de.unirostock.sems.bives.statsgenerator.algorithm

Class RepositoryProcessor

java.lang.Object

de.unirostock.sems.bives.statsgenerator.algorithm.RepositoryProcessor

public class RepositoryProcessor
extends Object

The Class BiomodelsProcessor.

Author:

martin

Constructor Summary

Constructors

Constructor and Description
RepositoryProcessor(File storageDir, File workingDir, de.unirostock.sems.bives.sbml.algorithm.SBMLValidator valSBML, de.unirostock.sems.bives.cellml.algorithm.CellMLValidator valCellMl, FileStatsWriter fsw, DiffStatsWriter dsw, Map<String,ComodiTermCounter> comodiTerms) Instantiates a new biomodels processor.

Method Summary

Modifier and Type	Method and Description
static void	clean(Map<String,Model> models) Clean.
boolean	compare(ModelVersion originalVersion, ModelVersion modifiedVersion, Model m, File workingDir) Compare.
void	generateFileStats(ModelVersion modelVersion, Date date, Model m) Do file stats.
void	process() Process.
void	process(File dir) Process biomodels.
void	processModel(Model m) Process model.
void	processWorkingDir(File f) Process model.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

RepositoryProcessor

public RepositoryProcessor(File storageDir,
                           File workingDir,
                           de.unirostock.sems.bives.sbml.algorithm.SBMLValidator valSBML,
                           de.unirostock.sems.bives.cellml.algorithm.CellMLValidator valCellMl,
                           FileStatsWriter fsw,
                           DiffStatsWriter dsw,
                           Map<String,ComodiTermCounter> comodiTerms)

Instantiates a new biomodels processor.

Parameters:

storageDir - the storage dir

workingDir - the working dir

valSBML - the val sbml

valCellMl - the val cell ml

fsw - the fsw

dsw - the dsw

comodiTerms - the comodi terms

Method Detail

process

public void process()

Process.

process

public void process(File dir)

Process biomodels.

Parameters:

dir - the dir

processWorkingDir

public void processWorkingDir(File f)
                       throws FileNotFoundException,
                              IOException,
                              org.json.simple.parser.ParseException

Process model.

Parameters:

f - the f

Throws:

FileNotFoundException - the file not found exception

IOException - Signals that an I/O exception has occurred.

org.json.simple.parser.ParseException - the parse exception

clean

public static void clean(Map<String,Model> models)

Clean.

Parameters:

models - the models

processModel

public void processModel(Model m)

Process model.

Parameters:

m - the m

compare

public boolean compare(ModelVersion originalVersion,
                       ModelVersion modifiedVersion,
                       Model m,
                       File workingDir)

Compare.

Parameters:

originalVersion - the original version

modifiedVersion - the modified version

m - the m

workingDir - the working dir

Returns:

true, if successful

generateFileStats

public void generateFileStats(ModelVersion modelVersion,
                              Date date,
                              Model m)

Do file stats.

Parameters:

modelVersion - the model version

date - the date

m - the m