//Module importance measure
	public void ModuleImportance(ArrayList Diseasegene,ArrayList GenesetsGene,ArrayList DiffExpGene,int modulenum, String outpath,String filepath)
	{
		
		FileReader filereader=null;
		BufferedReader bufferedreader=null;
		FileWriter filewriter=null;
		BufferedWriter bufferedwriter=null;
		ArrayList modulename=new ArrayList();
		double NCR[]=new double[modulenum];
		double ECR[]=new double[modulenum];
		double MCR[]=new double[modulenum];
			try
			{
				filereader=new FileReader(filepath);
				bufferedreader=new BufferedReader(filereader);
			
				String string=new String();
				String nstring="";
				int num=0;
				
				while((string=bufferedreader.readLine())!=null)
				{
					String split[]=string.split("	");
					int number=0;
					
					modulename.add(string);
					int diffgenenum=0;
					for(int i=1;i<split.length;i++)
					{
						if(DiffExpGene.contains(split[i]))
						{
							diffgenenum++;
						}
						if(Diseasegene.contains(split[i]))
						{
							number++;
						}
					}
					//System.out.println(split.length);
					NCR[num]=(double)diffgenenum/(split.length-1);
					int diffedgesnumber=Diffedgenum("D:\\DiffCorData\\GeneSetsExp\\"+num+"-Result.txt");
					ECR[num]=(double)diffedgesnumber/((split.length-1)*(split.length-2)/2);
					
					MCR[num]=(((NCR[num]+ECR[num]))/2)*((double)(number+1)/(split.length-1));//效果很好166/500
					
					System.out.println(MCR[num]);
			       num++;
					
				}
				
			}catch(Exception e)
			{
				e.printStackTrace();
			}finally
			{
				try {
					filereader.close();
					bufferedreader.close();
					
				} catch (IOException e) {
					//  Auto-generated catch block
					e.printStackTrace();
				}
			}
			
	//Sort the modules by importance value
			int []order=new int[modulename.size()];
			for(int i=0;i<order.length;i++)
			{
				order[i]=i;
			}
			for(int i=0;i<MCR.length;i++)
			{
				for(int j=i+1;j<MCR.length;j++)
				{
					if(MCR[i]<MCR[j])
					{
						double temp=MCR[i];
						MCR[i]=MCR[j];
						MCR[j]=temp;
						int temp2=order[i];
						order[i]=order[j];
						order[j]=temp2;
					}
				}
			}
		
		try
		{
			filewriter=new FileWriter(outpath+"DiffMoudle-result-final.txt");
			bufferedwriter=new BufferedWriter(filewriter);
			for(int i=0;i<modulenum;i++)
			{
				bufferedwriter.write(modulename.get(order[i])+"	"+MCR[i]+"\r\n");
			}
			
		}catch(Exception e)
		{
			e.printStackTrace();
		}finally
		{
			try {
				
				bufferedwriter.close();
				filewriter.close();
			} catch (IOException e) {
				//  Auto-generated catch block
				e.printStackTrace();
			}
	
	}
	
}







//Module gene importance measure and sort.
	public void ModuleGeneorder(String modulepath,String DESeq2resultpath,String Diffcorrpath, String outputfilepath,ArrayList diseasegene,ArrayList[]GOHuman, ArrayList GOHumanGene,ArrayList GOHumanGO,ArrayList GOHumanDensity)
	{
		FileReader filereader=null;
		BufferedReader bufferedreader=null;
		ArrayList diffgene=ReadtoArray3(DESeq2resultpath,0);
		ArrayList diffgenevalue=ReadtoArray3(DESeq2resultpath,1);
		
		FileWriter filewriter=null;
		BufferedWriter bufferedwriter=null;
		try
		{
			String filepath2=modulepath;
			filereader=new FileReader(filepath2);
			bufferedreader=new BufferedReader(filereader);
			filewriter=new FileWriter(outputfilepath+"Module-gene-ordered.txt");
			bufferedwriter=new BufferedWriter(filewriter);
			String string=new String();
			int row=0;
			while((string=bufferedreader.readLine())!=null)
			{
				String split[]=string.split("	");
				ArrayList geneinmodule=new ArrayList();
				for(int i=1;i<split.length-1;i++)
				{
					geneinmodule.add(split[i]);
				}
				BigDecimal diffvalue[]=returndiffgenevalue(diffgene,diffgenevalue,geneinmodule);
				BigDecimal diffedgevalue[]=ReadtoArray4(Diffcorrpath+row+"-Result.txt",geneinmodule);
				
				
				BigDecimal govalue[]=returngovalue(geneinmodule, diseasegene, GOHuman, GOHumanGene,GOHumanGO,GOHumanDensity);
				
				ArrayList returnlist=returnoutputarray(diffvalue,diffedgevalue,govalue,geneinmodule);
				
				returnlist.add(0, split[0]);
				returnlist.add(returnlist.size(), split[split.length-1]);
				System.out.println(returnlist);
				for(int y=0;y<(returnlist.size()-1);y++)
				{
					bufferedwriter.write(returnlist.get(y).toString()+"#");
				}
				bufferedwriter.write(returnlist.get(returnlist.size()-1)+"\r\n");
				row++;
			}
	
	}catch(Exception e)
	{
		e.printStackTrace();
	}finally
	{
		try {
			filereader.close();
			bufferedreader.close();
			bufferedwriter.close();
			filewriter.close();
		} catch (IOException e) {
			// TODO Auto-generated catch block
			e.printStackTrace();
		}
	}
	}
	
	
	
	// Globel Gene Rank.
	public ArrayList globelrank(int genenumber, String moduleinfoinputpath)
	{
		ArrayList moduleinfoinput=ReadtoArray(moduleinfoinputpath);
		ArrayList returngene=new ArrayList();
		ArrayList tempreturngene=new ArrayList();
		BigDecimal []mij=new BigDecimal [moduleinfoinput.size()];
		for(int x=0;x<mij.length;x++)
		{
			
				mij[x]=new BigDecimal(0);
		
		}
		while(returngene.size()<genenumber)
		{
			System.out.println(returngene);
			int returngenesize=tempreturngene.size();
			//System.out.println(returngenesize);
			String tempgene=geneneedtoadd(returngenesize,moduleinfoinput, mij);
			String temp[]=tempgene.split("#");
			tempreturngene.add(temp[0]);
			int location=Integer.parseInt(temp[1]);
			mij[location]=mij[location].add(new BigDecimal(1));
			
			if(!returngene.contains(temp[0]))
			{
				returngene.add(temp[0]);
			}
			
		}
		
		
		
		return returngene;
	}