msf 0.1.0

data/lib/msf/models/spectrum_score.rb

@@ -0,0 +1,24 @@
+# ActiveRecord model of MSF SpectrumScore
+#
+#		Example:
+#
+#		SpectrumScore.first.protein_score
+class SpectrumScore < ActiveRecord::Base
+  def self.table_name
+    :SpectrumScores
+  end
+  def self.primary_key
+    [:ProcessingNodeNumber, :SpectrumID]
+  end
+  def processing_node_number
+    self.ProcessingNodeNumber
+  end
+  def spectrum_id
+    self.SpectrumID
+  end
+  def score
+    self.Score
+  end
+  belongs_to :spectrum,
+    :foreign_key => "SpectrumID"
+end

data/lib/msf/models/taxonomy_name.rb

@@ -0,0 +1,26 @@
+# ActiveRecord model of MSF TaxonomyName
+#
+#		Example:
+#
+#   TaxonomyName.find(1)
+#   TaxonomyName.first.name
+class TaxonomyName < ActiveRecord::Base
+  def self.table_name
+    :TaxonomyNames
+  end
+  def self.primary_key
+    :TaxonomyID
+  end
+  def taxonomy_id
+    self.TaxonomyID
+  end
+  def name
+    self.Name
+  end
+  def name_category
+    self.NameCategory
+  end
+  # associations
+  belongs_to :taxonomy_names,
+    :foreign_key => "TaxonomyID"
+end

data/lib/msf/models/workflow_info.rb

@@ -0,0 +1,46 @@
+# ActiveRecord model of MSF WorkflowInfo
+#
+#		Example:
+#
+#		WorkflowInfo.first.workflow_description
+class WorkflowInfo < ActiveRecord::Base
+  def self.table_name
+    :WorkflowInfo
+  end
+  def workflow_name
+    self.WorkflowName
+  end
+  def workflow_description
+    self.WorkflowDescription
+  end
+  def workflow_state
+    self.WorkflowState
+  end
+  def workflow_start_date
+    self.WorkflowStartDate
+  end
+  def workflow_template
+    self.WorkflowTemplate
+  end
+  def user
+    self.User
+  end
+  def workflow_guid
+    self.WorkflowGUID
+  end
+  def machine_guid
+    self.MachineGUID
+  end
+  def machine_name
+    self.MachineName
+  end
+  def merge_similar_identification_results
+    self.MergeSimilarIdentificationResults
+  end
+  def is_valid
+    self.IsValid
+  end
+  def version
+    self.Version
+  end
+end

data/lib/msf/models/workflow_message.rb

@@ -0,0 +1,31 @@
+# ActiveRecord model of MSF WorkflowMessage
+#
+#		Example:
+#
+#		WorkflowMessage.first.message
+class WorkflowMessage < ActiveRecord::Base
+  def self.table_name
+    :WorkflowMessages
+  end
+  def self.primary_key
+    :MessageID
+  end
+  def message_id
+    self.MessageID
+  end
+  def processing_node_id
+    self.ProcessingNodeID
+  end
+  def processing_node_number
+    self.ProcessingNodeNumber
+  end
+  def time
+    self.Time
+  end
+  def message_kind
+    self.MessageKind
+  end
+  def message
+    self.Message
+  end
+end

data/lib/msf/msf.rb

@@ -0,0 +1,32 @@
+require 'active_record'
+
+# This class establishes an ActiveRecord connection to an MSF file (sqlite3 database) at the specified path.
+class MSF
+
+  # filesystem PATH to an MSF file
+  attr_accessor :path
+  # the resulting ActiveRecord::Base.connection
+  attr_reader :connection
+
+  # * assign any passed attributes
+  # * define connection
+  #
+  #		Example:
+	#
+	#		msf = MSF.new({
+  #   :path => './my.msf'
+	#		})
+  #   msf.connection.tables
+  #   msf.connection.disconnect!
+  #   msf.reconnect
+  def initialize(attributes={})
+    attributes.each do |name, value|
+      send("#{name}=", value)
+    end
+    @connection = ActiveRecord::Base.establish_connection(:adapter => 'sqlite3', :database => @path).connection
+  end
+  # reconnect to the MSF file (sqlite3 database)
+  def reconnect
+    @connection = ActiveRecord::Base.establish_connection(:adapter => 'sqlite3', :database => @path).connection
+  end
+end

data/lib/msf/sql/enzyme_cleavage_specificity.rb

@@ -0,0 +1,16 @@
+module ThermoMSF
+  module Model
+    class EnzymeCleavageSpecificity < Sequel::Model(:EnzymesCleavageSpecificities)
+        set_primary_key [:EnzymeID, :Specificity]
+      # ruby style accessors
+      def enzyme_id
+        self.EnzymeID
+      end
+      def specificity
+        self.Specificity
+      end
+      # associations
+      many_to_one enzyme, :key => :EnzymeID
+    end
+  end
+end

data/lib/msf/sql/false_discovery_rate.rb

@@ -0,0 +1,24 @@
+module ThermoMSF
+  module Model
+    class FalseDiscoveryRate < Sequel::Model(:FalseDiscoveryRates)
+        set_primary_key [:ProcessingNodeNumber, :ConfidenceLevel]
+      # ruby style accessors
+      def processing_node_number
+        self.ProcessingNodeNumber
+      end
+      def confidence_level
+        self.ConfidenceLevel
+      end
+      def true_count
+        self.TrueCount
+      end
+      def false_count
+        self.FalseCount
+      end
+      def target
+        self.Target
+      end
+      # associations
+    end
+  end
+end

data/lib/msf/sql/fasta_file_protein_annotation.rb

@@ -0,0 +1,17 @@
+module ThermoMSF
+  module Model
+    class FastaFileProteinAnnotation < Sequel::Model(:FastaFilesProteinAnnotations)
+        set_primary_key [:FastaFileID, :ProteinAnnotationID]
+      # ruby style accessors
+      def fasta_file_id
+        self.FastaFileID
+      end
+      def protein_annotation_id
+        self.ProteinAnnotationID
+      end
+      # associations
+      many_to_one fasta_file, :key => :FastaFileID
+      many_to_one protein_annotation, :key => :ProteinAnnotationID
+    end
+  end
+end

data/lib/msf/sql/mass_peak_relation.rb

@@ -0,0 +1,17 @@
+module ThermoMSF
+  module Model
+    class MassPeakRelation < Sequel::Model(:MassPeakRelations)
+        set_primary_key [:MassPeakID, :RelatedMassPeakID]
+      # ruby style accessors
+      def mass_peak_id
+        self.MassPeakID
+      end
+      def related_mass_peak_id
+        self.RelatedMassPeakID
+      end
+      # associations
+      many_to_one mass_peak, :key => :MassPeakID
+      many_to_one related_mass_peak, :key => :RelatedMassPeakID
+    end
+  end
+end

data/lib/msf/sql/peptide_amino_acid_modification_decoy.rb

@@ -0,0 +1,23 @@
+module ThermoMSF
+  module Model
+    class PeptideAminoAcidModificationDecoy < Sequel::Model(:PeptidesAminoAcidModifications_decoy)
+        set_primary_key :
+      # ruby style accessors
+      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
+      # associations
+      many_to_one peptide, :key => :PeptideID
+      many_to_one amino_acid_modification, :key => :AminoAcidModificationID
+    end
+  end
+end

data/lib/msf/sql/peptide_decoy.rb

@@ -0,0 +1,32 @@
+module ThermoMSF
+  module Model
+    class PeptideDecoy < Sequel::Model(:Peptides_decoy)
+        set_primary_key :
+      # ruby style accessors
+      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 sequence
+        self.Sequence
+      end
+      # associations
+      many_to_one peptide, :key => :PeptideID
+      many_to_one spectrum, :key => :SpectrumID
+    end
+  end
+end

data/lib/msf/sql/peptide_terminal_modification_decoy.rb

@@ -0,0 +1,20 @@
+module ThermoMSF
+  module Model
+    class PeptideTerminalModificationDecoy < Sequel::Model(:PeptidesTerminalModifications_decoy)
+        set_primary_key :
+      # ruby style accessors
+      def processing_node_number
+        self.ProcessingNodeNumber
+      end
+      def peptide_id
+        self.PeptideID
+      end
+      def terminal_modification_id
+        self.TerminalModificationID
+      end
+      # associations
+      many_to_one peptide, :key => :PeptideID
+      many_to_one terminal_modification, :key => :TerminalModificationID
+    end
+  end
+end

data/lib/msf/sql/precursor_ion_quan_result.rb

@@ -0,0 +1,29 @@
+module ThermoMSF
+  module Model
+    class PrecursorIonQuanResult < Sequel::Model(:PrecursorIonQuanResults)
+        set_primary_key :
+      # ruby style accessors
+      def quan_channel_id
+        self.QuanChannelID
+      end
+      def quan_result_id
+        self.QuanResultID
+      end
+      def mass
+        self.Mass
+      end
+      def charge
+        self.Charge
+      end
+      def area
+        self.Area
+      end
+      def retention_time
+        self.RetentionTime
+      end
+      # associations
+      many_to_one quan_channel, :key => :QuanChannelID
+      many_to_one quan_result, :key => :QuanResultID
+    end
+  end
+end

data/lib/msf/sql/precursor_ion_quan_result_event_spectrum.rb

@@ -0,0 +1,17 @@
+module ThermoMSF
+  module Model
+    class PrecursorIonQuanResultEventSpectrum < Sequel::Model(:PrecursorIonQuanResultsEventSpectra)
+        set_primary_key :
+      # ruby style accessors
+      def quan_result_id
+        self.QuanResultID
+      end
+      def quan_spectrum_id
+        self.QuanSpectrumID
+      end
+      # associations
+      many_to_one quan_result, :key => :QuanResultID
+      many_to_one quan_spectrum, :key => :QuanSpectrumID
+    end
+  end
+end

data/lib/msf/sql/precursor_ion_quan_result_search_spectrum.rb

@@ -0,0 +1,20 @@
+module ThermoMSF
+  module Model
+    class PrecursorIonQuanResultSearchSpectrum < Sequel::Model(:PrecursorIonQuanResultsSearchSpectra)
+        set_primary_key :
+      # ruby style accessors
+      def processing_node_number
+        self.ProcessingNodeNumber
+      end
+      def quan_result_id
+        self.QuanResultID
+      end
+      def search_spectrum_id
+        self.SearchSpectrumID
+      end
+      # associations
+      many_to_one quan_result, :key => :QuanResultID
+      many_to_one search_spectrum, :key => :SearchSpectrumID
+    end
+  end
+end

data/lib/msf/sql/processing_node_filter_parameter.rb

@@ -0,0 +1,29 @@
+module ThermoMSF
+  module Model
+    class ProcessingNodeFilterParameter < Sequel::Model(:ProcessingNodeFilterParameters)
+        set_primary_key [:ProcessingNodeNumber, :FilterParameterName]
+      # ruby style accessors
+      def processing_node_number
+        self.ProcessingNodeNumber
+      end
+      def filter_parameter_name
+        self.FilterParameterName
+      end
+      def filter_module_type_id
+        self.FilterModuleTypeID
+      end
+      def filter_module_number
+        self.FilterModuleNumber
+      end
+      def processing_node_id
+        self.ProcessingNodeID
+      end
+      def filter_parameter_value
+        self.FilterParameterValue
+      end
+      # associations
+      many_to_one filter_module_type, :key => :FilterModuleTypeID
+      many_to_one processing_node, :key => :ProcessingNodeID
+    end
+  end
+end

data/lib/msf/sql/processing_node_interface.rb

@@ -0,0 +1,19 @@
+module ThermoMSF
+  module Model
+    class ProcessingNodeInterface < Sequel::Model(:ProcessingNodeInterfaces)
+        set_primary_key :
+      # ruby style accessors
+      def processing_node_id
+        self.ProcessingNodeID
+      end
+      def interface_kind
+        self.InterfaceKind
+      end
+      def interface_name
+        self.InterfaceName
+      end
+      # associations
+      many_to_one processing_node, :key => :ProcessingNodeID
+    end
+  end
+end