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Matrix Science Mascot Parser toolkit
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Matrix Science Mascot Parser toolkit
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Modules | |
| Configuration files | |
| Examples for the configuration files module | |
| Fixed values for quantitation.xml | |
| Fixed values for crosslinking.xml | |
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_crosslinking_accession |
Accession element in crosslinking.xml More... | |
| class | ms_crosslinking_accessions |
Accessions element in crosslinking.xml More... | |
| class | ms_crosslinking_configfile |
This class represents the file crosslinking.xml. More... | |
| class | ms_crosslinking_does_not_pair_with |
mxm:does_not_pair_with element in crosslinking.xml More... | |
| class | ms_crosslinking_filters |
Filters element in crosslinking.xml More... | |
| class | ms_crosslinking_linker |
Linker element in crosslinking.xml More... | |
| class | ms_crosslinking_linkers |
Linkers element in crosslinking.xml More... | |
| class | ms_crosslinking_method |
Represents a method object in crosslinking.xml More... | |
| class | ms_crosslinking_monolink |
Monolink element in crosslinking.xml More... | |
| class | ms_crosslinking_parameter |
| Parameter name and value pair. More... | |
| class | ms_crosslinking_parameters |
A class that represents base parametersType in crosslinking_1.xsd. More... | |
| class | ms_crosslinking_scope |
Scope element in crosslinking.xml More... | |
| class | ms_crosslinking_settings |
Settings element in crosslinking.xml 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 and set affinity. 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_file_index |
Represents a file_index element. 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... | |
| class | ms_xml_parameter |
| Parameter name and value pair. More... | |
| class | ms_xml_parameters |
A class that represents a base parametersType. More... | |
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 , MOD_TYPE_______LAST = 9 } |
| enum | OPERATING_SYS { _OS_UNKNOWN = 0 , _OS_WINDOWS_NT = 1 , _OS_LINUX = 2 , _OS_NUM_OPERATING_SYS = 3 } |
| 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 , TAX_SPECIES_FORMAT_COUNT } |
| enum | WWW_TYPE { WWW_SEQ = 0 , WWW_REP = 1 } |
The Mascot configuration files module is used to simplify retrieving and saving information to the configuration files.
| anonymous enum |
Maximum number of variable mods.
See Using enumerated values and static const ints 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 and static const ints 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 and static const ints in Perl, Java, Python and C#.
| Enumerator | |
|---|---|
| MASS_TYPE_MONO | monoisotopic mass index |
| MASS_TYPE_AVE | average mass index |
| enum MOD_TYPES |
Definitions for possible modification types.
See Using enumerated values and static const ints in Perl, Java, Python and C#.
| 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 and static const ints in Perl, Java, Python and C#.
| Enumerator | |
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| _OS_UNKNOWN | Unknown OS. |
| _OS_WINDOWS_NT | WindowsXXX. |
| _OS_LINUX | Linux. |
| _OS_NUM_OPERATING_SYS | Placeholder. |
| enum TAX_NODE_FORMAT |
Possible formats for the nodes.dmp and gencode.dmp files.
See Using enumerated values and static const ints 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 and static const ints in Perl, Java, Python and C#.
| enum WWW_TYPE |
All supported types of entries in the WWW section.
See Using enumerated values and static const ints in Perl, Java, Python and C#.
| Enumerator | |
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| WWW_SEQ | Sequence string source. |
| WWW_REP | Full text report source. |
1.9.6