textractor.learning
Class AnnotationFormatReader

java.lang.Object
  textractor.learning.AnnotationFormatReader

All Implemented Interfaces:

Closeable

public final class AnnotationFormatReader
extends Object
implements Closeable

Reads text in a format suitable for human annotation and machine parsing. Provides a way to find the TextFragmentAnnotaion that correspond to the annotaions in the file, and update them with the annotation attributes parsed from the file. The format presents each text fragment as in the sample below. Lines that start with *--- indicate that the annotation has been modified by the human annotator and should be updated. Lines that start with --- have not been modified and will not be updated in the database.

 --- identifier --- annotation-attributes < enter here properties as inferred from evidence in the text below:
 text fragment (possibly multiple lines)
 --- identifier --- < enter here properties as inferred from evidence in the text below:
 text fragment (possibly multiple lines)
 

An actual example will look like this:

 --- 1 ---  R79K:mutation < enter here properties as inferred from evidence in the text below:
 However, two types of mutants were constructed one
 bears the R79K mutation on both the dAK and dGK subunits, while the
 other has the R79K mutation on the dGK subunit only (R79K:dGK).
 --- 2 ---  < enter here properties as inferred from evidence in the text below:
 Therefore, the R79K substitution seems to
 have a greater effect on dGuo binding than on that of dAdo, but dGK
 modification appears to produce a stimulatory conformational effect on
 the opposite subunit, resembling the known unidirectional activation of
 dAK by either dGuo or dGTP.
 class of enzymes.
 

Author:

Fabien Campagne

Constructor Summary

AnnotationFormatReader(TextractorManager tm, Reader reader)
Constructs an instance to write the format to the given reader.

Method Summary

void	close()
void	updateAnnotations() Writes a text fragment in a format suitable for annotation.

Methods inherited from class java.lang.Object

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

Constructor Detail

AnnotationFormatReader

public AnnotationFormatReader(TextractorManager tm,
                              Reader reader)
                       throws IOException,
                              ConfigurationException,
                              NoSuchMethodException,
                              IllegalAccessException,
                              InvocationTargetException,
                              InstantiationException,
                              ClassNotFoundException,
                              URISyntaxException

Constructs an instance to write the format to the given reader.

Parameters:

reader - The formatted text fragments will be written to.

Throws:

IOException

ConfigurationException

NoSuchMethodException

IllegalAccessException

InvocationTargetException

InstantiationException

ClassNotFoundException

URISyntaxException

Method Detail

updateAnnotations

public void updateAnnotations()
                       throws IOException,
                              SyntaxErrorException,
                              TextractorDatabaseException

Writes a text fragment in a format suitable for annotation.

Throws:

IOException

SyntaxErrorException

TextractorDatabaseException

close

public void close()

Specified by:

close in interface Closeable