www.pudn.com > DNA_Analysis.rar > DNA.java

/** 
 *  
 */ 
package dna.sequences.analysis; 
 
import java.io.*; 
import java.util.*; 
 
import jaligner.Alignment; 
import jaligner.Sequence; 
import jaligner.SmithWatermanGotoh; 
import jaligner.formats.Pair; 
import jaligner.matrix.MatrixLoader; 
import jaligner.util.SequenceParser; 
 
 
/** 
 * @author Administrator 
 * 
 */ 
public class DNA { 
 
	/** 
	 * @param args 
	 */ 
	@SuppressWarnings("unchecked") 
	public static void main(String[] args) { 
		 
		if(args.length !=3) 
		{ 
			System.out.println("args error! please check..."); 
			System.exit(1); 
		}	 
				 
//		put codontable to the hashmap 
		HashMap codonTable = new HashMap(); 
		 
		 
		File ct = new File("codontable"); 
		if(!ct.exists()) 
		{ 
			System.out.println("the file codontable not exits,please check!"); 
			System.exit(1); 
		} 
		 
		FileReader ctr = null; 
		BufferedReader cbr = null; 
		 
		try { 
			ctr = new FileReader(ct); 
			cbr = new BufferedReader(ctr); 
			 
		} catch (FileNotFoundException e1) { 
			e1.printStackTrace(); 
		} 
		 
		String strK = null; 
		String strV = null; 
		try { 
			while((strK = cbr.readLine()) != null && (strV = cbr.readLine()) != null) 
			{ 
				codonTable.put(strK.toUpperCase(),strV.toUpperCase()); 
			} 
		} catch (IOException e) { 
			e.printStackTrace(); 
		} 
		 
		//store the total number of DNA sequence  
		int totalSeq = 0; 
		 
		//read input file 
		File infile = null; 
		FileReader fr = null; 
		BufferedReader br = null; 
		 
		//write output file 
		File outfile = null; 
		FileWriter fw = null; 
		PrintWriter  out = null;	 
		 
		int seqNum = 0; 
		int baseTotal = 0; 
		String partOne = "PART 1: GENENATION INFORMATION \n"; 
		 
		String partTwo = "PART 2: SEQUENCE DETAILS \n"; 
		String seqTwo = null; 
		 
		String partThree = "PART 3: SEQUENCE ALIGNMENT \n"; 
		 
		if(args[0].toLowerCase().equals("simple")) 
		{ 
			infile = new File(args[1]); 
			try { 
				fr = new FileReader(infile); 
				br = new BufferedReader(fr); 
			} catch (FileNotFoundException e) { 
				e.printStackTrace(); 
			} 
			try { 
				while(br.readLine() != null) 
				{ 
					totalSeq ++; 
				} 
			} catch (IOException e1) { 
				e1.printStackTrace(); 
			} 
			 
			try { 
				fr.close(); 
				br.close(); 
			} catch (IOException e1) { 
				e1.printStackTrace(); 
			} 
			String []seqString = new String[totalSeq]; 
			 
			infile = new File(args[1]); 
			try { 
				fr = new FileReader(infile); 
				br = new BufferedReader(fr); 
			} catch (FileNotFoundException e) { 
				e.printStackTrace(); 
			} 
			 
			outfile = new File(args[2]); 
			try { 
				fw = new   FileWriter(outfile,true); 
				 
				out =  new  PrintWriter(fw);     
			                                                                                                                                                       
			} catch (IOException e) { 
				e.printStackTrace(); 
			}           
			 
			//start to read line from the input file 
			String line = null; 
			try { 
				while((line = br.readLine())!= null) 
				{ 
										 
					//part 1 
					baseTotal += line.length(); 
					seqNum ++; 
					 
					//part 2 
					partTwo = partTwo + "Sequence " + String.valueOf(seqNum) + "\n"; 
					partTwo = partTwo + "Number of bases : " + String.valueOf(line.length()) +"\n"; 
					partTwo = partTwo + "GC Percentage : " + String.valueOf(GCPercentage(line)) + "\n"; 
					partTwo = partTwo + "Base Details : " + " A: " + String.valueOf(BaseDetails('A',line)); 
					partTwo = partTwo + " C: "+String.valueOf(BaseDetails('C',line)); 
					partTwo = partTwo + " G: "+String.valueOf(BaseDetails('G',line)); 
					partTwo = partTwo + " T: "+String.valueOf(BaseDetails('T',line))+"\n"; 
					 
					boolean startT = false; 
					String subStrV = null; 
					String subStrK = null; 
					seqTwo = ""; 
					for(int i=0,j=i+3; i') 
						totalSeq ++; 
				} 
			} catch (IOException e1) { 
				e1.printStackTrace(); 
			} 
			 
			try { 
				fr.close(); 
				br.close(); 
			} catch (IOException e1) { 
				e1.printStackTrace(); 
			} 
			String []seqString = new String[totalSeq]; 
			String []seqItem = new String[totalSeq]; 
			String []seqAmino = new String[totalSeq]; 
			 
			infile = new File(args[1]); 
			try { 
				fr = new FileReader(infile); 
				br = new BufferedReader(fr); 
			} catch (FileNotFoundException e) { 
				e.printStackTrace(); 
			} 
			 
			outfile = new File(args[2]); 
			try { 
				fw = new   FileWriter(outfile,true); 
				 
				out =  new  PrintWriter(fw);     
			                                                                                                                                                       
			} catch (IOException e) { 
				e.printStackTrace(); 
			} 
			 
			String line = null; 
			String seqTemp = ""; 
			try { 
				while((line = br.readLine()) != null) 
				{				 
					//part 1 
					if(line.equals("")) 
						continue; 
					if(line.charAt(0) == '>') 
					{ 
						seqItem[seqNum] = line; 
						if(!seqTemp.equals("")) 
						{ 
							seqString[seqNum-1] = seqTemp; 
							seqTemp = ""; 
						} 
						 
						seqNum++; 
					} 
					else 
					{ 
						baseTotal += line.length(); 
						seqTemp += line; 
					} 
					 
				} 
				 
				seqString[seqNum-1] = seqTemp; 
				 
				//start to write part 1 result to the output file 
				partOne += "The file contains "; 
				partOne += String.valueOf(seqNum); 
				partOne += " sequence\n"; 
				 
				partOne += "There are a total of "; 
				partOne += String.valueOf(baseTotal); 
				partOne += " bases in all sequences\n"; 
				 
				partOne +="There are on average "; 
				partOne +=String.valueOf(baseTotal/seqNum); 
				partOne +=" bases in each sequence\n"; 
				 
				 
				out.println(partOne); 
				 
				//part 2 
				for(int i=0; i