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Classes | Modules | Enumerations

Mascot configuration files module

Classes

class  ms_clusterparams
 An instance of this class represents all the parameters specified in the Cluster section of mascot.dat. More...
class  ms_computeraddress
 The class serves as a container for computer address parameters for cluster mode. More...
class  ms_cronjob
 Represents a single entry from the cron section of mascot.dat. More...
class  ms_cronoptions
 Contains parameters from the cron section of mascot.dat. More...
class  ms_databaseoptions
 An instance of this class represents a single database definition from the Databases section of mascot.dat. More...
class  ms_databases
 An instance of this class represents the Databases section of mascot.dat. More...
class  ms_datfile
 Encapsulates the mascot.dat file that contains the most important parameters. More...
class  ms_dbprocessors
 Represent a single dabatase entry in the Processors section. More...
class  ms_enzyme
 Represent a single entry in the enzymes file. More...
class  ms_enzymefile
 Reads and parses the enzymes file that contains multiple enzyme definitions. More...
class  ms_fragmentationrules
 This class encapsulates a single entry (an instrument) from a fragmentation_rules file. More...
class  ms_fragrulesfile
 This class encapsulates a complete fragmentation_rules file. More...
class  ms_libraryoptions
 Represents the LibraryOptions section of mascot.dat. More...
class  ms_license
 The class provides access license details in read-only mode. More...
class  ms_mascotfiles
 An instance of this class contains configuration files paths (except for mascot.dat). More...
class  ms_mascotoptions
 An instance of this class represents all the parameters specified in the Options section of mascot.dat. More...
class  ms_masses
 Reads and parses the masses file with residue and atom masses. More...
class  ms_modfile
 Use this class in order to read in the amino acid modification file. More...
class  ms_modification
 The class represents a single modification-entry in mod_file. More...
class  ms_modvector
 General usage class for creating lists of modifications to be passed as parameters. More...
class  ms_obofile
 The class provides simplified access to ontology files in the .obo format. More...
class  ms_parseoptions
 Represents the PARSE section of mascot.dat. More...
class  ms_parserule
 Represents a single regular expression parsing rule. More...
class  ms_parserule_plus
 Represents regular expression parse rule plus some additional parameters. More...
class  ms_processoroptions
 An instance of this class represents all the parameters specified in the Processors section of mascot.dat. More...
class  ms_processors
 This class is designed to retrieve current CPU configuration on the computer. More...
class  ms_quant_average
 An object of this class represent a single "average" element in quantitation.xml. More...
class  ms_quant_component
 An object of this class represent a single component element in quantitation.xml. More...
class  ms_quant_composition
 Describes the compositionType type in quantitation.xml. More...
class  ms_quant_configfile
 Use this class in order to read/write quantitation.xml. More...
class  ms_quant_correction
 Represents a correction element. More...
class  ms_quant_element
 The element sub-element of compositionType in quantitation.xml. More...
class  ms_quant_integration
 An object of this class represent a single integration element in quantitation.xml. More...
class  ms_quant_isotope
 Represents an isotope element. More...
class  ms_quant_localdef
 Represents a local_definition element. More...
class  ms_quant_method
 An object of this class represent a single quantitation method from quantitation.xml. More...
class  ms_quant_modgroup
 An object of this class represent a single modification group element in quantitation.xml. More...
class  ms_quant_moverz
 Parameter name and value pair. More...
class  ms_quant_multiplex
 An object of this class represent a multiplex element in quantitation.xml. More...
class  ms_quant_neutralloss
 A neutral loss for the sequence ions, e.g. loss of phosphate. More...
class  ms_quant_normalisation
 An object of this class represent a single normalisation element in quantitation.xml. More...
class  ms_quant_normalisation_peptide
 An object of this class represent a single peptide element in quantitation.xml. More...
class  ms_quant_normalisation_peptides
 An object of this class represent a collection of peptide elements in quantitation.xml. More...
class  ms_quant_normalisation_protein
 An object of this class represent a single protein element in quantitation.xml. More...
class  ms_quant_normalisation_proteins
 An object of this class represent a collection of peptide elements in quantitation.xml. More...
class  ms_quant_numerator
 Represent numerator_component and denominator_component elements. More...
class  ms_quant_outliers
 An object of this class represent a single OUTLIERS element in quantitation.xml. More...
class  ms_quant_parameter
 Parameter name and value pair. More...
class  ms_quant_parameters
 A class that represents base parametersType in quantitation.xml. More...
class  ms_quant_pepneutralloss
 A neutral loss from the precursor. More...
class  ms_quant_precursor
 An object of this class represent a single precursor element in quantitation.xml. More...
class  ms_quant_protocol
 An object of this class represent a protocol element in quantitation.xml. More...
class  ms_quant_quality
 An object of this class represent a single quality element in quantitation.xml. More...
class  ms_quant_ratio
 Represents the ratioType type for the report_ratio element in quantitation.xml. More...
class  ms_quant_replicate
 An object of this class represent a single replicate element in quantitation.xml. More...
class  ms_quant_reporter
 An object of this class represents a single reporter element in quantitation.xml. More...
class  ms_quant_satellite
 An object of this class represent a single satellite element in quantitation.xml. More...
class  ms_quant_specificity
 Describes a specificity element in quantitation.xml (Unimod style specificity). More...
class  ms_quant_unmodified
 Describes an unmodified element in quantitation.xml. More...
class  ms_taxnodesfiles
 Filenames and formats for taxonomy nodes or genetic codes files. More...
class  ms_taxonomychoice
 The class represents a single taxonomy choice entry in the taxonomy file. More...
class  ms_taxonomyfile
 Use this class in order to read in a taxonomy file. More...
class  ms_taxonomyrules
 This class represents a single Taxonomy_XXX section in mascot.dat. More...
class  ms_taxonomytree
 The complete taxonomy tree as built from one or more files such as nodes.dmp. More...
class  ms_taxspeciesfiles
 An instance of this class describes one entry of taxonomy species files. More...
class  ms_umod_aminoacid
 Represents an "amino acid" object in unimod.xml. More...
class  ms_umod_composition
 Represents the composition type in unimod.xml. More...
class  ms_umod_configfile
 This class represents the file unimod.xml. More...
class  ms_umod_element
 Represents an element object in unimod.xml. More...
class  ms_umod_elemref
 Represents the elemref_t type in unimod.xml. More...
class  ms_umod_modbrick
 Represents a modification brick object in unimod.xml. More...
class  ms_umod_modification
 Represents a modif object in unimod.xml. More...
class  ms_umod_neutralloss
 Represents NeutralLoss and PepNeutralLoss objects in unimod.xml. More...
class  ms_umod_specificity
 Represents modification specificity objects in unimod.xml. More...
class  ms_umod_xref
 Represents the cross references objects in unimod.xml. More...
class  ms_unigeneoptions
 An instance of this class represents all the parameters specified in UniGene section of mascot.dat. More...
class  ms_wwwentry
 Represent a single entry in the WWW section of mascot.dat. More...
class  ms_wwwoptions
 Represents the whole WWW section. More...

Modules

 Configuration files
 Examples for the configuration files module
 Fixed values for quantitation.xml

Enumerations

enum  { MAX_VAR_MODS = 'W' -'A' + 10 }
 

Maximum number of variable mods.

More...
enum  DATABASE_TYPE {
  AA = 0,
  NA = 1,
  SL = 2,
  SLREF = 3
}
enum  MASS_TYPE {
  MASS_TYPE_MONO = 0x0000,
  MASS_TYPE_AVE = 0x0001
}
 

All possible mass types.

More...
enum  MOD_TYPES {
  MOD_TYPE_RESIDUE = 0,
  MOD_TYPE_N_TERM = 1,
  MOD_TYPE_C_TERM = 2,
  MOD_TYPE_N_PROTEIN = 3,
  MOD_TYPE_C_PROTEIN = 4,
  MOD_TYPE_N_TERM_RESIDUE = 5,
  MOD_TYPE_C_TERM_RESIDUE = 6,
  MOD_TYPE_N_PROTEIN_RESIDUE = 7,
  MOD_TYPE_C_PROTEIN_RESIDUE = 8
}
enum  OPERATING_SYS {
  _OS_AIX = 0,
  _OS_UNKNOWN = 1,
  _OS_WINDOWS_NT = 2,
  _OS_IRIX = 3,
  _OS_ALPHA_TRUE64 = 4,
  _OS_SOLARIS = 5,
  _OS_LINUX = 6,
  _OS_LINUXALPHA = 7,
  _OS_FREE_BSD_ = 8,
  _OS_NUM_OPERATING_SYS = 9
}
enum  TAX_NODE_FORMAT {
  TAX_NODE_NCBI,
  TAX_NODE_GENCODE
}
enum  TAX_SPECIES_FORMAT {
  TAX_SPECIES_NCBI,
  TAX_SPECIES_SWISSPROT,
  TAX_SPECIES_PDB,
  TAX_SPECIES_GI2TAXID,
  TAX_SPECIES_ACC2TAXID,
  TAX_SPECIES_EXPLICIT
}
enum  WWW_TYPE {
  WWW_SEQ = 0,
  WWW_REP = 1
}

Detailed Description

The Mascot configuration files module is used to simplify retrieving and saving information to the configuration files.


Enumeration Type Documentation

anonymous enum

Maximum number of variable mods.

See Using enumerated values in Perl, Java, Python and C#.

Enumerator:
MAX_VAR_MODS 

The results file uses 1..9 and A..W (1..32).

enum DATABASE_TYPE

Definition of all supported database types.

See Using enumerated values in Perl, Java, Python and C#.

Enumerator:
AA 

Protein sequence database (FASTA file, amino acid)

NA 

NA sequence database (FASTA file, nucleic acid)

SL 

Spectral Library (MSP file)

SLREF 

FASTA reference database of a Spectral Library.

enum MASS_TYPE

All possible mass types.

See Using enumerated values in Perl, Java, Python and C#.

Enumerator:
MASS_TYPE_MONO 

monoisotopic mass index

MASS_TYPE_AVE 

average mass index

Examples:
config_masses.cs, and tools_aahelper.cs.
enum MOD_TYPES

Definitions for possible modification types.

See Using enumerated values in Perl, Java, Python and C#.

Enumerator:
MOD_TYPE_RESIDUE 

Applies to specific residues, independent of position within the peptide.

MOD_TYPE_N_TERM 

Applies to the peptide N-terminus, independent of residue identity.

MOD_TYPE_C_TERM 

Applies to the peptide C-terminus, independent of residue identity.

MOD_TYPE_N_PROTEIN 

Applies to the protein N-terminus, independent of residue identity.

MOD_TYPE_C_PROTEIN 

Applies to the protein C-terminus, independent of residue identity.

MOD_TYPE_N_TERM_RESIDUE 

Applies to a specific residue only when that residue is at N-terminus.

MOD_TYPE_C_TERM_RESIDUE 

Applies to a specific residue only when that residue is at C-terminus.

MOD_TYPE_N_PROTEIN_RESIDUE 

Applies to a specific residue only when that residue is at N-terminus of a protein.

MOD_TYPE_C_PROTEIN_RESIDUE 

Applies to a specific residue only when that residue is at C-terminus of a protein.

enum OPERATING_SYS

List of all supported operating systems (past and present)

Mascot runs on a number of different operating systems. The following are currently supported.

See Using enumerated values in Perl, Java, Python and C#.

Enumerator:
_OS_AIX 

IBM AIX.

_OS_UNKNOWN 

Unknown OS.

_OS_WINDOWS_NT 

WindowsXXX.

_OS_IRIX 

Irix.

_OS_ALPHA_TRUE64 

Alpha Tru64.

_OS_SOLARIS 

Solaris.

_OS_LINUX 

Linux.

_OS_LINUXALPHA 

Alpha Linux.

_OS_FREE_BSD_ 

FreeBSD.

_OS_NUM_OPERATING_SYS 

Placeholder.

enum TAX_NODE_FORMAT

Possible formats for the nodes.dmp and gencode.dmp files.

See Using enumerated values in Perl, Java, Python and C#.

Enumerator:
TAX_NODE_NCBI 

NCBI nodes.dmp format.

TAX_NODE_GENCODE 

NCBI gencode.dmp format.

enum TAX_SPECIES_FORMAT

All possible taxonomy species file formats.

See Using enumerated values in Perl, Java, Python and C#.

Enumerator:
TAX_SPECIES_NCBI 

NCBI names.dmp taxonomy species files.

TAX_SPECIES_SWISSPROT 

SwissProt.

TAX_SPECIES_PDB 

PDB.

TAX_SPECIES_GI2TAXID 

GI2TAXID.

TAX_SPECIES_ACC2TAXID 

Simple 'accession taxID' (any whitespace).

TAX_SPECIES_EXPLICIT 

No lookup required, because the ID is given in the description line. For example: >IPI:IPI00000001.2 Tax_Id=9606 Double-stranded RNA ...

enum WWW_TYPE

All supported types of entries in the WWW section.

See Using enumerated values in Perl, Java, Python and C#.

Enumerator:
WWW_SEQ 

Sequence string source.

WWW_REP 

Full text report source.

Examples:
config_mascotdat.cs.
Copyright © 2016 Matrix Science Ltd.  All Rights Reserved. Generated on Fri Jun 2 2017 01:44:51