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