Package GNormPluslib

Class BioCDoc

java.lang.Object

GNormPluslib.BioCDoc

public class BioCDoc
extends Object

Field Summary

Fields

Modifier and Type	Field	Description
ArrayList<ArrayList<ArrayList<String>>>	Annotations
ArrayList<ArrayList<String>>	PassageContexts
ArrayList<ArrayList<String>>	PassageNames
ArrayList<ArrayList<Integer>>	PassageOffsets
ArrayList<String>	PMIDs

Constructor Summary

Constructors

Constructor	Description
BioCDoc()

Method Summary

Modifier and Type	Method	Description
void	BioC2PubTator(String input, String output)
void	BioC2PubTator(String original_input, String input, String output)
String	BioCFormatCheck(String InputFile)
void	BioCOutput(String input, String output, ArrayList<ArrayList<ArrayList<String>>> Annotations, boolean Final, boolean RemovePreviousAnno)
void	BioCReader(String input)
void	BioCReaderWithAnnotation(String input)
void	PubTator2BioC(String input, String output)

Methods inherited from class java.lang.Object

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

Field Detail

PMIDs

public ArrayList<String> PMIDs

PassageNames

public ArrayList<ArrayList<String>> PassageNames

PassageOffsets

public ArrayList<ArrayList<Integer>> PassageOffsets

PassageContexts

public ArrayList<ArrayList<String>> PassageContexts

Annotations

public ArrayList<ArrayList<ArrayList<String>>> Annotations

Constructor Detail

BioCDoc

public BioCDoc()

Method Detail

BioCFormatCheck

public String BioCFormatCheck(String InputFile)
                       throws IOException

Throws:

IOException

PubTator2BioC

public void PubTator2BioC(String input,
                          String output)
                   throws IOException,
                          XMLStreamException

Throws:

IOException

XMLStreamException

BioC2PubTator

public void BioC2PubTator(String input,
                          String output)
                   throws IOException,
                          XMLStreamException

Throws:

IOException

XMLStreamException

BioC2PubTator

public void BioC2PubTator(String original_input,
                          String input,
                          String output)
                   throws IOException,
                          XMLStreamException

Throws:

IOException

XMLStreamException

BioCReader

public void BioCReader(String input)
                throws IOException,
                       XMLStreamException

Throws:

IOException

XMLStreamException

BioCReaderWithAnnotation

public void BioCReaderWithAnnotation(String input)
                              throws IOException,
                                     XMLStreamException

Throws:

IOException

XMLStreamException

BioCOutput

public void BioCOutput(String input,
                       String output,
                       ArrayList<ArrayList<ArrayList<String>>> Annotations,
                       boolean Final,
                       boolean RemovePreviousAnno)
                throws IOException,
                       XMLStreamException

Throws:

IOException

XMLStreamException