/peptide_terminal_modification.rb +29 -0
- data/lib/msf/models/peptides_amino_acid_modifications.rb +32 -0
- data/lib/msf/models/peptides_proteins.rb +27 -0
- data/lib/msf/models/processing_node.rb +65 -0
- data/lib/msf/models/processing_node_score.rb +45 -0
- data/lib/msf/models/protein.rb +38 -0
- data/lib/msf/models/protein_annotation.rb +35 -0
- data/lib/msf/models/protein_identification_group.rb +19 -0
- data/lib/msf/models/protein_score.rb +34 -0
- data/lib/msf/models/reporter_ion_quan_result.rb +31 -0
- data/lib/msf/models/reporter_ion_quan_result_search_spectrum.rb +29 -0
- data/lib/msf/models/scan_event.rb +37 -0
- data/lib/msf/models/schema_info.rb +29 -0
- data/lib/msf/models/spectrum.rb +34 -0
- data/lib/msf/models/spectrum_header.rb +63 -0
- data/lib/msf/models/spectrum_score.rb +24 -0
- data/lib/msf/models/taxonomy_name.rb +26 -0
- data/lib/msf/models/workflow_info.rb +46 -0
- data/lib/msf/models/workflow_message.rb +31 -0
- data/lib/msf/msf.rb +32 -0
- data/lib/msf/sql/enzyme_cleavage_specificity.rb +16 -0
- data/lib/msf/sql/false_discovery_rate.rb +24 -0
- data/lib/msf/sql/fasta_file_protein_annotation.rb +17 -0
- data/lib/msf/sql/mass_peak_relation.rb +17 -0
- data/lib/msf/sql/peptide_amino_acid_modification_decoy.rb +23 -0
- data/lib/msf/sql/peptide_decoy.rb +32 -0
- data/lib/msf/sql/peptide_terminal_modification_decoy.rb +20 -0
- data/lib/msf/sql/precursor_ion_quan_result.rb +29 -0
- data/lib/msf/sql/precursor_ion_quan_result_event_spectrum.rb +17 -0
- data/lib/msf/sql/precursor_ion_quan_result_search_spectrum.rb +20 -0
- data/lib/msf/sql/processing_node_filter_parameter.rb +29 -0
- data/lib/msf/sql/processing_node_interface.rb +19 -0
- data/lib/msf/sql/processing_node_parameter.rb +46 -0
- data/lib/msf/sql/processing_node_spectrum.rb +16 -0
- data/lib/msf/sql/quan_result.rb +40 -0
- data/lib/msf/sql/result_filter_set.rb +12 -0
- data/lib/msf/sql/taxonomy_node.rb +26 -0
- data/msf.gemspec +143 -0
- data/spec/msf_spec.rb +7 -0
- data/spec/spec_helper.rb +14 -0
- metadata +275 -0
@@ -0,0 +1,27 @@
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# ActiveRecord model of MSF PeptidesProteins
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# Join table for Peptides and Proteins HABTM
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#
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# Example:
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#
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# PeptidesProteins.first
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class PeptidesProteins < ActiveRecord::Base
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def self.table_name
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:PeptidesProteins
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end
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def self.primary_keys
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[:ProcessingNodeNumber, :PeptideID, :ProteinID]
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end
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def processing_node_number
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self.ProcessingNodeNumber
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end
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def peptide_id
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self.PeptideID
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end
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def protein_id
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self.ProteinID
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end
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belongs_to :protein,
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:foreign_key => 'ProteinID'
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belongs_to :peptide,
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:foreign_key => 'PeptideID'
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end
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# ActiveRecord model of MSF ProcessingNode
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#
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# Example:
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#
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# ProcessingNode.find(1)
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# ProcessingNode.first.node_name
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# ProcessingNode.find_by_NodeName('Mascot').peptides
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# ProcessingNode.find_by_NodeName('Mascot').protein_scores
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# ProcessingNode.find_by_NodeName('Mascot').spectrum_scores
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class ProcessingNode < ActiveRecord::Base
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def self.table_name
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:ProcessingNodes
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end
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def self.primary_key
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:ProcessingNodeNumber
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end
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def processing_node_number
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self.ProcessingNodeNumber
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end
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def processing_node_id
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self.ProcessingNodeID
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end
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def processing_node_parent_number
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self.ProcessingNodeParentNumber
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end
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def node_name
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self.NodeName
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end
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def friendly_name
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self.FriendlyName
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end
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def major_version
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self.MajorVersion
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end
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def minor_version
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self.MinorVersion
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end
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def node_comment
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self.NodeComment
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end
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def node_guid
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self.NodeGUID
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end
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def processing_node_state
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self.ProcessingNodeState
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end
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def self.isobaric_tags
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@isobaric_tags ||= {
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'113' => {'channel_id' => 1, 'mono_mass' => 113.107873, 'average_mass' => 113.1808},
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'114' => {'channel_id' => 2, 'mono_mass' => 114.111228, 'average_mass' => 114.1735},
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'115' => {'channel_id' => 3, 'mono_mass' => 115.108263, 'average_mass' => 115.1669},
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'116' => {'channel_id' => 4, 'mono_mass' => 116.111618, 'average_mass' => 116.1595},
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'117' => {'channel_id' => 5, 'mono_mass' => 117.114973, 'average_mass' => 117.1522},
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'118' => {'channel_id' => 6, 'mono_mass' => 118.112008, 'average_mass' => 118.1456},
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'119' => {'channel_id' => 7, 'mono_mass' => 119.115363, 'average_mass' => 119.1383},
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'121' => {'channel_id' => 8, 'mono_mass' => 121.122072, 'average_mass' => 121.1236},
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}
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end
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has_many :peptides,
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:foreign_key => 'ProcessingNodeNumber'
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has_many :protein_scores,
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:foreign_key => 'ProcessingNodeNumber'
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has_many :spectrum_scores,
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:foreign_key => 'ProcessingNodeNumber'
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end
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# ActiveRecord model of MSF ProcessingNodeScore
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#
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# Example:
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#
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# ProcessingNodeScore.first.score_name
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class ProcessingNodeScore < ActiveRecord::Base
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def self.table_name
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:ProcessingNodeScores
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end
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def self.primary_key
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:ScoreID
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end
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def processing_node_id
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self.ProcessingNodeID
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end
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def score_id
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self.ScoreID
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end
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def score_name
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self.ScoreName
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end
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def friendly_name
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self.FriendlyName
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end
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def description
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self.Description
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end
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def format_string
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self.FormatString
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end
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def score_category
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self.ScoreCategory
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end
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def hidden
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self.Hidden
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end
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def is_main_score
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self.IsMainScore
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end
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def score_guid
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self.ScoreGUID
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end
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has_many :processing_nodes,
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:foreign_key => "ProcessingNodeID"
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end
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# ActiveRecord model of MSF Protein
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#
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# Example:
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#
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# Protein.find(1)
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# Protein.first.sequence
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# Protein.first.protein_score
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# Protein.first.protein_annotation
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# Protein.first.peptides
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class Protein < ActiveRecord::Base
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def self.table_name
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:Proteins
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end
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def self.primary_key
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:ProteinID
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end
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def protein_id
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self.ProteinID
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end
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def sequence
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self.Sequence
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end
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def sequence_hash_code
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self.SequenceHashCode
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end
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def is_master_protein
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self.IsMasterProtein
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end
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has_one :protein_score,
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:foreign_key => "ProteinID"
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has_one :protein_annotation,
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:foreign_key => "ProteinID"
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# HABTM join table for peptides
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has_many :peptides_proteins,
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:class_name => 'PeptidesProteins',
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:foreign_key => "ProteinID"
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has_many :peptides, :through => :peptides_proteins
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end
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# ActiveRecord model of MSF ProteinAnnotation
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#
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# Example:
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#
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# ProteinAnnotation.first.description
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class ProteinAnnotation < ActiveRecord::Base
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def self.table_name
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:ProteinAnnotations
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end
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def self.primary_key
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:ProteinAnnotationID
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end
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def protein_annotation_id
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self.ProteinAnnotationID
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end
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def protein_id
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self.ProteinID
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end
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def description_hash_code
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self.DescriptionHashCode
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end
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def description
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self.Description
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end
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def taxonomy_id
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self.TaxonomyID
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end
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def accession
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self.description.split('|')[1]
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end
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belongs_to :protein,
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:foreign_key => "ProteinID"
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belongs_to :taxonomy,
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:foreign_key => "TaxonomyID"
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end
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# ActiveRecord model of MSF ProteinIdentificationGroup
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#
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# Example:
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#
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# ProteinIdentificationGroup.first
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class ProteinIdentificationGroup < ActiveRecord::Base
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def self.table_name
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:ProteinIdentificationGroups
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end
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def self.primary_key
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[:ProteinIdentificationGroupId, :ProcessingNodeNumber]
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end
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def protein_identification_group_id
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self.ProteinIdentificationGroupId
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end
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def processing_node_number
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self.ProcessingNodeNumber
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end
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end
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# ActiveRecord model of MSF ProteinScore
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#
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# Example:
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#
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# ProteinScore.first.protein_score
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class ProteinScore < ActiveRecord::Base
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def self.table_name
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:ProteinScores
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end
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def self.primary_key
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[:ProcessingNodeNumber, :ProteinID]
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end
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def processing_node_number
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self.ProcessingNodeNumber
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end
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def protein_id
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self.ProteinID
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end
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def protein_identification_group_id
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self.ProteinIdentificationGroupID
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end
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def protein_score
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self.ProteinScore
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end
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def coverage
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self.Coverage
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end
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belongs_to :protein,
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:foreign_key => "ProteinID"
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belongs_to :protein_identification_group,
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:foreign_key => "ProteinIdentificationGroupID"
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belongs_to :processing_node,
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:foreign_key => "ProcessingNodeNumber"
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end
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# ActiveRecord model of MSF ReporterIonQuanResult
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#
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# Example:
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#
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# ReporterIonQuanResult.find(1)
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# ReporterIonQuanResult.first.reporter_ion_quan_results_search_spectra
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class ReporterIonQuanResult < ActiveRecord::Base
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def self.table_name
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:ReporterIonQuanResults
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end
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def self.primary_key
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[:ProcessingNodeNumber, :QuanChannelID, :SpectrumID]
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end
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def processing_node_number
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self.ProcessingNodeNumber
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end
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def quan_channel_id
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self.QuanChannelID
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end
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def spectrum_id
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self.SpectrumID
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end
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def mass
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self.Mass
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end
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def height
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self.Height
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end
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belongs_to :reporter_ion_quan_results_search_spectra,
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:foreign_key => 'SpectrumID'
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end
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# ActiveRecord model of MSF ReporterIonQuanResultsSearchSpectra
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# Join table for ReporterIonQuanResult and Spectrum HABTM
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3
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#
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# Example:
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5
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#
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# ReporterIonQuanResultsSearchSpectra.first
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class ReporterIonQuanResultsSearchSpectra < ActiveRecord::Base
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def self.table_name
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:ReporterIonQuanResultsSearchSpectra
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end
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def self.primary_key
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:SearchSpectrumID
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# [:ProcessingNodeNumber, :SpectrumID, :SearchSpectrumID]
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end
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def processing_node_number
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16
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self.ProcessingNodeNumber
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end
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def spectrum_id
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19
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self.SpectrumID
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end
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def search_spectrum_id
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self.SearchSpectrumID
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end
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has_many :reporter_ion_quan_results,
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|
+
:foreign_key => "SpectrumID",
|
26
|
+
:primary_key => "SpectrumID"
|
27
|
+
belongs_to :spectrum,
|
28
|
+
:foreign_key => 'UniqueSpectrumID'
|
29
|
+
end
|
@@ -0,0 +1,37 @@
|
|
1
|
+
# ActiveRecord model of MSF ScanEvent
|
2
|
+
#
|
3
|
+
# Example:
|
4
|
+
#
|
5
|
+
# ScanEvent.find(1)
|
6
|
+
# ScanEvent.first.scan_type
|
7
|
+
class ScanEvent < ActiveRecord::Base
|
8
|
+
def self.table_name
|
9
|
+
:ScanEvents
|
10
|
+
end
|
11
|
+
def self.primary_key
|
12
|
+
:ScanEventID
|
13
|
+
end
|
14
|
+
def scan_event_id
|
15
|
+
self.ScanEventID
|
16
|
+
end
|
17
|
+
def ms_level
|
18
|
+
self.MSLevel
|
19
|
+
end
|
20
|
+
def polarity
|
21
|
+
self.Polarity
|
22
|
+
end
|
23
|
+
def scan_type
|
24
|
+
self.ScanType
|
25
|
+
end
|
26
|
+
def ionization
|
27
|
+
self.Ionization
|
28
|
+
end
|
29
|
+
def mass_analyzer
|
30
|
+
self.MassAnalyzer
|
31
|
+
end
|
32
|
+
def activation_type
|
33
|
+
self.ActivationType
|
34
|
+
end
|
35
|
+
has_many :spectrum_headers,
|
36
|
+
:foreign_key => "ScanEventID"
|
37
|
+
end
|
@@ -0,0 +1,29 @@
|
|
1
|
+
# ActiveRecord model of MSF SchemaInfo
|
2
|
+
#
|
3
|
+
# Example:
|
4
|
+
#
|
5
|
+
# SchemaInfo.find(1)
|
6
|
+
# SchemaInfo.first.software_version
|
7
|
+
class SchemaInfo < ActiveRecord::Base
|
8
|
+
def self.table_name
|
9
|
+
:SchemaInfo
|
10
|
+
end
|
11
|
+
def self.primary_key
|
12
|
+
:Version
|
13
|
+
end
|
14
|
+
def version
|
15
|
+
self.Version
|
16
|
+
end
|
17
|
+
def kind
|
18
|
+
self.Kind
|
19
|
+
end
|
20
|
+
def date
|
21
|
+
self.Date
|
22
|
+
end
|
23
|
+
def software_version
|
24
|
+
self.SoftwareVersion
|
25
|
+
end
|
26
|
+
def comment
|
27
|
+
self.Comment
|
28
|
+
end
|
29
|
+
end
|
@@ -0,0 +1,34 @@
|
|
1
|
+
# ActiveRecord model of MSF Spectrum
|
2
|
+
#
|
3
|
+
# Example:
|
4
|
+
#
|
5
|
+
# Spectrum.find(1)
|
6
|
+
# Spectrum.first.spectrum
|
7
|
+
class Spectrum < ActiveRecord::Base
|
8
|
+
def self.table_name
|
9
|
+
:Spectra
|
10
|
+
end
|
11
|
+
def self.primary_key
|
12
|
+
:UniqueSpectrumID
|
13
|
+
end
|
14
|
+
def unique_spectrum_id
|
15
|
+
self.UniqueSpectrumID
|
16
|
+
end
|
17
|
+
def spectrum
|
18
|
+
self.Spectrum
|
19
|
+
end
|
20
|
+
def spectrum_hash_code
|
21
|
+
self.SpectrumHashCode
|
22
|
+
end
|
23
|
+
has_many :peptides,
|
24
|
+
:foreign_key => "SpectrumID",
|
25
|
+
:primary_key => "UniqueSpectrumID"
|
26
|
+
has_one :spectrum_header,
|
27
|
+
:foreign_key => "SpectrumID"
|
28
|
+
has_one :spectrum_score,
|
29
|
+
:foreign_key => "SpectrumID"
|
30
|
+
has_one :search_spectrum,
|
31
|
+
:class_name => 'ReporterIonQuanResultsSearchSpectra',
|
32
|
+
:foreign_key => "SearchSpectrumID",
|
33
|
+
:primary_key => "UniqueSpectrumID"
|
34
|
+
end
|
@@ -0,0 +1,63 @@
|
|
1
|
+
# ActiveRecord model of MSF SpectrumHeader
|
2
|
+
#
|
3
|
+
# Example:
|
4
|
+
#
|
5
|
+
# SpectrumHeader.find(1)
|
6
|
+
# SpectrumHeader.first.mass
|
7
|
+
class SpectrumHeader < ActiveRecord::Base
|
8
|
+
def self.table_name
|
9
|
+
:SpectrumHeaders
|
10
|
+
end
|
11
|
+
def self.primary_key
|
12
|
+
:SpectrumID
|
13
|
+
end
|
14
|
+
def spectrum_id
|
15
|
+
self.SpectrumID
|
16
|
+
end
|
17
|
+
def mass_peak_id
|
18
|
+
self.MassPeakID
|
19
|
+
end
|
20
|
+
def scan_event_id
|
21
|
+
self.ScanEventID
|
22
|
+
end
|
23
|
+
def last_scan
|
24
|
+
self.LastScan
|
25
|
+
end
|
26
|
+
def first_scan
|
27
|
+
self.FirstScan
|
28
|
+
end
|
29
|
+
def retention_time
|
30
|
+
self.RetentionTime
|
31
|
+
end
|
32
|
+
def hidden
|
33
|
+
self.Hidden
|
34
|
+
end
|
35
|
+
def scan_numbers
|
36
|
+
self.ScanNumbers
|
37
|
+
end
|
38
|
+
def charge
|
39
|
+
self.Charge
|
40
|
+
end
|
41
|
+
def mass
|
42
|
+
self.Mass
|
43
|
+
end
|
44
|
+
def creating_processing_node_number
|
45
|
+
self.CreatingProcessingNodeNumber
|
46
|
+
end
|
47
|
+
def unique_spectrum_id
|
48
|
+
self.UniqueSpectrumID
|
49
|
+
end
|
50
|
+
def title
|
51
|
+
self.mass_peak.file_info.file_basename + "_" + self.SpectrumID.to_s + "_" + self.FirstScan.to_s + "_" + self.Charge.to_s
|
52
|
+
end
|
53
|
+
# associations
|
54
|
+
belongs_to :spectrum,
|
55
|
+
:foreign_key => "SpectrumID"
|
56
|
+
belongs_to :mass_peak,
|
57
|
+
:foreign_key => "MassPeakID"
|
58
|
+
belongs_to :scan_event,
|
59
|
+
:foreign_key => "ScanEventID"
|
60
|
+
belongs_to :unique_spectrum,
|
61
|
+
:class_name => "Spectrum",
|
62
|
+
:foreign_key => "UniqueSpectrumID"
|
63
|
+
end
|