jpayne@68: package fileIO;
jpayne@68: import java.io.File;
jpayne@68: import java.io.InputStream;
jpayne@68: import java.util.ArrayList;
jpayne@68: 
jpayne@68: import shared.Shared;
jpayne@68: import structures.ListNum;
jpayne@68: 
jpayne@68: 
jpayne@68: public abstract class ByteFile {
jpayne@68: 	
jpayne@68: //	public static final ByteFile makeByteFile(String fname){
jpayne@68: //		return makeByteFile(fname, false, true);
jpayne@68: //	}
jpayne@68: 	
jpayne@68: 	public static final ByteFile makeByteFile1(String fname, boolean allowSubprocess){
jpayne@68: 		FileFormat ff=FileFormat.testInput(fname, FileFormat.TEXT, null, allowSubprocess, false);
jpayne@68: 		return new ByteFile1(ff);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public static final ByteFile makeByteFile(String fname, boolean allowSubprocess){
jpayne@68: 		FileFormat ff=FileFormat.testInput(fname, FileFormat.TEXT, null, allowSubprocess, false);
jpayne@68: 		return makeByteFile(ff);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public static final ByteFile makeByteFile(FileFormat ff){
jpayne@68: 		return makeByteFile(ff, 0);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public static final ByteFile makeByteFile(FileFormat ff, int type){
jpayne@68: 		if(type==1){return new ByteFile1(ff);}
jpayne@68: 		if(type==2){return new ByteFile2(ff);}
jpayne@68: 		if(!Shared.LOW_MEMORY && (FORCE_MODE_BF2 || (!FORCE_MODE_BF1 && Shared.threads()>4/* && (ReadWrite.isCompressed(fname) || ReadWrite.isSam(fname))*/))){
jpayne@68: //			if(allowSubprocess && ((ReadWrite.USE_UNPIGZ || ReadWrite.USE_GUNZIP) && (fname.endsWith(".gz") || fname.endsWith(".gzip")))){}
jpayne@68: 			return new ByteFile2(ff);
jpayne@68: 		}
jpayne@68: //		if(FORCE_MODE_BF3){return new QuickFile(ff);}
jpayne@68: 		return new ByteFile1(ff);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	protected ByteFile(FileFormat ff_){
jpayne@68: 		ff=ff_;
jpayne@68: 		assert(ff.read()) : ff;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public final ArrayList<byte[]> toByteLines(){
jpayne@68: 		
jpayne@68: 		byte[] s=null;
jpayne@68: 		ArrayList<byte[]> list=new ArrayList<byte[]>(4096);
jpayne@68: 		
jpayne@68: 		for(s=nextLine(); s!=null; s=nextLine()){
jpayne@68: 			list.add(s);
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		return list;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public static final ArrayList<byte[]> toLines(FileFormat ff){
jpayne@68: 		ByteFile bf=makeByteFile(ff);
jpayne@68: 		ArrayList<byte[]> lines=bf.toByteLines();
jpayne@68: 		bf.close();
jpayne@68: 		return lines;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public static final ArrayList<byte[]> toLines(String fname){
jpayne@68: 		FileFormat ff=FileFormat.testInput(fname, FileFormat.TEXT, null, true, false);
jpayne@68: 		return toLines(ff);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public final long countLines(){
jpayne@68: 		byte[] s=null;
jpayne@68: 		long count=0;
jpayne@68: 		for(s=nextLine(); s!=null; s=nextLine()){count++;}
jpayne@68: 		reset();
jpayne@68: 		
jpayne@68: 		return count;
jpayne@68: 	}
jpayne@68: 
jpayne@68: 	public abstract void reset();
jpayne@68: 	final void superReset(){
jpayne@68: 		nextID=0;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public synchronized final ListNum<byte[]> nextList(){
jpayne@68: 		byte[] line=nextLine();
jpayne@68: 		if(line==null){return null;}
jpayne@68: 		ArrayList<byte[]> list=new ArrayList<byte[]>(200);
jpayne@68: 		list.add(line);
jpayne@68: 		for(int i=1; i<200; i++){
jpayne@68: 			line=nextLine();
jpayne@68: 			if(line==null){break;}
jpayne@68: 			list.add(line);
jpayne@68: 		}
jpayne@68: 		ListNum<byte[]> ln=new ListNum<byte[]>(list, nextID);
jpayne@68: 		nextID++;
jpayne@68: 		return ln;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public final boolean exists(){
jpayne@68: 		return name().equals("stdin") || name().startsWith("stdin.") || name().startsWith("jar:") || new File(name()).exists(); //TODO Ugly and unsafe hack for files in jars
jpayne@68: 	}
jpayne@68: 
jpayne@68: 	public abstract InputStream is();
jpayne@68: 	public abstract long lineNum();
jpayne@68: 	
jpayne@68: 	/** Returns true if there was an error */
jpayne@68: 	public abstract boolean close();
jpayne@68: 	
jpayne@68: 	public abstract byte[] nextLine();
jpayne@68: 	
jpayne@68: //	public final void pushBack(byte[] line){
jpayne@68: //		assert(pushBack==null);
jpayne@68: //		pushBack=line;
jpayne@68: //	}
jpayne@68: 	
jpayne@68: 	public abstract void pushBack(byte[] line);
jpayne@68: 	
jpayne@68: 	public abstract boolean isOpen();
jpayne@68: 	
jpayne@68: 	public final String name(){return ff.name();}
jpayne@68: 	public final boolean allowSubprocess(){return ff.allowSubprocess();}
jpayne@68: 	
jpayne@68: 	public final FileFormat ff;
jpayne@68: 	
jpayne@68: 	/** Force usage of ByteFile1 */
jpayne@68: 	public static boolean FORCE_MODE_BF1=false;//!(Data.GENEPOOL || Data.DENOVO || Data.CORI || Shared.WINDOWS);
jpayne@68: 	
jpayne@68: 	/** Force usage of ByteFile2 */
jpayne@68: 	public static boolean FORCE_MODE_BF2=false;
jpayne@68: 	
jpayne@68: 	/** Unused */
jpayne@68: 	@Deprecated
jpayne@68: 	public static boolean FORCE_MODE_BF3=false;
jpayne@68: 	
jpayne@68: 	protected final static byte slashr='\r', slashn='\n', carrot='>', plus='+', at='@';//, tab='\t';
jpayne@68: 	
jpayne@68: //	byte[] pushBack=null;
jpayne@68: 	private long nextID=0;
jpayne@68: 	
jpayne@68: }