diff --git "a/src_Java/GNormPluslib/SimConcept.java" "b/src_Java/GNormPluslib/SimConcept.java"
--- "a/src_Java/GNormPluslib/SimConcept.java"
+++ "b/src_Java/GNormPluslib/SimConcept.java"
@@ -1,1524 +1,1524 @@
-/**
- * Project: GNormPlus
- * Function: SimConcept : Simplify Composite mentions
- */
-
-package GNormPluslib;
-
-import bioc.BioCAnnotation;
-import bioc.BioCCollection;
-import bioc.BioCDocument;
-import bioc.BioCLocation;
-import bioc.BioCPassage;
-
-import bioc.io.BioCDocumentWriter;
-import bioc.io.BioCFactory;
-import bioc.io.woodstox.ConnectorWoodstox;
-import java.io.BufferedReader;
-import java.io.BufferedWriter;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileOutputStream;
-import java.io.FileReader;
-import java.io.FileWriter;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.io.OutputStreamWriter;
-import java.text.BreakIterator;
-import java.time.LocalDate;
-import java.time.ZoneId;
-import java.text.DecimalFormat;
-import java.math.RoundingMode;
-
-import javax.xml.stream.XMLStreamException;
-
-import org.tartarus.snowball.SnowballStemmer;
-import org.tartarus.snowball.ext.englishStemmer;
-
-import java.util.Map;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Locale;
-
-public class SimConcept 
-{
-	/*
-	 * Feature Extraction
-	 */
-	public void FeatureExtraction_Train(String FilenameData) throws XMLStreamException
-	{
-		try 
-		{
-			/** output files */ 
-			BufferedWriter FileData = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(FilenameData), "UTF-8")); // .data
-			//NLP modules
-			SnowballStemmer stemmer = new englishStemmer();
-			/** PMIDs : i */
-			for (int i = 0; i < GNormPlus.BioCDocobj.PMIDs.size(); i++)
-			{
-				String Pmid = GNormPlus.BioCDocobj.PMIDs.get(i);
-				
-				/** Paragraphs : j */
-				for (int j = 0; j < GNormPlus.BioCDocobj.PassageNames.get(i).size(); j++)
-				{
-					ArrayList<String> Annotation = GNormPlus.BioCDocobj.Annotations.get(i).get(j);
-					/** Annotations : k 
-					 * 0 start
-					 * 1 last
-					 * 2 mention
-					 * 3 type
-					 * 4 id
-					 */
-					int Inital_Annotation_size=Annotation.size();
-					for (int k = 0; k < Annotation.size() ; k++)   // k : Annotations
-					{
-						String anno[]=Annotation.get(k).split("\\t",-1);
-						int MentionStart= Integer.parseInt(anno[0]);
-		        		int MentionLast= Integer.parseInt(anno[1]);
-		        		String Mention = anno[2];
-		        		String Type = anno[3];
-		        		if(anno.length>4)
-		        		{
-			        		String ID = anno[4];
-			        		
-			        		String TokenSTR = Mention;
-			        		TokenSTR = TokenSTR.replaceAll("([0-9])([A-Za-z])", "$1 $2");
-			        		TokenSTR = TokenSTR.replaceAll("([A-Za-z])([0-9])", "$1 $2");
-			        		TokenSTR = TokenSTR.replaceAll("([A-Z])([a-z])", "$1 $2");
-			        		TokenSTR = TokenSTR.replaceAll("([a-z])([A-Z])", "$1 $2");
-							TokenSTR = TokenSTR.replaceAll("([\\W])", " $1 ");
-			        		TokenSTR = TokenSTR.replaceAll("[ ]+", " ");
-			        		TokenSTR = TokenSTR.replaceAll("^[ ]+", "");
-			        		TokenSTR = TokenSTR.replaceAll("[ ]+$", "");
-			        		
-			        		/*
-			        		 * Only for Gene
-			        		 */
-			        		if(ID.equals("ASJAS") && k<Inital_Annotation_size)
-			        		{
-			        			Pattern ptmp = Pattern.compile("^([^ ][^ ][^ ]+) ([^ ]+) ([^\\W\\-\\_]+) ([^ ]+) ([^ ]+)$");
-								Matcher mtmp = ptmp.matcher(TokenSTR.toLowerCase());
-								if(mtmp.find())
-								{
-									String t1=mtmp.group(1);
-									String t2=mtmp.group(2);
-									String t3=mtmp.group(3);
-									String t4=mtmp.group(4);
-									String t5=mtmp.group(5);
-									String tmp_ment=t1+" "+t2+" "+t3+" - "+t5;
-									Annotation.add(MentionStart+"\t"+MentionLast+"\t"+tmp_ment+"\t"+Type+"\tASCOS");
-									tmp_ment=t1+" "+t2+" "+t3+" "+t4.substring(0, 1)+" "+t5;
-									Annotation.add(MentionStart+"\t"+MentionLast+"\t"+tmp_ment+"\t"+Type+"\tASCSS");
-									tmp_ment=t1+" "+t2+" / "+t5;
-									Annotation.add(MentionStart+"\t"+MentionLast+"\t"+tmp_ment+"\t"+Type+"\tASCS");
-									tmp_ment=t1+" "+t2+" or - "+t5;
-									Annotation.add(MentionStart+"\t"+MentionLast+"\t"+tmp_ment+"\t"+Type+"\tASCOS");
-									tmp_ment=t1+" I, II, and III";
-									Annotation.add(MentionStart+"\t"+MentionLast+"\t"+tmp_ment+"\t"+Type+"\tASCSCCS");
-									tmp_ment=t1+" B, D, and F";
-									Annotation.add(MentionStart+"\t"+MentionLast+"\t"+tmp_ment+"\t"+Type+"\tASCSCCS");
-									tmp_ment=t1+" A, B, C, D, E, and F";
-									Annotation.add(MentionStart+"\t"+MentionLast+"\t"+tmp_ment+"\t"+Type+"\tASCSCSCSCSCCS");
-									tmp_ment=t1+"1, -2, -4, -7, -9, and -12";
-									Annotation.add(MentionStart+"\t"+MentionLast+"\t"+tmp_ment+"\t"+Type+"\tASCOSCOSCOSCOSCCOS");
-									tmp_ment="B and G "+t1;
-									Annotation.add(MentionStart+"\t"+MentionLast+"\t"+tmp_ment+"\t"+Type+"\tSCSA");
-									tmp_ment="A/E "+t1;
-									Annotation.add(MentionStart+"\t"+MentionLast+"\t"+tmp_ment+"\t"+Type+"\tSCSA");
-									tmp_ment="alpha/beta "+t1;
-									Annotation.add(MentionStart+"\t"+MentionLast+"\t"+tmp_ment+"\t"+Type+"\tSCSA");
-									if(t5.matches("[0-9]") && t2.matches("[0-9]") && Integer.parseInt(t5)>Integer.parseInt(t2))
-									{
-										tmp_ment=t1+" "+t2+" to "+t5;
-										Annotation.add(MentionStart+"\t"+MentionLast+"\t"+tmp_ment+"\t"+Type+"\tASNS");
-										tmp_ment=t1+" "+t2+" to -"+t5;
-										Annotation.add(MentionStart+"\t"+MentionLast+"\t"+tmp_ment+"\t"+Type+"\tASNOS");
-										tmp_ment=t1+" -"+t2+" to -"+t5;
-										Annotation.add(MentionStart+"\t"+MentionLast+"\t"+tmp_ment+"\t"+Type+"\tAASNOS");
-										tmp_ment=t1+" "+t2+" to "+t1+" "+t5;
-										Annotation.add(MentionStart+"\t"+MentionLast+"\t"+tmp_ment+"\t"+Type+"\tASNAS");
-										tmp_ment=t1+" "+t2+"-"+t5;
-										Annotation.add(MentionStart+"\t"+MentionLast+"\t"+tmp_ment+"\t"+Type+"\tASNS");
-										tmp_ment=t1+" "+t2+", "+t5+", and "+(Integer.parseInt(t5)+2);
-										Annotation.add(MentionStart+"\t"+MentionLast+"\t"+tmp_ment+"\t"+Type+"\tASCSCCS");
-										tmp_ment=t1+" -"+t2+", -"+t5+", and -"+(Integer.parseInt(t5)+2);
-										Annotation.add(MentionStart+"\t"+MentionLast+"\t"+tmp_ment+"\t"+Type+"\tAASC0SCC0S");
-									}
-								}
-			        		}
-			        		
-			        		String Mention_tmp = Mention;
-							String tokens[]=TokenSTR.split(" ",-1);
-							
-							//For Repeat
-							HashMap <String,Integer> Token2Num = new HashMap <String,Integer>();
-							for(int p=0;p<tokens.length;p++)
-			                {
-								if(!Token2Num.containsKey(tokens[p]))
-								{
-									Token2Num.put(tokens[p], 0);
-								}
-								Token2Num.put(tokens[p], Token2Num.get(tokens[p])+1);
-							}
-							
-							//For Abbreviation
-							HashMap <Integer,String> AbbLFStatus_hash = new HashMap <Integer,String>();
-							for(String Pmid_LF : GNormPlus.PmidLF2Abb_hash.keySet())
-							{
-								String pf[] = Pmid_LF.split("\\t",-1);
-								if(pf[0].equals(Pmid))
-								{
-									String Abb = GNormPlus.PmidLF2Abb_hash.get(Pmid_LF);
-									String LF = pf[1];
-									
-									Abb = Abb.replaceAll("([0-9])([A-Za-z])", "$1 $2");
-									Abb = Abb.replaceAll("([A-Za-z])([0-9])", "$1 $2");
-					        		Abb = Abb.replaceAll("([A-Z])([a-z])", "$1 $2");
-					        		Abb = Abb.replaceAll("([a-z])([A-Z])", "$1 $2");
-					        		Abb = Abb.replaceAll("([\\W])", " $1 ");
-									Abb = Abb.replaceAll("[ ]+", " ");
-					        		Abb = Abb.replaceAll("^[ ]+", "");
-					        		
-					        		LF = LF.replaceAll("([0-9])([A-Za-z])", "$1 $2");
-					        		LF = LF.replaceAll("([A-Za-z])([0-9])", "$1 $2");
-					        		LF = LF.replaceAll("([A-Z])([a-z])", "$1 $2");
-					        		LF = LF.replaceAll("([a-z])([A-Z])", "$1 $2");
-					        		LF = LF.replaceAll("([\\W])", " $1 ");
-									LF = LF.replaceAll("[ ]+", " ");
-					        		LF = LF.replaceAll("^[ ]+", "");
-					        		LF = LF.replaceAll("[ ]+$", "");
-					        		
-									
-									Abb=Abb.replaceAll("([^A-Za-z0-9@ ])","\\\\$1");
-									LF=LF.replaceAll("([^A-Za-z0-9@ ])","\\\\$1");
-									Abb=Abb.toLowerCase();
-									LF=LF.toLowerCase();
-									Pattern ptmp1 = Pattern.compile("(.*)("+LF+")([ ]*\\([ ]*)("+Abb+")[ ]*\\).*");
-									Matcher mtmp1 = ptmp1.matcher(TokenSTR.toLowerCase());
-									Pattern ptmp2 = Pattern.compile("(.*)("+Abb+")([ ]*\\([ ]*)("+LF+")[ ]*\\).*");
-									Matcher mtmp2 = ptmp2.matcher(TokenSTR.toLowerCase());
-									int start_LF=0;
-									int last_LF=0;
-									int start_Abb=0;
-									int last_Abb=0;
-									if(mtmp1.find())
-									{
-										start_LF = mtmp1.group(1).length();
-										last_LF = start_LF+mtmp1.group(2).length();
-										start_Abb = last_LF+mtmp1.group(3).length();
-										last_Abb = start_Abb+mtmp1.group(4).length();
-									}
-									else if(mtmp2.find())
-									{
-										start_Abb = mtmp2.group(1).length();
-										last_Abb = start_LF+mtmp2.group(2).length();
-										start_LF = last_LF+mtmp2.group(3).length();
-										last_LF = start_Abb+mtmp2.group(4).length();
-									}
-									for(int l=start_LF;l<last_LF;l++)
-									{
-										AbbLFStatus_hash.put(l, "FullName");
-									}
-									for(int l=start_Abb;l<last_Abb;l++)
-									{
-										AbbLFStatus_hash.put(l, "Abbreviation");
-									}
-								}
-							}
-							
-							int Offset=0;
-							for(int p=0;p<tokens.length;p++) // p : toknes
-			                {
-								//white space
-			        			String WSB="WSB:N/A";
-			        			String WSF="WSF:N/A";
-			        			
-			        			if(p>0)
-			        			{
-			        				String B=tokens[p-1];
-			        				B=B.replaceAll("[A-Za-z]+", "A");
-			        				B=B.replaceAll("[0-9]+", "0");
-			        				WSB="WSB:"+B;
-			        			}
-			        			if(p<tokens.length-1)
-			        			{
-			        				String F=tokens[p+1];
-			        				F=F.replaceAll("[A-Za-z]+", "A");
-			        				F=F.replaceAll("[0-9]+", "0");
-			        				WSF="WSF:"+F;
-			        			}
-
-			        			//stemming
-								stemmer.setCurrent(tokens[p].toLowerCase());
-								stemmer.stem();
-								String stem=stemmer.getCurrent();
-								
-								//Number of Numbers [0-9]
-								String Num_num="";
-								String tmp=tokens[p];
-								tmp=tmp.replaceAll("[^0-9]","");
-								if(tmp.length()>3){Num_num="N:4+";}else{Num_num="N:"+ tmp.length();}
-								
-								//Number of Uppercase [A-Z]
-								String Num_Uc="";
-								tmp=tokens[p];
-								tmp=tmp.replaceAll("[^A-Z]","");
-								if(tmp.length()>3){Num_Uc="U:4+";}else{Num_Uc="U:"+ tmp.length();}
-								
-								//Number of Lowercase [a-z]
-								String Num_lc="";
-								tmp=tokens[p];
-								tmp=tmp.replaceAll("[^a-z]","");
-								if(tmp.length()>3){Num_lc="L:4+";}else{Num_lc="L:"+ tmp.length();}
-								
-								//Number of ALL char
-								String Num_All="";
-								if(tokens[p].length()>3){Num_All="A:4+";}else{Num_All="A:"+ tokens[p].length();}
-								
-								//specific character (;:,.->+_)
-								String SpecificC="__nil__";
-								if(tokens[p].equals(";") || tokens[p].equals(":") || tokens[p].equals(",") || tokens[p].equals(".") || tokens[p].equals("-") || tokens[p].equals(">") || tokens[p].equals("+") || tokens[p].equals("_"))
-								{
-									SpecificC="-SpecificC1-";
-								}
-								else if(tokens[p].equals("(") || tokens[p].equals(")"))
-								{
-									SpecificC="-SpecificC2-";
-								}
-								else if(tokens[p].equals("{") || tokens[p].equals("}"))
-								{
-									SpecificC="-SpecificC3-";
-								}
-								else if(tokens[p].equals("[") || tokens[p].equals("]"))
-								{
-									SpecificC="-SpecificC4-";
-								}
-								else if(tokens[p].equals("\\") || tokens[p].equals("/"))
-								{
-									SpecificC="-SpecificC5-";
-								}
-								
-								//Chemical Prefix/Suffix
-								String ChemPreSuf="__nil__";
-								if(tokens[p].matches(".*(yl|ylidyne|oyl|sulfonyl)")){ChemPreSuf="-CHEMinlineSuffix-";}
-								else if(tokens[p].matches("(meth|eth|prop|tetracos).*")){ChemPreSuf="-CHEMalkaneStem-";}
-								else if(tokens[p].matches("(di|tri|tetra).*")){ChemPreSuf="-CHEMsimpleMultiplier-";}
-								else if(tokens[p].matches("(benzen|pyridin|toluen).*")){ChemPreSuf="-CHEMtrivialRing-";}
-								else if(tokens[p].matches(".*(one|ol|carboxylic|amide|ate|acid|ium|ylium|ide|uide|iran|olan|inan|pyrid|acrid|amid|keten|formazan|fydrazin)(s|)")){ChemPreSuf="-CHEMsuffix-";}
-								
-								//MentionType
-								String MentionType="__nil__";
-								if(GNormPlus.SimConceptMention2Type_hash.containsKey(tokens[p]))
-								{
-									MentionType = "-"+GNormPlus.SimConceptMention2Type_hash.get(tokens[p])+"-";
-								}
-								
-								//Protein symbols
-								String ProteinSym="__nil__";
-								if(tokens[p].matches(".*(glutamine|glutamic|leucine|valine|isoleucine|lysine|alanine|glycine|aspartate|methionine|threonine|histidine|aspartic|asparticacid|arginine|asparagine|tryptophan|proline|phenylalanine|cysteine|serine|glutamate|tyrosine|stop|frameshift).*")){ChemPreSuf="-ProteinSymFull-";}
-								else if(tokens[p].matches("(cys|ile|ser|gln|met|asn|pro|lys|asp|thr|phe|ala|gly|his|leu|arg|trp|val|glu|tyr|fs|fsx)")){ChemPreSuf="-ProteinSymTri-";}
-								else if(tokens[p].matches("[CISQMNPKDTFAGHLRWVEYX]")){ChemPreSuf="-ProteinSymChar-";}
-								
-								//Repeat
-								String Repeat="__nil__";
-								if(Token2Num.get(tokens[p])>1 && tokens[p].length()>1 && (!tokens[p].matches("([\\W\\-\\_0-9]+|and|or|alpha|beta|gamma|theta|zeta|delta|kappa|II|VI|IV|III)")))
-								{
-									Repeat="-Repeat-";
-								}
-								
-								//Patterns
-								String Pattern1 = tokens[p];
-								if(Pattern1.matches(".*[\\W\\-\\_].*"))
-								{
-									Pattern1="__nil__";
-								}
-								else
-								{
-									Pattern1=Pattern1.replaceAll("[A-Z]", "A");
-									Pattern1=Pattern1.replaceAll("[a-z]", "a");
-									Pattern1=Pattern1.replaceAll("[0-9]", "0");
-									Pattern1="P1:"+Pattern1;
-								}
-								String Pattern2 = tokens[p];
-								if(Pattern2.matches(".*[\\W\\-\\_].*"))
-								{
-									Pattern2="__nil__";
-								}
-								else
-								{
-									Pattern2=Pattern2.replaceAll("[A-Za-z]", "a");
-									Pattern2=Pattern2.replaceAll("[0-9]", "0");
-									Pattern2="P2:"+Pattern2;
-								}
-								String Pattern3 = tokens[p];
-								if(Pattern3.matches(".*[\\W\\-\\_].*"))
-								{
-									Pattern3="__nil__";
-								}
-								else
-								{
-									Pattern3=Pattern3.replaceAll("[A-Z]+", "A");
-									Pattern3=Pattern3.replaceAll("[a-z]+", "a");
-									Pattern3=Pattern3.replaceAll("[0-9]+", "0");
-									Pattern3="P3:"+Pattern3;
-								}
-								String Pattern4 = tokens[p];
-								if(Pattern4.matches(".*[\\W\\-\\_].*"))
-								{
-									Pattern4="__nil__";
-								}
-								else
-								{
-									Pattern4=Pattern4.replaceAll("[A-Za-z]+", "a");
-									Pattern4=Pattern4.replaceAll("[0-9]+", "0");
-									Pattern4="P4:"+Pattern4;
-								}
-								
-								//prefix
-								String prefix="";
-								tmp=tokens[p];
-								if(tmp.length()>=1){ prefix=tmp.substring(0, 1);}else{prefix="__nil__";}
-								if(tmp.length()>=2){ prefix=prefix+" "+tmp.substring(0, 2);}else{prefix=prefix+" __nil__";}
-								if(tmp.length()>=3){ prefix=prefix+" "+tmp.substring(0, 3);}else{prefix=prefix+" __nil__";}
-								if(tmp.length()>=4){ prefix=prefix+" "+tmp.substring(0, 4);}else{prefix=prefix+" __nil__";}
-								if(tmp.length()>=5){ prefix=prefix+" "+tmp.substring(0, 5);}else{prefix=prefix+" __nil__";}
-								
-								//suffix
-								String suffix="";
-								tmp=tokens[p];
-								if(tmp.length()>=1){ suffix=tmp.substring(tmp.length()-1, tmp.length());}else{suffix="__nil__";}
-								if(tmp.length()>=2){ suffix=suffix+" "+tmp.substring(tmp.length()-2, tmp.length());}else{suffix=suffix+" __nil__";}
-								if(tmp.length()>=3){ suffix=suffix+" "+tmp.substring(tmp.length()-3, tmp.length());}else{suffix=suffix+" __nil__";}
-								if(tmp.length()>=4){ suffix=suffix+" "+tmp.substring(tmp.length()-4, tmp.length());}else{suffix=suffix+" __nil__";}
-								if(tmp.length()>=5){ suffix=suffix+" "+tmp.substring(tmp.length()-5, tmp.length());}else{suffix=suffix+" __nil__";}
-								
-								//Abbreviation & Long Form
-								String AbbLF="__nil__";
-								if(AbbLFStatus_hash.containsKey(Offset))
-								{
-									AbbLF=AbbLFStatus_hash.get(Offset);
-								}
-								
-								String Status = ID.substring(p, p+1);
-			        			FileData.write(tokens[p]+" "+WSB+" "+WSF+" "+stem
-			        					+" "+Num_num+" "+Num_num+" "+Num_Uc+" "+Num_lc+" "+Num_All+" "+SpecificC
-			        					+" "+ChemPreSuf+" "+MentionType+" "+ProteinSym+" "+Repeat
-			        					+" "+Pattern1+" "+Pattern2+" "+Pattern3+" "+Pattern4
-			        					+" "+prefix+" "+suffix+" "+AbbLF
-			        					+" "+Status+"\n");
-			        			Offset=Offset+tokens[p].length()+1;
-			        			if(ID.length()>tokens.length)
-			        			{
-			        				System.out.println(ID+"\t"+TokenSTR);
-			        			}
-			                }	
-			        		FileData.write("\n");
-		        		}
-					}
-	        		
-				}
-			}
-			FileData.close();
-		}
-		catch(IOException e1){ System.out.println("[MR]: Input file is not exist.");}
-	}
-	public void FeatureExtraction_Test(String FilenameData) throws XMLStreamException
-	{
-		try 
-		{
-			/** output files */ 
-			BufferedWriter FileData = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(FilenameData), "UTF-8")); // .data
-			//NLP modules
-			SnowballStemmer stemmer = new englishStemmer();
-			/** PMIDs : i */
-			for (int i = 0; i < GNormPlus.BioCDocobj.Annotations.size(); i++)
-			{
-				String Pmid = GNormPlus.BioCDocobj.PMIDs.get(i);
-				
-				/** Paragraphs : j */
-				for (int j = 0; j < GNormPlus.BioCDocobj.Annotations.get(i).size(); j++)
-				{
-					ArrayList<String> Annotation = GNormPlus.BioCDocobj.Annotations.get(i).get(j);
-					/** Annotations : k 
-					 * 0 start
-					 * 1 last
-					 * 2 mention
-					 * 3 type
-					 * 4 id
-					 */
-					for (int k = 0; k < Annotation.size() ; k++)   // k : Annotations
-					{
-						String anno[]=Annotation.get(k).split("\\t",-1);
-						String Mentions = anno[2];
-						String Type = anno[3];
-		        		String MentionArr[]=Mentions.split("\\|",-1);
-		        		if(Type.equals("Gene"))
-		        		{
-			        		for(int m=0;m<MentionArr.length;m++)
-			        		{
-			        			String Mention = MentionArr[m];
-			        			String TokenSTR = Mention;
-				        		TokenSTR = TokenSTR.replaceAll("([0-9])([A-Za-z])", "$1 $2");
-				        		TokenSTR = TokenSTR.replaceAll("([A-Za-z])([0-9])", "$1 $2");
-				        		TokenSTR = TokenSTR.replaceAll("([A-Z])([a-z])", "$1 $2");
-				        		TokenSTR = TokenSTR.replaceAll("([a-z])([A-Z])", "$1 $2");
-								TokenSTR = TokenSTR.replaceAll("([\\W])", " $1 ");
-				        		TokenSTR = TokenSTR.replaceAll("[ ]+", " ");
-				        		TokenSTR = TokenSTR.replaceAll("^[ ]+", "");
-				        		String Mention_tmp = Mention;
-								String tokens[]=TokenSTR.split(" ",-1);
-								
-								//For Repeat
-								HashMap <String,Integer> Token2Num = new HashMap <String,Integer>();
-								for(int p=0;p<tokens.length;p++)
-				                {
-									if(!Token2Num.containsKey(tokens[p]))
-									{
-										Token2Num.put(tokens[p], 0);
-									}
-									Token2Num.put(tokens[p], Token2Num.get(tokens[p])+1);
-								}
-								
-								//For Abbreviation
-								HashMap <Integer,String> AbbLFStatus_hash = new HashMap <Integer,String>();
-								for(String Pmid_LF : GNormPlus.PmidLF2Abb_hash.keySet())
-								{
-									String pf[] = Pmid_LF.split("\\t",-1);
-									if(pf[0].equals(Pmid))
-									{
-										String Abb = GNormPlus.PmidLF2Abb_hash.get(Pmid_LF);
-										String LF = pf[1];
-										
-										Abb = Abb.replaceAll("([0-9])([A-Za-z])", "$1 $2");
-										Abb = Abb.replaceAll("([A-Za-z])([0-9])", "$1 $2");
-						        		Abb = Abb.replaceAll("([A-Z])([a-z])", "$1 $2");
-						        		Abb = Abb.replaceAll("([a-z])([A-Z])", "$1 $2");
-						        		Abb = Abb.replaceAll("([\\W])", " $1 ");
-										Abb = Abb.replaceAll("[ ]+", " ");
-						        		Abb = Abb.replaceAll("^[ ]+", "");
-						        		
-						        		LF = LF.replaceAll("([0-9])([A-Za-z])", "$1 $2");
-						        		LF = LF.replaceAll("([A-Za-z])([0-9])", "$1 $2");
-						        		LF = LF.replaceAll("([A-Z])([a-z])", "$1 $2");
-						        		LF = LF.replaceAll("([a-z])([A-Z])", "$1 $2");
-						        		LF = LF.replaceAll("([\\W])", " $1 ");
-										LF = LF.replaceAll("[ ]+", " ");
-						        		LF = LF.replaceAll("^[ ]+", "");
-						        		
-										
-										Abb=Abb.replaceAll("([\\~\\!\\@\\#\\$\\%\\^\\&\\*\\(\\)\\_\\+\\-\\=\\[\\]\\;\\'\\,\\.\\/\\{\\}\\|\\:\\?])","\\\\$1");
-										LF=LF.replaceAll("([\\~\\!\\@\\#\\$\\%\\^\\&\\*\\(\\)\\_\\+\\-\\=\\[\\]\\;\\'\\,\\.\\/\\{\\}\\|\\:\\?])","\\\\$1");
-										Abb=Abb.toLowerCase();
-										LF=LF.toLowerCase();
-										Pattern ptmp1 = Pattern.compile("(.*)"
-														+ "("+LF+")"
-														+ "([ ]*\\([ ]*)"
-														+ "("+Abb+")"
-														+ "[ ]*\\).*");
-										Matcher mtmp1 = ptmp1.matcher(TokenSTR.toLowerCase());
-										Pattern ptmp2 = Pattern.compile("(.*)"
-														+ "("+Abb+")"
-														+ "([ ]*\\([ ]*)"
-														+ "("+LF+")"
-														+ "[ ]*\\).*");
-										Matcher mtmp2 = ptmp2.matcher(TokenSTR.toLowerCase());
-										int start_LF=0;
-										int last_LF=0;
-										int start_Abb=0;
-										int last_Abb=0;
-										if(mtmp1.find())
-										{
-											start_LF = mtmp1.group(1).length();
-											last_LF = start_LF+mtmp1.group(2).length();
-											start_Abb = last_LF+mtmp1.group(3).length();
-											last_Abb = start_Abb+mtmp1.group(4).length();
-										}
-										else if(mtmp2.find())
-										{
-											start_Abb = mtmp2.group(1).length();
-											last_Abb = start_LF+mtmp2.group(2).length();
-											start_LF = last_LF+mtmp2.group(3).length();
-											last_LF = start_Abb+mtmp2.group(4).length();
-										}
-										for(int l=start_LF;l<last_LF;l++)
-										{
-											AbbLFStatus_hash.put(l, "FullName");
-										}
-										for(int l=start_Abb;l<last_Abb;l++)
-										{
-											AbbLFStatus_hash.put(l, "Abbreviation");
-										}
-									}
-								}
-								
-								int Offset=0;
-								for(int p=0;p<tokens.length;p++) // p : toknes
-				                {
-									//white space
-				        			String WSB="WSB:N/A";
-				        			String WSF="WSF:N/A";
-				        			
-				        			if(p>0)
-				        			{
-				        				String B=tokens[p-1];
-				        				B=B.replaceAll("[A-Za-z]+", "A");
-				        				B=B.replaceAll("[0-9]+", "0");
-				        				WSB="WSB:"+B;
-				        			}
-				        			if(p<tokens.length-1)
-				        			{
-				        				String F=tokens[p+1];
-				        				F=F.replaceAll("[A-Za-z]+", "A");
-				        				F=F.replaceAll("[0-9]+", "0");
-				        				WSF="WSF:"+F;
-				        			}
-				        			
-				        			//stemming
-									stemmer.setCurrent(tokens[p].toLowerCase());
-									stemmer.stem();
-									String stem=stemmer.getCurrent();
-									
-									//Number of Numbers [0-9]
-									String Num_num="";
-									String tmp=tokens[p];
-									tmp=tmp.replaceAll("[^0-9]","");
-									if(tmp.length()>3){Num_num="N:4+";}else{Num_num="N:"+ tmp.length();}
-									
-									//Number of Uppercase [A-Z]
-									String Num_Uc="";
-									tmp=tokens[p];
-									tmp=tmp.replaceAll("[^A-Z]","");
-									if(tmp.length()>3){Num_Uc="U:4+";}else{Num_Uc="U:"+ tmp.length();}
-									
-									//Number of Lowercase [a-z]
-									String Num_lc="";
-									tmp=tokens[p];
-									tmp=tmp.replaceAll("[^a-z]","");
-									if(tmp.length()>3){Num_lc="L:4+";}else{Num_lc="L:"+ tmp.length();}
-									
-									//Number of ALL char
-									String Num_All="";
-									if(tokens[p].length()>3){Num_All="A:4+";}else{Num_All="A:"+ tokens[p].length();}
-									
-									//specific character (;:,.->+_)
-									String SpecificC="__nil__";
-									if(tokens[p].equals(";") || tokens[p].equals(":") || tokens[p].equals(",") || tokens[p].equals(".") || tokens[p].equals("-") || tokens[p].equals(">") || tokens[p].equals("+") || tokens[p].equals("_"))
-									{
-										SpecificC="-SpecificC1-";
-									}
-									else if(tokens[p].equals("(") || tokens[p].equals(")"))
-									{
-										SpecificC="-SpecificC2-";
-									}
-									else if(tokens[p].equals("{") || tokens[p].equals("}"))
-									{
-										SpecificC="-SpecificC3-";
-									}
-									else if(tokens[p].equals("[") || tokens[p].equals("]"))
-									{
-										SpecificC="-SpecificC4-";
-									}
-									else if(tokens[p].equals("\\") || tokens[p].equals("/"))
-									{
-										SpecificC="-SpecificC5-";
-									}
-									
-									//Chemical Prefix/Suffix
-									String ChemPreSuf="__nil__";
-									if(tokens[p].matches(".*(yl|ylidyne|oyl|sulfonyl)")){ChemPreSuf="-CHEMinlineSuffix-";}
-									else if(tokens[p].matches("(meth|eth|prop|tetracos).*")){ChemPreSuf="-CHEMalkaneStem-";}
-									else if(tokens[p].matches("(di|tri|tetra).*")){ChemPreSuf="-CHEMsimpleMultiplier-";}
-									else if(tokens[p].matches("(benzen|pyridin|toluen).*")){ChemPreSuf="-CHEMtrivialRing-";}
-									else if(tokens[p].matches(".*(one|ol|carboxylic|amide|ate|acid|ium|ylium|ide|uide|iran|olan|inan|pyrid|acrid|amid|keten|formazan|fydrazin)(s|)")){ChemPreSuf="-CHEMsuffix-";}
-									
-									//MentionType
-									String MentionType="__nil__";
-									if(GNormPlus.SimConceptMention2Type_hash.containsKey(tokens[p]))
-									{
-										MentionType = "-"+GNormPlus.SimConceptMention2Type_hash.get(tokens[p])+"-";
-									}
-									
-									//Protein symbols
-									String ProteinSym="__nil__";
-									if(tokens[p].matches(".*(glutamine|glutamic|leucine|valine|isoleucine|lysine|alanine|glycine|aspartate|methionine|threonine|histidine|aspartic|asparticacid|arginine|asparagine|tryptophan|proline|phenylalanine|cysteine|serine|glutamate|tyrosine|stop|frameshift).*")){ChemPreSuf="-ProteinSymFull-";}
-									else if(tokens[p].matches("(cys|ile|ser|gln|met|asn|pro|lys|asp|thr|phe|ala|gly|his|leu|arg|trp|val|glu|tyr|fs|fsx)")){ChemPreSuf="-ProteinSymTri-";}
-									else if(tokens[p].matches("[CISQMNPKDTFAGHLRWVEYX]")){ChemPreSuf="-ProteinSymChar-";}
-									
-									//Repeat
-									String Repeat="__nil__";
-									if(Token2Num.get(tokens[p])>1 && tokens[p].length()>1 && (!tokens[p].matches("([\\W\\-\\_0-9]+|and|or|alpha|beta|gamma|theta|zeta|delta|kappa|II|VI|IV|III)")))
-									{
-										Repeat="-Repeat-";
-									}
-									
-									//Patterns
-									String Pattern1 = tokens[p];
-									if(Pattern1.matches(".*[\\W\\-\\_].*"))
-									{
-										Pattern1="__nil__";
-									}
-									else
-									{
-										Pattern1=Pattern1.replaceAll("[A-Z]", "A");
-										Pattern1=Pattern1.replaceAll("[a-z]", "a");
-										Pattern1=Pattern1.replaceAll("[0-9]", "0");
-										Pattern1="P1:"+Pattern1;
-									}
-									String Pattern2 = tokens[p];
-									if(Pattern2.matches(".*[\\W\\-\\_].*"))
-									{
-										Pattern2="__nil__";
-									}
-									else
-									{
-										Pattern2=Pattern2.replaceAll("[A-Za-z]", "a");
-										Pattern2=Pattern2.replaceAll("[0-9]", "0");
-										Pattern2="P2:"+Pattern2;
-									}
-									String Pattern3 = tokens[p];
-									if(Pattern3.matches(".*[\\W\\-\\_].*"))
-									{
-										Pattern3="__nil__";
-									}
-									else
-									{
-										Pattern3=Pattern3.replaceAll("[A-Z]+", "A");
-										Pattern3=Pattern3.replaceAll("[a-z]+", "a");
-										Pattern3=Pattern3.replaceAll("[0-9]+", "0");
-										Pattern3="P3:"+Pattern3;
-									}
-									String Pattern4 = tokens[p];
-									if(Pattern4.matches(".*[\\W\\-\\_].*"))
-									{
-										Pattern4="__nil__";
-									}
-									else
-									{
-										Pattern4=Pattern4.replaceAll("[A-Za-z]+", "a");
-										Pattern4=Pattern4.replaceAll("[0-9]+", "0");
-										Pattern4="P4:"+Pattern4;
-									}
-									
-									//prefix
-									String prefix="";
-									tmp=tokens[p];
-									if(tmp.length()>=1){ prefix=tmp.substring(0, 1);}else{prefix="__nil__";}
-									if(tmp.length()>=2){ prefix=prefix+" "+tmp.substring(0, 2);}else{prefix=prefix+" __nil__";}
-									if(tmp.length()>=3){ prefix=prefix+" "+tmp.substring(0, 3);}else{prefix=prefix+" __nil__";}
-									if(tmp.length()>=4){ prefix=prefix+" "+tmp.substring(0, 4);}else{prefix=prefix+" __nil__";}
-									if(tmp.length()>=5){ prefix=prefix+" "+tmp.substring(0, 5);}else{prefix=prefix+" __nil__";}
-									
-									//suffix
-									String suffix="";
-									tmp=tokens[p];
-									if(tmp.length()>=1){ suffix=tmp.substring(tmp.length()-1, tmp.length());}else{suffix="__nil__";}
-									if(tmp.length()>=2){ suffix=suffix+" "+tmp.substring(tmp.length()-2, tmp.length());}else{suffix=suffix+" __nil__";}
-									if(tmp.length()>=3){ suffix=suffix+" "+tmp.substring(tmp.length()-3, tmp.length());}else{suffix=suffix+" __nil__";}
-									if(tmp.length()>=4){ suffix=suffix+" "+tmp.substring(tmp.length()-4, tmp.length());}else{suffix=suffix+" __nil__";}
-									if(tmp.length()>=5){ suffix=suffix+" "+tmp.substring(tmp.length()-5, tmp.length());}else{suffix=suffix+" __nil__";}
-									
-									//Abbreviation & Long Form
-									String AbbLF="__nil__";
-									if(AbbLFStatus_hash.containsKey(Offset))
-									{
-										AbbLF=AbbLFStatus_hash.get(Offset);
-									}
-									
-									FileData.write(tokens[p]+" "+WSB+" "+WSF+" "+stem
-				        					+" "+Num_num+" "+Num_num+" "+Num_Uc+" "+Num_lc+" "+Num_All+" "+SpecificC
-				        					+" "+ChemPreSuf+" "+MentionType+" "+ProteinSym+" "+Repeat
-				        					+" "+Pattern1+" "+Pattern2+" "+Pattern3+" "+Pattern4
-				        					+" "+prefix+" "+suffix+" "+AbbLF+"\n");
-				        			Offset=Offset+tokens[p].length()+1;
-				                }
-								FileData.write("\n");
-				        	}
-		        		}
-					}
-	        		
-				}
-			}
-			FileData.close();
-		}
-		catch(IOException e1){ System.out.println("[MR]: Input file is not exist.");}
-	}
-	public void CRF_test(String model, String FilenameData,String FilenameOutput) throws IOException 
-	{
-		File f = new File(FilenameOutput);
-        BufferedWriter fr = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(f), "UTF-8"));
-		
-		Runtime runtime = Runtime.getRuntime();
-	    
-		String cmd ="CRF/crf_test -m "+model+" -o "+FilenameOutput+" "+FilenameData;
-	    
-	    try {
-	    	Process process = runtime.exec(cmd);
-	    	InputStream is = process.getInputStream();
-	    	InputStreamReader isr = new InputStreamReader(is, "UTF-8");
-	    	BufferedReader br = new BufferedReader(isr);
-	    	String line="";
-		    while ( (line = br.readLine()) != null) 
-		    {
-		    	fr.write(line);
-		    	fr.newLine();
-		        fr.flush();
-		    }
-		    is.close();
-		    isr.close();
-		    br.close();
-		    fr.close();
-	    }
-	    catch (IOException e) {
-	    	System.out.println(e);
-	    	runtime.exit(0);
-	    }
-	}
-	public void CRF_learn(String model,String FilenameData) throws IOException 
-	{
-		Runtime runtime = Runtime.getRuntime();
-	    
-	    Process process = null;
-	    String line = null;
-	    InputStream is = null;
-	    InputStreamReader isr = null;
-	    BufferedReader br = null;
-	    String cmd = "CRF/crf_learn -f 3 -c 4.0 CRF/template_SimConcept "+FilenameData+" "+model; 
-	    
-	    try {
-	    	process = runtime.exec(cmd);
-		    is = process.getInputStream();
-		    isr = new InputStreamReader(is, "UTF-8");
-		    br = new BufferedReader(isr);
-		    while ( (line = br.readLine()) != null) 
-		    {
-		    	System.out.println(line);
-		        System.out.flush();
-		    }
-		    is.close();
-		    isr.close();
-		    br.close();
-	    }
-	    catch (IOException e) {
-	    	System.out.println(e);
-	    	runtime.exit(0);
-	    }
-	}
-	public void ReadCRFresult(String Filename,String FilenameOutput,String FilenameBioC) throws XMLStreamException, IOException
-	{
-		/** load CRF output */
-		ArrayList<String> outputArr1 = new ArrayList<String>();
-		BufferedReader inputfile = new BufferedReader(new InputStreamReader(new FileInputStream(FilenameOutput), "UTF-8"));
-		String line;
-		while ((line = inputfile.readLine()) != null)  
-		{	
-			outputArr1.add(line);
-		}
-		inputfile.close();
-		
-		/**
-		 * Recognize the mentions which can be simplified
-		 */
-		int Count_mention=0;
-		boolean Simplified=false;
-		String Mention="";
-		String Mention_NoSpace="";
-		String States="";
-		HashMap<String,String> Mentions_hash = new HashMap<String,String>();
-		HashMap<String,String> States_hash = new HashMap<String,String>();
-		HashMap<String,String> Output_Split_mention_Ind = new HashMap<String,String>();
-		HashMap<String,String> Output_Split_mention = new HashMap<String,String>();
-		for(int i=0;i<outputArr1.size();i++)
-		{
-			String outputsRow[]=outputArr1.get(i).split("\\t",-1);
-			String Token = outputsRow[0]; // 1st column: Token
-			String TknState = outputsRow[outputsRow.length-1]; // last column: state
-			
-			if(TknState.matches("[CJBEFN]")) //  Simplify-able
-			{
-				Simplified = true;
-			}
-			
-			if(outputsRow.length<=1) //the end of a mention
-			{
-				if(Simplified == true)
-				{
-					/*
-					 * update BF states :
-					 * 
-					 *  AABAFA
-					 *  AWXWOA
-					 * 
-					 */
-					for (String PmidAbb : GNormPlus.PmidAbb2LF_hash.keySet())
-					{
-						String PmidAbbs[]=PmidAbb.split("\\t",-1);
-						String Abb = PmidAbbs[1];
-						String LF = GNormPlus.PmidAbb2LF_hash.get(PmidAbb);
-
-						Abb = Abb.replaceAll("([0-9])([A-Za-z])", "$1 $2");
-						Abb = Abb.replaceAll("([A-Za-z])([0-9])", "$1 $2");
-		        		Abb = Abb.replaceAll("([A-Z])([a-z])", "$1 $2");
-		        		Abb = Abb.replaceAll("([a-z])([A-Z])", "$1 $2");
-		        		Abb = Abb.replaceAll("([\\W])", " $1 ");
-						Abb = Abb.replaceAll("[ ]+", " ");
-		        		Abb = Abb.replaceAll("^[ ]+", "");
-		        		LF = LF.replaceAll("([0-9])([A-Za-z])", "$1 $2");
-		        		LF = LF.replaceAll("([A-Za-z])([0-9])", "$1 $2");
-		        		LF = LF.replaceAll("([A-Z])([a-z])", "$1 $2");
-		        		LF = LF.replaceAll("([a-z])([A-Z])", "$1 $2");
-		        		LF = LF.replaceAll("([\\W])", " $1 ");
-						LF = LF.replaceAll("[ ]+", " ");
-		        		LF = LF.replaceAll("^[ ]+", "");
-		        		Abb=Abb.replaceAll("([^A-Za-z0-9@ ])","\\\\$1");
-						LF=LF.replaceAll("([^A-Za-z0-9@ ])","\\\\$1");
-						
-						Pattern ptmp1 = Pattern.compile("^(.*)("+LF+") \\( ("+Abb+") \\) (.*)$");
-						Matcher mtmp1 = ptmp1.matcher(Mention);
-						Pattern ptmp2 = Pattern.compile("^(.*)("+Abb+") \\( ("+LF+") \\) (.*)$");
-						Matcher mtmp2 = ptmp2.matcher(Mention);
-						if(mtmp1.find())
-						{
-							int t1_len=0;
-							if(!mtmp1.group(1).equals(""))
-							{
-								t1_len=mtmp1.group(1).split(" ",-1).length;
-							}
-							String t2[] = mtmp1.group(2).split(" ",-1);
-							String t3[] = mtmp1.group(3).split(" ",-1);
-							
-							String N1 ="";String N2 ="";String N3 ="";String N4 ="";
-							N1=States.substring(0,t1_len);
-							for(int t=0;t<t2.length;t++){N2=N2+"W";}
-							for(int t=0;t<t3.length;t++){N3=N3+"W";}
-							N4=States.substring(N1.length()+N2.length()+N3.length()+2);
-							States=N1+N2+"X"+N3+"O"+N4;
-						}
-						else if(mtmp2.find())
-						{
-							int t1_len=0;
-							if(!mtmp2.group(1).equals(""))
-							{
-								t1_len=mtmp2.group(1).split(" ",-1).length;
-							}
-							String t2[] = mtmp2.group(2).split(" ",-1);
-							String t3[] = mtmp2.group(3).split(" ",-1);
-							
-							String N1 ="";String N2 ="";String N3 ="";String N4 ="";
-							N1=States.substring(0,t1_len);
-							for(int t=0;t<t2.length;t++){N2=N2+"W";}
-							for(int t=0;t<t3.length;t++){N3=N3+"W";}
-							N4=States.substring(N1.length()+N2.length()+N3.length()+2);
-							States=N1+N2+"X"+N3+"O"+N4;
-						}
-						else
-						{
-							//System.out.println(Mention+"\t"+LF+"\t"+Abb);
-						}
-					}
-					States_hash.put(Mention_NoSpace, States);
-					Mentions_hash.put(Mention_NoSpace, Mention);
-				}
-				//Initial
-				Simplified= false;
-				Mention="";
-				Mention_NoSpace="";
-				Count_mention++;
-				States="";
-			}
-			else
-			{
-				if(Mention.equals(""))
-				{
-					Mention = Token;
-				}
-				else
-				{
-					Mention = Mention +" "+Token;
-				}
-				States=States+TknState;
-				Mention_NoSpace=Mention_NoSpace+Token;
-			}
-		}
-		
-		for (String MNoSpace : Mentions_hash.keySet()) // mention : i
-		{
-			ArrayList<String> Split_mention = new ArrayList<String>();
-			ArrayList<String> Split_state = new ArrayList<String>();
-			String tmp_mention="";
-			String tmp_state="";
-			/**
-			 * count = Mentions_count.get(i) : # of the mention in the corpus (543)
-			 * Mentions_hash.get(count) : Original Mention (ORP - 1 to ORP - 6)
-			 * States_hash.get(count) : States (AASNOOS)
-			 */
-			
-			String TokenArr[]=Mentions_hash.get(MNoSpace).split(" ",-1);
-			String StateArr[]=States_hash.get(MNoSpace).split("",-1);
-			
-			//refinement : isn't used
-			Pattern ptmp1 = Pattern.compile("^([S]+)([CN])([S]+)$");
-			Matcher mtmp1 = ptmp1.matcher(States_hash.get(MNoSpace));
-			if(mtmp1.find())
-			{
-				States_hash.put(MNoSpace, mtmp1.group(1)+"J"+mtmp1.group(3));
-			}
-
-			//Split BE
-			int len=TokenArr.length;
-			if(StateArr.length<TokenArr.length){len=StateArr.length;}
-			for(int s=0;s<len;s++) // token/state : s
-			{
-				if(StateArr[s].matches("[BE]"))
-				{
-					if(tmp_mention.length()>0)
-					{
-						Split_mention.add(tmp_mention);
-						Split_state.add(tmp_state);
-					}
-					tmp_mention = "";
-					tmp_state = "";
-				}
-				else //CNBF
-				{
-					tmp_mention = tmp_mention + TokenArr[s] + " ";
-					tmp_state = tmp_state + StateArr[s];
-				}
-			}
-			if(!tmp_mention.equals(""))
-			{	
-				Split_mention.add(tmp_mention);
-				Split_state.add(tmp_state);
-			}
-			
-			//Split B/F
-			for(int m=0;m<Split_mention.size();m++)// m mention
-			{
-				String A="";
-				String X="";
-				String STAA="";
-				String strainX="";
-				String STAstrainX="";
-				int X_continous=0;
-				ArrayList<String> strainsX = new ArrayList<String>();
-				ArrayList<String> STAstrainsX = new ArrayList<String>();
-				String each_token[] = Split_mention.get(m).split(" ");
-				String each_state[] = Split_state.get(m).split("");
-				for(int s=0;s<each_state.length;s++) //s token
-				{
-					if(each_state[s].matches("[ACNS]"))
-					{
-						A=A+each_token[s]+" ";
-						STAA =STAA+each_state[s];
-					}
-					else if(each_state[s].equals("W"))
-					{
-						A=A+"STRAINXXX";
-						STAA=STAA+"@";
-						strainX=strainX+each_token[s]+" ";
-						STAstrainX=STAstrainX+each_state[s];
-						X_continous=0;
-					}
-					else if(each_state[s].equals("X") && X_continous==0)
-					{
-						X=each_state[s];
-						strainsX.add(strainX);
-						STAstrainsX.add(STAstrainX);
-						strainX="";
-						STAstrainX="";
-						X_continous++;
-					}
-				}
-				if(!strainX.equals("")){strainsX.add(strainX);}
-				if(!STAstrainX.equals("")){STAstrainsX.add(STAstrainX);}
-				A=A.replaceAll("(STRAINXXX){1,}", "STRAINXXX");
-				STAA=STAA.replaceAll("(@){1,}", "@");
-				
-				if(X.equals("X"))
-				{
-					for(int x=0;x<strainsX.size();x++) //x token
-					{
-						String strain=strainsX.get(x);
-						String state=STAstrainsX.get(x);
-						String tkns = A;
-						strain = strain.replaceAll("([\\W\\-\\_])", "\\\\$1");
-						tkns=tkns.replaceAll("STRAINXXX", strain);
-						tkns=tkns.replaceAll("  ", " ");
-						if(tkns.substring(tkns.length()-1,tkns.length()-1).equals(" ")){tkns=tkns.substring(0,tkns.length()-2);}
-						String STAAs=STAA;
-						STAAs=STAAs.replaceAll("@", state);
-						Split_mention.add(tkns);
-						Split_state.add(STAAs);
-					}
-					Split_mention.remove(m);
-					Split_state.remove(m);
-				}
-			}
-			for(int s=0;s<Split_state.size();s++)
-			{
-				Split_state.set(s,Split_state.get(s).replaceAll("W","A"));
-			}
-			
-			//Split J
-			for(int m=0;m<Split_mention.size();m++)// m mention
-			{
-				String each_token[] = Split_mention.get(m).split(" ",-1);
-				String each_state[] = Split_state.get(m).split("",-1);
-				String sub_mention="";
-				boolean found_J = false;
-				for(int k=0;k<each_state.length;k++)
-				{
-					if(each_state[k].equals("J"))
-					{
-						found_J = true;
-						if(Output_Split_mention_Ind.containsKey(MNoSpace))
-						{
-							Output_Split_mention_Ind.put(MNoSpace, Output_Split_mention_Ind.get(MNoSpace)+"|"+sub_mention);
-						}
-						else
-						{
-							Output_Split_mention_Ind.put(MNoSpace,sub_mention);
-						}
-						sub_mention="";
-					}
-					else 
-					{
-						sub_mention=sub_mention+each_token[k]+" ";
-					}
-				}
-				
-				if(found_J == true)
-				{
-					if(Output_Split_mention_Ind.containsKey(MNoSpace))
-					{
-						Output_Split_mention_Ind.put(MNoSpace, Output_Split_mention_Ind.get(MNoSpace)+"|"+sub_mention);
-					}
-					else
-					{
-						Output_Split_mention_Ind.put(MNoSpace,sub_mention);
-					}
-				}
-			}
-			
-			//Split CN
-			for(int m=0;m<Split_mention.size();m++) // s split mention
-			{
-				String A="";
-				String strainCN="";
-				int CNO_continous=0;
-				ArrayList<String> strainsCN = new ArrayList<String>();
-				String CorN="";
-				
-				String each_token[] = Split_mention.get(m).split(" ",-1);
-				String each_state[] = Split_state.get(m).split("",-1);
-				
-				for(int k=0;k<each_state.length;k++)
-				{
-					if(each_state[k].equals("A"))
-					{
-						A=A+each_token[k]+" ";
-					}
-					else if(each_state[k].equals("S"))
-					{
-						if(A.length()>=4)
-						{
-							A=A.replace("s $", "");
-						}
-						A=A+"STRAINXXX";
-						strainCN=strainCN+each_token[k]+" ";
-						CNO_continous=0;
-					}
-					else if(each_state[k].matches("[CN]") && CNO_continous==0)
-					{
-						CorN=each_state[k];
-						strainsCN.add(strainCN);
-						strainCN="";
-						CNO_continous++;
-					}
-					else if(each_state[k].equals("J"))
-					{
-						if(!strainCN.equals("")){strainsCN.add(strainCN);}
-						
-						A=A.replaceAll("STRAINXXXSTRAINXXX","STRAINXXX");
-						A=A.replaceAll("STRAINXXXSTRAINXXX","STRAINXXX");
-						
-						ptmp1 = Pattern.compile("^(.+)s (.*)$");
-						mtmp1 = ptmp1.matcher(A);
-						if(mtmp1.find() && mtmp1.group(1).length()>=3 )
-						{
-							A = mtmp1.group(1)+ " "+mtmp1.group(2);
-						}
-						
-						if(CorN.equals("C"))
-						{
-							for(int x=0;x<strainsCN.size();x++)
-							{
-								String tmp = A;
-								String strainsCN_tmp=strainsCN.get(x).replaceAll("([^A-Za-z0-9@ ])", "\\\\$1");
-								tmp = tmp.replaceAll("STRAINXXX", strainsCN_tmp);
-								tmp = tmp.replaceAll("[ ]+", " ");
-								if(tmp.length()>2 && (tmp.substring(tmp.length()-2, tmp.length()-2).equals(" ")))
-								{
-									tmp = tmp.substring(0,tmp.length()-2);
-								}
-								if(Output_Split_mention_Ind.containsKey(MNoSpace))
-								{
-									Output_Split_mention_Ind.put(MNoSpace, Output_Split_mention_Ind.get(MNoSpace)+"|"+tmp);
-								}
-								else
-								{
-									Output_Split_mention_Ind.put(MNoSpace, tmp);
-								}
-							}
-						}
-						else if(CorN.equals("N"))
-						{
-							if(strainsCN.contains(0) && strainsCN.contains(1))
-							{
-								String strain1= strainsCN.get(0).replaceAll(" ", "");
-								String strain2= strainsCN.get(1).replaceAll(" ", "");
-								if(strain1.matches("[0-9]+") && strain2.matches("[0-9]+"))
-								{
-									if(Integer.parseInt(strain2)-Integer.parseInt(strain1)<=20)
-									{
-										for(int strCount=Integer.parseInt(strain1);strCount<=Integer.parseInt(strain2);strCount++)
-										{
-											String tmp=A;
-											tmp = tmp.replace("STRAINXXX", Integer.toString(strCount));
-											tmp = tmp.replaceAll("[ ]+"," ");
-											if(tmp.length()>2 && tmp.substring(tmp.length()-2, tmp.length()-2).equals(" "))
-											{
-												tmp = tmp.substring(0,tmp.length()-2);
-											}
-											if(Output_Split_mention_Ind.containsKey(MNoSpace))
-											{
-												Output_Split_mention_Ind.put(MNoSpace, Output_Split_mention_Ind.get(MNoSpace)+"|"+tmp);
-											}
-											else
-											{
-												Output_Split_mention_Ind.put(MNoSpace, tmp);
-											}
-										}
-									}
-								}
-								else if(strain1.matches("[A-Z]+ ") && strain2.matches("[A-Z]+ "))
-								{
-									int strInt1 = (int) strain1.replaceAll(" ", "").charAt(0);
-									int strInt2 = (int) strain2.replaceAll(" ", "").charAt(0);
-									if(strInt2-strInt1<=20)
-									{
-										for(int strCount=strInt1;strCount<=strInt2;strCount++)
-										{
-											String tmp=A;
-											tmp = tmp.replace("STRAINXXX", Integer.toString(strCount));
-											tmp = tmp.replaceAll("[ ]+"," ");
-											if(tmp.length()>2 && tmp.substring(tmp.length()-2, tmp.length()-2).equals(" "))
-											{
-												tmp = tmp.substring(0,tmp.length()-2);
-											}
-											if(Output_Split_mention_Ind.containsKey(MNoSpace))
-											{
-												Output_Split_mention_Ind.put(MNoSpace, Output_Split_mention_Ind.get(MNoSpace)+"|"+tmp);
-											}
-											else
-											{
-												Output_Split_mention_Ind.put(MNoSpace, tmp);
-											}
-										}
-									}
-								}
-								else
-								{
-									if(Output_Split_mention.containsKey(MNoSpace))
-									{
-										Output_Split_mention.put(MNoSpace, Output_Split_mention.get(MNoSpace)+"|"+Split_mention.get(m));
-									}
-									else
-									{
-										Output_Split_mention.put(MNoSpace, Split_mention.get(m));
-									}
-								}
-							}
-						}
-						else
-						{
-							if(Output_Split_mention.containsKey(MNoSpace))
-							{
-								Output_Split_mention.put(MNoSpace, Output_Split_mention.get(MNoSpace)+"|"+Split_mention.get(m));
-							}
-							else
-							{
-								Output_Split_mention.put(MNoSpace, Split_mention.get(m));
-							}
-						}
-						
-						A="";
-						strainCN="";
-						CNO_continous=0;
-						strainsCN = new ArrayList<String>();
-						CorN="";
-					}
-				}
-				if(!strainCN.equals("")){strainsCN.add(strainCN);}
-				
-				A=A.replaceAll("(STRAINXXX){2,}","STRAINXXX");
-				
-				ptmp1 = Pattern.compile("^(.+)s (.*)$");
-				mtmp1 = ptmp1.matcher(A);
-				if(mtmp1.find() && mtmp1.group(1).length()>=3 )
-				{
-					A = mtmp1.group(1)+ " "+mtmp1.group(2);
-				}
-				
-				if(CorN.equals("C"))
-				{
-					for(int x=0;x<strainsCN.size();x++)
-					{
-						String tmp = A;
-						tmp = tmp.replaceAll("\\$", " ");
-						strainsCN.set(x,strainsCN.get(x).replaceAll("\\$", " "));
-						tmp = tmp.replaceAll("STRAINXXX", strainsCN.get(x));
-						tmp = tmp.replaceAll("[ ]+", " ");
-						if(tmp.length()>2 && (tmp.substring(tmp.length()-2, tmp.length()-2).equals(" ")))
-						{
-							tmp = tmp.substring(0,tmp.length()-2);
-						}
-						if(Output_Split_mention_Ind.containsKey(MNoSpace))
-						{
-							Output_Split_mention_Ind.put(MNoSpace, Output_Split_mention_Ind.get(MNoSpace)+"|"+tmp);
-						}
-						else
-						{
-							Output_Split_mention_Ind.put(MNoSpace, tmp);
-						}
-					}
-				}
-				else if(CorN.equals("N"))
-				{
-					if(strainsCN.size()==2)
-					{
-						String strain1= strainsCN.get(0).replaceAll(" ", "");
-						String strain2= strainsCN.get(1).replaceAll(" ", "");
-						if(strain1.matches("[0-9]{1,7}") && strain2.matches("[0-9]{1,7}"))
-						{
-							if(Integer.parseInt(strain2)-Integer.parseInt(strain1)<=20)
-							{
-								for(int strCount=Integer.parseInt(strain1);strCount<=Integer.parseInt(strain2);strCount++)
-								{
-									String tmp=A;
-									tmp = tmp.replace("STRAINXXX", Integer.toString(strCount));
-									tmp = tmp.replaceAll("[ ]+"," ");
-									if(tmp.length()>2 && tmp.substring(tmp.length()-2, tmp.length()-2).equals(" "))
-									{
-										tmp = tmp.substring(0,tmp.length()-2);
-									}
-									if(Output_Split_mention_Ind.containsKey(MNoSpace))
-									{
-										Output_Split_mention_Ind.put(MNoSpace, Output_Split_mention_Ind.get(MNoSpace)+"|"+tmp);
-									}
-									else
-									{
-										Output_Split_mention_Ind.put(MNoSpace, tmp);
-									}
-								}
-							}
-						}
-						else if(strain1.matches("[A-Z]+ ") && strain2.matches("[A-Z]+ "))
-						{
-							int strInt1 = (int) strain1.replaceAll(" ", "").charAt(0);
-							int strInt2 = (int) strain2.replaceAll(" ", "").charAt(0);
-							if(strInt2-strInt1<=20)
-							{
-								for(int strCount=strInt1;strCount<=strInt2;strCount++)
-								{
-									String tmp=A;
-									tmp = tmp.replace("STRAINXXX", Integer.toString(strCount));
-									tmp = tmp.replaceAll("[ ]+"," ");
-									if(tmp.length()>2 && tmp.substring(tmp.length()-2, tmp.length()-2).equals(" "))
-									{
-										tmp = tmp.substring(0,tmp.length()-2);
-									}
-									if(Output_Split_mention_Ind.containsKey(MNoSpace))
-									{
-										Output_Split_mention_Ind.put(MNoSpace, Output_Split_mention_Ind.get(MNoSpace)+"|"+tmp);
-									}
-									else
-									{
-										Output_Split_mention_Ind.put(MNoSpace, tmp);
-									}
-								}
-							}
-						}
-						else
-						{
-							if(Output_Split_mention.containsKey(MNoSpace))
-							{
-								Output_Split_mention.put(MNoSpace, Output_Split_mention.get(MNoSpace)+"|"+Split_mention.get(m));
-							}
-							else
-							{
-								Output_Split_mention.put(MNoSpace, Split_mention.get(m));
-							}
-						}
-					}
-				}
-				else
-				{
-					if(Output_Split_mention.containsKey(MNoSpace))
-					{
-						Output_Split_mention.put(MNoSpace, Output_Split_mention.get(MNoSpace)+"|"+Split_mention.get(m));
-					}
-					else
-					{
-						Output_Split_mention.put(MNoSpace, Split_mention.get(m));
-					}
-				}
-			}
-		}
-		
-		for (int i = 0; i < GNormPlus.BioCDocobj.Annotations.size(); i++)
-		{
-			for (int j = 0; j < GNormPlus.BioCDocobj.Annotations.get(i).size(); j++)
-			{
-				int Annotation_Num = GNormPlus.BioCDocobj.Annotations.get(i).get(j).size();
-				for (int k = 0; k < Annotation_Num ; k++)   // k : Annotations
-				{
-					String anno[]=GNormPlus.BioCDocobj.Annotations.get(i).get(j).get(k).split("\\t"); //Mention
-					String MenArr[]=anno[2].split("\\|");
-	        		for(int m=0;m<MenArr.length;m++)
-	        		{
-	        			String MNoSpace = MenArr[m];
-	        			MNoSpace = MNoSpace.replaceAll("[ ]+",  "");
-	        			if(Output_Split_mention_Ind.containsKey(MNoSpace))
-	        			{
-	        				if(anno.length==5)
-	        				{
-	        					String split_men[]=Output_Split_mention_Ind.get(MNoSpace).split("\\|"); 
-	        					for(int s=0;s<split_men.length;s++)
-	        					{
-	        						String anno2 = anno[2] +"|"+split_men[s];
-		        					GNormPlus.BioCDocobj.Annotations.get(i).get(j).add(anno[0]+"\t"+anno[1]+"\t"+anno2+"\t"+anno[3]+"\t"+anno[4]);
-		        				}
-	        				}
-	        				else if(anno.length<5)
-	        				{
-	        					String split_men[]=Output_Split_mention_Ind.get(MNoSpace).split("\\|"); 
-	        					for(int s=0;s<split_men.length;s++)
-	        					{
-	        						String anno2 = anno[2] +"|"+split_men[s];
-		        					GNormPlus.BioCDocobj.Annotations.get(i).get(j).add(anno[0]+"\t"+anno[1]+"\t"+anno2+"\t"+anno[3]);
-	        					}
-	        				}
-	        			}
-	        			else if(Output_Split_mention.containsKey(MNoSpace))
-	        			{
-	        				if(anno.length==5)
-	        				{
-	        					String anno2 = anno[2] +"|"+Output_Split_mention.get(MNoSpace);
-	        					GNormPlus.BioCDocobj.Annotations.get(i).get(j).set(k, anno[0]+"\t"+anno[1]+"\t"+anno2+"\t"+anno[3]+"\t"+anno[4]);
-	        				}
-	        				else if(anno.length<5)
-	        				{
-	        					GNormPlus.BioCDocobj.Annotations.get(i).get(j).set(k, anno[0]+"\t"+anno[1]+"\t"+anno[2]+"\t"+anno[3]);
-	        				}
-	        			} 
-	        		}
-	        	}
-			}
-		}
-		
-		/**
-		 * suffixprefix_orig2modified
-		 */
-		for (int i = 0; i < GNormPlus.BioCDocobj.Annotations.size(); i++)
-		{
-			for (int j = 0; j < GNormPlus.BioCDocobj.Annotations.get(i).size(); j++)
-			{
-				int Annotation_Num = GNormPlus.BioCDocobj.Annotations.get(i).get(j).size();
-				for (int k = 0; k < Annotation_Num ; k++)   // k : Annotations
-				{
-					String anno[]=GNormPlus.BioCDocobj.Annotations.get(i).get(j).get(k).split("\\t"); //Mention
-					String MenArr[]=anno[2].split("\\|");
-					ArrayList <String> Mentions = new ArrayList<String>();
-					for(int m=0;m<MenArr.length;m++)
-	        		{
-						Mentions.add(MenArr[m]);
-						for(String orig_mention : GNormPlus.suffixprefix_orig2modified.keySet())
-						{
-							String modi_mention=GNormPlus.suffixprefix_orig2modified.get(orig_mention);
-							if(MenArr[m].equals(orig_mention))
-							{
-								Mentions.add(modi_mention);
-								break;
-							}
-						}
-					}
-					String mens="";
-					for(int m=0;m<Mentions.size();m++)
-					{
-						String mention=Mentions.get(m);
-						if(mens.equals(""))
-						{
-							mens=mention;
-						}
-						else
-						{
-							mens=mens+"|"+mention;
-						}
-					}
-					if(anno.length==5)
-    				{
-    					GNormPlus.BioCDocobj.Annotations.get(i).get(j).set(k, anno[0]+"\t"+anno[1]+"\t"+mens+"\t"+anno[3]+"\t"+anno[4]);
-    				}
-    				else if(anno.length<5)
-    				{
-    					GNormPlus.BioCDocobj.Annotations.get(i).get(j).set(k, anno[0]+"\t"+anno[1]+"\t"+mens+"\t"+anno[3]);
-    				}
-				}
-			}
-		}
-		
-		/*
-		// 2 --> ii
-		// ii --> 2
-		for (int i = 0; i < GNormPlus.BioCDocobj.Annotations.size(); i++)
-		{
-			for (int j = 0; j < GNormPlus.BioCDocobj.Annotations.get(i).size(); j++)
-			{
-				int Annotation_Num = GNormPlus.BioCDocobj.Annotations.get(i).get(j).size();
-				for (int k = 0; k < Annotation_Num ; k++)   // k : Annotations
-				{
-					String anno[]=GNormPlus.BioCDocobj.Annotations.get(i).get(j).get(k).split("\\t"); //Mention
-					String MenArr[]=anno[2].split("\\|");
-					HashMap<String,String> Mentions = new HashMap<String,String>();
-					for(int m=0;m<MenArr.length;m++)
-	        		{
-						Mentions.put(MenArr[m], "");
-						for(String suffix : GNormPlus.SuffixTranslationMap2_hash.keySet())
-						{
-							String Men_rev=MenArr[m].replaceAll(suffix, GNormPlus.SuffixTranslationMap2_hash.get(suffix));
-							Mentions.put(Men_rev, "");
-						}
-					}
-					String mens="";
-					for(String mention : Mentions.keySet())
-					{
-						if(mens.equals(""))
-						{
-							mens=mention;
-						}
-						else
-						{
-							mens=mens+"|"+mention;
-						}
-					}
-				}
-			}
-		}
-		*/
-		GNormPlus.BioCDocobj.BioCOutput(Filename,FilenameBioC,GNormPlus.BioCDocobj.Annotations,false,true);
-	}
+/**
+ * Project: GNormPlus
+ * Function: SimConcept : Simplify Composite mentions
+ */
+
+package GNormPluslib;
+
+import bioc.BioCAnnotation;
+import bioc.BioCCollection;
+import bioc.BioCDocument;
+import bioc.BioCLocation;
+import bioc.BioCPassage;
+
+import bioc.io.BioCDocumentWriter;
+import bioc.io.BioCFactory;
+import bioc.io.woodstox.ConnectorWoodstox;
+import java.io.BufferedReader;
+import java.io.BufferedWriter;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileOutputStream;
+import java.io.FileReader;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.io.OutputStreamWriter;
+import java.text.BreakIterator;
+import java.time.LocalDate;
+import java.time.ZoneId;
+import java.text.DecimalFormat;
+import java.math.RoundingMode;
+
+import javax.xml.stream.XMLStreamException;
+
+import org.tartarus.snowball.SnowballStemmer;
+import org.tartarus.snowball.ext.englishStemmer;
+
+import java.util.Map;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Locale;
+
+public class SimConcept 
+{
+	/*
+	 * Feature Extraction
+	 */
+	public void FeatureExtraction_Train(String FilenameData) throws XMLStreamException
+	{
+		try 
+		{
+			/** output files */ 
+			BufferedWriter FileData = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(FilenameData), "UTF-8")); // .data
+			//NLP modules
+			SnowballStemmer stemmer = new englishStemmer();
+			/** PMIDs : i */
+			for (int i = 0; i < GNormPlus.BioCDocobj.PMIDs.size(); i++)
+			{
+				String Pmid = GNormPlus.BioCDocobj.PMIDs.get(i);
+				
+				/** Paragraphs : j */
+				for (int j = 0; j < GNormPlus.BioCDocobj.PassageNames.get(i).size(); j++)
+				{
+					ArrayList<String> Annotation = GNormPlus.BioCDocobj.Annotations.get(i).get(j);
+					/** Annotations : k 
+					 * 0 start
+					 * 1 last
+					 * 2 mention
+					 * 3 type
+					 * 4 id
+					 */
+					int Inital_Annotation_size=Annotation.size();
+					for (int k = 0; k < Annotation.size() ; k++)   // k : Annotations
+					{
+						String anno[]=Annotation.get(k).split("\\t",-1);
+						int MentionStart= Integer.parseInt(anno[0]);
+		        		int MentionLast= Integer.parseInt(anno[1]);
+		        		String Mention = anno[2];
+		        		String Type = anno[3];
+		        		if(anno.length>4)
+		        		{
+			        		String ID = anno[4];
+			        		
+			        		String TokenSTR = Mention;
+			        		TokenSTR = TokenSTR.replaceAll("([0-9])([A-Za-z])", "$1 $2");
+			        		TokenSTR = TokenSTR.replaceAll("([A-Za-z])([0-9])", "$1 $2");
+			        		TokenSTR = TokenSTR.replaceAll("([A-Z])([a-z])", "$1 $2");
+			        		TokenSTR = TokenSTR.replaceAll("([a-z])([A-Z])", "$1 $2");
+							TokenSTR = TokenSTR.replaceAll("([\\W])", " $1 ");
+			        		TokenSTR = TokenSTR.replaceAll("[ ]+", " ");
+			        		TokenSTR = TokenSTR.replaceAll("^[ ]+", "");
+			        		TokenSTR = TokenSTR.replaceAll("[ ]+$", "");
+			        		
+			        		/*
+			        		 * Only for Gene
+			        		 */
+			        		if(ID.equals("ASJAS") && k<Inital_Annotation_size)
+			        		{
+			        			Pattern ptmp = Pattern.compile("^([^ ][^ ][^ ]+) ([^ ]+) ([^\\W\\-\\_]+) ([^ ]+) ([^ ]+)$");
+								Matcher mtmp = ptmp.matcher(TokenSTR.toLowerCase());
+								if(mtmp.find())
+								{
+									String t1=mtmp.group(1);
+									String t2=mtmp.group(2);
+									String t3=mtmp.group(3);
+									String t4=mtmp.group(4);
+									String t5=mtmp.group(5);
+									String tmp_ment=t1+" "+t2+" "+t3+" - "+t5;
+									Annotation.add(MentionStart+"\t"+MentionLast+"\t"+tmp_ment+"\t"+Type+"\tASCOS");
+									tmp_ment=t1+" "+t2+" "+t3+" "+t4.substring(0, 1)+" "+t5;
+									Annotation.add(MentionStart+"\t"+MentionLast+"\t"+tmp_ment+"\t"+Type+"\tASCSS");
+									tmp_ment=t1+" "+t2+" / "+t5;
+									Annotation.add(MentionStart+"\t"+MentionLast+"\t"+tmp_ment+"\t"+Type+"\tASCS");
+									tmp_ment=t1+" "+t2+" or - "+t5;
+									Annotation.add(MentionStart+"\t"+MentionLast+"\t"+tmp_ment+"\t"+Type+"\tASCOS");
+									tmp_ment=t1+" I, II, and III";
+									Annotation.add(MentionStart+"\t"+MentionLast+"\t"+tmp_ment+"\t"+Type+"\tASCSCCS");
+									tmp_ment=t1+" B, D, and F";
+									Annotation.add(MentionStart+"\t"+MentionLast+"\t"+tmp_ment+"\t"+Type+"\tASCSCCS");
+									tmp_ment=t1+" A, B, C, D, E, and F";
+									Annotation.add(MentionStart+"\t"+MentionLast+"\t"+tmp_ment+"\t"+Type+"\tASCSCSCSCSCCS");
+									tmp_ment=t1+"1, -2, -4, -7, -9, and -12";
+									Annotation.add(MentionStart+"\t"+MentionLast+"\t"+tmp_ment+"\t"+Type+"\tASCOSCOSCOSCOSCCOS");
+									tmp_ment="B and G "+t1;
+									Annotation.add(MentionStart+"\t"+MentionLast+"\t"+tmp_ment+"\t"+Type+"\tSCSA");
+									tmp_ment="A/E "+t1;
+									Annotation.add(MentionStart+"\t"+MentionLast+"\t"+tmp_ment+"\t"+Type+"\tSCSA");
+									tmp_ment="alpha/beta "+t1;
+									Annotation.add(MentionStart+"\t"+MentionLast+"\t"+tmp_ment+"\t"+Type+"\tSCSA");
+									if(t5.matches("[0-9]") && t2.matches("[0-9]") && Integer.parseInt(t5)>Integer.parseInt(t2))
+									{
+										tmp_ment=t1+" "+t2+" to "+t5;
+										Annotation.add(MentionStart+"\t"+MentionLast+"\t"+tmp_ment+"\t"+Type+"\tASNS");
+										tmp_ment=t1+" "+t2+" to -"+t5;
+										Annotation.add(MentionStart+"\t"+MentionLast+"\t"+tmp_ment+"\t"+Type+"\tASNOS");
+										tmp_ment=t1+" -"+t2+" to -"+t5;
+										Annotation.add(MentionStart+"\t"+MentionLast+"\t"+tmp_ment+"\t"+Type+"\tAASNOS");
+										tmp_ment=t1+" "+t2+" to "+t1+" "+t5;
+										Annotation.add(MentionStart+"\t"+MentionLast+"\t"+tmp_ment+"\t"+Type+"\tASNAS");
+										tmp_ment=t1+" "+t2+"-"+t5;
+										Annotation.add(MentionStart+"\t"+MentionLast+"\t"+tmp_ment+"\t"+Type+"\tASNS");
+										tmp_ment=t1+" "+t2+", "+t5+", and "+(Integer.parseInt(t5)+2);
+										Annotation.add(MentionStart+"\t"+MentionLast+"\t"+tmp_ment+"\t"+Type+"\tASCSCCS");
+										tmp_ment=t1+" -"+t2+", -"+t5+", and -"+(Integer.parseInt(t5)+2);
+										Annotation.add(MentionStart+"\t"+MentionLast+"\t"+tmp_ment+"\t"+Type+"\tAASC0SCC0S");
+									}
+								}
+			        		}
+			        		
+			        		String Mention_tmp = Mention;
+							String tokens[]=TokenSTR.split(" ",-1);
+							
+							//For Repeat
+							HashMap <String,Integer> Token2Num = new HashMap <String,Integer>();
+							for(int p=0;p<tokens.length;p++)
+			                {
+								if(!Token2Num.containsKey(tokens[p]))
+								{
+									Token2Num.put(tokens[p], 0);
+								}
+								Token2Num.put(tokens[p], Token2Num.get(tokens[p])+1);
+							}
+							
+							//For Abbreviation
+							HashMap <Integer,String> AbbLFStatus_hash = new HashMap <Integer,String>();
+							for(String Pmid_LF : GNormPlus.PmidLF2Abb_hash.keySet())
+							{
+								String pf[] = Pmid_LF.split("\\t",-1);
+								if(pf[0].equals(Pmid))
+								{
+									String Abb = GNormPlus.PmidLF2Abb_hash.get(Pmid_LF);
+									String LF = pf[1];
+									
+									Abb = Abb.replaceAll("([0-9])([A-Za-z])", "$1 $2");
+									Abb = Abb.replaceAll("([A-Za-z])([0-9])", "$1 $2");
+					        		Abb = Abb.replaceAll("([A-Z])([a-z])", "$1 $2");
+					        		Abb = Abb.replaceAll("([a-z])([A-Z])", "$1 $2");
+					        		Abb = Abb.replaceAll("([\\W])", " $1 ");
+									Abb = Abb.replaceAll("[ ]+", " ");
+					        		Abb = Abb.replaceAll("^[ ]+", "");
+					        		
+					        		LF = LF.replaceAll("([0-9])([A-Za-z])", "$1 $2");
+					        		LF = LF.replaceAll("([A-Za-z])([0-9])", "$1 $2");
+					        		LF = LF.replaceAll("([A-Z])([a-z])", "$1 $2");
+					        		LF = LF.replaceAll("([a-z])([A-Z])", "$1 $2");
+					        		LF = LF.replaceAll("([\\W])", " $1 ");
+									LF = LF.replaceAll("[ ]+", " ");
+					        		LF = LF.replaceAll("^[ ]+", "");
+					        		LF = LF.replaceAll("[ ]+$", "");
+					        		
+									
+									Abb=Abb.replaceAll("([^A-Za-z0-9@ ])","\\\\$1");
+									LF=LF.replaceAll("([^A-Za-z0-9@ ])","\\\\$1");
+									Abb=Abb.toLowerCase();
+									LF=LF.toLowerCase();
+									Pattern ptmp1 = Pattern.compile("(.*)("+LF+")([ ]*\\([ ]*)("+Abb+")[ ]*\\).*");
+									Matcher mtmp1 = ptmp1.matcher(TokenSTR.toLowerCase());
+									Pattern ptmp2 = Pattern.compile("(.*)("+Abb+")([ ]*\\([ ]*)("+LF+")[ ]*\\).*");
+									Matcher mtmp2 = ptmp2.matcher(TokenSTR.toLowerCase());
+									int start_LF=0;
+									int last_LF=0;
+									int start_Abb=0;
+									int last_Abb=0;
+									if(mtmp1.find())
+									{
+										start_LF = mtmp1.group(1).length();
+										last_LF = start_LF+mtmp1.group(2).length();
+										start_Abb = last_LF+mtmp1.group(3).length();
+										last_Abb = start_Abb+mtmp1.group(4).length();
+									}
+									else if(mtmp2.find())
+									{
+										start_Abb = mtmp2.group(1).length();
+										last_Abb = start_LF+mtmp2.group(2).length();
+										start_LF = last_LF+mtmp2.group(3).length();
+										last_LF = start_Abb+mtmp2.group(4).length();
+									}
+									for(int l=start_LF;l<last_LF;l++)
+									{
+										AbbLFStatus_hash.put(l, "FullName");
+									}
+									for(int l=start_Abb;l<last_Abb;l++)
+									{
+										AbbLFStatus_hash.put(l, "Abbreviation");
+									}
+								}
+							}
+							
+							int Offset=0;
+							for(int p=0;p<tokens.length;p++) // p : toknes
+			                {
+								//white space
+			        			String WSB="WSB:N/A";
+			        			String WSF="WSF:N/A";
+			        			
+			        			if(p>0)
+			        			{
+			        				String B=tokens[p-1];
+			        				B=B.replaceAll("[A-Za-z]+", "A");
+			        				B=B.replaceAll("[0-9]+", "0");
+			        				WSB="WSB:"+B;
+			        			}
+			        			if(p<tokens.length-1)
+			        			{
+			        				String F=tokens[p+1];
+			        				F=F.replaceAll("[A-Za-z]+", "A");
+			        				F=F.replaceAll("[0-9]+", "0");
+			        				WSF="WSF:"+F;
+			        			}
+
+			        			//stemming
+								stemmer.setCurrent(tokens[p].toLowerCase());
+								stemmer.stem();
+								String stem=stemmer.getCurrent();
+								
+								//Number of Numbers [0-9]
+								String Num_num="";
+								String tmp=tokens[p];
+								tmp=tmp.replaceAll("[^0-9]","");
+								if(tmp.length()>3){Num_num="N:4+";}else{Num_num="N:"+ tmp.length();}
+								
+								//Number of Uppercase [A-Z]
+								String Num_Uc="";
+								tmp=tokens[p];
+								tmp=tmp.replaceAll("[^A-Z]","");
+								if(tmp.length()>3){Num_Uc="U:4+";}else{Num_Uc="U:"+ tmp.length();}
+								
+								//Number of Lowercase [a-z]
+								String Num_lc="";
+								tmp=tokens[p];
+								tmp=tmp.replaceAll("[^a-z]","");
+								if(tmp.length()>3){Num_lc="L:4+";}else{Num_lc="L:"+ tmp.length();}
+								
+								//Number of ALL char
+								String Num_All="";
+								if(tokens[p].length()>3){Num_All="A:4+";}else{Num_All="A:"+ tokens[p].length();}
+								
+								//specific character (;:,.->+_)
+								String SpecificC="__nil__";
+								if(tokens[p].equals(";") || tokens[p].equals(":") || tokens[p].equals(",") || tokens[p].equals(".") || tokens[p].equals("-") || tokens[p].equals(">") || tokens[p].equals("+") || tokens[p].equals("_"))
+								{
+									SpecificC="-SpecificC1-";
+								}
+								else if(tokens[p].equals("(") || tokens[p].equals(")"))
+								{
+									SpecificC="-SpecificC2-";
+								}
+								else if(tokens[p].equals("{") || tokens[p].equals("}"))
+								{
+									SpecificC="-SpecificC3-";
+								}
+								else if(tokens[p].equals("[") || tokens[p].equals("]"))
+								{
+									SpecificC="-SpecificC4-";
+								}
+								else if(tokens[p].equals("\\") || tokens[p].equals("/"))
+								{
+									SpecificC="-SpecificC5-";
+								}
+								
+								//Chemical Prefix/Suffix
+								String ChemPreSuf="__nil__";
+								if(tokens[p].matches(".*(yl|ylidyne|oyl|sulfonyl)")){ChemPreSuf="-CHEMinlineSuffix-";}
+								else if(tokens[p].matches("(meth|eth|prop|tetracos).*")){ChemPreSuf="-CHEMalkaneStem-";}
+								else if(tokens[p].matches("(di|tri|tetra).*")){ChemPreSuf="-CHEMsimpleMultiplier-";}
+								else if(tokens[p].matches("(benzen|pyridin|toluen).*")){ChemPreSuf="-CHEMtrivialRing-";}
+								else if(tokens[p].matches(".*(one|ol|carboxylic|amide|ate|acid|ium|ylium|ide|uide|iran|olan|inan|pyrid|acrid|amid|keten|formazan|fydrazin)(s|)")){ChemPreSuf="-CHEMsuffix-";}
+								
+								//MentionType
+								String MentionType="__nil__";
+								if(GNormPlus.SimConceptMention2Type_hash.containsKey(tokens[p]))
+								{
+									MentionType = "-"+GNormPlus.SimConceptMention2Type_hash.get(tokens[p])+"-";
+								}
+								
+								//Protein symbols
+								String ProteinSym="__nil__";
+								if(tokens[p].matches(".*(glutamine|glutamic|leucine|valine|isoleucine|lysine|alanine|glycine|aspartate|methionine|threonine|histidine|aspartic|asparticacid|arginine|asparagine|tryptophan|proline|phenylalanine|cysteine|serine|glutamate|tyrosine|stop|frameshift).*")){ChemPreSuf="-ProteinSymFull-";}
+								else if(tokens[p].matches("(cys|ile|ser|gln|met|asn|pro|lys|asp|thr|phe|ala|gly|his|leu|arg|trp|val|glu|tyr|fs|fsx)")){ChemPreSuf="-ProteinSymTri-";}
+								else if(tokens[p].matches("[CISQMNPKDTFAGHLRWVEYX]")){ChemPreSuf="-ProteinSymChar-";}
+								
+								//Repeat
+								String Repeat="__nil__";
+								if(Token2Num.get(tokens[p])>1 && tokens[p].length()>1 && (!tokens[p].matches("([\\W\\-\\_0-9]+|and|or|alpha|beta|gamma|theta|zeta|delta|kappa|II|VI|IV|III)")))
+								{
+									Repeat="-Repeat-";
+								}
+								
+								//Patterns
+								String Pattern1 = tokens[p];
+								if(Pattern1.matches(".*[\\W\\-\\_].*"))
+								{
+									Pattern1="__nil__";
+								}
+								else
+								{
+									Pattern1=Pattern1.replaceAll("[A-Z]", "A");
+									Pattern1=Pattern1.replaceAll("[a-z]", "a");
+									Pattern1=Pattern1.replaceAll("[0-9]", "0");
+									Pattern1="P1:"+Pattern1;
+								}
+								String Pattern2 = tokens[p];
+								if(Pattern2.matches(".*[\\W\\-\\_].*"))
+								{
+									Pattern2="__nil__";
+								}
+								else
+								{
+									Pattern2=Pattern2.replaceAll("[A-Za-z]", "a");
+									Pattern2=Pattern2.replaceAll("[0-9]", "0");
+									Pattern2="P2:"+Pattern2;
+								}
+								String Pattern3 = tokens[p];
+								if(Pattern3.matches(".*[\\W\\-\\_].*"))
+								{
+									Pattern3="__nil__";
+								}
+								else
+								{
+									Pattern3=Pattern3.replaceAll("[A-Z]+", "A");
+									Pattern3=Pattern3.replaceAll("[a-z]+", "a");
+									Pattern3=Pattern3.replaceAll("[0-9]+", "0");
+									Pattern3="P3:"+Pattern3;
+								}
+								String Pattern4 = tokens[p];
+								if(Pattern4.matches(".*[\\W\\-\\_].*"))
+								{
+									Pattern4="__nil__";
+								}
+								else
+								{
+									Pattern4=Pattern4.replaceAll("[A-Za-z]+", "a");
+									Pattern4=Pattern4.replaceAll("[0-9]+", "0");
+									Pattern4="P4:"+Pattern4;
+								}
+								
+								//prefix
+								String prefix="";
+								tmp=tokens[p];
+								if(tmp.length()>=1){ prefix=tmp.substring(0, 1);}else{prefix="__nil__";}
+								if(tmp.length()>=2){ prefix=prefix+" "+tmp.substring(0, 2);}else{prefix=prefix+" __nil__";}
+								if(tmp.length()>=3){ prefix=prefix+" "+tmp.substring(0, 3);}else{prefix=prefix+" __nil__";}
+								if(tmp.length()>=4){ prefix=prefix+" "+tmp.substring(0, 4);}else{prefix=prefix+" __nil__";}
+								if(tmp.length()>=5){ prefix=prefix+" "+tmp.substring(0, 5);}else{prefix=prefix+" __nil__";}
+								
+								//suffix
+								String suffix="";
+								tmp=tokens[p];
+								if(tmp.length()>=1){ suffix=tmp.substring(tmp.length()-1, tmp.length());}else{suffix="__nil__";}
+								if(tmp.length()>=2){ suffix=suffix+" "+tmp.substring(tmp.length()-2, tmp.length());}else{suffix=suffix+" __nil__";}
+								if(tmp.length()>=3){ suffix=suffix+" "+tmp.substring(tmp.length()-3, tmp.length());}else{suffix=suffix+" __nil__";}
+								if(tmp.length()>=4){ suffix=suffix+" "+tmp.substring(tmp.length()-4, tmp.length());}else{suffix=suffix+" __nil__";}
+								if(tmp.length()>=5){ suffix=suffix+" "+tmp.substring(tmp.length()-5, tmp.length());}else{suffix=suffix+" __nil__";}
+								
+								//Abbreviation & Long Form
+								String AbbLF="__nil__";
+								if(AbbLFStatus_hash.containsKey(Offset))
+								{
+									AbbLF=AbbLFStatus_hash.get(Offset);
+								}
+								
+								String Status = ID.substring(p, p+1);
+			        			FileData.write(tokens[p]+" "+WSB+" "+WSF+" "+stem
+			        					+" "+Num_num+" "+Num_num+" "+Num_Uc+" "+Num_lc+" "+Num_All+" "+SpecificC
+			        					+" "+ChemPreSuf+" "+MentionType+" "+ProteinSym+" "+Repeat
+			        					+" "+Pattern1+" "+Pattern2+" "+Pattern3+" "+Pattern4
+			        					+" "+prefix+" "+suffix+" "+AbbLF
+			        					+" "+Status+"\n");
+			        			Offset=Offset+tokens[p].length()+1;
+			        			if(ID.length()>tokens.length)
+			        			{
+			        				System.out.println(ID+"\t"+TokenSTR);
+			        			}
+			                }	
+			        		FileData.write("\n");
+		        		}
+					}
+	        		
+				}
+			}
+			FileData.close();
+		}
+		catch(IOException e1){ System.out.println("[MR]: Input file is not exist.");}
+	}
+	public void FeatureExtraction_Test(String FilenameData) throws XMLStreamException
+	{
+		try 
+		{
+			/** output files */ 
+			BufferedWriter FileData = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(FilenameData), "UTF-8")); // .data
+			//NLP modules
+			SnowballStemmer stemmer = new englishStemmer();
+			/** PMIDs : i */
+			for (int i = 0; i < GNormPlus.BioCDocobj.Annotations.size(); i++)
+			{
+				String Pmid = GNormPlus.BioCDocobj.PMIDs.get(i);
+				
+				/** Paragraphs : j */
+				for (int j = 0; j < GNormPlus.BioCDocobj.Annotations.get(i).size(); j++)
+				{
+					ArrayList<String> Annotation = GNormPlus.BioCDocobj.Annotations.get(i).get(j);
+					/** Annotations : k 
+					 * 0 start
+					 * 1 last
+					 * 2 mention
+					 * 3 type
+					 * 4 id
+					 */
+					for (int k = 0; k < Annotation.size() ; k++)   // k : Annotations
+					{
+						String anno[]=Annotation.get(k).split("\\t",-1);
+						String Mentions = anno[2];
+						String Type = anno[3];
+		        		String MentionArr[]=Mentions.split("\\|",-1);
+		        		if(Type.equals("Gene"))
+		        		{
+			        		for(int m=0;m<MentionArr.length;m++)
+			        		{
+			        			String Mention = MentionArr[m];
+			        			String TokenSTR = Mention;
+				        		TokenSTR = TokenSTR.replaceAll("([0-9])([A-Za-z])", "$1 $2");
+				        		TokenSTR = TokenSTR.replaceAll("([A-Za-z])([0-9])", "$1 $2");
+				        		TokenSTR = TokenSTR.replaceAll("([A-Z])([a-z])", "$1 $2");
+				        		TokenSTR = TokenSTR.replaceAll("([a-z])([A-Z])", "$1 $2");
+								TokenSTR = TokenSTR.replaceAll("([\\W])", " $1 ");
+				        		TokenSTR = TokenSTR.replaceAll("[ ]+", " ");
+				        		TokenSTR = TokenSTR.replaceAll("^[ ]+", "");
+				        		String Mention_tmp = Mention;
+								String tokens[]=TokenSTR.split(" ",-1);
+								
+								//For Repeat
+								HashMap <String,Integer> Token2Num = new HashMap <String,Integer>();
+								for(int p=0;p<tokens.length;p++)
+				                {
+									if(!Token2Num.containsKey(tokens[p]))
+									{
+										Token2Num.put(tokens[p], 0);
+									}
+									Token2Num.put(tokens[p], Token2Num.get(tokens[p])+1);
+								}
+								
+								//For Abbreviation
+								HashMap <Integer,String> AbbLFStatus_hash = new HashMap <Integer,String>();
+								for(String Pmid_LF : GNormPlus.PmidLF2Abb_hash.keySet())
+								{
+									String pf[] = Pmid_LF.split("\\t",-1);
+									if(pf[0].equals(Pmid))
+									{
+										String Abb = GNormPlus.PmidLF2Abb_hash.get(Pmid_LF);
+										String LF = pf[1];
+										
+										Abb = Abb.replaceAll("([0-9])([A-Za-z])", "$1 $2");
+										Abb = Abb.replaceAll("([A-Za-z])([0-9])", "$1 $2");
+						        		Abb = Abb.replaceAll("([A-Z])([a-z])", "$1 $2");
+						        		Abb = Abb.replaceAll("([a-z])([A-Z])", "$1 $2");
+						        		Abb = Abb.replaceAll("([\\W])", " $1 ");
+										Abb = Abb.replaceAll("[ ]+", " ");
+						        		Abb = Abb.replaceAll("^[ ]+", "");
+						        		
+						        		LF = LF.replaceAll("([0-9])([A-Za-z])", "$1 $2");
+						        		LF = LF.replaceAll("([A-Za-z])([0-9])", "$1 $2");
+						        		LF = LF.replaceAll("([A-Z])([a-z])", "$1 $2");
+						        		LF = LF.replaceAll("([a-z])([A-Z])", "$1 $2");
+						        		LF = LF.replaceAll("([\\W])", " $1 ");
+										LF = LF.replaceAll("[ ]+", " ");
+						        		LF = LF.replaceAll("^[ ]+", "");
+						        		
+										
+										Abb=Abb.replaceAll("([\\~\\!\\@\\#\\$\\%\\^\\&\\*\\(\\)\\_\\+\\-\\=\\[\\]\\;\\'\\,\\.\\/\\{\\}\\|\\:\\?])","\\\\$1");
+										LF=LF.replaceAll("([\\~\\!\\@\\#\\$\\%\\^\\&\\*\\(\\)\\_\\+\\-\\=\\[\\]\\;\\'\\,\\.\\/\\{\\}\\|\\:\\?])","\\\\$1");
+										Abb=Abb.toLowerCase();
+										LF=LF.toLowerCase();
+										Pattern ptmp1 = Pattern.compile("(.*)"
+														+ "("+LF+")"
+														+ "([ ]*\\([ ]*)"
+														+ "("+Abb+")"
+														+ "[ ]*\\).*");
+										Matcher mtmp1 = ptmp1.matcher(TokenSTR.toLowerCase());
+										Pattern ptmp2 = Pattern.compile("(.*)"
+														+ "("+Abb+")"
+														+ "([ ]*\\([ ]*)"
+														+ "("+LF+")"
+														+ "[ ]*\\).*");
+										Matcher mtmp2 = ptmp2.matcher(TokenSTR.toLowerCase());
+										int start_LF=0;
+										int last_LF=0;
+										int start_Abb=0;
+										int last_Abb=0;
+										if(mtmp1.find())
+										{
+											start_LF = mtmp1.group(1).length();
+											last_LF = start_LF+mtmp1.group(2).length();
+											start_Abb = last_LF+mtmp1.group(3).length();
+											last_Abb = start_Abb+mtmp1.group(4).length();
+										}
+										else if(mtmp2.find())
+										{
+											start_Abb = mtmp2.group(1).length();
+											last_Abb = start_LF+mtmp2.group(2).length();
+											start_LF = last_LF+mtmp2.group(3).length();
+											last_LF = start_Abb+mtmp2.group(4).length();
+										}
+										for(int l=start_LF;l<last_LF;l++)
+										{
+											AbbLFStatus_hash.put(l, "FullName");
+										}
+										for(int l=start_Abb;l<last_Abb;l++)
+										{
+											AbbLFStatus_hash.put(l, "Abbreviation");
+										}
+									}
+								}
+								
+								int Offset=0;
+								for(int p=0;p<tokens.length;p++) // p : toknes
+				                {
+									//white space
+				        			String WSB="WSB:N/A";
+				        			String WSF="WSF:N/A";
+				        			
+				        			if(p>0)
+				        			{
+				        				String B=tokens[p-1];
+				        				B=B.replaceAll("[A-Za-z]+", "A");
+				        				B=B.replaceAll("[0-9]+", "0");
+				        				WSB="WSB:"+B;
+				        			}
+				        			if(p<tokens.length-1)
+				        			{
+				        				String F=tokens[p+1];
+				        				F=F.replaceAll("[A-Za-z]+", "A");
+				        				F=F.replaceAll("[0-9]+", "0");
+				        				WSF="WSF:"+F;
+				        			}
+				        			
+				        			//stemming
+									stemmer.setCurrent(tokens[p].toLowerCase());
+									stemmer.stem();
+									String stem=stemmer.getCurrent();
+									
+									//Number of Numbers [0-9]
+									String Num_num="";
+									String tmp=tokens[p];
+									tmp=tmp.replaceAll("[^0-9]","");
+									if(tmp.length()>3){Num_num="N:4+";}else{Num_num="N:"+ tmp.length();}
+									
+									//Number of Uppercase [A-Z]
+									String Num_Uc="";
+									tmp=tokens[p];
+									tmp=tmp.replaceAll("[^A-Z]","");
+									if(tmp.length()>3){Num_Uc="U:4+";}else{Num_Uc="U:"+ tmp.length();}
+									
+									//Number of Lowercase [a-z]
+									String Num_lc="";
+									tmp=tokens[p];
+									tmp=tmp.replaceAll("[^a-z]","");
+									if(tmp.length()>3){Num_lc="L:4+";}else{Num_lc="L:"+ tmp.length();}
+									
+									//Number of ALL char
+									String Num_All="";
+									if(tokens[p].length()>3){Num_All="A:4+";}else{Num_All="A:"+ tokens[p].length();}
+									
+									//specific character (;:,.->+_)
+									String SpecificC="__nil__";
+									if(tokens[p].equals(";") || tokens[p].equals(":") || tokens[p].equals(",") || tokens[p].equals(".") || tokens[p].equals("-") || tokens[p].equals(">") || tokens[p].equals("+") || tokens[p].equals("_"))
+									{
+										SpecificC="-SpecificC1-";
+									}
+									else if(tokens[p].equals("(") || tokens[p].equals(")"))
+									{
+										SpecificC="-SpecificC2-";
+									}
+									else if(tokens[p].equals("{") || tokens[p].equals("}"))
+									{
+										SpecificC="-SpecificC3-";
+									}
+									else if(tokens[p].equals("[") || tokens[p].equals("]"))
+									{
+										SpecificC="-SpecificC4-";
+									}
+									else if(tokens[p].equals("\\") || tokens[p].equals("/"))
+									{
+										SpecificC="-SpecificC5-";
+									}
+									
+									//Chemical Prefix/Suffix
+									String ChemPreSuf="__nil__";
+									if(tokens[p].matches(".*(yl|ylidyne|oyl|sulfonyl)")){ChemPreSuf="-CHEMinlineSuffix-";}
+									else if(tokens[p].matches("(meth|eth|prop|tetracos).*")){ChemPreSuf="-CHEMalkaneStem-";}
+									else if(tokens[p].matches("(di|tri|tetra).*")){ChemPreSuf="-CHEMsimpleMultiplier-";}
+									else if(tokens[p].matches("(benzen|pyridin|toluen).*")){ChemPreSuf="-CHEMtrivialRing-";}
+									else if(tokens[p].matches(".*(one|ol|carboxylic|amide|ate|acid|ium|ylium|ide|uide|iran|olan|inan|pyrid|acrid|amid|keten|formazan|fydrazin)(s|)")){ChemPreSuf="-CHEMsuffix-";}
+									
+									//MentionType
+									String MentionType="__nil__";
+									if(GNormPlus.SimConceptMention2Type_hash.containsKey(tokens[p]))
+									{
+										MentionType = "-"+GNormPlus.SimConceptMention2Type_hash.get(tokens[p])+"-";
+									}
+									
+									//Protein symbols
+									String ProteinSym="__nil__";
+									if(tokens[p].matches(".*(glutamine|glutamic|leucine|valine|isoleucine|lysine|alanine|glycine|aspartate|methionine|threonine|histidine|aspartic|asparticacid|arginine|asparagine|tryptophan|proline|phenylalanine|cysteine|serine|glutamate|tyrosine|stop|frameshift).*")){ChemPreSuf="-ProteinSymFull-";}
+									else if(tokens[p].matches("(cys|ile|ser|gln|met|asn|pro|lys|asp|thr|phe|ala|gly|his|leu|arg|trp|val|glu|tyr|fs|fsx)")){ChemPreSuf="-ProteinSymTri-";}
+									else if(tokens[p].matches("[CISQMNPKDTFAGHLRWVEYX]")){ChemPreSuf="-ProteinSymChar-";}
+									
+									//Repeat
+									String Repeat="__nil__";
+									if(Token2Num.get(tokens[p])>1 && tokens[p].length()>1 && (!tokens[p].matches("([\\W\\-\\_0-9]+|and|or|alpha|beta|gamma|theta|zeta|delta|kappa|II|VI|IV|III)")))
+									{
+										Repeat="-Repeat-";
+									}
+									
+									//Patterns
+									String Pattern1 = tokens[p];
+									if(Pattern1.matches(".*[\\W\\-\\_].*"))
+									{
+										Pattern1="__nil__";
+									}
+									else
+									{
+										Pattern1=Pattern1.replaceAll("[A-Z]", "A");
+										Pattern1=Pattern1.replaceAll("[a-z]", "a");
+										Pattern1=Pattern1.replaceAll("[0-9]", "0");
+										Pattern1="P1:"+Pattern1;
+									}
+									String Pattern2 = tokens[p];
+									if(Pattern2.matches(".*[\\W\\-\\_].*"))
+									{
+										Pattern2="__nil__";
+									}
+									else
+									{
+										Pattern2=Pattern2.replaceAll("[A-Za-z]", "a");
+										Pattern2=Pattern2.replaceAll("[0-9]", "0");
+										Pattern2="P2:"+Pattern2;
+									}
+									String Pattern3 = tokens[p];
+									if(Pattern3.matches(".*[\\W\\-\\_].*"))
+									{
+										Pattern3="__nil__";
+									}
+									else
+									{
+										Pattern3=Pattern3.replaceAll("[A-Z]+", "A");
+										Pattern3=Pattern3.replaceAll("[a-z]+", "a");
+										Pattern3=Pattern3.replaceAll("[0-9]+", "0");
+										Pattern3="P3:"+Pattern3;
+									}
+									String Pattern4 = tokens[p];
+									if(Pattern4.matches(".*[\\W\\-\\_].*"))
+									{
+										Pattern4="__nil__";
+									}
+									else
+									{
+										Pattern4=Pattern4.replaceAll("[A-Za-z]+", "a");
+										Pattern4=Pattern4.replaceAll("[0-9]+", "0");
+										Pattern4="P4:"+Pattern4;
+									}
+									
+									//prefix
+									String prefix="";
+									tmp=tokens[p];
+									if(tmp.length()>=1){ prefix=tmp.substring(0, 1);}else{prefix="__nil__";}
+									if(tmp.length()>=2){ prefix=prefix+" "+tmp.substring(0, 2);}else{prefix=prefix+" __nil__";}
+									if(tmp.length()>=3){ prefix=prefix+" "+tmp.substring(0, 3);}else{prefix=prefix+" __nil__";}
+									if(tmp.length()>=4){ prefix=prefix+" "+tmp.substring(0, 4);}else{prefix=prefix+" __nil__";}
+									if(tmp.length()>=5){ prefix=prefix+" "+tmp.substring(0, 5);}else{prefix=prefix+" __nil__";}
+									
+									//suffix
+									String suffix="";
+									tmp=tokens[p];
+									if(tmp.length()>=1){ suffix=tmp.substring(tmp.length()-1, tmp.length());}else{suffix="__nil__";}
+									if(tmp.length()>=2){ suffix=suffix+" "+tmp.substring(tmp.length()-2, tmp.length());}else{suffix=suffix+" __nil__";}
+									if(tmp.length()>=3){ suffix=suffix+" "+tmp.substring(tmp.length()-3, tmp.length());}else{suffix=suffix+" __nil__";}
+									if(tmp.length()>=4){ suffix=suffix+" "+tmp.substring(tmp.length()-4, tmp.length());}else{suffix=suffix+" __nil__";}
+									if(tmp.length()>=5){ suffix=suffix+" "+tmp.substring(tmp.length()-5, tmp.length());}else{suffix=suffix+" __nil__";}
+									
+									//Abbreviation & Long Form
+									String AbbLF="__nil__";
+									if(AbbLFStatus_hash.containsKey(Offset))
+									{
+										AbbLF=AbbLFStatus_hash.get(Offset);
+									}
+									
+									FileData.write(tokens[p]+" "+WSB+" "+WSF+" "+stem
+				        					+" "+Num_num+" "+Num_num+" "+Num_Uc+" "+Num_lc+" "+Num_All+" "+SpecificC
+				        					+" "+ChemPreSuf+" "+MentionType+" "+ProteinSym+" "+Repeat
+				        					+" "+Pattern1+" "+Pattern2+" "+Pattern3+" "+Pattern4
+				        					+" "+prefix+" "+suffix+" "+AbbLF+"\n");
+				        			Offset=Offset+tokens[p].length()+1;
+				                }
+								FileData.write("\n");
+				        	}
+		        		}
+					}
+	        		
+				}
+			}
+			FileData.close();
+		}
+		catch(IOException e1){ System.out.println("[MR]: Input file is not exist.");}
+	}
+	public void CRF_test(String model, String FilenameData,String FilenameOutput) throws IOException 
+	{
+		File f = new File(FilenameOutput);
+        BufferedWriter fr = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(f), "UTF-8"));
+		
+		Runtime runtime = Runtime.getRuntime();
+	    
+		String cmd ="CRF/crf_test -m "+model+" -o "+FilenameOutput+" "+FilenameData;
+	    
+	    try {
+	    	Process process = runtime.exec(cmd);
+	    	InputStream is = process.getInputStream();
+	    	InputStreamReader isr = new InputStreamReader(is, "UTF-8");
+	    	BufferedReader br = new BufferedReader(isr);
+	    	String line="";
+		    while ( (line = br.readLine()) != null) 
+		    {
+		    	fr.write(line);
+		    	fr.newLine();
+		        fr.flush();
+		    }
+		    is.close();
+		    isr.close();
+		    br.close();
+		    fr.close();
+	    }
+	    catch (IOException e) {
+	    	System.out.println(e);
+	    	runtime.exit(0);
+	    }
+	}
+	public void CRF_learn(String model,String FilenameData) throws IOException 
+	{
+		Runtime runtime = Runtime.getRuntime();
+	    
+	    Process process = null;
+	    String line = null;
+	    InputStream is = null;
+	    InputStreamReader isr = null;
+	    BufferedReader br = null;
+	    String cmd = "CRF/crf_learn -f 3 -c 4.0 CRF/template_SimConcept "+FilenameData+" "+model; 
+	    
+	    try {
+	    	process = runtime.exec(cmd);
+		    is = process.getInputStream();
+		    isr = new InputStreamReader(is, "UTF-8");
+		    br = new BufferedReader(isr);
+		    while ( (line = br.readLine()) != null) 
+		    {
+		    	System.out.println(line);
+		        System.out.flush();
+		    }
+		    is.close();
+		    isr.close();
+		    br.close();
+	    }
+	    catch (IOException e) {
+	    	System.out.println(e);
+	    	runtime.exit(0);
+	    }
+	}
+	public void ReadCRFresult(String Filename,String FilenameOutput,String FilenameBioC) throws XMLStreamException, IOException
+	{
+		/** load CRF output */
+		ArrayList<String> outputArr1 = new ArrayList<String>();
+		BufferedReader inputfile = new BufferedReader(new InputStreamReader(new FileInputStream(FilenameOutput), "UTF-8"));
+		String line;
+		while ((line = inputfile.readLine()) != null)  
+		{	
+			outputArr1.add(line);
+		}
+		inputfile.close();
+		
+		/**
+		 * Recognize the mentions which can be simplified
+		 */
+		int Count_mention=0;
+		boolean Simplified=false;
+		String Mention="";
+		String Mention_NoSpace="";
+		String States="";
+		HashMap<String,String> Mentions_hash = new HashMap<String,String>();
+		HashMap<String,String> States_hash = new HashMap<String,String>();
+		HashMap<String,String> Output_Split_mention_Ind = new HashMap<String,String>();
+		HashMap<String,String> Output_Split_mention = new HashMap<String,String>();
+		for(int i=0;i<outputArr1.size();i++)
+		{
+			String outputsRow[]=outputArr1.get(i).split("\\t",-1);
+			String Token = outputsRow[0]; // 1st column: Token
+			String TknState = outputsRow[outputsRow.length-1]; // last column: state
+			
+			if(TknState.matches("[CJBEFN]")) //  Simplify-able
+			{
+				Simplified = true;
+			}
+			
+			if(outputsRow.length<=1) //the end of a mention
+			{
+				if(Simplified == true)
+				{
+					/*
+					 * update BF states :
+					 * 
+					 *  AABAFA
+					 *  AWXWOA
+					 * 
+					 */
+					for (String PmidAbb : GNormPlus.PmidAbb2LF_hash.keySet())
+					{
+						String PmidAbbs[]=PmidAbb.split("\\t",-1);
+						String Abb = PmidAbbs[1];
+						String LF = GNormPlus.PmidAbb2LF_hash.get(PmidAbb);
+
+						Abb = Abb.replaceAll("([0-9])([A-Za-z])", "$1 $2");
+						Abb = Abb.replaceAll("([A-Za-z])([0-9])", "$1 $2");
+		        		Abb = Abb.replaceAll("([A-Z])([a-z])", "$1 $2");
+		        		Abb = Abb.replaceAll("([a-z])([A-Z])", "$1 $2");
+		        		Abb = Abb.replaceAll("([\\W])", " $1 ");
+						Abb = Abb.replaceAll("[ ]+", " ");
+		        		Abb = Abb.replaceAll("^[ ]+", "");
+		        		LF = LF.replaceAll("([0-9])([A-Za-z])", "$1 $2");
+		        		LF = LF.replaceAll("([A-Za-z])([0-9])", "$1 $2");
+		        		LF = LF.replaceAll("([A-Z])([a-z])", "$1 $2");
+		        		LF = LF.replaceAll("([a-z])([A-Z])", "$1 $2");
+		        		LF = LF.replaceAll("([\\W])", " $1 ");
+						LF = LF.replaceAll("[ ]+", " ");
+		        		LF = LF.replaceAll("^[ ]+", "");
+		        		Abb=Abb.replaceAll("([^A-Za-z0-9@ ])","\\\\$1");
+						LF=LF.replaceAll("([^A-Za-z0-9@ ])","\\\\$1");
+						
+						Pattern ptmp1 = Pattern.compile("^(.*)("+LF+") \\( ("+Abb+") \\) (.*)$");
+						Matcher mtmp1 = ptmp1.matcher(Mention);
+						Pattern ptmp2 = Pattern.compile("^(.*)("+Abb+") \\( ("+LF+") \\) (.*)$");
+						Matcher mtmp2 = ptmp2.matcher(Mention);
+						if(mtmp1.find())
+						{
+							int t1_len=0;
+							if(!mtmp1.group(1).equals(""))
+							{
+								t1_len=mtmp1.group(1).split(" ",-1).length;
+							}
+							String t2[] = mtmp1.group(2).split(" ",-1);
+							String t3[] = mtmp1.group(3).split(" ",-1);
+							
+							String N1 ="";String N2 ="";String N3 ="";String N4 ="";
+							N1=States.substring(0,t1_len);
+							for(int t=0;t<t2.length;t++){N2=N2+"W";}
+							for(int t=0;t<t3.length;t++){N3=N3+"W";}
+							N4=States.substring(N1.length()+N2.length()+N3.length()+2);
+							States=N1+N2+"X"+N3+"O"+N4;
+						}
+						else if(mtmp2.find())
+						{
+							int t1_len=0;
+							if(!mtmp2.group(1).equals(""))
+							{
+								t1_len=mtmp2.group(1).split(" ",-1).length;
+							}
+							String t2[] = mtmp2.group(2).split(" ",-1);
+							String t3[] = mtmp2.group(3).split(" ",-1);
+							
+							String N1 ="";String N2 ="";String N3 ="";String N4 ="";
+							N1=States.substring(0,t1_len);
+							for(int t=0;t<t2.length;t++){N2=N2+"W";}
+							for(int t=0;t<t3.length;t++){N3=N3+"W";}
+							N4=States.substring(N1.length()+N2.length()+N3.length()+2);
+							States=N1+N2+"X"+N3+"O"+N4;
+						}
+						else
+						{
+							//System.out.println(Mention+"\t"+LF+"\t"+Abb);
+						}
+					}
+					States_hash.put(Mention_NoSpace, States);
+					Mentions_hash.put(Mention_NoSpace, Mention);
+				}
+				//Initial
+				Simplified= false;
+				Mention="";
+				Mention_NoSpace="";
+				Count_mention++;
+				States="";
+			}
+			else
+			{
+				if(Mention.equals(""))
+				{
+					Mention = Token;
+				}
+				else
+				{
+					Mention = Mention +" "+Token;
+				}
+				States=States+TknState;
+				Mention_NoSpace=Mention_NoSpace+Token;
+			}
+		}
+		
+		for (String MNoSpace : Mentions_hash.keySet()) // mention : i
+		{
+			ArrayList<String> Split_mention = new ArrayList<String>();
+			ArrayList<String> Split_state = new ArrayList<String>();
+			String tmp_mention="";
+			String tmp_state="";
+			/**
+			 * count = Mentions_count.get(i) : # of the mention in the corpus (543)
+			 * Mentions_hash.get(count) : Original Mention (ORP - 1 to ORP - 6)
+			 * States_hash.get(count) : States (AASNOOS)
+			 */
+			
+			String TokenArr[]=Mentions_hash.get(MNoSpace).split(" ",-1);
+			String StateArr[]=States_hash.get(MNoSpace).split("",-1);
+			
+			//refinement : isn't used
+			Pattern ptmp1 = Pattern.compile("^([S]+)([CN])([S]+)$");
+			Matcher mtmp1 = ptmp1.matcher(States_hash.get(MNoSpace));
+			if(mtmp1.find())
+			{
+				States_hash.put(MNoSpace, mtmp1.group(1)+"J"+mtmp1.group(3));
+			}
+
+			//Split BE
+			int len=TokenArr.length;
+			if(StateArr.length<TokenArr.length){len=StateArr.length;}
+			for(int s=0;s<len;s++) // token/state : s
+			{
+				if(StateArr[s].matches("[BE]"))
+				{
+					if(tmp_mention.length()>0)
+					{
+						Split_mention.add(tmp_mention);
+						Split_state.add(tmp_state);
+					}
+					tmp_mention = "";
+					tmp_state = "";
+				}
+				else //CNBF
+				{
+					tmp_mention = tmp_mention + TokenArr[s] + " ";
+					tmp_state = tmp_state + StateArr[s];
+				}
+			}
+			if(!tmp_mention.equals(""))
+			{	
+				Split_mention.add(tmp_mention);
+				Split_state.add(tmp_state);
+			}
+			
+			//Split B/F
+			for(int m=0;m<Split_mention.size();m++)// m mention
+			{
+				String A="";
+				String X="";
+				String STAA="";
+				String strainX="";
+				String STAstrainX="";
+				int X_continous=0;
+				ArrayList<String> strainsX = new ArrayList<String>();
+				ArrayList<String> STAstrainsX = new ArrayList<String>();
+				String each_token[] = Split_mention.get(m).split(" ");
+				String each_state[] = Split_state.get(m).split("");
+				for(int s=0;s<each_state.length;s++) //s token
+				{
+					if(each_state[s].matches("[ACNS]"))
+					{
+						A=A+each_token[s]+" ";
+						STAA =STAA+each_state[s];
+					}
+					else if(each_state[s].equals("W"))
+					{
+						A=A+"STRAINXXX";
+						STAA=STAA+"@";
+						strainX=strainX+each_token[s]+" ";
+						STAstrainX=STAstrainX+each_state[s];
+						X_continous=0;
+					}
+					else if(each_state[s].equals("X") && X_continous==0)
+					{
+						X=each_state[s];
+						strainsX.add(strainX);
+						STAstrainsX.add(STAstrainX);
+						strainX="";
+						STAstrainX="";
+						X_continous++;
+					}
+				}
+				if(!strainX.equals("")){strainsX.add(strainX);}
+				if(!STAstrainX.equals("")){STAstrainsX.add(STAstrainX);}
+				A=A.replaceAll("(STRAINXXX){1,}", "STRAINXXX");
+				STAA=STAA.replaceAll("(@){1,}", "@");
+				
+				if(X.equals("X"))
+				{
+					for(int x=0;x<strainsX.size();x++) //x token
+					{
+						String strain=strainsX.get(x);
+						String state=STAstrainsX.get(x);
+						String tkns = A;
+						strain = strain.replaceAll("([\\W\\-\\_])", "\\\\$1");
+						tkns=tkns.replaceAll("STRAINXXX", strain);
+						tkns=tkns.replaceAll("  ", " ");
+						if(tkns.substring(tkns.length()-1,tkns.length()-1).equals(" ")){tkns=tkns.substring(0,tkns.length()-2);}
+						String STAAs=STAA;
+						STAAs=STAAs.replaceAll("@", state);
+						Split_mention.add(tkns);
+						Split_state.add(STAAs);
+					}
+					Split_mention.remove(m);
+					Split_state.remove(m);
+				}
+			}
+			for(int s=0;s<Split_state.size();s++)
+			{
+				Split_state.set(s,Split_state.get(s).replaceAll("W","A"));
+			}
+			
+			//Split J
+			for(int m=0;m<Split_mention.size();m++)// m mention
+			{
+				String each_token[] = Split_mention.get(m).split(" ",-1);
+				String each_state[] = Split_state.get(m).split("",-1);
+				String sub_mention="";
+				boolean found_J = false;
+				for(int k=0;k<each_state.length;k++)
+				{
+					if(each_state[k].equals("J"))
+					{
+						found_J = true;
+						if(Output_Split_mention_Ind.containsKey(MNoSpace))
+						{
+							Output_Split_mention_Ind.put(MNoSpace, Output_Split_mention_Ind.get(MNoSpace)+"|"+sub_mention);
+						}
+						else
+						{
+							Output_Split_mention_Ind.put(MNoSpace,sub_mention);
+						}
+						sub_mention="";
+					}
+					else 
+					{
+						sub_mention=sub_mention+each_token[k]+" ";
+					}
+				}
+				
+				if(found_J == true)
+				{
+					if(Output_Split_mention_Ind.containsKey(MNoSpace))
+					{
+						Output_Split_mention_Ind.put(MNoSpace, Output_Split_mention_Ind.get(MNoSpace)+"|"+sub_mention);
+					}
+					else
+					{
+						Output_Split_mention_Ind.put(MNoSpace,sub_mention);
+					}
+				}
+			}
+			
+			//Split CN
+			for(int m=0;m<Split_mention.size();m++) // s split mention
+			{
+				String A="";
+				String strainCN="";
+				int CNO_continous=0;
+				ArrayList<String> strainsCN = new ArrayList<String>();
+				String CorN="";
+				
+				String each_token[] = Split_mention.get(m).split(" ",-1);
+				String each_state[] = Split_state.get(m).split("",-1);
+				
+				for(int k=0;k<each_state.length;k++)
+				{
+					if(each_state[k].equals("A"))
+					{
+						A=A+each_token[k]+" ";
+					}
+					else if(each_state[k].equals("S"))
+					{
+						if(A.length()>=4)
+						{
+							A=A.replace("s $", "");
+						}
+						A=A+"STRAINXXX";
+						strainCN=strainCN+each_token[k]+" ";
+						CNO_continous=0;
+					}
+					else if(each_state[k].matches("[CN]") && CNO_continous==0)
+					{
+						CorN=each_state[k];
+						strainsCN.add(strainCN);
+						strainCN="";
+						CNO_continous++;
+					}
+					else if(each_state[k].equals("J"))
+					{
+						if(!strainCN.equals("")){strainsCN.add(strainCN);}
+						
+						A=A.replaceAll("STRAINXXXSTRAINXXX","STRAINXXX");
+						A=A.replaceAll("STRAINXXXSTRAINXXX","STRAINXXX");
+						
+						ptmp1 = Pattern.compile("^(.+)s (.*)$");
+						mtmp1 = ptmp1.matcher(A);
+						if(mtmp1.find() && mtmp1.group(1).length()>=3 )
+						{
+							A = mtmp1.group(1)+ " "+mtmp1.group(2);
+						}
+						
+						if(CorN.equals("C"))
+						{
+							for(int x=0;x<strainsCN.size();x++)
+							{
+								String tmp = A;
+								String strainsCN_tmp=strainsCN.get(x).replaceAll("([^A-Za-z0-9@ ])", "\\\\$1");
+								tmp = tmp.replaceAll("STRAINXXX", strainsCN_tmp);
+								tmp = tmp.replaceAll("[ ]+", " ");
+								if(tmp.length()>2 && (tmp.substring(tmp.length()-2, tmp.length()-2).equals(" ")))
+								{
+									tmp = tmp.substring(0,tmp.length()-2);
+								}
+								if(Output_Split_mention_Ind.containsKey(MNoSpace))
+								{
+									Output_Split_mention_Ind.put(MNoSpace, Output_Split_mention_Ind.get(MNoSpace)+"|"+tmp);
+								}
+								else
+								{
+									Output_Split_mention_Ind.put(MNoSpace, tmp);
+								}
+							}
+						}
+						else if(CorN.equals("N"))
+						{
+							if(strainsCN.contains(0) && strainsCN.contains(1))
+							{
+								String strain1= strainsCN.get(0).replaceAll(" ", "");
+								String strain2= strainsCN.get(1).replaceAll(" ", "");
+								if(strain1.matches("[0-9]+") && strain2.matches("[0-9]+"))
+								{
+									if(Integer.parseInt(strain2)-Integer.parseInt(strain1)<=20)
+									{
+										for(int strCount=Integer.parseInt(strain1);strCount<=Integer.parseInt(strain2);strCount++)
+										{
+											String tmp=A;
+											tmp = tmp.replace("STRAINXXX", Integer.toString(strCount));
+											tmp = tmp.replaceAll("[ ]+"," ");
+											if(tmp.length()>2 && tmp.substring(tmp.length()-2, tmp.length()-2).equals(" "))
+											{
+												tmp = tmp.substring(0,tmp.length()-2);
+											}
+											if(Output_Split_mention_Ind.containsKey(MNoSpace))
+											{
+												Output_Split_mention_Ind.put(MNoSpace, Output_Split_mention_Ind.get(MNoSpace)+"|"+tmp);
+											}
+											else
+											{
+												Output_Split_mention_Ind.put(MNoSpace, tmp);
+											}
+										}
+									}
+								}
+								else if(strain1.matches("[A-Z]+ ") && strain2.matches("[A-Z]+ "))
+								{
+									int strInt1 = (int) strain1.replaceAll(" ", "").charAt(0);
+									int strInt2 = (int) strain2.replaceAll(" ", "").charAt(0);
+									if(strInt2-strInt1<=20)
+									{
+										for(int strCount=strInt1;strCount<=strInt2;strCount++)
+										{
+											String tmp=A;
+											tmp = tmp.replace("STRAINXXX", Integer.toString(strCount));
+											tmp = tmp.replaceAll("[ ]+"," ");
+											if(tmp.length()>2 && tmp.substring(tmp.length()-2, tmp.length()-2).equals(" "))
+											{
+												tmp = tmp.substring(0,tmp.length()-2);
+											}
+											if(Output_Split_mention_Ind.containsKey(MNoSpace))
+											{
+												Output_Split_mention_Ind.put(MNoSpace, Output_Split_mention_Ind.get(MNoSpace)+"|"+tmp);
+											}
+											else
+											{
+												Output_Split_mention_Ind.put(MNoSpace, tmp);
+											}
+										}
+									}
+								}
+								else
+								{
+									if(Output_Split_mention.containsKey(MNoSpace))
+									{
+										Output_Split_mention.put(MNoSpace, Output_Split_mention.get(MNoSpace)+"|"+Split_mention.get(m));
+									}
+									else
+									{
+										Output_Split_mention.put(MNoSpace, Split_mention.get(m));
+									}
+								}
+							}
+						}
+						else
+						{
+							if(Output_Split_mention.containsKey(MNoSpace))
+							{
+								Output_Split_mention.put(MNoSpace, Output_Split_mention.get(MNoSpace)+"|"+Split_mention.get(m));
+							}
+							else
+							{
+								Output_Split_mention.put(MNoSpace, Split_mention.get(m));
+							}
+						}
+						
+						A="";
+						strainCN="";
+						CNO_continous=0;
+						strainsCN = new ArrayList<String>();
+						CorN="";
+					}
+				}
+				if(!strainCN.equals("")){strainsCN.add(strainCN);}
+				
+				A=A.replaceAll("(STRAINXXX){2,}","STRAINXXX");
+				
+				ptmp1 = Pattern.compile("^(.+)s (.*)$");
+				mtmp1 = ptmp1.matcher(A);
+				if(mtmp1.find() && mtmp1.group(1).length()>=3 )
+				{
+					A = mtmp1.group(1)+ " "+mtmp1.group(2);
+				}
+				
+				if(CorN.equals("C"))
+				{
+					for(int x=0;x<strainsCN.size();x++)
+					{
+						String tmp = A;
+						tmp = tmp.replaceAll("\\$", " ");
+						strainsCN.set(x,strainsCN.get(x).replaceAll("\\$", " "));
+						tmp = tmp.replaceAll("STRAINXXX", strainsCN.get(x));
+						tmp = tmp.replaceAll("[ ]+", " ");
+						if(tmp.length()>2 && (tmp.substring(tmp.length()-2, tmp.length()-2).equals(" ")))
+						{
+							tmp = tmp.substring(0,tmp.length()-2);
+						}
+						if(Output_Split_mention_Ind.containsKey(MNoSpace))
+						{
+							Output_Split_mention_Ind.put(MNoSpace, Output_Split_mention_Ind.get(MNoSpace)+"|"+tmp);
+						}
+						else
+						{
+							Output_Split_mention_Ind.put(MNoSpace, tmp);
+						}
+					}
+				}
+				else if(CorN.equals("N"))
+				{
+					if(strainsCN.size()==2)
+					{
+						String strain1= strainsCN.get(0).replaceAll(" ", "");
+						String strain2= strainsCN.get(1).replaceAll(" ", "");
+						if(strain1.matches("[0-9]{1,7}") && strain2.matches("[0-9]{1,7}"))
+						{
+							if(Integer.parseInt(strain2)-Integer.parseInt(strain1)<=20)
+							{
+								for(int strCount=Integer.parseInt(strain1);strCount<=Integer.parseInt(strain2);strCount++)
+								{
+									String tmp=A;
+									tmp = tmp.replace("STRAINXXX", Integer.toString(strCount));
+									tmp = tmp.replaceAll("[ ]+"," ");
+									if(tmp.length()>2 && tmp.substring(tmp.length()-2, tmp.length()-2).equals(" "))
+									{
+										tmp = tmp.substring(0,tmp.length()-2);
+									}
+									if(Output_Split_mention_Ind.containsKey(MNoSpace))
+									{
+										Output_Split_mention_Ind.put(MNoSpace, Output_Split_mention_Ind.get(MNoSpace)+"|"+tmp);
+									}
+									else
+									{
+										Output_Split_mention_Ind.put(MNoSpace, tmp);
+									}
+								}
+							}
+						}
+						else if(strain1.matches("[A-Z]+ ") && strain2.matches("[A-Z]+ "))
+						{
+							int strInt1 = (int) strain1.replaceAll(" ", "").charAt(0);
+							int strInt2 = (int) strain2.replaceAll(" ", "").charAt(0);
+							if(strInt2-strInt1<=20)
+							{
+								for(int strCount=strInt1;strCount<=strInt2;strCount++)
+								{
+									String tmp=A;
+									tmp = tmp.replace("STRAINXXX", Integer.toString(strCount));
+									tmp = tmp.replaceAll("[ ]+"," ");
+									if(tmp.length()>2 && tmp.substring(tmp.length()-2, tmp.length()-2).equals(" "))
+									{
+										tmp = tmp.substring(0,tmp.length()-2);
+									}
+									if(Output_Split_mention_Ind.containsKey(MNoSpace))
+									{
+										Output_Split_mention_Ind.put(MNoSpace, Output_Split_mention_Ind.get(MNoSpace)+"|"+tmp);
+									}
+									else
+									{
+										Output_Split_mention_Ind.put(MNoSpace, tmp);
+									}
+								}
+							}
+						}
+						else
+						{
+							if(Output_Split_mention.containsKey(MNoSpace))
+							{
+								Output_Split_mention.put(MNoSpace, Output_Split_mention.get(MNoSpace)+"|"+Split_mention.get(m));
+							}
+							else
+							{
+								Output_Split_mention.put(MNoSpace, Split_mention.get(m));
+							}
+						}
+					}
+				}
+				else
+				{
+					if(Output_Split_mention.containsKey(MNoSpace))
+					{
+						Output_Split_mention.put(MNoSpace, Output_Split_mention.get(MNoSpace)+"|"+Split_mention.get(m));
+					}
+					else
+					{
+						Output_Split_mention.put(MNoSpace, Split_mention.get(m));
+					}
+				}
+			}
+		}
+		
+		for (int i = 0; i < GNormPlus.BioCDocobj.Annotations.size(); i++)
+		{
+			for (int j = 0; j < GNormPlus.BioCDocobj.Annotations.get(i).size(); j++)
+			{
+				int Annotation_Num = GNormPlus.BioCDocobj.Annotations.get(i).get(j).size();
+				for (int k = 0; k < Annotation_Num ; k++)   // k : Annotations
+				{
+					String anno[]=GNormPlus.BioCDocobj.Annotations.get(i).get(j).get(k).split("\\t"); //Mention
+					String MenArr[]=anno[2].split("\\|");
+	        		for(int m=0;m<MenArr.length;m++)
+	        		{
+	        			String MNoSpace = MenArr[m];
+	        			MNoSpace = MNoSpace.replaceAll("[ ]+",  "");
+	        			if(Output_Split_mention_Ind.containsKey(MNoSpace))
+	        			{
+	        				if(anno.length==5)
+	        				{
+	        					String split_men[]=Output_Split_mention_Ind.get(MNoSpace).split("\\|"); 
+	        					for(int s=0;s<split_men.length;s++)
+	        					{
+	        						String anno2 = anno[2] +"|"+split_men[s];
+		        					GNormPlus.BioCDocobj.Annotations.get(i).get(j).add(anno[0]+"\t"+anno[1]+"\t"+anno2+"\t"+anno[3]+"\t"+anno[4]);
+		        				}
+	        				}
+	        				else if(anno.length<5)
+	        				{
+	        					String split_men[]=Output_Split_mention_Ind.get(MNoSpace).split("\\|"); 
+	        					for(int s=0;s<split_men.length;s++)
+	        					{
+	        						String anno2 = anno[2] +"|"+split_men[s];
+		        					GNormPlus.BioCDocobj.Annotations.get(i).get(j).add(anno[0]+"\t"+anno[1]+"\t"+anno2+"\t"+anno[3]);
+	        					}
+	        				}
+	        			}
+	        			else if(Output_Split_mention.containsKey(MNoSpace))
+	        			{
+	        				if(anno.length==5)
+	        				{
+	        					String anno2 = anno[2] +"|"+Output_Split_mention.get(MNoSpace);
+	        					GNormPlus.BioCDocobj.Annotations.get(i).get(j).set(k, anno[0]+"\t"+anno[1]+"\t"+anno2+"\t"+anno[3]+"\t"+anno[4]);
+	        				}
+	        				else if(anno.length<5)
+	        				{
+	        					GNormPlus.BioCDocobj.Annotations.get(i).get(j).set(k, anno[0]+"\t"+anno[1]+"\t"+anno[2]+"\t"+anno[3]);
+	        				}
+	        			} 
+	        		}
+	        	}
+			}
+		}
+		
+		/**
+		 * suffixprefix_orig2modified
+		 */
+		for (int i = 0; i < GNormPlus.BioCDocobj.Annotations.size(); i++)
+		{
+			for (int j = 0; j < GNormPlus.BioCDocobj.Annotations.get(i).size(); j++)
+			{
+				int Annotation_Num = GNormPlus.BioCDocobj.Annotations.get(i).get(j).size();
+				for (int k = 0; k < Annotation_Num ; k++)   // k : Annotations
+				{
+					String anno[]=GNormPlus.BioCDocobj.Annotations.get(i).get(j).get(k).split("\\t"); //Mention
+					String MenArr[]=anno[2].split("\\|");
+					ArrayList <String> Mentions = new ArrayList<String>();
+					for(int m=0;m<MenArr.length;m++)
+	        		{
+						Mentions.add(MenArr[m]);
+						for(String orig_mention : GNormPlus.suffixprefix_orig2modified.keySet())
+						{
+							String modi_mention=GNormPlus.suffixprefix_orig2modified.get(orig_mention);
+							if(MenArr[m].equals(orig_mention))
+							{
+								Mentions.add(modi_mention);
+								break;
+							}
+						}
+					}
+					String mens="";
+					for(int m=0;m<Mentions.size();m++)
+					{
+						String mention=Mentions.get(m);
+						if(mens.equals(""))
+						{
+							mens=mention;
+						}
+						else
+						{
+							mens=mens+"|"+mention;
+						}
+					}
+					if(anno.length==5)
+    				{
+    					GNormPlus.BioCDocobj.Annotations.get(i).get(j).set(k, anno[0]+"\t"+anno[1]+"\t"+mens+"\t"+anno[3]+"\t"+anno[4]);
+    				}
+    				else if(anno.length<5)
+    				{
+    					GNormPlus.BioCDocobj.Annotations.get(i).get(j).set(k, anno[0]+"\t"+anno[1]+"\t"+mens+"\t"+anno[3]);
+    				}
+				}
+			}
+		}
+		
+		/*
+		// 2 --> ii
+		// ii --> 2
+		for (int i = 0; i < GNormPlus.BioCDocobj.Annotations.size(); i++)
+		{
+			for (int j = 0; j < GNormPlus.BioCDocobj.Annotations.get(i).size(); j++)
+			{
+				int Annotation_Num = GNormPlus.BioCDocobj.Annotations.get(i).get(j).size();
+				for (int k = 0; k < Annotation_Num ; k++)   // k : Annotations
+				{
+					String anno[]=GNormPlus.BioCDocobj.Annotations.get(i).get(j).get(k).split("\\t"); //Mention
+					String MenArr[]=anno[2].split("\\|");
+					HashMap<String,String> Mentions = new HashMap<String,String>();
+					for(int m=0;m<MenArr.length;m++)
+	        		{
+						Mentions.put(MenArr[m], "");
+						for(String suffix : GNormPlus.SuffixTranslationMap2_hash.keySet())
+						{
+							String Men_rev=MenArr[m].replaceAll(suffix, GNormPlus.SuffixTranslationMap2_hash.get(suffix));
+							Mentions.put(Men_rev, "");
+						}
+					}
+					String mens="";
+					for(String mention : Mentions.keySet())
+					{
+						if(mens.equals(""))
+						{
+							mens=mention;
+						}
+						else
+						{
+							mens=mens+"|"+mention;
+						}
+					}
+				}
+			}
+		}
+		*/
+		GNormPlus.BioCDocobj.BioCOutput(Filename,FilenameBioC,GNormPlus.BioCDocobj.Annotations,false,true);
+	}
 }
\ No newline at end of file