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package icecream;
import java.util.ArrayList;
import shared.Tools;
import stream.Read;
import stream.SamLine;
import structures.IntList;
/**
* Container for the list of reads from a single
* PacBio ZMW.
* @author Brian Bushnell
* @date June 5, 2020
*/
public class ZMW extends ArrayList<Read> {
/**
* For serialization.
*/
private static final long serialVersionUID = -2580124131008824113L;
public ZMW(){super();}
public ZMW(int initialSize){super(initialSize);}
public long countBases(){
long x=0;
for(Read r : this){
x+=r.length();
}
return x;
}
public int medianLength(boolean includeDiscarded){
if(size()<3){return -1;}
IntList lengths=new IntList(size()-2);
for(int i=1; i<size()-1; i++){
Read r=get(i);
if(includeDiscarded || !r.discarded()){
lengths.add(get(i).length());
}
}
lengths.sort();
int median=lengths.get(lengths.size/2);
return median;
}
public int longestLength(boolean includeDiscarded){
int max=0;
for(Read r : this){
if(includeDiscarded || !r.discarded()){
max=Tools.max(max, r.length());
}
}
return max;
}
public Read medianRead(boolean includeDiscarded){
int len=medianLength(includeDiscarded);
if(len<0){return longestRead(includeDiscarded);}
for(int i=1; i<size()-1; i++){
Read r=get(i);
if((includeDiscarded || !r.discarded()) && r.length()==len){
return r;
}
}
return null;
}
public Read longestRead(boolean includeDiscarded){
Read max=null;
for(Read r : this){
if((includeDiscarded || !r.discarded()) && (max==null || r.length()>max.length())){max=r;}
}
return max;
}
public int zid(){
if(zid==-1){parseZID();}
return zid;
}
private int parseZID(){
return (size()<1 ? -1 : PBHeader.parseZMW(get(0).id));
}
public static void fixReadHeader(Read r, int leftTrim, int rightTrim){
leftTrim=Tools.max(0, leftTrim);
rightTrim=Tools.max(0, rightTrim);
if(leftTrim<1 && rightTrim<1){return;}
final int idx=r.id.lastIndexOf('/');
if(idx>0 && idx<r.id.length()-3){
String prefix=r.id.substring(0, idx+1);
String suffix=r.id.substring(idx+1);
if(suffix.indexOf('_')>0){
String coords=suffix, comment="";
int tab=suffix.indexOf('\t');
if(tab<0){tab=suffix.indexOf(' ');}
if(tab>0){
coords=coords.substring(0, tab);
comment=coords.substring(tab);
}
String[] split=Tools.underscorePattern.split(coords);
int left=Integer.parseInt(split[0]);
int right=Integer.parseInt(split[1]);
left+=leftTrim;
right-=rightTrim;
if(left>right){left=right;}
if(right-left!=r.length()){right=left+r.length();}
// System.err.println(r.length()+", "+(right-left));
r.id=prefix+left+"_"+right+comment;
final SamLine sl=r.samline;
if(sl!=null){
sl.qname=r.id;
if(sl.optional!=null){
for(int i=0; i<sl.optional.size(); i++){
String s=sl.optional.get(i);
if(s.startsWith("qe:i:")){
s="qe:i:"+right;
sl.optional.set(i, s);
}else if(s.startsWith("qs:i:")){
s="qs:i:"+left;
sl.optional.set(i, s);
}
}
}
}
}
}
}
public void setDiscarded(boolean b){
for(Read r : this){
r.setDiscarded(b);
}
}
public int[] lengths() {
final int size=size();
int[] array=new int[size];
for(int i=0; i<size; i++){
Read r=get(i);
array[i]=r==null ? -1 : r.length();
}
return array;
}
public float estimatePasses(){
final int size=size();
if(size<1){return 0;}
else if(size==1){return 0.25f;}
else if(size==2){return 0.5f;}
int median=medianLength(true);
int first=first().length();
int last=last().length();
return size-2+estimatePasses(first, median)+estimatePasses(last, median);
}
private float estimatePasses(int len, int median){
float ratio=len/(float)median;
//TODO: I want this to be more asymptotic
return Tools.min(0.99f, ratio/(1+0.05f*ratio));
}
public boolean discarded() {
for(Read r : this){
if(!r.discarded()){return false;}
}
return true;
}
/**
* Identifier assigned by streamer, not by PacBio.
* First identifier is 0, then 1, etc.
*/
public long id;
/**
* ZMW ID assigned by PacBio.
*/
private int zid=-1;
public Read first(){return get(0);}
public Read last(){return get(size()-1);}
}
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