package GNormPluslib;

import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileOutputStream;
import java.io.FileReader;
import java.io.IOException;
import java.io.OutputStreamWriter;
import java.sql.SQLException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.regex.Matcher;
import java.util.regex.Pattern;

import javax.xml.stream.XMLStreamException;

import GNormPluslib.PrefixTree;
import GNormPluslib.GNR;
import GNormPluslib.SR;

public class GNormPlus
{
	public static BioCDoc BioCDocobj = new BioCDoc();
	public static PrefixTree PT_Species = new PrefixTree();
	public static PrefixTree PT_Cell = new PrefixTree();
	public static PrefixTree PT_CTDGene = new PrefixTree();
	public static PrefixTree PT_Gene = new PrefixTree();
	public static PrefixTree PT_GeneChromosome = new PrefixTree();
	public static PrefixTree PT_FamilyName = new PrefixTree();
	public static HashMap<String, String> ent_hash = new HashMap<String, String>();
	public static HashMap<String, String> GenusID_hash = new HashMap<String, String>();
	public static HashMap<String, String> PrefixID_hash = new HashMap<String, String>();
	public static HashMap<String, Double> TaxFreq_hash = new HashMap<String, Double>();
	public static HashMap<String, String> GeneScoring_hash = new HashMap<String, String>();
	public static HashMap<String, Double> GeneScoringDF_hash = new HashMap<String, Double>();
	public static HashMap<String, String> GeneIDs_hash = new HashMap<String, String>();
	public static HashMap<String, String> Normalization2Protein_hash = new HashMap<String, String>();
	public static HashMap<String, String> HomologeneID_hash = new HashMap<String, String>();
	public static HashMap<String,String> SuffixTranslationMap_hash = new HashMap<String,String>();
	public static HashMap<String,String> SuffixTranslationMap2_hash = new HashMap<String,String>();
	public static HashMap<String, String> Pmid2Abb_hash = new HashMap<String, String>();
	public static HashMap<String, String> PmidAbb2LF_lc_hash = new HashMap<String, String>();
	public static HashMap<String, String> PmidLF2Abb_lc_hash = new HashMap<String, String>();
	public static HashMap<String, String> PmidAbb2LF_hash = new HashMap<String, String>();
	public static HashMap<String, String> PmidLF2Abb_hash = new HashMap<String, String>();
	public static HashMap<String, String> Pmid2ChromosomeGene_hash = new HashMap<String, String>();
	public static HashMap<String, String> SimConceptMention2Type_hash = new HashMap<String, String>();
	public static HashMap<String, String> Filtering_hash = new HashMap<String, String>();
	public static HashMap<String, String> Filtering_WithLongForm_hash = new HashMap<String, String>();
	public static HashMap<String, String> SP_Virus2Human_hash = new HashMap<String, String>();
	public static HashMap<String, String> GeneWithoutSPPrefix_hash = new HashMap<String, String>();
	public static ArrayList <String> taxid4gene = new ArrayList <String>();
	public static HashMap<String, String> setup_hash = new HashMap<String, String>();
	public static HashMap<String, String> suffixprefix_orig2modified = new HashMap<String, String>();
	public static HashMap<String, String> Abb2Longformtok_hash = new HashMap<String, String>();
	public static HashMap<String, String> StrainID_ancestor2tax_hash = new HashMap<String, String>();
	public static HashMap<String, String> StrainID_taxid2names_hash = new HashMap<String, String>();
	
	public static String SetupFile = "setup.txt";
	public static void main(String [] args) throws IOException, InterruptedException, XMLStreamException, SQLException 
	{
		String InputFolder="input";
		String OutputFolder="output";
		String tmpFolder="tmp";
		String FocusSpecies = "";
		if(args.length<2)
		{
			System.out.println("\n$ java -Xmx30G -Xms10G -jar GNormPlus.jar [InputFolder] [OutputFolder] [SetupFile]");
			System.out.println("[InputFolder] Default : input");
			System.out.println("[OutputFolder] Default : output");
			System.out.println("[SetupFile] Default : setup.txt\n\n");
		}
		else
		{
			/*
			 * Parameters
			 */
			InputFolder=args[0];
			OutputFolder=args[1];
			if(args.length>=3)
			{
				SetupFile = args[2];
			}
			if(args.length>=4)
			{
				FocusSpecies=args[3];
			}
		}
		
		BufferedReader br = new BufferedReader(new FileReader(SetupFile));
		String line="";
		Pattern ptmp = Pattern.compile("^	([A-Za-z0-9]+) = ([^ \\t\\n\\r]+)$");
		while ((line = br.readLine()) != null)  
		{
			Matcher mtmp = ptmp.matcher(line);
			if(mtmp.find())
			{
				setup_hash.put(mtmp.group(1), mtmp.group(2));
			}
		}
		br.close();
		if(!setup_hash.containsKey("GeneIDMatch"))
		{
			setup_hash.put("GeneIDMatch","True");
		}
		if(!setup_hash.containsKey("HomologeneID"))
		{
			setup_hash.put("HomologeneID","False");
		}
		if(!FocusSpecies.equals(""))
		{
			setup_hash.put("FocusSpecies",FocusSpecies);
		}
		if(!setup_hash.containsKey("ShowUnNormalizedMention"))
		{
			setup_hash.put("ShowUnNormalizedMention","False");
		}
		if(setup_hash.containsKey("tmpFolder"))
		{
			tmpFolder=setup_hash.get("tmpFolder");
		}
		
		/*
		 * Time stamp - start : All
		 */
		double startTime,endTime,totTime;
		startTime = System.currentTimeMillis();//start time
	
		int NumFiles=0;
		File folder = new File(InputFolder);
		File[] listOfFiles = folder.listFiles();
		for (int i = 0; i < listOfFiles.length; i++)
		{
			if (listOfFiles[i].isFile()) 
			{
				String InputFile = listOfFiles[i].getName();
				File f = new File(OutputFolder+"/"+InputFile);
				if(f.exists() && !f.isDirectory()) 
				{ 
				}
				else
				{
					NumFiles++;
				}
			}
		}
		
		System.out.println("Total "+NumFiles+" file(s) wait(s) for process.");
		
		if(NumFiles>0)
		{
			/* 
			 * Start & Load Dictionary
			 */
			String TrainTest = "Test";
			if(setup_hash.containsKey("TrainTest"))
			{
				TrainTest = setup_hash.get("TrainTest");
			}
			
			
			/** Load Dictionary */
			if(setup_hash.containsKey("GeneRecognition") && setup_hash.get("GeneRecognition").toLowerCase().equals("true"))
			{
				System.out.print("Loading Gene NER Dictionary : Processing ... \r");
				/** CTDGene  */
				if(setup_hash.containsKey("IgnoreNER") && setup_hash.get("IgnoreNER").toLowerCase().equals("true")){} // not NER (entities are pre-annotated)
				else if(setup_hash.containsKey("SpeciesAssignmentOnly") && setup_hash.get("SpeciesAssignmentOnly").toLowerCase().equals("true")) {} // species assignment 
				else
				{
					PT_CTDGene.TreeFile2Tree(setup_hash.get("DictionaryFolder")+"/PT_CTDGene.txt");
				}
				/** ent */
				br = new BufferedReader(new FileReader(setup_hash.get("DictionaryFolder")+"/ent.rev.txt"));
				line="";
				while ((line = br.readLine()) != null)  
				{
					String l[]=line.split("\t"); //&#x00391;	Alpha
					ent_hash.put(l[0], l[1]);
				}
				br.close();	
	
				/** FamilyName */
				if((!setup_hash.containsKey("IgnoreNER")) || setup_hash.get("IgnoreNER").toLowerCase() != "true")
				{
					PT_FamilyName.TreeFile2Tree(setup_hash.get("DictionaryFolder")+"/PT_FamilyName.txt");
				}
			
				/** GeneChromosome */
				//PT_GeneChromosome.TreeFile2Tree(setup_hash.get("DictionaryFolder")+"/PT_GeneChromosome.txt");
				System.out.println("Loading Gene NER Dictionary : Processing ... done.");
			}
			
			if(setup_hash.containsKey("SpeciesRecognition") && setup_hash.get("SpeciesRecognition").toLowerCase().equals("true"))
			{
				System.out.print("Loading Species NER Dictionary : Processing ... \r");
				/** Species */
				PT_Species.TreeFile2Tree(setup_hash.get("DictionaryFolder")+"/PT_Species.txt");

				/** Cell */
				PT_Cell.TreeFile2Tree(setup_hash.get("DictionaryFolder")+"/PT_Cell.txt");
				
				/** Genus */
				br = new BufferedReader(new FileReader(setup_hash.get("DictionaryFolder")+"/SPGenus.txt"));
				line="";
				while ((line = br.readLine()) != null)  
				{
					String l[]=line.split("\t");
					GenusID_hash.put(l[0], l[1]); // tax id -> Genus
				}
				br.close();	
				
				/** taxid4gene */
				br = new BufferedReader(new FileReader(setup_hash.get("DictionaryFolder")+"/tax4gene.txt"));
				line="";
				while ((line = br.readLine()) != null)  
				{
					taxid4gene.add(line); // tax id -> Genus
				}
				br.close();	
				System.out.println("Loading Species NER Dictionary : Processing ... done.");
				
			}
			
			if(setup_hash.containsKey("SpeciesAssignment") && setup_hash.get("SpeciesAssignment").toLowerCase().equals("true"))
			{
				System.out.print("Loading Species Assignment Dictionary : Processing ... \r");
				/** GeneWithoutSPPrefix */
				br = new BufferedReader(new FileReader(setup_hash.get("DictionaryFolder")+"/GeneWithoutSPPrefix.txt"));
				line="";
				while ((line = br.readLine()) != null)  
				{
					GeneWithoutSPPrefix_hash.put(line, "");
				}
				br.close();	
				
				/** Prefix */
				br = new BufferedReader(new FileReader(setup_hash.get("DictionaryFolder")+"/SPPrefix.txt"));
				line="";
				while ((line = br.readLine()) != null)  
				{
					String l[]=line.split("\t");
					PrefixID_hash.put(l[0], l[1]); //tax id -> prefix
				}
				br.close();
				PrefixID_hash.put("9606", "h");
				PrefixID_hash.put("10090", "m");
				PrefixID_hash.put("10116", "r");
				PrefixID_hash.put("4932", "y");
				PrefixID_hash.put("7227", "d");
				PrefixID_hash.put("7955", "z|dr|Dr|Zf|zf");
				PrefixID_hash.put("3702", "at|At");
				
				/** Frequency */
				br = new BufferedReader(new FileReader(setup_hash.get("DictionaryFolder")+"/taxonomy_freq.txt"));
				line="";
				while ((line = br.readLine()) != null)  
				{
					String l[]=line.split("\t");
					TaxFreq_hash.put(l[0], Double.parseDouble(l[1])/200000000); //tax id -> prefix
				}
				br.close();	
				
				/** SP_Virus2Human_hash */
				br = new BufferedReader(new FileReader(setup_hash.get("DictionaryFolder")+"/SP_Virus2HumanList.txt"));
				line="";
				while ((line = br.readLine()) != null)  
				{
					SP_Virus2Human_hash.put(line,"9606");
				}
				br.close();	
				
				/** SPStrain */
				/*
				br = new BufferedReader(new FileReader(setup_hash.get("DictionaryFolder")+"/SPStrain.txt"));
				line="";
				while ((line = br.readLine()) != null)  
				{
					String l[]=line.split("\t");
					String ancestor_id = l[0];
					String tax_id = l[1];
					String tax_names = l[2];
					StrainID_ancestor2tax_hash.put(ancestor_id, tax_id); // ancestor -> tax_id
					StrainID_taxid2names_hash.put(tax_id, tax_names); // tax id -> strain
				}
				br.close();
				*/
				System.out.println("Loading Species Assignment Dictionary : Processing ... done.");
				
			}
			
			if(setup_hash.containsKey("GeneNormalization") && setup_hash.get("GeneNormalization").toLowerCase().equals("true"))
			{
				System.out.print("Loading Gene normalization Dictionary : Processing ... \r");
				/** gene_prefix & gene_suffix */
				br = new BufferedReader(new FileReader(setup_hash.get("DictionaryFolder")+"/PrefixSuffix.txt"));
				line="";
				while ((line = br.readLine()) != null)  
				{
					String l[]=line.split("\t");
					String org=l[0];
					String mod=l[1];
					suffixprefix_orig2modified.put(org,mod);
				}
				br.close();	
				
				/** gene_prefix & gene_suffix */
				br = new BufferedReader(new FileReader(setup_hash.get("DictionaryFolder")+"/NonGeneAbbr.txt"));
				line="";
				while ((line = br.readLine()) != null)  
				{
					String l[]=line.split("\t");
					String shortform=l[0];
					String longform_toks=l[1];
					Abb2Longformtok_hash.put(shortform,longform_toks);
				}
				br.close();
				
				/** SimConcept.MentionType */
				br = new BufferedReader(new FileReader(setup_hash.get("DictionaryFolder")+"/SimConcept.MentionType.txt"));
				line="";
				while ((line = br.readLine()) != null)  
				{
					String l[]=line.split("\t");
					SimConceptMention2Type_hash.put(l[0], l[1]);
				}
				br.close();	
				
				/** Filtering */
				br = new BufferedReader(new FileReader(setup_hash.get("DictionaryFolder")+"/Filtering.txt"));
				line="";
				while ((line = br.readLine()) != null)  
				{
					Filtering_hash.put(line, "");
				}
				br.close();	
				
				/** Filtering_WithLongForm.txt */
				br = new BufferedReader(new FileReader(setup_hash.get("DictionaryFolder")+"/Filtering_WithLongForm.txt"));
				line="";
				while ((line = br.readLine()) != null)  
				{
					String l[]=line.split("\t");
					Filtering_WithLongForm_hash.put(l[0], l[1]);
				}
				br.close();	
				
				/** Gene Dictionary */
				if(setup_hash.containsKey("FocusSpecies") && !setup_hash.get("FocusSpecies").equals("All"))
				{
					PT_Gene.TreeFile2Tree(setup_hash.get("DictionaryFolder")+"/PT_Gene."+setup_hash.get("FocusSpecies")+".txt");
				}
				else if((!FocusSpecies.equals("")) && (!FocusSpecies.equals("All")))
				{
					PT_Gene.TreeFile2Tree(setup_hash.get("DictionaryFolder")+"/PT_Gene."+FocusSpecies+".txt");
				}
				else
				{
					PT_Gene.TreeFile2Tree(setup_hash.get("DictionaryFolder")+"/PT_Gene.txt");
				}
			
				/** GeneScoring */
				String FileName=setup_hash.get("DictionaryFolder")+"/GeneScoring.txt";
				
				if(setup_hash.containsKey("FocusSpecies") && !setup_hash.get("FocusSpecies").equals("All"))
				{
					FileName = setup_hash.get("DictionaryFolder")+"/GeneScoring."+setup_hash.get("FocusSpecies")+".txt";
				}
				else if((!FocusSpecies.equals("")) && (!FocusSpecies.equals("All")))
				{
					FileName = setup_hash.get("DictionaryFolder")+"/GeneScoring."+FocusSpecies+".txt";
				}
				br = new BufferedReader(new FileReader(FileName));
				line="";
				while ((line = br.readLine()) != null)  
				{
					String l[]=line.split("\t");
					GeneScoring_hash.put(l[0], l[1]+"\t"+l[2]+"\t"+l[3]+"\t"+l[4]+"\t"+l[5]+"\t"+l[6]);
				}
				br.close();	
				
				/** GeneScoring.DF */
				FileName=setup_hash.get("DictionaryFolder")+"/GeneScoring.DF.txt";
				if(setup_hash.containsKey("FocusSpecies") && !setup_hash.get("FocusSpecies").equals("All"))
				{
					FileName = setup_hash.get("DictionaryFolder")+"/GeneScoring.DF."+setup_hash.get("FocusSpecies")+".txt";
				}
				else if((!FocusSpecies.equals("")) && (!FocusSpecies.equals("All")))
				{
					FileName = setup_hash.get("DictionaryFolder")+"/GeneScoring.DF."+FocusSpecies+".txt";
				}
				br = new BufferedReader(new FileReader(FileName));
				double Sum = Double.parseDouble(br.readLine());
				while ((line = br.readLine()) != null)  
				{
					String l[]=line.split("\t");
					// token -> idf
					GeneScoringDF_hash.put(l[0], Math.log10(Sum/Double.parseDouble(l[1])));
				}
				br.close();
				
				/** Suffix Translation */
				SuffixTranslationMap_hash.put("alpha","a");
				SuffixTranslationMap_hash.put("a","alpha");
				SuffixTranslationMap_hash.put("beta","b");
				SuffixTranslationMap_hash.put("b","beta");
				SuffixTranslationMap_hash.put("delta","d");
				SuffixTranslationMap_hash.put("d","delta");
				SuffixTranslationMap_hash.put("z","zeta");
				SuffixTranslationMap_hash.put("zeta","z");
				SuffixTranslationMap_hash.put("gamma","g");
				SuffixTranslationMap_hash.put("g","gamma");
				SuffixTranslationMap_hash.put("r","gamma");
				SuffixTranslationMap_hash.put("y","gamma");
				
				SuffixTranslationMap2_hash.put("2","ii");
				SuffixTranslationMap2_hash.put("ii","2");
				SuffixTranslationMap2_hash.put("II","2");
				SuffixTranslationMap2_hash.put("1","i");
				SuffixTranslationMap2_hash.put("i","1");
				SuffixTranslationMap2_hash.put("I","1");
				
				/** GeneID */
				if(setup_hash.containsKey("GeneIDMatch") && setup_hash.get("GeneIDMatch").toLowerCase().equals("true"))
				{
					br = new BufferedReader(new FileReader(setup_hash.get("DictionaryFolder")+"/GeneIDs.txt"));
					line="";
					while ((line = br.readLine()) != null)  
					{
						String l[]=line.split("\t");
						GeneIDs_hash.put(l[0],l[1]);
					}
					br.close();
				}
				
				/** Normalization2Protein */
				if(setup_hash.containsKey("Normalization2Protein") && setup_hash.get("Normalization2Protein").toLowerCase().equals("true"))
				{
					br = new BufferedReader(new FileReader(setup_hash.get("DictionaryFolder")+"/Gene2Protein.txt"));
					line="";
					while ((line = br.readLine()) != null)  
					{
						String l[]=line.split("\t");
						Normalization2Protein_hash.put(l[0],l[1]);
					}
					br.close();
				}
				
				/** HomologeneID */
				if(setup_hash.containsKey("HomologeneID") && setup_hash.get("HomologeneID").toLowerCase().equals("true"))
				{
					br = new BufferedReader(new FileReader(setup_hash.get("DictionaryFolder")+"/Gene2Homoid.txt"));
					line="";
					while ((line = br.readLine()) != null)  
					{
						String l[]=line.split("\t");
						HomologeneID_hash.put(l[0],l[1]);
					}
					br.close();
				}
				System.out.println("Loading Gene normalization Dictionary : Processing ... done.");
			}
			
			endTime = System.currentTimeMillis();
			totTime = endTime - startTime;
			System.out.println("Loading Dictionary : Processing Time:"+totTime/1000+"sec");
			
			folder = new File(InputFolder);
			listOfFiles = folder.listFiles();
			for (int i = 0; i < listOfFiles.length; i++)
			{
				if (listOfFiles[i].isFile()) 
				{
					String InputFile = listOfFiles[i].getName();
					File f = new File(OutputFolder+"/"+InputFile);
					if(f.exists() && !f.isDirectory()) 
					{ 
						System.out.println(InputFolder+"/"+InputFile+" - Done. (The output file exists in output folder)");
					}
					else
					{
						String path=tmpFolder; 
				        File file = new File(path);
				        File[] files = file.listFiles(); 
				        for (File ftmp:files) 
				        {
				        	if (ftmp.isFile() && ftmp.exists()) 
				            {
				        		if(ftmp.toString().matches(tmpFolder+"/"+InputFile+".*"))
					        	{
				        			ftmp.delete();
					        	}
				        	}
				        }
						
						BioCDocobj = new BioCDoc();
						
						/*
						 * Format Check 
						 */
						String Format = "";
						String checkR = BioCDocobj.BioCFormatCheck(InputFolder+"/"+InputFile);
						if(checkR.equals("BioC"))
						{
							Format = "BioC";
						}
						else if(checkR.equals("PubTator"))
						{
							Format = "PubTator";
						}
						else
						{
							System.out.println(checkR);
							System.exit(0);
						}
						
						System.out.print(InputFolder+"/"+InputFile+" - ("+Format+" format) : Processing ... \r");
						
						/** PubTator2BioC*/
						if(Format.equals("PubTator"))
						{
							BioCDocobj.PubTator2BioC(InputFolder+"/"+InputFile,tmpFolder+"/"+InputFile);
						}
						else
						{
							br = new BufferedReader(new FileReader(InputFolder+"/"+InputFile));
							BufferedWriter fr = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(tmpFolder+"/"+InputFile), "UTF-8"));
							line="";
							while ((line = br.readLine()) != null)  
							{
								fr.write(line);
							}
							br.close();
							fr.close();
						}
						
						/** load file */
						GNR GNRobj = new GNR();
						GNRobj.LoadInputFile(tmpFolder+"/"+InputFile,tmpFolder+"/"+InputFile+".Abb",TrainTest);
						SR SRobj = new SR();
						SimConcept SCobj = new SimConcept();
						GN GNobj = new GN();
						String FinalStep="";
						
						/** SpeciesRecognition */
						if(setup_hash.containsKey("SpeciesRecognition")  && setup_hash.get("SpeciesRecognition").toLowerCase().equals("true") ) // pre-annotated name entities
						{
							SRobj.SpeciesRecognition(tmpFolder+"/"+InputFile,tmpFolder+"/"+InputFile+".SR.xml",setup_hash.get("DictionaryFolder")+"/SPStrain.txt",setup_hash.get("FilterAntibody"));
							FinalStep="SpeciesRecognition";
						}
						
						/** GeneRecognition */
						if( setup_hash.containsKey("GeneRecognition") && setup_hash.get("GeneRecognition").toLowerCase().equals("true") )
						{
							GNRobj.FeatureExtraction(tmpFolder+"/"+InputFile+".data",tmpFolder+"/"+InputFile+".loca",TrainTest);
							GNRobj.CRF_test(setup_hash.get("GNRModel"),tmpFolder+"/"+InputFile+".data",tmpFolder+"/"+InputFile+".output","top3"); //top3
							GNRobj.ReadCRFresult(tmpFolder+"/"+InputFile,tmpFolder+"/"+InputFile+".loca",tmpFolder+"/"+InputFile+".output",tmpFolder+"/"+InputFile+".GNR.xml",0.005,0.05); //0.005,0.05
							f = new File(tmpFolder+"/"+InputFile+".SR.xml");
							if(f.exists()) 
							{
								GNRobj.PostProcessing(tmpFolder+"/"+InputFile+".SR.xml",tmpFolder+"/"+InputFile+".GNR.xml");
							}
							else
							{
								GNRobj.PostProcessing(tmpFolder+"/"+InputFile,tmpFolder+"/"+InputFile+".GNR.xml");
							}
							FinalStep="GeneRecognition";
						}
						
						/** SpeciesAssignment */
						if(setup_hash.containsKey("SpeciesAssignment")  && setup_hash.get("SpeciesAssignment").toLowerCase().equals("true") ) // pre-annotated name entities
						{
							if(setup_hash.containsKey("FocusSpecies") && !setup_hash.get("FocusSpecies").equals("All")) // FocusSpecies
							{
								f = new File(tmpFolder+"/"+InputFile+".GNR.xml");
								if(f.exists()) 
								{
									SRobj.SpeciesAssignment(tmpFolder+"/"+InputFile+".GNR.xml",tmpFolder+"/"+InputFile+".SA.xml",setup_hash.get("FocusSpecies"));
								}
								else
								{
									SRobj.SpeciesAssignment(tmpFolder+"/"+InputFile,tmpFolder+"/"+InputFile+".SA.xml",setup_hash.get("FocusSpecies"));
								}
							}
							else// All Species
							{
								f = new File(tmpFolder+"/"+InputFile+".GNR.xml");
								if(f.exists()) 
								{
									SRobj.SpeciesAssignment(tmpFolder+"/"+InputFile+".GNR.xml",tmpFolder+"/"+InputFile+".SA.xml");
								}
								else
								{
									SRobj.SpeciesAssignment(tmpFolder+"/"+InputFile,tmpFolder+"/"+InputFile+".SA.xml");
								}
							}
							FinalStep="SpeciesAssignment";
						}
						
						/** GeneNormalization */
						if((setup_hash.containsKey("GeneNormalization")) && setup_hash.get("GeneNormalization").toLowerCase().equals("true") )
						{
							/** SimConcept */
							{
								SCobj.FeatureExtraction_Test(tmpFolder+"/"+InputFile+".SC.data");
								SCobj.CRF_test(setup_hash.get("SCModel"),tmpFolder+"/"+InputFile+".SC.data",tmpFolder+"/"+InputFile+".SC.output");
								SCobj.ReadCRFresult(tmpFolder+"/"+InputFile,tmpFolder+"/"+InputFile+".SC.output",tmpFolder+"/"+InputFile+".SC.xml");
							}
							
							/** GeneNormalization */
							{
								GNobj.PreProcessing4GN(InputFolder+"/"+InputFile,tmpFolder+"/"+InputFile+".PreProcessing4GN.xml");
								GNobj.ChromosomeRecognition(InputFolder+"/"+InputFile,tmpFolder+"/"+InputFile+".GN.xml");
								if(setup_hash.containsKey("GeneIDMatch") && setup_hash.get("GeneIDMatch").equals("True"))
								{
									
									GNobj.GeneNormalization(tmpFolder+"/"+InputFile,tmpFolder+"/"+InputFile+".GN.xml",true);
									GNobj.GeneIDRecognition(tmpFolder+"/"+InputFile,tmpFolder+"/"+InputFile+".GN.xml");
								}
								else
								{
									GNobj.GeneNormalization(tmpFolder+"/"+InputFile,tmpFolder+"/"+InputFile+".GN.xml",false);
								}
							}
							FinalStep="GeneNormalization";
						}
						
						/** BioC2PubTator*/
						String final_output="";
						if(FinalStep.equals("GeneNormalization"))
						{
							final_output=tmpFolder+"/"+InputFile+".GN.xml";
						}
						else if(FinalStep.equals("SpeciesAssignment"))
						{
							final_output=tmpFolder+"/"+InputFile+".SA.xml";
						}
						else if(FinalStep.equals("SpeciesRecognition"))
						{
							final_output=tmpFolder+"/"+InputFile+".SR.xml";
						}
						else if(FinalStep.equals("GeneRecognition"))
						{
							final_output=tmpFolder+"/"+InputFile+".GNR.xml";
						}
						
						if(Format.equals("PubTator"))
						{
							BioCDocobj.BioC2PubTator(final_output,OutputFolder+"/"+InputFile);
						}
						else
						{
							br = new BufferedReader(new FileReader(final_output));
							BufferedWriter fr = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(OutputFolder+"/"+InputFile), "UTF-8"));
							line="";
							while ((line = br.readLine()) != null)  
							{
								fr.write(line);
							}
							br.close();
							fr.close();
						}
						
						/*
						 * remove tmp files
						 */
						if((!setup_hash.containsKey("DeleteTmp")) || setup_hash.get("DeleteTmp").toLowerCase().equals("true"))
						{
							path="tmp"; 
					        file = new File(path);
					        files = file.listFiles(); 
					        for (File ftmp:files) 
					        {
					        	if (ftmp.isFile() && ftmp.exists()) 
					            {
					        		if(ftmp.toString().matches(tmpFolder+"/"+InputFile+".*"))
						        	{
					        			ftmp.delete();
						        	}
					        	}
					        }
						}
						
						/*
						 * Time stamp - last
						 */
						endTime = System.currentTimeMillis();
						totTime = endTime - startTime;
						System.out.println(InputFolder+"/"+InputFile+" - ("+Format+" format) : Processing Time:"+totTime/1000+"sec");
					}
				}
			}
		}
	}
}