Definitions

descFileRead(fileName)

This function provides the same raw output as tdfread from the statistics toolbox, making sure, that we don’t need that as a prerequesite

USAGE:

[raw] = descFileRead(fileName)

INPUT:

fileName: The filename of a tab delimited data file. The

first row of the file will be considered to be headers (with spaces being replaced by ‘_’.

OUTPUTS:

raw: A struct with one field per header and a char

array of all data listed in the column.

getAnnotationFieldName(annotatedField, database, annotationQualifier, qualifierSelection, invertSelection)

Get the cobra field corresponding to the given database for the annotion Qualifier and the given annotated field.

USAGE:

fieldName = getAnnotationFieldName(annotatedField,database,annotationQualifier)

INPUTS:

annotationField: The base field that is being annotated

(e.g. ‘rxn’, ‘model’, ‘comp’, …)

database: The database names of the annotation. (e.g.

kegg)

annotationQualifier: The annotation qualifier (see

http://co.mbine.org/standards/qualifiers for possible qualifiers)

OPTIONAL INPUTS:

qualifierSelection: Exclude the qualifiers from mappings (default: {}). invertSelection: Invert the qualifierSelection i.e. use

only those specified (default: false);

OUTPUTS:

fieldNames: The name of the field corresponding to the

given annotation.

dbIDs: A Cell array with the DB IDs relations: The relations the field has with the db

names (for defined fields, this can be a multiple tpes separated by ‘;’

getRegisteredDatabases()

Get all databases registered with identifiers.org along with their pattern and and prefix data.

USAGE:

identifiersDBs = getRegisteredDatabases()

OUPUTS:

identifiersDBs: A Struct with data on each database registered

with identifiers.org (needs web access). The struct will have the following fields:

• .name: The name of the database

• .pattern: A regexp pattern allowed with the db.

• .prefix: The prefix of the db on identifiers.org