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Public Member Functions

ms_taxonomyrules Class Reference
[Mascot configuration files module]

This class represents a single Taxonomy_XXX section in mascot.dat. More...

#include <ms_taxonomyrules.hpp>

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List of all members.

Public Member Functions

 ms_taxonomyrules ()
 Default constructor.
 ms_taxonomyrules (const ms_taxonomyrules &src)
 Copying constructor.
 ~ms_taxonomyrules ()
 Destructor.
void appendGencodeFile (const ms_taxnodesfiles *item)
 Adds an entry into the GencodeFiles list.
void appendNoBreakDescLineIf (const char *str)
 Adds an entry into the NoBreakDescLineIf list.
void appendNodesFile (const ms_taxnodesfiles *item)
 Adds an entry into the NodesFiles list.
void appendPerDbSrcRule (const ms_parserule_plus *item)
 Adds a new database source string into the list.
void appendPrefixRemove (const char *item)
 Adds an entry into the PrefixRemoves list.
void appendSpeciesFile (const ms_taxspeciesfiles *item)
 Adds an entry into the SpeciesFiles list.
void appendStrFile (const ms_taxspeciesfiles *item)
void appendSuffixRemove (const char *item)
 Adds an entry into the SuffixRemoves list.
void clearDBLevelTaxId ()
 Deletes DBLevelTaxId; it will not be saved in the file.
void clearGencodeFiles ()
 Deletes all GencodeFiles entries.
void clearNoBreakDescLineIf ()
 Deletes all NoBreakDescLineIf entries.
void clearNodesFiles ()
 Deletes all NodesFiles entries.
void clearPerDbSrcRules ()
 Deletes all database source strings.
void clearPrefixRemoves ()
 Deletes all PrefixRemoves entries.
void clearSpeciesFiles ()
 Deletes all entries for SpeciesFiles.
void clearSuffixRemoves ()
 Deletes all SuffixRemoves entries.
void copyFrom (const ms_taxonomyrules *right)
 Can be used to create a copy of another object.
void defaultValues ()
 Initialises the instance with default values.
const ms_parserulegetAccFromSpeciesLine () const
 Returns the value of AccFromSpeciesLine.
int getDBLevelTaxId () const
 Returns the value of DBLevelTaxId.
const ms_parserule_plusgetDefaultRule () const
 Returns the value of DefaultRule.
char getDescriptionLineSep () const
 Returns the value of DescriptionLineSep.
const ms_parserulegetDoThisRuleFirst () const
 Returns the value of DoThisRuleFirst.
int getErrorLevel () const
 Returns the value of ErrorLevel.
const ms_taxnodesfilesgetGencodeFile (const int index) const
 Returns an instance of ms_taxnodesfiles describing an entry in GencodeFiles.
std::string getIdentifier () const
 Returns the value of Identifier.
std::string getNoBreakDescLineIf (const int index) const
 Returns a NoBreakDescLineIf entry by its number.
const ms_taxnodesfilesgetNodesFile (const int index) const
 Returns an instance of ms_taxnodesfiles describing an entry in NodesFiles.
int getNumberOfGencodeFiles () const
 Returns the number of file names specified in GencodeFiles.
int getNumberOfNoBreakDescLineIf () const
 Returns the number of NoBreakDescLineIf entries.
int getNumberOfNodesFiles () const
 Returns the number of file names specified in NodesFiles.
int getNumberOfPerDbSrcRules () const
 Returns the number of database source strings.
int getNumberOfPrefixRemoves () const
 Returns the number of PrefixRemoves entries.
int getNumberOfSpeciesFiles () const
 Returns the number of file names specified in SpeciesFiles.
int getNumberOfStrFiles () const
int getNumberOfSuffixRemoves () const
 Returns the number of SuffixRemoves entries.
const ms_parserule_plusgetPerDbSrcRule (const int index) const
 Returns a database source string by its number.
std::string getPreceedingComments () const
 Returns any comments preceeding the section.
std::string getPrefixRemove (const int index) const
 Returns the PrefixRemoves string by number.
std::string getQuickRefSearch () const
 Returns the value of QuickRefSearch.
const ms_taxspeciesfilesgetSpeciesFile (const int index) const
 Returns an instance of ms_taxspeciesfiles describing an entry in SpeciesFiles.
std::string getSpeciesFormatRegex (const TAX_SPECIES_FORMAT format) const
 Returns a regular expression, if any for the species format.
const ms_parserulegetSrcDatabaseRule () const
 Returns the value of SrcDatabaseRule.
const ms_taxspeciesfilesgetStrFile (const int index) const
const ms_parserule_plusgetStrRule () const
std::string getSuffixRemove (const int index) const
 Returns a SuffixRemoves string by number.
bool isConcatRefFileLines () const
 Returns TRUE if ConcatRefFileLines parameter is set to 1 and FALSE otherwise.
bool isDBLevelTaxId () const
 Returns TRUE if there is a database level taxonomy ID in the file.
bool isEnabled () const
 Returns TRUE if Enabled parameter is set to 1 and FALSE otherwise.
bool isFromRefFile () const
 Returns TRUE if FromRefFile parameter is set to 1 and FALSE otherwise.
bool isMitochondrialTranslation () const
 Returns TRUE if MitochondrialTranslation parameter is set to 1 and FALSE otherwise.
bool isSectionAvailable () const
 Checks whether the section has been actually read from the file.
ms_taxonomyrulesoperator= (const ms_taxonomyrules &right)
 Assignment operator for C++ client applications.
void setAccFromSpeciesLine (const ms_parserule *src)
 Change the value of AccFromSpeciesLine.
void setConcatRefFileLines (const bool flag)
 Change the value of ConcatRefFileLines.
void setDBLevelTaxId (const int value)
 Change the value of DBLevelTaxId.
void setDefaultRule (const ms_parserule_plus *src)
 Change the value of DefaultRule.
void setDescriptionLineSep (const char value)
 Change the value of DescriptionLineSep.
void setDoThisRuleFirst (const ms_parserule *src)
 Change the value of DoThisRuleFirst.
void setEnabled (const bool flag)
 Change the value of Enabled.
void setErrorLevel (const int value)
 Change the value of ErrorLevel.
void setFromRefFile (const bool flag)
 Change the value of FromRefFile.
void setIdentifier (const char *str)
 Change the value of Identifier.
void setMitochondrialTranslation (const bool flag)
 Set the value of MitochondrialTranslation.
void setPreceedingComments (const std::string &comments)
 Sets any comments preceeding the section.
void setQuickRefSearch (const char *str)
 Change the value of QuickRefSearch.
void setSectionAvailable (const bool value)
 Changes availability of the section, i.e. whether it should be saved in a file.
void setSpeciesFormatRegex (const TAX_SPECIES_FORMAT format, const std::string regex)
 Set the regular expression, if any, for the species format.
void setSrcDatabaseRule (const ms_parserule *src)
 Change the value of SrcDatabaseRule.
void setStrRule (const ms_parserule_plus *src)

Detailed Description

This class represents a single Taxonomy_XXX section in mascot.dat.

The Taxonomy section defines a set of taxonomy rules that can be selected for a database. Usage of taxonomy rules can be turned off by setting Enabled property to 0. See isEnabled() for more information.

Instances of this class are created in ms_datfile.

Also get yourselves acquainted with the base class ms_customproperty. It facilitates the following tasks:

More functionality is described in the documentation for ms_customproperty.


Member Function Documentation

void appendGencodeFile ( const ms_taxnodesfiles item )

Adds an entry into the GencodeFiles list.

See getGencodeFile() for more information.

Parameters:
iteman item to add a copy of into the list.
void appendNoBreakDescLineIf ( const char *  str )

Adds an entry into the NoBreakDescLineIf list.

See getNoBreakDescLineIf() for more information.

Parameters:
stran item to add a copy of into the list.
void appendNodesFile ( const ms_taxnodesfiles item )

Adds an entry into the NodesFiles list.

See getNodesFile() for more information.

Parameters:
iteman item to add a copy of into the list.
void appendPerDbSrcRule ( const ms_parserule_plus item )

Adds a new database source string into the list.

See getPerDbSrcRule() for more information.

Parameters:
iteman item to add a copy of into the list
void appendPrefixRemove ( const char *  item )

Adds an entry into the PrefixRemoves list.

See getPrefixRemove() for more information.

Parameters:
iteman item to add a copy of into the list.
void appendSpeciesFile ( const ms_taxspeciesfiles item )

Adds an entry into the SpeciesFiles list.

See getSpeciesFile() for more information.

Parameters:
iteman item to add a copy of into the list.
void appendStrFile ( const ms_taxspeciesfiles item )
Parameters:
itempointer to a taxonomy species file
void appendSuffixRemove ( const char *  item )

Adds an entry into the SuffixRemoves list.

See getSuffixRemove() for more information.

Parameters:
iteman item to add a copy of into the list.
void clearGencodeFiles (  )

Deletes all GencodeFiles entries.

See getGencodeFile() for more information.

void clearNoBreakDescLineIf (  )

Deletes all NoBreakDescLineIf entries.

See getNoBreakDescLineIf() for more information.

void clearNodesFiles (  )

Deletes all NodesFiles entries.

See getNodesFile() for more information.

void clearPerDbSrcRules (  )

Deletes all database source strings.

See getPerDbSrcRule() for more information.

void clearPrefixRemoves (  )

Deletes all PrefixRemoves entries.

See getPrefixRemove() for more information.

void clearSpeciesFiles (  )

Deletes all entries for SpeciesFiles.

See getSpeciesFile() for more information.

void clearSuffixRemoves (  )

Deletes all SuffixRemoves entries.

See getSuffixRemove() for more information.

const ms_parserule * getAccFromSpeciesLine (  ) const

Returns the value of AccFromSpeciesLine.

MSDB database explicitly associates each species line with the accession string of the primary database entry. A further rule, AccFromSpeciesLine, is used to extract this accession string.

Returns:
pointer to a parser rule
int getDBLevelTaxId (  ) const

Returns the value of DBLevelTaxId.

Database level taxonomy ID can be specified in order to find proper NA translation table without names.dmp and nodes.dmp files usage.

Default is -1, which is not a valid taxonomy ID.

Returns:
database level taxonomy id
const ms_parserule_plus * getDefaultRule (  ) const

Returns the value of DefaultRule.

The DefaultRule describes how to find the species name in the line of text in the reference file. The string in quotes is a regular expression. All words in the PrefixRemoves and SuffixRemoves keywords should be removed before trying to do a match. For more detailed information on how to specify this parameter consult Mascot manual.

If specified, DoThisRuleFirst is applied first, and the default rule would only be used if this failed.

See also:
getQuickRefSearch(), getDoThisRuleFirst(), getAccFromSpeciesLine()
Returns:
pointer to a parser rule
char getDescriptionLineSep (  ) const

Returns the value of DescriptionLineSep.

The line that contains the species IDs has multiple IDs, separated by a character, whose ASCII code is specified by DescriptionLineSep.

There is no default value for this parameter.

Returns:
description line separator for this taxonomy
const ms_parserule * getDoThisRuleFirst (  ) const

Returns the value of DoThisRuleFirst.

See getDefaultRule().

Returns:
a pointer to the parser rule for which to do this rule first
int getErrorLevel (  ) const

Returns the value of ErrorLevel.

ErrorLevel indicates the type of warnings or errors that are found when creating the taxonomy information. Possible values and their meanings:

  • 0 - an entry is put into the NoTaxonomyMatch.txt file for every sequence where no taxonomy information is found.
  • 1+ (severe) - an entry is put into the NoTaxonomyMatch.txt file for every sequence that had any accession string without a match. Since some sequences in NCBI will have up to 200 gi numbers (sources), there is a reasonable chance that some of these entries will not have species information, and this would cause the errors files to become very large.

Default is 1.

Returns:
error level
const ms_taxnodesfiles * getGencodeFile ( const int  index ) const

Returns an instance of ms_taxnodesfiles describing an entry in GencodeFiles.

The GencodeFiles file is used to find a proper NA translation table for a given taxonomy. For more detailed information on how to configure this parameter consult Mascot manual and documentation for ms_taxnodesfiles.

By default the list of files is empty.

Parameters:
indexfile number from 0 to (getNumberOfGencodeFiles()-1).
Returns:
instance of ms_taxnodesfiles class describing one of the files specified in GencodeFiles parameter of the Taxonomy section.
std::string getIdentifier (  ) const

Returns the value of Identifier.

This parameter contains a symbolic name for the taxonomy specification as seen, for instance, in the database GUI utility.

By default this is empty.

Returns:
identifier of the taxonomy
Examples:
config_mascotdat.cpp.
std::string getNoBreakDescLineIf ( const int  index ) const

Returns a NoBreakDescLineIf entry by its number.

NoBreakDescLineIf specifies keywords that prevent description line from being broken into separate words.

By default this is an empty list.

Parameters:
indexnumber of entry from 0 to (getNumberOfNoBreakDescLineIf()-1).
Returns:
a string value.
const ms_taxnodesfiles * getNodesFile ( const int  index ) const

Returns an instance of ms_taxnodesfiles describing an entry in NodesFiles.

The NodesFiles file is used to traverse taxonomy hierarchy. It contains taxonomy ID nodes together with their parents IDs. For more detailed information on how to configure this parameter consult Mascot manual and documentation for ms_taxnodesfiles.

By default the list of files is empty.

Parameters:
indexfile number from 0 to (getNumberOfNodesFiles()-1).
Returns:
instance of ms_taxnodesfiles class describing one of the files specified in NodesFiles parameter of the Taxonomy section.
int getNumberOfGencodeFiles (  ) const

Returns the number of file names specified in GencodeFiles.

See getGencodeFile() and documentation for ms_taxnodesfiles.

Returns:
number of gencode files
int getNumberOfNoBreakDescLineIf (  ) const

Returns the number of NoBreakDescLineIf entries.

See getNoBreakDescLineIf() for explanations.

Returns:
number of keywords which prevent breaking description lines
int getNumberOfNodesFiles (  ) const

Returns the number of file names specified in NodesFiles.

See getNodesFile() and documentation for ms_taxnodesfiles.

Returns:
number of nodes files
int getNumberOfPerDbSrcRules (  ) const

Returns the number of database source strings.

See getPerDbSrcRule() and documentation for ms_parserule_plus.

Returns:
number of database source strings
int getNumberOfPrefixRemoves (  ) const

Returns the number of PrefixRemoves entries.

See getPrefixRemove().

Returns:
number of prefix removes
int getNumberOfSpeciesFiles (  ) const

Returns the number of file names specified in SpeciesFiles.

See getSpeciesFile() and documentation for ms_taxspeciesfiles.

Returns:
number of species files
int getNumberOfStrFiles (  ) const
Returns:
number of taxonomy species files
int getNumberOfSuffixRemoves (  ) const

Returns the number of SuffixRemoves entries.

See getSuffixRemove().

Returns:
number of suffix removes
const ms_parserule_plus * getPerDbSrcRule ( const int  index ) const

Returns a database source string by its number.

Database source strings contained in taxonomy section all look like RULE_XXX or OTHERRULE.

By default the list of rules is empty.

Parameters:
indexdatabase source string number from 0 to (getNumberOfPerDbSrcRules()-1).
Returns:
pointer to a parser rule
std::string getPreceedingComments (  ) const [inherited]

Returns any comments preceeding the section.

Sections in the mascot.dat file may have comments preceeding them. In most cases, these comments need to stay 'attached' to the section.

Multiple line comments are supported by having a single string with newline characters

See also:
setPreceedingComments()
Returns:
any comments preceeding the section
std::string getPrefixRemove ( const int  index ) const

Returns the PrefixRemoves string by number.

See getDefaultRule() for information on this parameter.

By default the list of prefixes is empty.

Parameters:
indexnumber of a string specified in the parameter from 0 to (getNumberOfPrefixRemoves()-1).
Returns:
one of the string specifed in the parameter.
std::string getQuickRefSearch (  ) const

Returns the value of QuickRefSearch.

The QuickRefSearch string is used to speed up the compressing of the database. Rather than use the regular expression for each line in the .ref file, this text is used for a fast compare to the string C;Species. Other lines are ignored.

By default this is empty.

Returns:
quick ref search for the taxonomy rule
const ms_taxspeciesfiles * getSpeciesFile ( const int  index ) const

Returns an instance of ms_taxspeciesfiles describing an entry in SpeciesFiles.

The SpeciesFiles file is used to convert a species name to a taxonomy ID. For more detailed information on how to configure this parameter consult Mascot manual and documentation for ms_taxspeciesfiles.

By default the list is empty.

Parameters:
indexfile number from 0 to (getNumberOfSpeciesFiles()-1).
Returns:
instance of ms_taxspeciesfiles class describing one of the files specified in SpeciesFiles parameter of the Taxonomy section.
std::string getSpeciesFormatRegex ( const TAX_SPECIES_FORMAT  format ) const

Returns a regular expression, if any for the species format.

Introduced in Mascot 2.4, allows the use of a regular expression for a species file. The regular expression needs to return two values: the 'accession' or 'id' and the taxonomy_id

For example, in the Taxonomy_X section of mascot.dat, there is, for example an entry:

 * SWISSPROTRegex "^\\([A-Z0-9]*\\) *[ABEV] *\\([0-9]*\\):" 

which has two bracketed expressions intended to extract AADNV and 648330 from

 AADNV V 648330: N=Aedes albopictus densovirus (isolate Boublik/1994) 

If there is no value for SWISSPROTRegex in the mascot.dat file, then the value returned is the default as shown above.

Parameters:
formatcan be any TAX_SPECIES_FORMAT value, although only TAX_SPECIES_SWISSPROT is currently supported in Mascot Server.
Returns:
the regular expression or an empty string.
const ms_parserule * getSrcDatabaseRule (  ) const

Returns the value of SrcDatabaseRule.

The parameter is used for finding database source string with regular expression.

See also:
getPerDbSrcRule()
Returns:
pointer to a parser rule
const ms_taxspeciesfiles * getStrFile ( const int  index ) const
Parameters:
indexfile index to look for
Returns:
taxonomy species file
const ms_parserule_plus * getStrRule (  ) const
Returns:
pointer to a parser rule
std::string getSuffixRemove ( const int  index ) const

Returns a SuffixRemoves string by number.

See getDefaultRule() for information on this parameter.

By default the list of suffixes is empty.

Parameters:
indexnumber of a string specified in the parameter from 0 to (getNumberOfSuffixRemoves()-1).
Returns:
one of the string specifed in the parameter.
bool isConcatRefFileLines (  ) const

Returns TRUE if ConcatRefFileLines parameter is set to 1 and FALSE otherwise.

A value of 1 (default) means that there might be multiple lines in reference file describing the same entry of the database.

See also:
isFromRefFile(), getDescriptionLineSep().
Returns:
true is ConcatRefFileLines equals 1, false otherwise
bool isEnabled (  ) const

Returns TRUE if Enabled parameter is set to 1 and FALSE otherwise.

Set Enabled parameter to 0 to disable the taxonomy. Most of the other parameters will be ignored although the taxonomy will be available for a database to select in database maintenance utility.

Default is 0.

Returns:
true if taxonomy rules are enabled, false otherwise
bool isFromRefFile (  ) const

Returns TRUE if FromRefFile parameter is set to 1 and FALSE otherwise.

FromRefFile is set to 0 to indicate that the taxonomy should be found in the .fasta file rather than in a reference file.

Default is 0.

See also:
isConcatRefFileLines(), getDescriptionLineSep().
Returns:
true if the taxonomy should be found in the fasta file, false otherwise
bool isMitochondrialTranslation (  ) const

Returns TRUE if MitochondrialTranslation parameter is set to 1 and FALSE otherwise.

Two types of NA translation tables can be used: nuclear and mitochondrial. Setting this parameter to 0 indicates the first type whereas 1 indicates the second one.

Default is 0.

Returns:
true if NA translation tables used are mitochondrial, false if they are nuclear
bool isSectionAvailable (  ) const

Checks whether the section has been actually read from the file.

By default a Taxonomy section is unavailable until it has been set to a different state.

Returns:
true if the section has been set to available
void setAccFromSpeciesLine ( const ms_parserule src )

Change the value of AccFromSpeciesLine.

See getAccFromSpeciesLine() for more information.

Parameters:
srcpointer to a parser rule
void setConcatRefFileLines ( const bool  flag )

Change the value of ConcatRefFileLines.

See isConcatRefFileLines() for more information.

Parameters:
flagboolean value to set whether there might be multiple lines for the same entry
void setDefaultRule ( const ms_parserule_plus src )

Change the value of DefaultRule.

See getDefaultRule().

Parameters:
srcpointer to a parser rule
void setDescriptionLineSep ( const char  value )

Change the value of DescriptionLineSep.

See getDescriptionLineSep() for more information.

Parameters:
valuedescription line separator
void setDoThisRuleFirst ( const ms_parserule src )

Change the value of DoThisRuleFirst.

See getDoThisRuleFirst().

Parameters:
srcpointer to a parser rule for which it should do this rule first
void setEnabled ( const bool  flag )

Change the value of Enabled.

See isEnabled() for more information.

Parameters:
flagwhether the taxonomy rules are enabled or not
void setErrorLevel ( const int  value )

Change the value of ErrorLevel.

See getErrorLevel() for more information.

Parameters:
valueerror level
void setFromRefFile ( const bool  flag )

Change the value of FromRefFile.

See isFromRefFile() for more information.

Parameters:
flagboolean value to define if the taxonomy should be found in the fasta file
void setIdentifier ( const char *  str )

Change the value of Identifier.

For more information see getIdentifier().

Parameters:
stridentifier for the taxonomy
void setMitochondrialTranslation ( const bool  flag )

Set the value of MitochondrialTranslation.

See isMitochondrialTranslation().

Parameters:
flagtrue if NA translation tables used are mitochondrial, false if they are nuclear
void setPreceedingComments ( const std::string &  comments ) [inherited]

Sets any comments preceeding the section.

Sections in the mascot.dat file may have comments preceeding them. In most cases, these comments need to stay 'attached' to the section.

Multiple line comments are supported by having a single string with newline characters

See also:
getPreceedingComments()
Parameters:
commentsany comments preceeding the section
void setQuickRefSearch ( const char *  str )

Change the value of QuickRefSearch.

See getQuickRefSearch().

Parameters:
strstring used to speed up database compression
void setSpeciesFormatRegex ( const TAX_SPECIES_FORMAT  format,
const std::string  regex 
)

Set the regular expression, if any, for the species format.

Instroduced in Mascot 2.4, allows the use of a regular expression for a species file. The regular expression needs to return two values: the 'accession' or 'id' and the taxonomy_id

For example, in the Taxonomy_X section of mascot.dat, there is, for example an entry:

 * SWISSPROTRegex "^\\([A-Z0-9]*\\) *[ABEV] *\\([0-9]*\\):" 

which has two bracketed expressions intended to extract AADNV and 648330 from

 AADNV V 648330: N=Aedes albopictus densovirus (isolate Boublik/1994) 
Parameters:
formatcan be any TAX_SPECIES_FORMAT value, although only TAX_SPECIES_SWISSPROT is currently supported in Mascot Server.
regexis the new regular expression or an empty string.
void setSrcDatabaseRule ( const ms_parserule src )

Change the value of SrcDatabaseRule.

See getSrcDatabaseRule().

Parameters:
srcpointer to a parser rule
void setStrRule ( const ms_parserule_plus src )
Parameters:
srcpointer to a parser str rule

The documentation for this class was generated from the following files:
Copyright © 2016 Matrix Science Ltd.  All Rights Reserved. Generated on Fri Jun 2 2017 01:44:54