msf 0.1.0

data/lib/msf/models/peptides_proteins.rb

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+# ActiveRecord model of MSF PeptidesProteins
+# Join table for Peptides and Proteins HABTM
+#
+#		Example:
+#
+#		PeptidesProteins.first
+class PeptidesProteins < ActiveRecord::Base
+  def self.table_name
+    :PeptidesProteins
+  end
+  def self.primary_keys
+    [:ProcessingNodeNumber, :PeptideID, :ProteinID]
+  end
+  def processing_node_number
+    self.ProcessingNodeNumber
+  end
+  def peptide_id
+    self.PeptideID
+  end
+  def protein_id
+    self.ProteinID
+  end
+  belongs_to :protein,
+    :foreign_key => 'ProteinID'
+  belongs_to :peptide,
+    :foreign_key => 'PeptideID'
+end

data/lib/msf/models/processing_node.rb

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+# ActiveRecord model of MSF ProcessingNode
+#
+#		Example:
+#
+#   ProcessingNode.find(1)
+#		ProcessingNode.first.node_name
+#   ProcessingNode.find_by_NodeName('Mascot').peptides
+#   ProcessingNode.find_by_NodeName('Mascot').protein_scores
+#   ProcessingNode.find_by_NodeName('Mascot').spectrum_scores
+class ProcessingNode < ActiveRecord::Base
+  def self.table_name
+    :ProcessingNodes
+  end
+  def self.primary_key
+    :ProcessingNodeNumber
+  end
+  def processing_node_number
+    self.ProcessingNodeNumber
+  end
+  def processing_node_id
+    self.ProcessingNodeID
+  end
+  def processing_node_parent_number
+    self.ProcessingNodeParentNumber
+  end
+  def node_name
+    self.NodeName
+  end
+  def friendly_name
+    self.FriendlyName
+  end
+  def major_version
+    self.MajorVersion
+  end
+  def minor_version
+    self.MinorVersion
+  end
+  def node_comment
+    self.NodeComment
+  end
+  def node_guid
+    self.NodeGUID
+  end
+  def processing_node_state
+    self.ProcessingNodeState
+  end
+  def self.isobaric_tags
+    @isobaric_tags ||= {
+      '113' => {'channel_id' => 1, 'mono_mass' => 113.107873, 'average_mass' => 113.1808},
+      '114' => {'channel_id' => 2, 'mono_mass' => 114.111228, 'average_mass' => 114.1735},
+      '115' => {'channel_id' => 3, 'mono_mass' => 115.108263, 'average_mass' => 115.1669},
+      '116' => {'channel_id' => 4, 'mono_mass' => 116.111618, 'average_mass' => 116.1595},
+      '117' => {'channel_id' => 5, 'mono_mass' => 117.114973, 'average_mass' => 117.1522},
+      '118' => {'channel_id' => 6, 'mono_mass' => 118.112008, 'average_mass' => 118.1456},
+      '119' => {'channel_id' => 7, 'mono_mass' => 119.115363, 'average_mass' => 119.1383},
+      '121' => {'channel_id' => 8, 'mono_mass' => 121.122072, 'average_mass' => 121.1236},
+    }
+  end
+  has_many :peptides,
+    :foreign_key => 'ProcessingNodeNumber'
+  has_many :protein_scores,
+    :foreign_key => 'ProcessingNodeNumber'
+  has_many :spectrum_scores,
+    :foreign_key => 'ProcessingNodeNumber'
+end

data/lib/msf/models/processing_node_score.rb

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+# ActiveRecord model of MSF ProcessingNodeScore
+#
+#		Example:
+#
+#		ProcessingNodeScore.first.score_name
+class ProcessingNodeScore < ActiveRecord::Base
+  def self.table_name
+    :ProcessingNodeScores
+  end
+  def self.primary_key
+    :ScoreID
+  end
+  def processing_node_id
+    self.ProcessingNodeID
+  end
+  def score_id
+    self.ScoreID
+  end
+  def score_name
+    self.ScoreName
+  end
+  def friendly_name
+    self.FriendlyName
+  end
+  def description
+    self.Description
+  end
+  def format_string
+    self.FormatString
+  end
+  def score_category
+    self.ScoreCategory
+  end
+  def hidden
+    self.Hidden
+  end
+  def is_main_score
+    self.IsMainScore
+  end
+  def score_guid
+    self.ScoreGUID
+  end
+  has_many :processing_nodes,
+    :foreign_key => "ProcessingNodeID"
+end

data/lib/msf/models/protein.rb

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+# ActiveRecord model of MSF Protein
+#
+#   Example:
+#
+#   Protein.find(1)
+#   Protein.first.sequence
+#   Protein.first.protein_score
+#   Protein.first.protein_annotation
+#   Protein.first.peptides
+class Protein < ActiveRecord::Base
+  def self.table_name
+    :Proteins
+  end
+  def self.primary_key
+    :ProteinID
+  end
+  def protein_id
+    self.ProteinID
+  end
+  def sequence
+    self.Sequence
+  end
+  def sequence_hash_code
+    self.SequenceHashCode
+  end
+  def is_master_protein
+    self.IsMasterProtein
+  end
+  has_one :protein_score,
+    :foreign_key => "ProteinID"
+  has_one :protein_annotation,
+    :foreign_key => "ProteinID"
+  # HABTM join table for peptides
+  has_many :peptides_proteins,
+    :class_name => 'PeptidesProteins',
+    :foreign_key => "ProteinID"
+  has_many :peptides, :through => :peptides_proteins
+end

data/lib/msf/models/protein_annotation.rb

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+# ActiveRecord model of MSF ProteinAnnotation
+#
+#		Example:
+#
+#		ProteinAnnotation.first.description
+class ProteinAnnotation < ActiveRecord::Base
+  def self.table_name
+    :ProteinAnnotations
+  end
+  def self.primary_key
+    :ProteinAnnotationID
+  end
+  def protein_annotation_id
+    self.ProteinAnnotationID
+  end
+  def protein_id
+    self.ProteinID
+  end
+  def description_hash_code
+    self.DescriptionHashCode
+  end
+  def description
+    self.Description
+  end
+  def taxonomy_id
+    self.TaxonomyID
+  end
+  def accession
+    self.description.split('|')[1]
+  end
+  belongs_to :protein,
+    :foreign_key => "ProteinID"
+  belongs_to :taxonomy,
+    :foreign_key => "TaxonomyID"
+end

data/lib/msf/models/protein_identification_group.rb

@@ -0,0 +1,19 @@
+# ActiveRecord model of MSF ProteinIdentificationGroup
+#
+#		Example:
+#
+#		ProteinIdentificationGroup.first
+class ProteinIdentificationGroup < ActiveRecord::Base
+  def self.table_name
+    :ProteinIdentificationGroups
+  end
+  def self.primary_key
+    [:ProteinIdentificationGroupId, :ProcessingNodeNumber]
+  end
+  def protein_identification_group_id
+    self.ProteinIdentificationGroupId
+  end
+  def processing_node_number
+    self.ProcessingNodeNumber
+  end
+end

data/lib/msf/models/protein_score.rb

@@ -0,0 +1,34 @@
+# ActiveRecord model of MSF ProteinScore
+#
+#		Example:
+#
+#		ProteinScore.first.protein_score
+class ProteinScore < ActiveRecord::Base
+  def self.table_name
+    :ProteinScores
+  end
+  def self.primary_key
+    [:ProcessingNodeNumber, :ProteinID]
+  end
+  def processing_node_number
+    self.ProcessingNodeNumber
+  end
+  def protein_id
+    self.ProteinID
+  end
+  def protein_identification_group_id
+    self.ProteinIdentificationGroupID
+  end
+  def protein_score
+    self.ProteinScore
+  end
+  def coverage
+    self.Coverage
+  end
+  belongs_to :protein,
+    :foreign_key => "ProteinID"
+  belongs_to :protein_identification_group,
+    :foreign_key => "ProteinIdentificationGroupID"
+  belongs_to :processing_node,
+    :foreign_key => "ProcessingNodeNumber"
+end

data/lib/msf/models/reporter_ion_quan_result.rb

@@ -0,0 +1,31 @@
+# ActiveRecord model of MSF ReporterIonQuanResult
+#
+#		Example:
+#
+#   ReporterIonQuanResult.find(1)
+#		ReporterIonQuanResult.first.reporter_ion_quan_results_search_spectra
+class ReporterIonQuanResult < ActiveRecord::Base
+  def self.table_name
+    :ReporterIonQuanResults
+  end
+  def self.primary_key
+    [:ProcessingNodeNumber, :QuanChannelID, :SpectrumID]
+  end
+  def processing_node_number
+    self.ProcessingNodeNumber
+  end
+  def quan_channel_id
+    self.QuanChannelID
+  end
+  def spectrum_id
+    self.SpectrumID
+  end
+  def mass
+    self.Mass
+  end
+  def height
+    self.Height
+  end
+  belongs_to :reporter_ion_quan_results_search_spectra,
+    :foreign_key => 'SpectrumID'
+end

data/lib/msf/models/reporter_ion_quan_result_search_spectrum.rb

@@ -0,0 +1,29 @@
+# ActiveRecord model of MSF ReporterIonQuanResultsSearchSpectra
+# Join table for ReporterIonQuanResult and Spectrum HABTM
+#
+#		Example:
+#
+#		ReporterIonQuanResultsSearchSpectra.first
+class ReporterIonQuanResultsSearchSpectra < ActiveRecord::Base
+  def self.table_name
+    :ReporterIonQuanResultsSearchSpectra
+  end
+  def self.primary_key
+    :SearchSpectrumID
+    # [:ProcessingNodeNumber, :SpectrumID, :SearchSpectrumID]
+  end
+  def processing_node_number
+    self.ProcessingNodeNumber
+  end
+  def spectrum_id
+    self.SpectrumID
+  end
+  def search_spectrum_id
+    self.SearchSpectrumID
+  end
+  has_many :reporter_ion_quan_results,
+    :foreign_key => "SpectrumID",
+    :primary_key => "SpectrumID"
+  belongs_to :spectrum,
+    :foreign_key => 'UniqueSpectrumID'
+end

data/lib/msf/models/scan_event.rb

@@ -0,0 +1,37 @@
+# ActiveRecord model of MSF ScanEvent
+#
+#		Example:
+#
+#   ScanEvent.find(1)
+#		ScanEvent.first.scan_type
+class ScanEvent < ActiveRecord::Base
+  def self.table_name
+    :ScanEvents
+  end
+  def self.primary_key
+    :ScanEventID
+  end
+  def scan_event_id
+    self.ScanEventID
+  end
+  def ms_level
+    self.MSLevel
+  end
+  def polarity
+    self.Polarity
+  end
+  def scan_type
+    self.ScanType
+  end
+  def ionization
+    self.Ionization
+  end
+  def mass_analyzer
+    self.MassAnalyzer
+  end
+  def activation_type
+    self.ActivationType
+  end
+  has_many :spectrum_headers,
+    :foreign_key => "ScanEventID"
+end

data/lib/msf/models/schema_info.rb

@@ -0,0 +1,29 @@
+# ActiveRecord model of MSF SchemaInfo
+#
+#		Example:
+#
+#   SchemaInfo.find(1)
+#		SchemaInfo.first.software_version
+class SchemaInfo < ActiveRecord::Base
+  def self.table_name
+    :SchemaInfo
+  end
+  def self.primary_key
+    :Version
+  end
+  def version
+    self.Version
+  end
+  def kind
+    self.Kind
+  end
+  def date
+    self.Date
+  end
+  def software_version
+    self.SoftwareVersion
+  end
+  def comment
+    self.Comment
+  end
+end

data/lib/msf/models/spectrum.rb

@@ -0,0 +1,34 @@
+# ActiveRecord model of MSF Spectrum
+#
+#   Example:
+#
+#   Spectrum.find(1)
+#   Spectrum.first.spectrum
+class Spectrum < ActiveRecord::Base
+  def self.table_name
+    :Spectra
+  end
+  def self.primary_key
+    :UniqueSpectrumID
+  end
+  def unique_spectrum_id
+    self.UniqueSpectrumID
+  end
+  def spectrum
+    self.Spectrum
+  end
+  def spectrum_hash_code
+    self.SpectrumHashCode
+  end
+  has_many :peptides,
+    :foreign_key => "SpectrumID",
+    :primary_key => "UniqueSpectrumID"
+  has_one :spectrum_header,
+    :foreign_key => "SpectrumID"
+  has_one :spectrum_score,
+    :foreign_key => "SpectrumID"
+  has_one :search_spectrum,
+    :class_name => 'ReporterIonQuanResultsSearchSpectra',
+    :foreign_key => "SearchSpectrumID",
+    :primary_key => "UniqueSpectrumID"
+end

data/lib/msf/models/spectrum_header.rb

@@ -0,0 +1,63 @@
+# ActiveRecord model of MSF SpectrumHeader
+#
+#   Example:
+#
+#   SpectrumHeader.find(1)
+#   SpectrumHeader.first.mass
+class SpectrumHeader < ActiveRecord::Base
+  def self.table_name
+    :SpectrumHeaders
+  end
+  def self.primary_key
+    :SpectrumID
+  end
+  def spectrum_id
+    self.SpectrumID
+  end
+  def mass_peak_id
+    self.MassPeakID
+  end
+  def scan_event_id
+    self.ScanEventID
+  end
+  def last_scan
+    self.LastScan
+  end
+  def first_scan
+    self.FirstScan
+  end
+  def retention_time
+    self.RetentionTime
+  end
+  def hidden
+    self.Hidden
+  end
+  def scan_numbers
+    self.ScanNumbers
+  end
+  def charge
+    self.Charge
+  end
+  def mass
+    self.Mass
+  end
+  def creating_processing_node_number
+    self.CreatingProcessingNodeNumber
+  end
+  def unique_spectrum_id
+    self.UniqueSpectrumID
+  end
+  def title
+    self.mass_peak.file_info.file_basename + "_" + self.SpectrumID.to_s + "_" + self.FirstScan.to_s + "_" + self.Charge.to_s
+  end
+  # associations
+  belongs_to :spectrum,
+    :foreign_key => "SpectrumID"
+  belongs_to :mass_peak,
+    :foreign_key => "MassPeakID"
+  belongs_to :scan_event,
+    :foreign_key => "ScanEventID"
+  belongs_to :unique_spectrum,
+    :class_name => "Spectrum",
+    :foreign_key => "UniqueSpectrumID"
+end