Package org.cy3sbml.gui

Class SBaseHTMLFactory

java.lang.Object

org.cy3sbml.gui.SBaseHTMLFactory

public class SBaseHTMLFactory
extends Object

Creates HTML information for given SBase. Core information is parsed from the NamedSBase object, with additional information like resources retrieved via web services (MIRIAM).

Here the HTML information string is created which is displayed on selection of SBML objects in the graph.

Field Summary

Fields

Modifier and Type	Field	Description
static final String	CY3SBML
static final String	delim
static final String	FILENAME_NAMESPACE
static final String	IDENTIFIERS_BASE
static final String	SBO

Constructor Summary

Constructors

Constructor	Description
SBaseHTMLFactory(String baseDir, MiriamRegistry miriamRegistry, OlsClient olsClient, UniprotAccess uniprotAccess, ChebiAccess chebiAccess)	Creates the factory.
SBaseHTMLFactory(String baseDir, MiriamRegistry miriamRegistry, OlsClient olsClient, UniprotAccess uniprotAccess, ChebiAccess chebiAccess, CompTargets compTargets)	Creates the factory, which shows the targets of the comp references.
SBaseHTMLFactory(String baseDir, MiriamRegistry miriamRegistry, OlsClient olsClient, UniprotAccess uniprotAccess, ChebiAccess chebiAccess, CompTargets compTargets, Function<org.sbml.jsbml.SBMLDocument,Optional<ArchiveImport>> archives)	Creates the factory, which shows the targets of the comp references and the COMBINE archive a document was imported from.

Method Summary

Modifier and Type	Method	Description
static String	baseDirFromAppDir(File appDir)	Returns the base URL of the gui resources in the given application directory.
static String	booleanHTML(boolean b)	Creates true or false HTML depending on boolean.
String	createHTMLText(String text)	Creates HTML text.
String	createHTMLText(String text, String title)	Creates HTML for given text String.
String	createInfo(org.sbml.jsbml.SBase sbase)	Creates the HTML information for the given SBase.
String	createSecondaryInformation(Namespace dataType, String identifier)	Resolves secondary resourses and returns the HTML.
static String	getPrefixValue(String keyToFind)

Methods inherited from class java.lang.Object

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

Field Details

SBO

public static final String SBO

See Also:

• Constant Field Values

CY3SBML

public static final String CY3SBML

See Also:

• Constant Field Values

IDENTIFIERS_BASE

public static final transient String IDENTIFIERS_BASE

See Also:

• Constant Field Values

FILENAME_NAMESPACE

public static final String FILENAME_NAMESPACE

See Also:

• Constant Field Values

delim

public static final String delim

See Also:

• Constant Field Values

Constructor Details

SBaseHTMLFactory

public SBaseHTMLFactory(String baseDir,
 MiriamRegistry miriamRegistry,
 OlsClient olsClient,
 UniprotAccess uniprotAccess,
 ChebiAccess chebiAccess)

Creates the factory.

Parameters:

baseDir - base URL of the gui resources, which resolves the relative resources within the WebView

miriamRegistry - data collections for resolving annotation URIs

olsClient - resolves ontology terms for display

uniprotAccess - resolves UniProt accessions for display

chebiAccess - resolves ChEBI ids for display

SBaseHTMLFactory

public SBaseHTMLFactory(String baseDir,
 MiriamRegistry miriamRegistry,
 OlsClient olsClient,
 UniprotAccess uniprotAccess,
 ChebiAccess chebiAccess,
 CompTargets compTargets)

Creates the factory, which shows the targets of the comp references.

Parameters:

compTargets - the comp references of the open documents, may be null

SBaseHTMLFactory

public SBaseHTMLFactory(String baseDir,
 MiriamRegistry miriamRegistry,
 OlsClient olsClient,
 UniprotAccess uniprotAccess,
 ChebiAccess chebiAccess,
 CompTargets compTargets,
 Function<org.sbml.jsbml.SBMLDocument,Optional<ArchiveImport>> archives)

Creates the factory, which shows the targets of the comp references and the COMBINE archive a document was imported from.

Parameters:

compTargets - the comp references of the open documents, may be null

archives - the archive of a document, may be null

Method Details

baseDirFromAppDir

public static String baseDirFromAppDir(File appDir)

Returns the base URL of the gui resources in the given application directory.

createHTMLText

public String createHTMLText(String text,
 String title)

Creates HTML for given text String.

createHTMLText

public String createHTMLText(String text)

Creates HTML text.

createInfo

public String createInfo(org.sbml.jsbml.SBase sbase)
                  throws IOException

Creates the HTML information for the given SBase.

Throws:

IOException

createSecondaryInformation

public String createSecondaryInformation(Namespace dataType,
 String identifier)

Resolves secondary resourses and returns the HTML.

Returns:

html string

booleanHTML

public static String booleanHTML(boolean b)

Creates true or false HTML depending on boolean.

getPrefixValue

public static String getPrefixValue(String keyToFind)