msf 0.1.0

data/lib/msf/models/custom_data_protein.rb

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+# ActiveRecord model of MSF CustomDataProtein
+#
+#		Example:
+#
+#   CustomDataProtein.find(1)
+#		CustomDataProtein.first.field_value
+class CustomDataProtein < ActiveRecord::Base
+  def self.table_name
+    :CustomDataProteins
+  end
+  def self.primary_key
+    [:FieldID, :ProteinID]
+  end
+  def field_id
+    self.FieldID
+  end
+  def protein_id
+    self.ProteinID
+  end
+  def field_value
+    self.FieldValue
+  end
+  belongs_to :custom_data_field,
+    :foreign_key => "FieldID"
+end

data/lib/msf/models/custom_data_spectrum.rb

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+# ActiveRecord model of MSF CustomDataSpectrum
+#
+#		Example:
+#
+#   CustomDataSpectrum.find(1)
+#		CustomDataSpectrum.first.field_value
+class CustomDataSpectrum < ActiveRecord::Base
+  def self.table_name
+    :CustomDataSpectra
+  end
+  def self.primary_key
+    [:FieldID, :SpectrumID]
+  end
+  def field_id
+    self.FieldID
+  end
+  def spectrum_id
+    self.SpectrumID
+  end
+  def field_value
+    self.FieldValue
+  end
+  belongs_to :custom_data_field,
+    :foreign_key => "FieldID"
+end

data/lib/msf/models/enzyme.rb

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+# ActiveRecord model of MSF Enzyme
+#
+#		Example:
+#
+#   Enzyme.find(1)
+#		Enzyme.all.first.name
+class Enzyme < ActiveRecord::Base
+  def self.table_name
+    :Enzymes
+  end
+  def self.primary_key
+    :EnzymeID
+  end
+  def enzyme_id
+    self.EnzymeID
+  end
+  def name
+    self.Name
+  end
+  def abbreviation
+    self.Abbreviation
+  end
+  def seperator
+    self.Seperator
+  end
+  def non_seperator
+    self.NonSeperator
+  end
+  def offset
+    self.Offset
+  end
+end

data/lib/msf/models/fasta_file.rb

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+# ActiveRecord model of MSF FastaFile
+#
+#		Example:
+#
+#   FastaFile.find(1)
+#		FastaFile.first.file_name
+class FastaFile < ActiveRecord::Base
+  def self.table_name
+    :FastaFiles
+  end
+  def self.primary_key
+    :FastaFileID
+  end
+  def fasta_file_id
+    self.FastaFileID
+  end
+  def file_name
+    self.FileName
+  end
+  def state
+    self.State
+  end
+  def virtual_file_name
+    self.VirtualFileName
+  end
+  def file_size
+    self.FileSize
+  end
+  def file_time
+    self.FileTime
+  end
+  def number_of_proteins
+    self.NumberOfProteins
+  end
+  def number_of_amino_acids
+    self.NumberOfAminoAcids
+  end
+  def file_hash_code
+    self.FileHashCode
+  end
+  def hidden
+    self.Hidden
+  end
+  def is_srf_import
+    self.IsSrfImport
+  end
+  def is_scheduled_for_deletion
+    self.IsScheduledForDeletion
+  end
+end

data/lib/msf/models/file_info.rb

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+# ActiveRecord model of MSF FileInfo
+#
+#		Example:
+#
+#   FileInfo.find(1)
+#		FileInfo.first.file_name
+#   FileInfo.first.chromatograms.first.trace_type
+class FileInfo < ActiveRecord::Base
+  def self.table_name
+    :FileInfos
+  end
+  def self.primary_key
+    :FileID
+  end
+  def file_id
+    self.FileID
+  end
+  def file_name
+    self.FileName
+  end
+  def file_basename
+    path = self.FileName.gsub("\\","/")
+    File.basename(path,File.extname(path))
+  end
+  def file_time
+    self.FileTime
+  end
+  def file_size
+    self.FileSize
+  end
+  def physical_file_name
+    self.PhysicalFileName
+  end
+  def file_type
+    self.FileType
+  end
+  has_many :chromatograms,
+    :foreign_key => "FileID"
+  has_many :mass_peaks,
+    :foreign_key => "FileID"
+end

data/lib/msf/models/mass_peak.rb

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+# ActiveRecord model of MSF MassPeak
+#
+#   Example:
+#
+#   MassPeak.find(1)
+#   MassPeak.first.charge
+class MassPeak < ActiveRecord::Base
+  def self.table_name
+    :MassPeaks
+  end
+  def self.primary_key
+    :MassPeakID
+  end
+  def mass_peak_id
+    self.MassPeakID
+  end
+  def charge
+    self.Charge
+  end
+  def intensity
+    self.Intensity
+  end
+  def mass
+    self.Mass
+  end
+  def scan_numbers
+    self.ScanNumbers
+  end
+  def file_id
+    self.FileID
+  end
+  belongs_to :file_info,
+    :foreign_key => "FileID"
+  has_one :spectrum_header,
+    :foreign_key => "MassPeakID"
+end

data/lib/msf/models/peptide.rb

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+# ActiveRecord model of MSF Peptide
+#
+#   Example:
+#
+#   Peptide.find(1)
+#   Peptide.first.sequence
+#   Peptide.first.internal_modifications
+#   Peptide.first.terminal_modification
+class Peptide < ActiveRecord::Base
+  def self.table_name
+    :Peptides
+  end
+  def self.primary_key
+    :PeptideID
+  end
+  def processing_node_number
+    self.ProcessingNodeNumber
+  end
+  def peptide_id
+    self.PeptideID
+  end
+  def spectrum_id
+    self.SpectrumID
+  end
+  def total_ions_count
+    self.TotalIonsCount
+  end
+  def matched_ions_count
+    self.MatchedIonsCount
+  end
+  def confidence_level
+    self.ConfidenceLevel
+  end
+  def search_engine_rank
+    self.SearchEngineRank
+  end
+  def hidden
+    self.Hidden
+  end
+  def sequence
+    self.Sequence
+  end
+  def annotation
+    self.Annotation
+  end
+  def unique_peptide_sequence_id
+    self.UniquePeptideSequenceID
+  end
+  def missed_cleavages
+    self.MissedCleavages
+  end
+  def theoretical_mass
+    mass = 0
+    charge = self.spectrum.spectrum_header.charge
+    self.sequence.split(//).each do |aa|
+      mass += AminoAcid.mass_for_one_letter_code(aa)
+    end
+    self.peptides_amino_acid_modifications.each do |modification|
+      mass += modification.internal_modification.delta_mass
+    end
+    unless self.terminal_modification.nil?
+      mass += self.terminal_modification.delta_mass
+    end
+    mass += 1.007825 + 15.994910 + 1.007825
+    mass = (mass  + (charge * 1.007825)) / charge
+  end
+  def modified_sequence
+    nterm = ''
+    cterm = '-COOH'
+    if self.terminal_modification.nil?
+      nterm = "NH2-"
+    else
+      nterm = "#{self.terminal_modification.modification_name}-"
+    end
+    sequence_amino_acids = self.sequence.split(//)
+    self.peptides_amino_acid_modifications.each do |modification|
+      sequence_amino_acids[modification.position] = "#{sequence_amino_acids[modification.position]}<#{modification.internal_modification.modification_name}>"
+    end
+    nterm + sequence_amino_acids.join("") + cterm
+  end
+  def isobar_sequence
+    nterm = ''
+    unless self.terminal_modification.nil?
+      nterm = "#{self.terminal_modification.modification_name}:"
+    end
+    sequence_amino_acids = self.sequence.split(//)
+    isobar_amino_acids = []
+    sequence_amino_acids.count.times { isobar_amino_acids << ":"}
+    self.peptides_amino_acid_modifications.each do |modification|
+      isobar_amino_acids[modification.position] = "#{modification.internal_modification.modification_name}_#{sequence_amino_acids[modification.position]}:"
+    end
+    nterm + isobar_amino_acids.join("")
+  end
+  belongs_to :spectrum,
+    :foreign_key => "SpectrumID"
+  has_one :peptide_score,
+    :foreign_key => "PeptideID"
+  # HABTM join table for proteins
+  has_many :peptides_proteins,
+    :class_name => 'PeptidesProteins',
+    :foreign_key => "PeptideID"
+  has_many :proteins, :through => :peptides_proteins
+  # HABTM join table for internal_modifications
+  has_many :peptides_amino_acid_modifications,
+    :class_name => 'PeptidesAminoAcidModifications',
+    :foreign_key => "PeptideID"
+  has_many :internal_modifications, :through => :peptides_amino_acid_modifications,
+    :class_name => 'AminoAcidModification',
+    :foreign_key => 'PeptideID'
+  # join table for terminal_modifications
+  has_one :peptide_terminal_modification,
+    :class_name => 'PeptideTerminalModification',
+    :foreign_key => "PeptideID"
+  has_one :terminal_modification, :through => :peptide_terminal_modification,
+    :class_name => 'AminoAcidModification',
+    :foreign_key => 'PeptideID'
+
+end

data/lib/msf/models/peptide_score.rb

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+# ActiveRecord model of MSF PeptideScore
+#
+#		Example:
+#
+#		PeptideScore.first.score
+class PeptideScore < ActiveRecord::Base
+  def self.table_name
+    :PeptideScores
+  end
+  def self.primary_key
+    [:ProcessingNodeNumber, :PeptideID, :ScoreID]
+  end
+  def processing_node_number
+    self.ProcessingNodeNumber
+  end
+  def peptide_id
+    self.PeptideID
+  end
+  def score_id
+    self.ScoreID
+  end
+  def processing_node_id
+    self.ProcessingNodeID
+  end
+  def score_value
+    self.ScoreValue
+  end
+  belongs_to :peptide,
+    :foreign_key => "PeptideID"
+  belongs_to :processing_node,
+    :foreign_key => "ProcessingNodeNumber"
+  belongs_to :processing_node_score,
+    :foreign_key => "ScoreID"
+end

data/lib/msf/models/peptide_score_decoy.rb

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+# ActiveRecord model of MSF PeptideScoreDecoy
+#
+#		Example:
+#
+#		PeptideScoreDecoy.first.score
+class PeptideScoreDecoy < ActiveRecord::Base
+  def self.table_name
+    :PeptideScores_decoy
+  end
+  def self.primary_key
+    [:ProcessingNodeNumber, :PeptideID, :ScoreID]
+  end
+  def processing_node_number
+    self.ProcessingNodeNumber
+  end
+  def peptide_id
+    self.PeptideID
+  end
+  def score_id
+    self.ScoreID
+  end
+  def processing_node_id
+    self.ProcessingNodeID
+  end
+  def score_value
+    self.ScoreValue
+  end
+  belongs_to :peptide,
+    :foreign_key => "PeptideID"
+  belongs_to :processing_node,
+    :foreign_key => "ProcessingNodeNumber"
+  belongs_to :processing_node_score,
+    :foreign_key => "ScoreID"
+end

data/lib/msf/models/peptide_terminal_modification.rb

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+# ActiveRecord model of MSF PeptideTerminalModification
+#
+#		Example:
+#
+#		PeptideTerminalModification.first
+class PeptideTerminalModification < ActiveRecord::Base
+  def self.table_name
+    :PeptidesTerminalModifications
+  end
+  def self.primary_key
+    [:ProcessingNodeNumber, :PeptideID, :TerminalModificationID]
+  end
+  def processing_node_number
+    self.ProcessingNodeNumber
+  end
+  def peptide_id
+    self.PeptideID
+  end
+  def terminal_modification_id
+    self.TerminalModificationID
+  end
+  belongs_to :peptide,
+    :foreign_key => "PeptideID"
+  belongs_to :terminal_modification,
+    :class_name => 'AminoAcidModification',
+    :foreign_key => 'TerminalModificationID'  
+  belongs_to :processing_node,
+    :foreign_key => 'ProcessingNodeNumber'  
+end

data/lib/msf/models/peptides_amino_acid_modifications.rb

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+# ActiveRecord model of MSF PeptidesAminoAcidModifications
+# Join table for Peptides and AminoAcidModifications HABTM
+#
+#		Example:
+#
+#		PeptidesAminoAcidModifications.first.position
+class PeptidesAminoAcidModifications < ActiveRecord::Base
+  def self.table_name
+    :PeptidesAminoAcidModifications
+  end
+  def self.primary_key
+    # [:AminoAcidModificationID, :PeptideID]
+    [:ProcessingNodeNumber, :PeptideID, :AminoAcidModificationID, :Position]
+  end
+  def processing_node_number
+    self.ProcessingNodeNumber
+  end
+  def peptide_id
+    self.PeptideID
+  end
+  def amino_acid_modification_id
+    self.AminoAcidModificationID
+  end
+  def position
+    self.Position
+  end
+  belongs_to :peptide,
+    :foreign_key => 'PeptideID'
+  belongs_to :internal_modification,
+    :class_name => 'AminoAcidModification',
+    :foreign_key => 'AminoAcidModificationID'  
+end