jpayne@68: package fileIO;
jpayne@68: 
jpayne@68: import java.io.File;
jpayne@68: 
jpayne@68: import dna.Data;
jpayne@68: import shared.Parse;
jpayne@68: import shared.PreParser;
jpayne@68: 
jpayne@68: /**
jpayne@68:  * Tests to see if a summary file matches a reference fasta file, based on date, size, and name
jpayne@68:  * @author Brian Bushnell
jpayne@68:  * @date Mar 11, 2013
jpayne@68:  *
jpayne@68:  */
jpayne@68: public class SummaryFile {
jpayne@68: 	
jpayne@68: 	public static void main(String[] args){
jpayne@68: 		if(args.length==0){
jpayne@68: 			System.out.println("Usage: SummaryFile <summary file> <reference fasta>");
jpayne@68: 			System.exit(0);
jpayne@68: 		}
jpayne@68: 
jpayne@68: 		{//Preparse block for help, config files, and outstream
jpayne@68: 			PreParser pp=new PreParser(args, new Object() { }.getClass().getEnclosingClass(), false);
jpayne@68: 			args=pp.args;
jpayne@68: 			//outstream=pp.outstream;
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		String summary=null, ref=null;
jpayne@68: 		
jpayne@68: 		for(int i=0; i<args.length; i++){
jpayne@68: 
jpayne@68: 			if(args[i].contains("=")){
jpayne@68: 				final String arg=args[i];
jpayne@68: 				final String[] split=arg.split("=");
jpayne@68: 				String a=split[0].toLowerCase();
jpayne@68: 				String b=split.length>1 ? split[1] : null;
jpayne@68: 				
jpayne@68: 				if(a.equals("summary")){
jpayne@68: 					summary=b;
jpayne@68: 				}else if(a.equals("ref") || a.equals("reference")){
jpayne@68: 					ref=b;
jpayne@68: 				}else{
jpayne@68: 					throw new RuntimeException("Unknown parameter: "+args[i]);
jpayne@68: 				}
jpayne@68: 
jpayne@68: 			}else{
jpayne@68: 				if(args[i].endsWith("summary.txt")){
jpayne@68: 					summary=args[i];
jpayne@68: 				}else{
jpayne@68: 					ref=args[i];
jpayne@68: 				}
jpayne@68: 			}
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		if(summary==null && args.length>0){
jpayne@68: 			summary=args[0];
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		if(summary==null){
jpayne@68: 			System.out.println("Usage: SummaryFile <summary file> <reference fasta>");
jpayne@68: 			System.exit(0);
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		if(ref==null){
jpayne@68: 			
jpayne@68: 		}
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public boolean compare(final String refName){
jpayne@68: 		try {
jpayne@68: 			File ref=new File(refName);
jpayne@68: 			if(!ref.exists()){
jpayne@68: 				if(refName.startsWith("stdin")){return false;}
jpayne@68: 				else{
jpayne@68: 					assert(false) : "No such file: "+refName;
jpayne@68: 				}
jpayne@68: 			}
jpayne@68: //			if(!refName.equals(source) && !Files.isSameFile(ref.toPath(), new File(source).toPath())){ //This is Java-7 specific.
jpayne@68: ////				assert(false) : refName+", "+source+": "+(Files.isSameFile(ref.toPath(), new File(source).toPath()))+
jpayne@68: ////						"\n"+ref.getCanonicalPath()+", "+new File(source).getCanonicalPath()+": "+(ref.getCanonicalPath().equals(new File(source).getCanonicalPath()));
jpayne@68: //				return false;
jpayne@68: //
jpayne@68: //			}
jpayne@68: 			if(!refName.equals(source) && !ref.getCanonicalPath().equals(new File(source).getCanonicalPath())){
jpayne@68: //				assert(false) : refName+", "+source+": "+(Files.isSameFile(ref.toPath(), new File(source).toPath()))+
jpayne@68: //						"\n"+ref.getCanonicalPath()+", "+new File(source).getCanonicalPath()+": "+(ref.getCanonicalPath().equals(new File(source).getCanonicalPath()));
jpayne@68: 				return false;
jpayne@68: 				
jpayne@68: 			}
jpayne@68: 			if(bytes!=ref.length()){
jpayne@68: //				assert(false) : bytes+", "+ref.length();
jpayne@68: 				return false;
jpayne@68: 			}
jpayne@68: 			if(modified!=ref.lastModified()){
jpayne@68: //				assert(false) : modified+", "+ref.lastModified();
jpayne@68: 				return false;
jpayne@68: 			}
jpayne@68: 		} catch (Exception e) {
jpayne@68: 			// TODO Auto-generated catch block
jpayne@68: 			e.printStackTrace();
jpayne@68: 			return false;
jpayne@68: 		}
jpayne@68: 		return true;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public static boolean compare(final String summaryName, final String refName){
jpayne@68: 		assert(refName!=null) : "Null reference file name.";
jpayne@68: 		if(!new File(summaryName).exists()){
jpayne@68: //			assert(false);
jpayne@68: 			return false;
jpayne@68: 		}
jpayne@68: 		SummaryFile sf=new SummaryFile(summaryName);
jpayne@68: 		return sf.compare(refName);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public static String getName(){
jpayne@68: 		return getName(Data.GENOME_BUILD);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public static String getName(int build){
jpayne@68: 		return Data.ROOT_GENOME+build+"/summary.txt";
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public SummaryFile(String path){
jpayne@68: 		summaryFname=path;
jpayne@68: 		String s;
jpayne@68: 		TextFile tf=new TextFile(summaryFname, false);
jpayne@68: 		for(s=tf.nextLine(); s!=null; s=tf.nextLine()){
jpayne@68: 			if(s.charAt(0)=='#'){
jpayne@68: 				if(s.startsWith("#Version")){
jpayne@68: 					String[] split=s.split("\t");
jpayne@68: 					version=(split.length>1 ? Integer.parseInt(split[1]) : 0);
jpayne@68: 				}
jpayne@68: 			}else{
jpayne@68: 				String[] split=s.split("\t");
jpayne@68: 				String a=split[0];
jpayne@68: 				String b=split[1];
jpayne@68: 				if(a.equalsIgnoreCase("chroms")){chroms=(int)Long.parseLong(b);}
jpayne@68: 				else if(a.equalsIgnoreCase("bases")){bases=Long.parseLong(b);}
jpayne@68: 				else if(a.equalsIgnoreCase("version")){version=Integer.parseInt(b);}
jpayne@68: 				else if(a.equalsIgnoreCase("defined")){definedBases=Long.parseLong(b);}
jpayne@68: 				else if(a.equalsIgnoreCase("contigs")){contigs=Integer.parseInt(b);}
jpayne@68: 				else if(a.equalsIgnoreCase("scaffolds")){scaffolds=Integer.parseInt(b);}
jpayne@68: 				else if(a.equalsIgnoreCase("interpad")){interpad=Integer.parseInt(b);}
jpayne@68: 				else if(a.equalsIgnoreCase("undefined")){undefinedBases=Long.parseLong(b);}
jpayne@68: 				else if(a.equalsIgnoreCase("name")){name=b;}
jpayne@68: 				else if(a.equalsIgnoreCase("source")){source=b;}
jpayne@68: 				else if(a.equalsIgnoreCase("bytes")){bytes=Long.parseLong(b);}
jpayne@68: 				else if(a.equalsIgnoreCase("last modified")){modified=Long.parseLong(b);}
jpayne@68: 				else if(a.equalsIgnoreCase("scafprefixes")){scafprefixes=Parse.parseBoolean(b);}
jpayne@68: 				else{throw new RuntimeException("In file "+tf.name+": Unknown term "+s);}
jpayne@68: 			}
jpayne@68: 		}
jpayne@68: 		tf.close();
jpayne@68: 	}
jpayne@68: 
jpayne@68: 	public final String summaryFname;
jpayne@68: 
jpayne@68: 	public int chroms;
jpayne@68: 	public long contigs;
jpayne@68: 	public long scaffolds;
jpayne@68: 	public int interpad;
jpayne@68: 	public long bases;
jpayne@68: 	public long definedBases;
jpayne@68: 	public long undefinedBases;
jpayne@68: 	public String name;
jpayne@68: 	public String source;
jpayne@68: 	public int version;
jpayne@68: 	public long bytes;
jpayne@68: 	public long modified;
jpayne@68: 	public boolean scafprefixes;
jpayne@68: 	
jpayne@68: }