import java.io.FileNotFoundException;

import java.io.FileReader;

import java.io.IOException;

import java.io.PrintWriter;

import java.util.HashMap;

import java.util.Iterator;

import java.util.Map;

import java.util.Scanner;

import java.util.StringTokenizer;

/**

* @author alvin567

*/

public class AnnotationParser {

/**

* @param args the command line arguments

*/

public static void main(String[] args) throws FileNotFoundException, IOException {

//Folder folder = new Folder("BioNLP-ST_2011_genia_test_data");//read all files from a list

//store all annotations in a hashmap

String fname[] = {"PMID-9619918.a1","PMID-9619918.a2"};

Annotations anns = readFile(fname);

PrintWriter r = new PrintWriter("recievedFile.txt");

Iterator it = anns.getAnn().entrySet().iterator();

while (it.hasNext()) {

Map.Entry pairs = (Map.Entry)it.next();

r.println(pairs.getKey() + " = " + pairs.getValue());

it.remove();

}

r.flush();

}

public static Annotations readFile(String [] readFile) throws FileNotFoundException{

Annotations anns = new Annotations();

HashMap hp = new HashMap();

for(int a = 0; a < readFile.length;a++){

FileReader file = new FileReader(readFile[a]);

Scanner sc = new Scanner(file);//read files

String lineOfData;

while(sc.hasNextLine()){

lineOfData = sc.nextLine();

Annotation annotation = null;

StringTokenizer token = new StringTokenizer(lineOfData,"\t");

String annotationID = token.nextToken();

//rest of annotation

StringTokenizer rest_of = new StringTokenizer(token.nextToken());

if(annotationID.startsWith("T")){//entity annotations

String type = rest_of.nextToken();

int setStart_offset = Integer.parseInt(rest_of.nextToken());

int setEnd_offset = Integer.parseInt(rest_of.nextToken());

String term = token.nextToken();

annotation = new Entity(annotationID,type,setStart_offset,setEnd_offset,term);

}

if(annotationID.startsWith("M")){//modification

String type = rest_of.nextToken();

String eventID = rest_of.nextToken();

annotation = new Modification(annotationID,type,eventID);

}

if(annotationID.startsWith("E")){

String [] textbound = rest_of.nextToken().split(":");

String type = textbound[0];

String trigger = textbound[1];

int tokenSize = rest_of.countTokens();

HashMap <String,Annotation> arguements = new HashMap();

//Represented in standoff as ID\tTYPE:TRIGGER [ROLE1:PART1 ROLE2:PART2 ...]

for(int x = 0;x < tokenSize;x++){

String roleID = rest_of.nextToken();

String [] arguement = roleID.split(":");

String roles = arguement[0];

String part = arguement[1];

Annotation parts = (Annotation) hp.get(part);

arguements.put(roles,parts);

}

annotation = new Event(annotationID,type,trigger,arguements);

}

if(annotationID.startsWith("*")){//equivalence relationshi

String type = rest_of.nextToken();//ignore token

String annID1 = rest_of.nextToken();

String annID2 = rest_of.nextToken();

annotation = new Equivalence(annotationID,type,annID1,annID2);

}

if(annotationID.startsWith("R")){

String type = rest_of.nextToken();

String [] splitTerm = rest_of.nextToken().split(":");

annotation = new Relation(annotationID,type,splitTerm[0],splitTerm[1]);

}

hp.put(annotationID, annotation);

}

}

anns.setAnn(hp);

return anns;

}

}