org.sbml.jsbml.xml.parsers

Class PackageUtil

java.lang.Object

org.sbml.jsbml.xml.parsers.PackageUtil

public class PackageUtil
extends java.lang.Object

Since:

1.1

Author:

Nicolas Rodriguez

Field Summary

Fields

Modifier and Type	Field and Description
private static org.apache.log4j.Logger	logger Log4j logger

Constructor Summary

Constructors

Constructor and Description
PackageUtil()

Method Summary

Modifier and Type	Method and Description
static void	checkPackages(SBase sbase, java.util.List<java.lang.String> packageNamespaces, boolean silent, boolean fix) Checks the given SBase, including all it's siblings, to make sure that the package version and namespace is set properly.
private static void	checkPackages(SBase sbase, java.util.Map<java.lang.String,PackageInfo> prefixMap, java.util.Map<java.lang.String,PackageInfo> namespaceMap, boolean silent, boolean fix) Checks the given SBase, including all it's siblings, to make sure that the package version and namespace is set properly.
static void	checkPackages(SBMLDocument doc) Checks the whole SBMLDocument, including all siblings, to make sure that the package version and namespace is set properly.
static void	checkPackages(SBMLDocument doc, boolean silent, boolean fix) Checks the whole SBMLDocument, including all siblings, to make sure that the package version and namespace is set properly.
static int	extractPackageVersion(java.lang.String namespace)
private static PackageInfo	getPackageInfo(SBase sbase, java.lang.String packageName, int packageVersion, java.lang.String elementNamespace, java.util.Map<java.lang.String,PackageInfo> prefixMap, java.util.Map<java.lang.String,PackageInfo> namespaceMap, boolean silent, boolean fix)

Methods inherited from class java.lang.Object

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

Field Detail

logger

private static final transient org.apache.log4j.Logger logger

Log4j logger

Constructor Detail

PackageUtil

public PackageUtil()

Method Detail

checkPackages

public static void checkPackages(SBMLDocument doc)

Checks the whole SBMLDocument, including all siblings, to make sure that the package version and namespace is set properly.

It will print warnings or errors when problems are found, nothing will be changed.

Parameters:

doc - the SBMLDocument to check.

checkPackages

public static void checkPackages(SBMLDocument doc,
                                 boolean silent,
                                 boolean fix)

Checks the whole SBMLDocument, including all siblings, to make sure that the package version and namespace is set properly.

The given boolean parameters will indicate if the method will print warnings or errors when problems are found, and if it will try to fix problems.

Parameters:

doc - the SBMLDocument to check.

silent - boolean to indicate if errors and warnings should be shown.

fix - boolean to indicate if encountered problems should be fixed.

checkPackages

public static void checkPackages(SBase sbase,
                                 java.util.List<java.lang.String> packageNamespaces,
                                 boolean silent,
                                 boolean fix)

Checks the given SBase, including all it's siblings, to make sure that the package version and namespace is set properly.

The given boolean parameters will indicate if the method will print warnings or errors when problems are found, and if it will try to fix problems.

Parameters:

sbase - the SBase to check.

packageNamespaces - the List of namespaces that are expected to be found SBML L3 packages.

silent - boolean to indicate if errors and warnings should be shown.

fix - boolean to indicate if encountered problems should be fixed.

checkPackages

private static void checkPackages(SBase sbase,
                                  java.util.Map<java.lang.String,PackageInfo> prefixMap,
                                  java.util.Map<java.lang.String,PackageInfo> namespaceMap,
                                  boolean silent,
                                  boolean fix)

Checks the given SBase, including all it's siblings, to make sure that the package version and namespace is set properly.

The given boolean parameters will indicate if the method will print warnings or errors when problems are found, and if it will try to fix problems.

Parameters:

sbase - the SBase to check.

prefixMap - map between package name (or prefix or label) and a PackageInfo object, representing the package name, namespace and version

namespaceMap - map between package namespace and a PackageInfo object, representing the package name, namespace and version

silent - boolean to indicate if errors and warnings should be shown.

fix - boolean to indicate if encountered problems should be fixed.

extractPackageVersion

public static int extractPackageVersion(java.lang.String namespace)

Parameters:

namespace -

Returns:

getPackageInfo

private static PackageInfo getPackageInfo(SBase sbase,
                                          java.lang.String packageName,
                                          int packageVersion,
                                          java.lang.String elementNamespace,
                                          java.util.Map<java.lang.String,PackageInfo> prefixMap,
                                          java.util.Map<java.lang.String,PackageInfo> namespaceMap,
                                          boolean silent,
                                          boolean fix)

Parameters:

sbase -

packageName -

packageVersion -

elementNamespace -

prefixMap -

namespaceMap -

silent -

fix -

Returns: