chemaxon.naming.document.annotate

Class DocumentAnnotator

java.lang.Object

chemaxon.naming.document.annotate.DocumentAnnotator

All Implemented Interfaces:

chemaxon.marvin.io.formats.MoleculeImporterIface, java.lang.AutoCloseable

@PublicAPI
public class DocumentAnnotator
extends java.lang.Object
implements chemaxon.marvin.io.formats.MoleculeImporterIface, java.lang.AutoCloseable

Generate a chemically annotated HTML view of a document.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	DocumentAnnotator.DocumentType
static interface	DocumentAnnotator.Listener
static class	DocumentAnnotator.ProgressInfo

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	MOL_UID_PROPERTY

Constructor Summary

Constructors

Constructor and Description
DocumentAnnotator(java.io.File sourceDocument) Constructs a DocumentAnnotator to annotate the given document file.
DocumentAnnotator(java.io.InputStream sourceDocument) Constructs a DocumentAnnotator to annotate the given document.
DocumentAnnotator(java.io.InputStream sourceDocument, DocumentAnnotator.DocumentType documentType) Constructs a DocumentAnnotator to annotate the given document.

Method Summary

Modifier and Type	Method and Description
void	close()
static DocumentAnnotator	fromPlainText(java.io.Reader source) Constructs a DocumentAnnotator to annotate the given text.
boolean	isAnnotationSupported()
void	process() Process the complete input at once, generating the annotated document.
Molecule	read() Find the next structure in the source document and return it, or null when the end of the document has been reached.
boolean	setAnnotatedOutput(java.io.File destination) Set the destination file where an annotated version of the source document should be written.
boolean	setAnnotatedOutput(java.io.OutputStream destination) Set the destination output stream where an annotated version of the source document should be written.
java.io.File	setAnnotatedOutputDirectory(java.io.File annotateDirectory) Set the directory where the annotated document and associated resources will be placed.
java.io.File	setAnnotatedOutputDirectory(java.io.File annotateDirectory, boolean keepOriginalExtension) Set the directory where the annotated document and associated resources will be placed.
void	setCustomHtmlToXmlConverter(chemaxon.naming.document.annotate.XmlToHtmlConverter customConverter) Provide a custom converter from XML to HTML, to be used instead of the default one.
void	setD2SOptions(chemaxon.naming.document.DocumentToStructureOptions options)
void	setD2SOptions(java.lang.String options) Deprecated. use setD2SOptions(D2S.Options) instead An option String can be parsed to a D2S.Options object using D2SOptionParser.parseOptions().
void	setMolconvert(java.io.File molconvert)
void	setOptions(DocumentAnnotatorOptions options)
void	setResourceDirectory(java.io.File resourceDirectory) Set the directory where resources will be stored.
void	usePopups(boolean addPopups)

Methods inherited from class java.lang.Object

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

Methods inherited from interface chemaxon.marvin.io.formats.MoleculeImporterIface

getMDocumentStream, getMolStream

Field Detail

MOL_UID_PROPERTY

public static final java.lang.String MOL_UID_PROPERTY

See Also:

Constant Field Values

Constructor Detail

DocumentAnnotator

public DocumentAnnotator(java.io.File sourceDocument)
                  throws java.io.FileNotFoundException

Constructs a DocumentAnnotator to annotate the given document file. The document format (PDF, HTML, XML) will be autodetected.

Parameters:

sourceDocument - the document to annotate

Throws:

java.io.FileNotFoundException - if the document does not exist

DocumentAnnotator

public DocumentAnnotator(java.io.InputStream sourceDocument)
                  throws java.io.IOException

Constructs a DocumentAnnotator to annotate the given document. The document format (PDF, HTML, XML) will be autodetected. If annotation of plain text is desired, please use: new DocumentAnnotator(sourceDocument, DocumentAnnotator.DocumentType.TXT)

Parameters:

sourceDocument - the document to annotate

Throws:

java.io.IOException

DocumentAnnotator

public DocumentAnnotator(java.io.InputStream sourceDocument,
                         DocumentAnnotator.DocumentType documentType)

Constructs a DocumentAnnotator to annotate the given document.

Parameters:

sourceDocument - the document to annotate

documentType - the type of the source document

Method Detail

fromPlainText

public static DocumentAnnotator fromPlainText(java.io.Reader source)

Constructs a DocumentAnnotator to annotate the given text.

Parameters:

source - a Reader representing the source document

setOptions

public void setOptions(DocumentAnnotatorOptions options)

isAnnotationSupported

public boolean isAnnotationSupported()

setAnnotatedOutput

public boolean setAnnotatedOutput(java.io.File destination)
                           throws java.io.IOException

Set the destination file where an annotated version of the source document should be written. Since not all type of source documents are supported for annotation, this method can return false, in which case no annotated document will be generated.

Returns:

true if annotation is supported for the source document, false otherwise.

Throws:

java.io.IOException - if the file exists but is a directory rather than a regular file, does not exist but cannot be created, or cannot be opened for any other reason

See Also:

isAnnotationSupported()

setAnnotatedOutput

public boolean setAnnotatedOutput(java.io.OutputStream destination)

Set the destination output stream where an annotated version of the source document should be written. Since not all type of source documents are supported for annotation, this method can return false, in which case no annotated document will be generated.

Returns:

true if annotation is supported for the source document, false otherwise.

See Also:

isAnnotationSupported()

setAnnotatedOutputDirectory

public java.io.File setAnnotatedOutputDirectory(java.io.File annotateDirectory)
                                         throws java.io.IOException

Set the directory where the annotated document and associated resources will be placed. The name of the annotated document is based on the source document file name, if known. Otherwise, it will be an arbitrary file name, which is returned as the result of this method.

Parameters:

annotateDirectory - the destination directory

Returns:

the File inside the directory where the main document will be stored, or null if annotation is not supported for the source document.

Throws:

java.io.IOException - if the directory cannot be used to store files.

setAnnotatedOutputDirectory

public java.io.File setAnnotatedOutputDirectory(java.io.File annotateDirectory,
                                                boolean keepOriginalExtension)
                                         throws java.io.IOException

Set the directory where the annotated document and associated resources will be placed. The name of the annotated document is based on the source document file name, if known. Otherwise, it will be an arbitrary file name, which is returned as the result of this method.

Parameters:

annotateDirectory - the destination directory

Returns:

the File inside the directory where the main document will be stored, or null if annotation is not supported for the source document.

Throws:

java.io.IOException - if the directory cannot be used to store files.

setResourceDirectory

public void setResourceDirectory(java.io.File resourceDirectory)
                          throws java.io.IOException

Set the directory where resources will be stored.

Throws:

java.io.IOException - if the directory cannot be used to store files.

setD2SOptions

public void setD2SOptions(chemaxon.naming.document.DocumentToStructureOptions options)

setD2SOptions

@Deprecated
public void setD2SOptions(java.lang.String options)

Deprecated. use setD2SOptions(D2S.Options) instead An option String can be parsed to a D2S.Options object using D2SOptionParser.parseOptions().

usePopups

public void usePopups(boolean addPopups)

Parameters:

addPopups - whether a popup should be generated for each hit

setMolconvert

public void setMolconvert(java.io.File molconvert)

setCustomHtmlToXmlConverter

public void setCustomHtmlToXmlConverter(chemaxon.naming.document.annotate.XmlToHtmlConverter customConverter)

Provide a custom converter from XML to HTML, to be used instead of the default one.

read

public Molecule read()
              throws java.io.IOException

Find the next structure in the source document and return it, or null when the end of the document has been reached. If an annotated document is being generated, calling read() might also lead to the corresponding portion of the annotated document to be written to the destination.

Specified by:

read in interface chemaxon.marvin.io.formats.MoleculeImporterIface

Returns:

the next structure found in the source document, or null if the document has been fully processed.

Throws:

java.io.IOException

close

public void close()
           throws java.io.IOException

Specified by:

close in interface chemaxon.marvin.io.formats.MoleculeImporterIface

Specified by:

close in interface java.lang.AutoCloseable

Throws:

java.io.IOException

process

public void process()
             throws java.io.IOException

Process the complete input at once, generating the annotated document.

Throws:

java.io.IOException

See Also:

Used the read() method instead if you want to also get access to the structures found in the document.