chemaxon.naming

Class DocumentExtractor

java.lang.Object

chemaxon.naming.DocumentExtractor

Deprecated.

use chemaxon.formats.MolImporter or chemaxon.naming.DocumentToStructure instead.

public class DocumentExtractor
extends Object

Extracts chemical names from text documents and converts them to chemical structures. Example usage:

// We have a document to process
java.io.Reader document = ...;

DocumentExtractor x = new DocumentExtractor();
x.processHTML(document); // or processPlainText(document) for input in plain text format

// Iterate through the hits (using a Java 1.5 feature, otherwise use an java.util.Iterator)
for (Hit hit : x.getHits()) {
  System.out.println(hit.position + ": " + hit.text + ": " + hit.structure.toFormat("smiles"));
}

The field hit.position contains the position of the first character of the name in the document.

Note that hit.text contains the name as it appears in the source document. A cleaned version (of possible OCR errors, typos, ...) can be retrieved with hit.structure.getName().

This class can also be called on the command-line. It then expects the name of a plain text file as the first argument (or from the standard input when absent). The list of hits is printed on the standard output.

Author:

Daniel Bonniot

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
class	DocumentExtractor.Hit Deprecated. An occurrence of a chemical name in the processed document.
static class	DocumentExtractor.ProgressInfo Deprecated.
static interface	DocumentExtractor.ProgressListener Deprecated.

Field Summary

Fields

Modifier and Type	Field and Description
static String	propertyPage Deprecated.
static String	propertySourceDocument Deprecated.

Constructor Summary

Constructors

Constructor and Description
DocumentExtractor() Deprecated. Creates a new document extractor.
DocumentExtractor(File document) Deprecated. If the file name ends with ".gz", the content will be uncompressed automatically.
DocumentExtractor(File document, String encoding) Deprecated. If the file name ends with ".gz", the content will be uncompressed automatically.
DocumentExtractor(Reader r) Deprecated.
DocumentExtractor(String text) Deprecated. Extract structures from a String.
DocumentExtractor(URL document) Deprecated.
DocumentExtractor(URLConnection document) Deprecated. Create a document extractor for the given URL connection.

Method Summary

Methods

Modifier and Type	Method and Description
void	acceptElements(boolean on) Deprecated.
void	acceptGenericNames(boolean on) Deprecated. Whether to accept generic, frequent names like "water".
void	acceptGroups(boolean on) Deprecated.
void	acceptIons(boolean on) Deprecated.
void	clearHits() Deprecated. Clears the list of hits.
List<DocumentExtractor.Hit>	getHits() Deprecated. Returns the hits found in the documents processed so far.
static void	main(String[] args) Deprecated. Expects the name of a plain text file as the first argument (or from the standard input when absent).
static void	printEncodingError() Deprecated.
void	processHTML() Deprecated. Extract names from an HTML document.
void	processHTML(DocumentExtractor.ProgressListener progressListener) Deprecated. Extract names from an HTML document.
void	processHTML(Reader r) Deprecated. Extract names from an HTML document.
void	processPlainText() Deprecated. Extract names from a plain text document.
void	processPlainText(DocumentExtractor.ProgressListener progressListener) Deprecated. Extract names from a plain text document.
void	processPlainText(Reader r) Deprecated. Extract names from a plain text document.
static DocumentExtractor	readPDF(File pdf) Deprecated. Creates a DocumentExtractor to process the given PDF document.
static DocumentExtractor	readPDF(InputStream pdfStream) Deprecated. Creates a DocumentExtractor to process the given PDF document.
void	setCasNumberLookup(boolean value) Deprecated. Enable or disable the lookup of CAS numbers (requires network access).

Methods inherited from class java.lang.Object

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

Field Detail

propertySourceDocument

public static final String propertySourceDocument

Deprecated.

See Also:

Constant Field Values

propertyPage

public static final String propertyPage

Deprecated.

See Also:

Constant Field Values

Constructor Detail

DocumentExtractor

public DocumentExtractor()

Deprecated.

Creates a new document extractor.

DocumentExtractor

public DocumentExtractor(File document)
                  throws IOException

Deprecated.

If the file name ends with ".gz", the content will be uncompressed automatically. The getEstimatedTotalCharacters() will be wrong in this case though (to be implemented, request if needed).

Throws:

IOException

DocumentExtractor

public DocumentExtractor(File document,
                 String encoding)
                  throws IOException

Deprecated.

If the file name ends with ".gz", the content will be uncompressed automatically. The getEstimatedTotalCharacters() will be wrong in this case though (to be implemented, request if needed).

Throws:

IOException

DocumentExtractor

public DocumentExtractor(URL document)
                  throws IOException

Deprecated.

Throws:

IOException

DocumentExtractor

public DocumentExtractor(URLConnection document)
                  throws IOException

Deprecated.

Create a document extractor for the given URL connection. This constructor is also useful when using a java.net.Proxy class, by using the URL.openConnection(java.net.Proxy) method to obtain the URLConnection.

Throws:

IOException

DocumentExtractor

public DocumentExtractor(Reader r)

Deprecated.

DocumentExtractor

public DocumentExtractor(String text)

Deprecated.

Extract structures from a String.

Since:

5.8

Method Detail

setCasNumberLookup

public void setCasNumberLookup(boolean value)

Deprecated.

Enable or disable the lookup of CAS numbers (requires network access). Disabled by default.

acceptElements

public void acceptElements(boolean on)

Deprecated.

acceptIons

public void acceptIons(boolean on)

Deprecated.

acceptGenericNames

public void acceptGenericNames(boolean on)

Deprecated.

Whether to accept generic, frequent names like "water".

acceptGroups

public void acceptGroups(boolean on)

Deprecated.

main

public static void main(String[] args)

Deprecated.

Expects the name of a plain text file as the first argument (or from the standard input when absent). The list of hits is printed on the standard output.

printEncodingError

public static void printEncodingError()

Deprecated.

processPlainText

public void processPlainText(Reader r)
                      throws IOException

Deprecated.

Extract names from a plain text document. Buffering is done internally, so passing a BufferedReader is not necessary.

Throws:

IOException

processPlainText

public void processPlainText()
                      throws IOException

Deprecated.

Extract names from a plain text document.

Throws:

IOException

processPlainText

public void processPlainText(DocumentExtractor.ProgressListener progressListener)
                      throws IOException

Deprecated.

Extract names from a plain text document. Buffering is done internally, so passing a BufferedReader is not necessary.

Throws:

IOException

processHTML

public void processHTML(Reader r)
                 throws IOException

Deprecated.

Extract names from an HTML document. Buffering is done internally, so passing a BufferedReader is not necessary.

Throws:

IOException

processHTML

public void processHTML()
                 throws IOException

Deprecated.

Extract names from an HTML document. Buffering is done internally, so passing a BufferedReader is not necessary.

Throws:

IOException

processHTML

public void processHTML(DocumentExtractor.ProgressListener progressListener)
                 throws IOException

Deprecated.

Extract names from an HTML document. Buffering is done internally, so passing a BufferedReader is not necessary.

Throws:

IOException

getHits

public List<DocumentExtractor.Hit> getHits()

Deprecated.

Returns the hits found in the documents processed so far.

clearHits

public void clearHits()

Deprecated.

Clears the list of hits.

readPDF

public static DocumentExtractor readPDF(File pdf)
                                 throws IOException

Deprecated.

Creates a DocumentExtractor to process the given PDF document.

Throws:

IOException

readPDF

public static DocumentExtractor readPDF(InputStream pdfStream)
                                 throws IOException

Deprecated.

Creates a DocumentExtractor to process the given PDF document.

Throws:

IOException