Top Level Namespace

Includes:

LibXML, Rake::DSL

Defined Under Namespace

Modules: ProteinToGenomeMapper Classes: CommandRunner, Constants, ConvertUtil, Decoymaker, FastaDB, FastaDatabase, GFFDB, GalaxyStager, GalaxyUtil, ManageDBTool, MascotUtil, MzMLParser, OMSSAUtil, OpenMSDefaults, PepXML, Peptide, PeptideNotInProteinError, PlasmoDB, ProphetTool, ProtXMLToGFFTool, Protein, Randomize, SearchTool, SetupTool, String, SwissprotDatabase, TandemSearchTool, Tool, UniprotMapper

Instance Method Summary

• #rubygems ⇒ Object

  We start the columns off with the header name newColumns={‘recname’=>[“Primary Name”],‘cd’=>[“CD Antigen Name”],‘altnames’=>[“Alternate Names”], ‘accessions’ =>[“Swissprot Accessions”], ‘location’ => [“Subcellular Location”], ‘function’ => [“Known Function”], ‘ipi’ => [“IPI”], ‘intact’ => [“Interactions”], ‘pride’ => [‘Pride’], ‘ensembl’=> [‘Ensembl’], ‘refsMASS SPEC’=>[“MS Refs”], ‘refsGLYCOSYLATION’=>[“Glyco Refs”], ‘refsNUCLEOTIDE SEQUENCE’=>[“Nucleotide Refs”], ‘refsX-RAY CRYSTALLOGRAPHY’=>[“Crystallography Refs”], ‘refs3D-STRUCTURE MODELLING’=>[“3D-Modelling Refs”], ‘refsPROTEIN SEQUENCE’=>[“Protein sequence Refs”], ‘glycosites’=>[“Glycosylation Sites”] }.

Instance Method Details

#rubygems ⇒ Object

We start the columns off with the header name newColumns=Name”],‘cd’=>[“CD Antigen Name”],‘altnames’=>[“Alternate Names”],

'accessions' =>["Swissprot Accessions"],
'location' => ["Subcellular Location"],
'function' => ["Known Function"],
'ipi' => ["IPI"],
'intact' => ["Interactions"],
'pride' => ['Pride'],
'ensembl'=> ['Ensembl'],
'refsMASS SPEC'=>["MS Refs"], 
'refsGLYCOSYLATION'=>["Glyco Refs"], 
'refsNUCLEOTIDE SEQUENCE'=>["Nucleotide Refs"], 
'refsX-RAY CRYSTALLOGRAPHY'=>["Crystallography Refs"],
'refs3D-STRUCTURE MODELLING'=>["3D-Modelling Refs"],
'refsPROTEIN SEQUENCE'=>["Protein sequence Refs"],
'glycosites'=>["Glycosylation Sites"]

# File 'lib/protk/bio_sptr_extensions.rb', line 24

require 'rubygems'