The complete taxonomy tree as built from one or more files such as nodes.dmp. More...

#include <ms_taxonomyrules.hpp>

Inheritance diagram for ms_taxonomytree:

Collaboration diagram for ms_taxonomytree:

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Public Member Functions
	ms_taxonomytree (const ms_taxonomyrules taxonomyRules, const char taxonomyDirectory="../taxonomy", const bool useIndex=true, const bool createList=false, const char preparingDirectory="../taxonomy/preparing", const char oldDirectory="../taxonomy/old")
	Create a taxonomy tree based on the rules specified in mascot.dat.

	ms_taxonomytree (const ms_taxonomytree &src)
	Copying constructor.

	~ms_taxonomytree ()
	Destructor.

void	appendErrors (const ms_errors &src)
	Copies all errors from another instance and appends them at the end of own list.

void	clearAllErrors ()
	Remove all errors from the current list of errors.

void	copyFrom (const ms_errors *right)
	Use this member to make a copy of another instance.

void	copyFrom (const ms_taxonomytree *right)
	Can be used to create a copy of another instance.

const ms_errs *	getErrorHandler () const
	Retrive the error object using this function to get access to all errors and error parameters.

int	getLastError () const
	Return the error description of the last error that occurred.

std::string	getLastErrorString () const
	Return the error description of the last error that occurred.

bool	getParent (const int id, int &ttParent, int &ttGenTable) const
	Return the parent id and translation table id for a species.

TAX_TREE_NODES *	getTaxIDArray ()
	Return a raw array of TAX_TREE_NODE values, with the array index being the id.

bool	isIncludedIn (const int id, const ms_taxonomychoice *choice) const
	Return true if the taxonomy id is included in the choice.

bool	isSpeciesDescendantOf (const int parentID, const int id) const
	Determine if a particular id is a child of the parentID.

bool	isValid () const
	Call this function to determine if there have been any errors.

ms_taxonomytree &	operator= (const ms_taxonomytree &right)
	Assignment operator for C++ client applications.

Detailed Description

The complete taxonomy tree as built from one or more files such as nodes.dmp.

Used for determining the taxonomy lineage. This class is used to load all of the files specified in a specified taxonomy section in mascot.dat, for example:

NodesFiles          NCBI:nodes.dmp, NCBI:merged.dmp

Index files are created using ms_tinycdb to improve performance in cases where a moderate number of parent id's are required. Index files are created in the same directory as the text files, with an additional 'extension' of ".cdb". Error or warning messages in ms_tinycdb are concatenated into the ms_taxonomytree object. If, for example, the process does not have write access to the directory with the taxonomy files , then an error ms_errs:: is generated, but the object is still valid and will continue with just the text files.

Other possible errors include: ms_errs::ERR_MSP_TAXONOMY_CONFLICT_PARENTS ms_errs::ERR_MSP_TAXONOMY_INVALID_NODE_FILE ms_errs::ERR_MSP_TAXONOMY_MISSING_NODE_FILE

The nodes.dmp file also contains the genetic code translation table id to be used when translating from nucleic acid to protein.

Example code to see if Homo Sapiens (9606) are mammals (40674):

my $datfile = new msparser::ms_datfile("../config/mascot.dat");
my $taxonomy_rules = $datfile->getTaxonomyRules(3);
my $tree = new msparser::ms_taxonomytree($taxonomy_rules);
if ($tree->isValid()) {
  my $human = 9606;
  my $mammalia = 40674;
  if ($tree->isSpeciesDescendantOf($mammalia, $human)) {
    print "Indeed, we are mammals\n";
  }
}

Constructor & Destructor Documentation

◆ ms_taxonomytree()

ms_taxonomytree	(	const ms_taxonomyrules *	taxonomyRules,
		const char *	taxonomyDirectory = `"../taxonomy"`,
		const bool	useIndex = `true`,
		const bool	createList = `false`,
		const char *	preparingDirectory = `"../taxonomy/preparing"`,
		const char *	oldDirectory = `"../taxonomy/old"`
	)

Create a taxonomy tree based on the rules specified in mascot.dat.

The complete taxonomy tree as built from one or more files such as nodes.dmp

Parameters

taxonomyRules	contains the list of NodesFiles specified in the taxonomy section of mascot.dat. These files are all loaded by this constructor. The names are retrieved using ms_taxonomyrules::getNodesFile
taxonomyDirectory	specifies the directory to look in for the files. The names in mascot.dat do not normally include path information since the files are generally in the ../taxonomy directory
useIndex	will normally be set to true. If just a handful of 'parent ids' are required, then it is most efficient to use the index files. See getTaxIDArray() for a situation where this should be set to false.
createList	will normally be set to false. It is used to create the list of nodes in memory even if the cache file is used.
preparingDirectory	optional parameter to specify a directory to look for new files and create temporary index files. Once the index files have been created, the new file and the created index files are moved to taxonomyDirectory. If this parameter is an empty string, or if there are no taxonomy files in this directory, new files will be looked for in taxonomyDirectory instead, and the index files will be created directly in taxonomyDirectory.
oldDirectory	optional parameter to archive existing files once index files have been created for a new file. If this parameter is an empty string, no archiving will be done.

Member Function Documentation

◆ appendErrors()

void appendErrors ( const ms_errors & src )

inherited

Copies all errors from another instance and appends them at the end of own list.

Parameters

src	The object to copy the errors across from. See Maintaining object references: two rules of thumb.

◆ clearAllErrors()

void clearAllErrors ( )

inherited

Remove all errors from the current list of errors.

The list of 'errors' can include fatal errors, warning messages, information messages and different levels of debugging messages.

All messages are accumulated into a list in this object, until clearAllErrors() is called.

See Error Handling.

See also: isValid(), getLastError(), getLastErrorString(), getErrorHandler()

Examples: common_error.cpp, resfile_error.cpp, and resfile_summary.cpp.

◆ copyFrom() [1/2]

void copyFrom ( const ms_errors * right )

inherited

Use this member to make a copy of another instance.

Parameters

right is the source to initialise from

◆ copyFrom() [2/2]

void copyFrom ( const ms_taxonomytree * right )

Can be used to create a copy of another instance.

Useful from Perl or scripting languages

Parameters

right is the object to copy from

◆ getErrorHandler()

const ms_errs * getErrorHandler ( ) const

inherited

Retrive the error object using this function to get access to all errors and error parameters.

See Error Handling.

Returns: Constant pointer to the error handler

See also: isValid(), getLastError(), getLastErrorString(), clearAllErrors(), getErrorHandler()

Examples: common_error.cpp, and http_helper_getstring.cpp.

◆ getLastError()

int getLastError ( ) const

inherited

Return the error description of the last error that occurred.

All errors are accumulated into a list in this object, until clearAllErrors() is called. This function returns the last error that occurred.

See Error Handling.

See also: isValid(), getLastErrorString(), clearAllErrors(), getErrorHandler()

Returns: the error number of the last error, or 0 if there have been no errors.

◆ getLastErrorString()

std::string getLastErrorString ( ) const

inherited

Return the error description of the last error that occurred.

All errors are accumulated into a list in this object, until clearAllErrors() is called. This function returns the last error that occurred.

Returns: Most recent error, warning, information or debug message

See Error Handling.

See also: isValid(), getLastError(), clearAllErrors(), getErrorHandler()

Examples: common_error.cpp, config_enzymes.cpp, config_fragrules.cpp, config_license.cpp, config_mascotdat.cpp, config_masses.cpp, config_modfile.cpp, config_procs.cpp, config_quantitation.cpp, config_taxonomy.cpp, http_helper_getstring.cpp, and tools_aahelper.cpp.

◆ getParent()

bool getParent	(	const int	id,
		int &	ttParent,
		int &	ttGenTable
	)		const

Return the parent id and translation table id for a species.

See Multiple return values in Perl, Java, Python and C#.

Parameters

[in]	id	is the NCBI taxonomy id for which to find the parent and translation table.
[out]	ttParent	is the parent id. This will be set to 0 if an entry is not found for id.
[out]	ttGenTable	is the genetic code translation table to be used for converting nucleic acid sequences to protein sequences.

Returns: false if the id is < 1 or greater than the number of entries or if the id is not found in any of the tables.

◆ getTaxIDArray()

ms_taxonomytree::TAX_TREE_NODES * getTaxIDArray ( )

Return a raw array of TAX_TREE_NODE values, with the array index being the id.

This function will only return a non zero value if the useIndex value passed to the constructor is set to false.

The calling function should not call delete on the pointer. The vector is deleted when the ms_taxonomytree object is deleted.

Returns: a pointer to the taxonomy tree nodes or NULL

◆ isIncludedIn()

bool isIncludedIn	(	const int	id,
		const ms_taxonomychoice *	choice
	)		const

Return true if the taxonomy id is included in the choice.

For example, take the definition of "Other Mammalia":

  Title:. . . . . . . . . . . . . . Other mammalia
  Include: 40674
  Exclude: 9443, 9989

If you pass 9606 (Human) and a choice of "Other Mammalia", this function would return false, because in this case, 9606 is part of 9443 (Primates).

Parameters

id	is the taxonomy id
choice	is the return from calling ms_taxonomyfile::getEntryByName

Returns: true if taxonomy id is included in taxonomy choice, false otherwise

◆ isSpeciesDescendantOf()

bool isSpeciesDescendantOf	(	const int	parentID,
		const int	id
	)		const

Determine if a particular id is a child of the parentID.

Parameters

parentID	is the taxonomy id of the parent
id	is the taxonomy id to be tested

Returns: true if the taxonomy is a descendent of the parentID

◆ isValid()

bool isValid ( ) const

inherited

Call this function to determine if there have been any errors.

This will return true unless there have been any fatal errors.

See Error Handling.

Returns: True if no fatal error occured

See also: getLastError(), getLastErrorString(), clearAllErrors(), getErrorHandler()

Examples: common_error.cpp, config_enzymes.cpp, config_fragrules.cpp, config_license.cpp, config_mascotdat.cpp, config_masses.cpp, config_modfile.cpp, config_procs.cpp, config_quantitation.cpp, config_taxonomy.cpp, http_helper_getstring.cpp, peptide_list.cpp, repeat_search.cpp, resfile_error.cpp, resfile_info.cpp, resfile_input.cpp, resfile_params.cpp, resfile_summary.cpp, and tools_aahelper.cpp.

◆ operator=()

ms_taxonomytree & operator= ( const ms_taxonomytree & right )

Assignment operator for C++ client applications.

Cannot be used from scripting languages

Parameters

right is the object to copy from

Returns: a reference to 'this'

The documentation for this class was generated from the following files:

ms_taxonomyrules.hpp
ms_taxonomyrules.cpp

Public Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ ms_taxonomytree()

Member Function Documentation

◆ appendErrors()

◆ clearAllErrors()

◆ copyFrom() [1/2]

◆ copyFrom() [2/2]

◆ getErrorHandler()

◆ getLastError()

◆ getLastErrorString()

◆ getParent()

◆ getTaxIDArray()

◆ isIncludedIn()

◆ isSpeciesDescendantOf()

◆ isValid()

◆ operator=()