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package align2;
import java.io.File;
import java.io.Serializable;
import fileIO.LoadThread;
import fileIO.ReadWrite;
import shared.KillSwitch;
/**
* @author Brian Bushnell
* @date Dec 23, 2012
*
*/
public class Block implements Serializable{
/**
*
*/
private static final long serialVersionUID = -1638122096023589384L;
public Block(int numSites_, int numStarts_){
numSites=numSites_;
numStarts=numStarts_;
sites=new int[numSites];
starts=new int[numStarts+1];
assert(Integer.bitCount(numStarts)==1 && Integer.bitCount(starts.length)==2) : numStarts;
}
public Block(int[] sites_, int[] starts_){
sites=sites_;
starts=starts_;
numSites=sites.length;
numStarts=starts.length-1;
assert(Integer.bitCount(numStarts)==1 && Integer.bitCount(starts.length)==2) : numStarts;
}
/** For legacy support */
public int[] getHitList(int key){
int len=length(key);
if(len==0){return null;}
int start=starts[key];
int[] r=KillSwitch.copyOfRange(sites, start, start+len);
return r;
}
/** For legacy support */
public int[] getHitList(int start, int stop){
int len=length(start, stop);
if(len==0){return null;}
assert(len>0) : len+", "+start+", "+stop;
int[] r=KillSwitch.copyOfRange(sites, start, start+len);
return r;
}
/** For legacy support */
public int[][] getHitLists(int[] start, int[] stop){
int[][] r=new int[start.length][];
for(int i=0; i<start.length; i++){r[i]=getHitList(start[i], stop[i]);}
return r;
}
public int length(int key){
int x=starts[key+1]-starts[key];
if(x==0){return 0;}
return sites[starts[key]]!=-1 ? x : 0; //Lists can be removed by making the first site -1.
}
public int length(int start, int stop){
if(start==stop || sites[start]==-1){return 0;}
return stop-start;
}
public boolean write(String fname, boolean overwrite){
String fname2=fname+"2.gz";
{
File f=new File(fname);
if(f.exists()){
if(!overwrite){
assert(false) : "Tried to overwrite file "+f.getAbsolutePath();
return false;
}
}
f=new File(fname2);
if(f.exists()){
if(!overwrite){
assert(false) : "Tried to overwrite file "+f.getAbsolutePath();
return false;
}
}
}
ReadWrite.writeObjectInThread(sites, fname, allowSubprocess);
if(!compress){
ReadWrite.writeObjectInThread(starts, fname+"2.gz", allowSubprocess);
}else{
if(copyOnWrite){
final int[] x;
x=new int[starts.length];
for(int i=1; i<x.length; i++){
x[i]=starts[i]-starts[i-1];
}
ReadWrite.writeObjectInThread(starts, fname+"2.gz", allowSubprocess);
}else{
compress(starts);
ReadWrite.writeAsync(starts, fname+"2.gz", allowSubprocess);
decompress(starts);
}
}
return true;
}
private static void compress(int[] x){
for(int i=x.length-1; i>0; i--){
x[i]=x[i]-x[i-1];
}
}
private static void decompress(int[] x){
int sum=x[0];
for(int i=1; i<x.length; i++){
sum+=x[i];
x[i]=sum;
}
}
public static Block read(String fname){
String fname2=fname+"2.gz";
final int[] a, b;
{
LoadThread<int[]> lta=LoadThread.load(fname, int[].class);
b=ReadWrite.read(int[].class, fname2, false);
lta.waitForThisToFinish();
a=lta.output;
}
// {
// LoadThread<int[]> lta=LoadThread.load(fname, int[].class);
// LoadThread<int[]> ltb=LoadThread.load(fname2, int[].class);
// lta.waitForThisToFinish();
// ltb.waitForThisToFinish();
// a=lta.output;
// b=ltb.output;
// }
// int[] a=ReadWrite.read(int[].class, fname);
// int[] b=ReadWrite.read(int[].class, fname2);
assert(a!=null && b!=null) : a+", "+b;
if(compress){
int sum=b[0];
for(int i=1; i<b.length; i++){
sum+=b[i];
b[i]=sum;
}
}
Block r=new Block(a, b);
assert(r.sites==a);
assert(r.starts==b);
return r;
}
public final int numSites;
public final int numStarts;
public final int[] sites;
public final int[] starts;
private static boolean allowSubprocess=false;
private static final boolean compress=true;
private static final boolean copyOnWrite=false;
}
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