import java.io.BufferedReader;
import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.IOException;
import java.io.PrintWriter;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import java.util.*;

public class Mrg2sig extends Thread{
	// Variablen
	String datei;
	int pmmm, bg;
	Thread t;
	// Hashmap für Werte Syntax: Atom_PM/MM [werte]
	String[] copy;
	HashMap<String,ArrayList>  gene = new HashMap<String,ArrayList> ();
	// Einlesen mrg Zeilenweise und einordnen in Hashtable
	@SuppressWarnings("unchecked")
	//Modifizierter Start
	public void start(Thread th)
	{
		this.t = th;
		super.start();
	}
	// Konstruktor
	// Start Parameter: Dateiname zum Einlesen, Verfahren (1 = PM-MM, 2 = PM), BG bearbeitet (1) oder nicht (2)
	public Mrg2sig(String datei, int pmmm, int bg)
	{
		this.datei = datei;
		this.pmmm = pmmm;
		this.bg = bg;
	}
	// Modifizierte Run
	public void run()
	{
		if(t != null)
		{
			try{t.join();t = null;}
			catch(InterruptedException e) {}
		}
		try 
		{
			int wo = datei.indexOf(".");
			String nuname = datei.substring(0,wo);
			if(bg == 1){datei = nuname+"minbg.mrg";}
			else if(bg == 2){datei = nuname+"celcdf.mrg";}
			nuname = nuname +"_m2s.mrg";
			readmrg(datei);
			if(pmmm == 1){calculate(nuname);}
			else{only_pm(nuname);}
		}
		catch (IOException e) 
		{
			e.printStackTrace();
		}
		catch (Exception es)
		{
			es.printStackTrace();
		}
		Stammfenster.progress.setValue(Stammfenster.progress.getValue()+5);
	}
	
	public void readmrg(String datei) throws IOException
	{
		System.out.println("ReadMRG..."+datei);
		String line = "", gen = "", pf = "", atom = "", mean = "";
		// READ
		BufferedReader mrg = new BufferedReader(new FileReader(datei));
		
		while(line != null)
		{
			Pattern pat = Pattern.compile("\\d+\\t+\\d+\\t+(\\d+)\\.\\d+\\t+(\\S+)\\t+(\\d+)\\t+\\w\\t+\\w\\t+\\w\\t+(\\w+)");//("\\d+\\s+\\d+\\s+(\\d+)\\s+(\\w+)\\s+(\\d+)\\s+\\w\\s+\\w\\s+\\w\\s+(\\w+)");
			Matcher mat = pat.matcher(line);
			if(mat.find())
			{
				//System.out.println("ESMATCHT!");
				mean = mat.group(1); gen = mat.group(2); atom = mat.group(3); pf = mat.group(4);
				//	Kommt ein Name zum ersten Mal vor, neuen Index erstellen
				if(!gene.containsKey(gen+'@'+pf))
				{
					gene.put(gen+'@'+pf,new ArrayList());
					gene.get(gen+'@'+pf).add(atom +"@"+ mean);
				}
				// Sonst die Werte zur Liste hinzufügen
				else
				{
					gene.get(gen +'@'+ pf).add(atom +'@'+ mean);
				}
			}
			line = mrg.readLine();
		}	
	}
	
	// Nur PM verwenden
	public void only_pm(String output)
	{
		// WRITE
		try {PrintWriter daten = new PrintWriter(output);
		ArrayList<String> pm;
		String[] atmeanPM = new String[2]; 
		String ind;
		double numean; 
		int count;
		ArrayList<String> s2sn = new ArrayList<String>();
		// Einlesen nach Einträgen
		for(String aKey : gene.keySet()) // Alle Indices durchgehen
		{
			// Wenn PM dann übernehmen
			if(aKey.endsWith("@PM"))
			{
				// pm-Werte aus der Arraylist des Gens übertragen in ArrayList pm
				pm = new ArrayList<String>();
				pm = gene.get(aKey);
				// Endung entfernen
				ind = aKey.replace("@PM","");
				ArrayList<String> tmp = new ArrayList<String>();
				count = 0;
				for(String val : pm)
				{
					atmeanPM = val.split("@");
					numean = Double.parseDouble(atmeanPM[1]);
					if(numean > 0 && numean < 10){numean = 10;}
					if(numean > 0)
					{
						tmp.add(new String(numean+""));
						count++;
						break;
					}
				}
				String[] tmpp = new String[tmp.size()];
				// Wichtig mit toArray(Objekt) absichern!
				tmp.toArray(tmpp);
				// daten.println(ind+"\t"+median(tmpp));
				s2sn.add(ind+"@"+median(tmpp));
				pm.clear(); tmp.clear(); tmpp = null;
			}
		}
		// Sig2Signorm
		String[] tmpp = new String[s2sn.size()];
		s2sn.toArray(tmpp);
		daten.print(s2snorm(tmpp));
		daten.close();
	  }
	  catch (FileNotFoundException e) 
	  {
	      e.printStackTrace();
	  }	
	}
	
	// MM von PM abziehen
	public void calculate(String output)
	{
		// WRITE
		try {PrintWriter daten = new PrintWriter(output);
		ArrayList<String> pm; ArrayList<String> mm;
		String[] atmeanPM, atmeanMM;
		atmeanPM = new String[2]; atmeanMM = new String[2];
		String ind;
		double numean; 
		int count;
		ArrayList<String> s2sn = new ArrayList<String>();
		// Einlesen nach Einträgen
		for(String aKey : gene.keySet()) // Alle Indices durchgehen
		{
			// Wenn PM dann passende MM suchen
			if(aKey.endsWith("@PM"))
			{
				pm = new ArrayList<String>();
				pm = gene.get(aKey);
				ind = aKey;
				ind = ind.replace("PM","MM");
				mm = new ArrayList<String>();
				mm = gene.get(ind);
				ArrayList<String> tmp = new ArrayList<String>();
				count = 0;
				for(String val : pm)
				{
					atmeanPM = val.split("@");
					for(String val2 : mm)
					{
						atmeanMM = val2.split("@");
						// Wenn die Atome übereinstimmen
						if(atmeanPM[0].equals(atmeanMM[0]))
						{
							// Neuen Wert ausrechenen PM-MM
							numean = Double.parseDouble(atmeanPM[1]) - Double.parseDouble(atmeanMM[1]);
							if(numean > 0 && numean < 10){numean = 10;}
							if(numean > 0)
							{
								tmp.add(new String(numean+""));
								count++;
								break;
							}
						}
					}
				}
				ind = ind.replace("@MM","");
				String[] tmpp = new String[tmp.size()];
				//  Wichtig mit toArray(Objekt) absichern!
				tmp.toArray(tmpp);
				// daten.println(ind+"\t"+median(tmpp));
				s2sn.add(ind+"@"+median(tmpp));
				mm.clear(); pm.clear(); tmp.clear(); tmpp = null;
			}
		}
		// Sig2Signorm
		String[] tmpp = new String[s2sn.size()];
		s2sn.toArray(tmpp);
		daten.print(s2snorm(tmpp));
		daten.close();
	  }
	  catch (FileNotFoundException e) 
	  {
	      e.printStackTrace();
	  }	
	}
	
	// Median
	public double median(String[] values)
	{
		double numean = 0;
		int cou = 0;
		double[] kase = new double[values.length];
		for(String m: values)
		{
			try{kase[cou] = Double.parseDouble(m);cou++;}
			catch(Exception e){}
		}
		// Sortieren
		Arrays.sort(kase);
		// Gerade
		if(kase.length > 0)
		{
			if(kase.length % 2 == 0 || kase.length == 1)
			{
				numean = kase[kase.length/2];
			}
			// Ungerade
			else
			{
				int ind1, ind2;
				ind1 = (int)(kase.length/2)-1;
				ind2 = (int)(kase.length/2);
				numean = ((kase[ind1]) + (kase[ind2]))/2;
			}
		}
		return(numean);
	}
	
	//Sig2Signorm
	public String s2snorm(String tmpp[])
	{
		String[] copy = new String[2];
		String[] index = new String[tmpp.length];
		String[] s2s = new String[tmpp.length];
		String[] cop = new String[tmpp.length];
		int za = 0;
		for(String bla:tmpp)
		{
			copy = bla.split("@");
			index[za] = copy[0];
			s2s[za] = copy[1];
			za++;
			copy = null;
		}
		double anz = 0;
		cop = s2s.clone();
		// Median aller Mediane berechnen
		anz = median(cop);
		za = 0;
		String out = "Normierung: " +anz+" \ns2s: "+s2s.length +"\ntmpp: "+tmpp.length +"\n";
		for(String va:s2s)
		{
			try{double nuu = Double.parseDouble(va);
			nuu = nuu/anz;
			//if(nuu < 0){nuu = 10;}
			//else{
			nuu = (nuu)*200;
			//}
			out += index[za] +"\t"+ nuu +"\n";
			za++;
			}catch(Exception e){}
		}
		return(out);
	}
}