Class ModelPolisherCLIL
- HTML tag correction in SBML files.
- SBML document validation and conversion.
- Annotation of models using external databases.
- - Output management including file writing, COMBINE archive creation, and compression.
+ - Output management including file writing, COMBINE archive creation, and outputType.
This class also handles error logging and provides detailed logging of the processing steps.
diff --git a/docs/edu/ucsd/sbrg/ModelPolisherOptions.Compression.html b/docs/edu/ucsd/sbrg/ModelPolisherOptions.OutputType.html
similarity index 86%
rename from docs/edu/ucsd/sbrg/ModelPolisherOptions.Compression.html
rename to docs/edu/ucsd/sbrg/ModelPolisherOptions.OutputType.html
index 40f1bea9..c94c5c5c 100644
--- a/docs/edu/ucsd/sbrg/ModelPolisherOptions.Compression.html
+++ b/docs/edu/ucsd/sbrg/ModelPolisherOptions.OutputType.html
@@ -2,10 +2,10 @@
-ModelPolisherOptions.Compression (ModelPolisher 2.1 API)
+ModelPolisherOptions.OutputType (ModelPolisher 2.1 API)
-
+
@@ -82,25 +82,25 @@
Returns the enum constant of this class with the specified name.
The string must match exactly an identifier used to declare an
enum constant in this class. (Extraneous whitespace characters are
diff --git a/docs/edu/ucsd/sbrg/ModelPolisherOptions.html b/docs/edu/ucsd/sbrg/ModelPolisherOptions.html
index adb1c8a6..73d1fb57 100644
--- a/docs/edu/ucsd/sbrg/ModelPolisherOptions.html
+++ b/docs/edu/ucsd/sbrg/ModelPolisherOptions.html
@@ -105,7 +105,7 @@
This switch allows users to specify if also those database cross-links
should be extracted from BiGG Models database for which currently no entry
in the MIRIAM exists.
Validates an SBML file either online or offline based on the provided parameters.
- Online validation refers to checking the file against a remote service or database, using specific parameters for the validation process.
- Offline validation involves reading the file locally, handling different compression formats if necessary, and validating the SBML document against local constraints.
- Errors encountered during the validation process are logged for further analysis.
Attempts to extract a BiGG ID that conforms to the BiGG ID specification from the BiGG knowledgebase. This method
processes annotations for biological entities such as Species, Reaction, or GeneProduct.
Each entity's annotations are provided as a list of URIs, which are then parsed to retrieve the BiGG ID.
Abstract method to check the validity of a BiGG ID. Implementations should return an Optional containing
the BiGG ID if it is valid, or an empty Optional if not.
Returns:
Optional containing the valid BiGG ID or empty if the ID is invalid.
Annotates the compartment with BiGG and SBO terms. If the compartment's name is not set or is set to "default",
it updates the name based on the BiGG database. This method only processes compartments that are recognized
within the BiGG Knowledgebase.
Delegates the annotation process for each reaction in the given SBML model.
This method iterates over all reactions in the model, updates the progress display,
and invokes the annotation for each reaction.
Annotates a reaction by setting its name, SBO term, and additional annotations. It also processes gene reaction rules
and subsystem information associated with the reaction. This method retrieves a BiGG ID for the reaction, either from
the reaction's ID directly or through associated annotations. If a valid BiGG ID is found, it proceeds with the
@@ -255,13 +259,16 @@
This method checks if the ID of the reaction is a valid BiGG ID and attempts to retrieve a corresponding
BiGG ID based on existing annotations. It first checks if the reaction ID matches the expected BiGG ID format
and verifies its existence in the database. If the ID does not match or is not found, it then attempts to
@@ -273,6 +280,8 @@
Sets the name of the reaction based on the provided BiGGId. It retrieves the reaction name using the abbreviation
from the BiGGId, polishes the name, and updates the reaction's name if the new name is different from the current name.
Parameters:
biggId - The BiGGId object containing the abbreviation used to fetch and potentially update the reaction's name.
Sets the SBO term for a reaction based on the given BiGGId.
If the reaction does not already have an SBO term set, it determines the appropriate SBO term
based on whether the reaction is a pseudoreaction or a generic process. Pseudoreactions are assigned
@@ -302,6 +315,8 @@
setSBOTerm
Parameters:
biggId - The BiGGId object containing the abbreviation used to check if the reaction is a pseudoreaction.
Parses gene reaction rules for a given reaction based on the BiGG database identifier.
This method retrieves gene reaction rules associated with the reaction's abbreviation
from the BiGG database and applies gene-protein-reaction (GPR) parsing to the reaction.
@@ -317,6 +333,8 @@
parseGeneReactionRules
Parameters:
biggId - The BiGG database identifier for the reaction, used to fetch and parse gene reaction rules.
Annotates an SBMLDocument using data from the BiGG Knowledgebase. This method processes various components of the
SBML model such as compartments, species, reactions, and gene products by adding relevant annotations from BiGG.
It also handles the addition of publications and notes related to the model.
Delegates annotation processing for all chemical species contained in the Model.
This method iterates over each species in the model and applies specific annotations.
This method annotates a species with various details fetched from the BiGG Knowledgebase. It performs the following:
1. Sets the species name based on the BiGGId. If the species does not have a name, it uses the BiGGId as the name.
2. Assigns an SBO (Systems Biology Ontology) term to the species based on the BiGGId.
@@ -247,13 +251,16 @@
Validates the species ID and attempts to retrieve a corresponding BiGGId based on existing annotations.
This method first tries to create a BiGGId from the species ID. If the species ID does not correspond to a known
BiGGId in the database, it then searches through the species' annotations to find a valid BiGGId.
Updates the name of the species based on data retrieved from the BiGG Knowledgebase. The species name is set only if it
has not been previously set or if the current name follows a default format that combines the BiGGId abbreviation and
compartment code. This method relies on the availability of a valid BiGGId for the species.
Parameters:
biggId - The BiGGId associated with the species, used to fetch the component name from the BiGG database.
This method handles the annotation of gene products in a given SBML model. It checks if the model has the FBC plugin
set and then proceeds to annotate each gene product found within the model. The progress bar is updated to reflect
the number of gene products being annotated.
Annotates a gene product by adding relevant metadata and references.
This method first checks the gene product's ID for validity and retrieves a corresponding BiGGId if available.
It then attempts to get a label for the gene product. If no label is found, the method returns early.
@@ -271,13 +275,16 @@
Validates the ID of a GeneProduct against the expected BiGG ID format and attempts to retrieve a
corresponding BiGGId from existing annotations if the initial ID does not conform to the BiGG format.
The method first checks if the gene product's ID matches the BiGG ID pattern. If it does not match, it then
@@ -288,6 +295,8 @@
Updates the label of a gene product and sets its name based on the retrieved gene name from the BiGG database.
If the current label is set to "None", it updates the label to the provided one. It then attempts to fetch
the gene name corresponding to this label from the BiGG database. If a gene name is found, it checks if the
@@ -321,6 +331,8 @@
setGPLabelName
Parameters:
label - The label to set or use for fetching the gene name. This label should correspond to a BiGGId
or be derived from AbstractSBase.getId().
Adds annotations to a gene product based on a given BiGGId. This method differentiates between
annotations that specify what the gene product 'is' and what it 'is encoded by'. Resources are fetched
from the BiGG database using the abbreviation from the provided BiGGId. Each resource URL is checked and
@@ -336,6 +349,8 @@
addAnnotations
Parameters:
biggId - The BiGGId associated with the gene product, typically derived from a species ID.
Retrieves a set of annotated URLs based on the type and BiGG ID provided.
This method queries the database to find matching annotations and constructs URLs using the retrieved data.
@@ -203,6 +204,8 @@
getAnnotations
Returns:
A sorted set of URLs that are annotations for the given BiGG ID. If the type is neither metabolite
nor reaction, or if an SQL exception occurs, an empty set is returned.
Retrieves a list of distinct subsystems associated with a specific model and reaction BiGG IDs.
This method executes a SQL query to fetch subsystems from the database where both the model and reaction
match the provided BiGG IDs. Only subsystems with a non-zero length are considered.
@@ -382,13 +386,16 @@
getSubsystems
reactionBiGGid - The BiGG ID of the reaction.
Returns:
A List of subsystem names as strings. Returns an empty list if no subsystems are found or if an error occurs.
Retrieves a list of distinct subsystems associated with a specific reaction BiGG ID.
This method executes a SQL query to fetch subsystems from the database where the reaction
matches the provided BiGG ID. Only subsystems with a non-zero length are considered.
@@ -397,6 +404,8 @@
getSubsystemsForReaction
reactionBiGGid - The BiGG ID of the reaction for which subsystems are to be retrieved.
Returns:
A List of subsystem names as strings. Returns an empty list if no subsystems are found or if an error occurs.
Retrieves the unique chemical formula for a given component within a specific compartment.
This method queries the database to find the distinct chemical formula associated with the specified
component and compartment IDs. It ensures that the formula is unique for the given parameters.
@@ -416,6 +426,8 @@
getChemicalFormulaByCompartment
Returns:
An Optional containing the chemical formula if exactly one unique formula is found,
otherwise an empty Optional if none or multiple formulas are found.
Retrieves the chemical formula for a given component within a specific model in the BiGG database.
This method executes a SQL query to find distinct chemical formulas associated with the component and model IDs provided.
If exactly one unique formula is found, it is returned. If none or multiple formulas are found, an empty Optional is returned.
@@ -434,13 +447,16 @@
getChemicalFormula
modelId - The BiGG ID of the model in which the component is present.
Returns:
An Optional<String> containing the chemical formula if exactly one is found, otherwise empty.
Retrieves the name of the compartment associated with the given BiGG ID from the database.
This method constructs a SQL query to select the compartment name where the BiGG ID matches
and the name is not an empty string.
@@ -449,6 +465,8 @@
getCompartmentName
biggId - The BiGGId object containing the abbreviation of the compartment.
Returns:
An Optional<String> containing the name of the compartment if found, otherwise empty.
Executes a SQL query with a single parameter and returns the result as an Optional.
This method is designed to handle queries that are expected to return a single result.
If multiple results are found, a severe log is recorded indicating the issue.
@@ -466,13 +485,16 @@
singleParamStatement
param - The parameter value to be used in the SQL query.
Returns:
An Optional<String> containing the result if exactly one result is found, otherwise empty.
Retrieves the name of the component associated with the given BiGG ID from the database.
This method constructs a SQL query to select the component name where the BiGG ID matches
and the name is not an empty string.
@@ -481,13 +503,16 @@
getComponentName
biggId - The BiGGId object containing the abbreviation of the component.
Returns:
An Optional<String> containing the name of the component if found, otherwise empty.
Retrieves the type of the component associated with the given BiGG ID from the database.
This method constructs a SQL query to select the component type where the BiGG ID matches
and the name field is not an empty string.
@@ -496,13 +521,16 @@
getComponentType
biggId - The BiGGId object containing the abbreviation of the component.
Returns:
An Optional<String> containing the type of the component if found, otherwise empty.
Retrieves all possible MIRIAM-compliant gene identifiers from the database based on a given label.
This method queries the database for gene identifiers that match the provided label and are compliant
with MIRIAM standards. Non-compliant entries are ignored.
@@ -511,13 +539,16 @@
getGeneIds
label - The label used to query gene identifiers.
Returns:
A TreeSet containing unique, sorted MIRIAM-compliant gene identifiers.
Retrieves the gene name from the database based on a given label.
This method constructs a SQL query to fetch the synonym of a gene that matches the given label,
ensuring that the gene is associated with a valid data source and genome region, and that the
@@ -528,6 +559,8 @@
getGeneName
label - The label used to query the gene name, typically a BIGG ID.
Returns:
An Optional containing the gene name if found, otherwise an empty Optional.
Retrieves formatted gene reaction rules for a specific reaction and model from the database.
This method constructs a SQL query to fetch and format the gene reaction rules associated with
the given reaction ID and model ID. The formatting includes replacing logical operators 'or' and 'and'
@@ -546,6 +580,8 @@
getGeneReactionRule
modelId - The ID of the model associated with the reaction.
Returns:
A list of formatted gene reaction rules as strings.
Executes a provided SQL query to retrieve gene reaction rules from the database.
This method prepares a statement with the given query, setting the specified reactionId and modelId as parameters.
It then executes the query and collects the results into a list of strings.
@@ -565,13 +602,16 @@
getReactionRules
modelId - The ID of the model to be used as the second parameter in the SQL query.
Returns:
A list of strings where each string is a gene reaction rule retrieved based on the given IDs.
Retrieves the organism associated with a given BiGG model abbreviation from the database.
This method constructs and executes a SQL query that joins the GENOME and MODEL tables to find the organism
corresponding to the specified model abbreviation.
@@ -580,13 +620,16 @@
getOrganism
abbreviation - The abbreviation of the model for which the organism is to be retrieved.
Returns:
An Optional containing the organism name if found, otherwise an empty Optional.
Retrieves a list of publications associated with a given BiGG model abbreviation from the database.
This method constructs and executes a SQL query that joins the PUBLICATION, PUBLICATION_MODEL, and MODEL tables
to find the publications related to the specified model abbreviation.
@@ -595,13 +638,16 @@
getPublications
abbreviation - The abbreviation of the model for which the publications are to be retrieved.
Returns:
A list of pairs where each pair consists of a publication type and its corresponding ID.
Retrieves the name of a reaction based on its BiGG ID abbreviation, ensuring the name is not empty.
This method constructs and executes a SQL query that selects the reaction name from the REACTION table
where the BIGG_ID matches the specified abbreviation and the name is not an empty string.
@@ -610,6 +656,8 @@
getReactionName
abbreviation - The abbreviation of the reaction for which the name is to be retrieved.
Returns:
An Optional containing the reaction name if found and not empty, otherwise an empty Optional.
Retrieves a set of resource URLs for a given BiGG ID, optionally filtering to include only those containing 'identifiers.org'.
This method constructs and executes a SQL query to fetch URLs from the database based on the type of BiGG ID (reaction or component).
It then filters these URLs based on the 'includeAnyURI' parameter.
@@ -629,13 +678,16 @@
getResources
isReaction - If true, the BiGG ID is treated as a reaction; if false, it is treated as a component.
Returns:
A sorted set of URLs as strings, potentially filtered by the 'identifiers.org' domain.
Retrieves the taxonomic identifier (taxon ID) for a given model based on its abbreviation.
This method queries the database to find the taxon ID associated with the model's abbreviation.
If multiple taxon IDs are found for the same abbreviation, a severe log message is generated.
@@ -644,13 +696,16 @@
getTaxonId
abbreviation - The abbreviation of the model for which the taxon ID is being queried.
Returns:
An Optional containing the taxon ID if found; otherwise, an empty Optional.
Retrieves the genome accession for a given model ID from the BiGG database.
The accession can be used to construct URLs for accessing genomic data from various sources.
The URLs can be formed using the accession ID with the following patterns:
@@ -663,13 +718,16 @@
getGenomeAccesion
Returns:
The accession string which can be appended to the base URLs mentioned above.
If the query fails or no accession is found, an empty string is returned.
Retrieves a set of unique BiGG IDs from a specified table in the database.
This method queries the database for all unique BiGG IDs in the specified table and returns them as a set.
The IDs are ordered by their natural ordering in the database.
@@ -679,6 +737,8 @@
getAllBiggIds
Returns:
A Set of strings containing unique BiGG IDs from the specified table. If an SQL error occurs,
the returned set will be empty.
Retrieves the charge associated with a specific component in a given compartment when the model ID is unknown.
This method executes a SQL query to find a distinct charge value for a component based on its BiGG ID and
the compartment's BiGG ID. The method ensures that the charge value is not empty and returns it if it is unique.
@@ -697,6 +758,8 @@
getChargeByCompartment
Returns:
An Optional containing the charge if it is unique and present; otherwise, an empty Optional.
If multiple unique charge values are found, a warning is logged.
Retrieves the charge for a given component and model from the database.
This method executes a SQL query to select distinct charge values associated with the specified component ID
and model ID. It ensures that the charge value is not null.
@@ -715,13 +779,16 @@
getCharge
Returns:
An Optional containing the charge if exactly one distinct charge is found, otherwise an empty Optional.
If multiple distinct charges are found, a warning is logged.
Determines if a given reaction ID corresponds to a pseudoreaction in the database.
A pseudoreaction is typically used to represent non-biochemical data flows such as biomass accumulation,
demand reactions, or exchange reactions.
@@ -730,6 +797,8 @@
isPseudoreaction
reactionId - The BiGG ID of the reaction to be checked.
Returns:
true if the reaction is a pseudoreaction, false otherwise.
diff --git a/docs/type-search-index.js b/docs/type-search-index.js
index f048b7d5..64f7b042 100644
--- a/docs/type-search-index.js
+++ b/docs/type-search-index.js
@@ -1 +1 @@
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