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package bin;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Iterator;
import java.util.Map.Entry;
import java.util.concurrent.ConcurrentHashMap;
import java.util.concurrent.atomic.AtomicLong;
import shared.Tools;
public class BinMap extends BinObject implements Iterable<Cluster> {
public BinMap(ArrayList<Contig> contigs) {contigList=contigs;}
/** Higher is less stringent; 1.0 is neutral, 0 is exact match */
public Cluster addOrMerge(Bin a, int minSizeToCompare, int minSizeToMerge,
int minSizeToAdd, Oracle oracle, Key key, int matrixRange) {
if(minSizeToMerge>=0 && a.size()>=minSizeToMerge) {
Cluster best=findBestCluster(a, minSizeToCompare, key, matrixRange, oracle);
if(best!=null) {
best.add(a);
return best;
}
}
if(minSizeToAdd>=0 && a.size()>=minSizeToAdd) {return add(a, key.set(a));}
residual.add(a);
return null;
}
void addAll(Collection<? extends Bin> bins, int minSize) {
Key key=new Key();
for(Bin b : bins) {
if(b.size()<minSize) {
residual.add(b);
}else {
add(b, key);
}
}
}
Cluster add(Bin a, Key key) {
Cluster c=a.toCluster();
if(key==null) {key=new Key();}
key.set(a);
ArrayList<Cluster> list=getOrMakeList(key);
synchronized(list) {list.add(c);}
return c;
}
public ArrayList<Cluster> getOrMakeList(Key key){
ArrayList<Cluster> list=map.get(key);
if(list==null) {
map.putIfAbsent((Key)(key.clone()), new ArrayList<Cluster>(8));
list=map.get(key);
minGridGC=Tools.min(minGridGC, key.gcLevel);
maxGridGC=Tools.max(maxGridGC, key.gcLevel);
minGridDepth=Tools.min(minGridDepth, key.covLevel, key.covLevel2);
maxGridDepth=Tools.max(maxGridDepth, key.covLevel, key.covLevel2);
assert(minGridGC<=maxGridGC) : minGridGC+", "+maxGridGC+", "+key;
assert(minGridDepth<=maxGridDepth);
}
return list;
}
public Cluster findBestCluster(Bin a, int minSizeToCompare, Key key, int matrixRange, Oracle oracle) {
if(key==null) {key=new Key();}
oracle.clear();
final float gc=a.gc();
final float depth=a.depth(0);
final float depth2=a.depth(1);
key.set(a);
float mult=Binner.sizeAdjustMult(a.size());
final float maxDepthRatio=1+(oracle.maxDepthRatio0-1)*mult;
final float maxGCDif=oracle.maxGCDif0*mult;
assert(maxDepthRatio>=1) : maxDepthRatio;
final int minDepthLevel=Tools.max(minGridDepth,
key.covLevel-matrixRange, Key.quantizeDepth(depth/maxDepthRatio));
final int maxDepthLevel=Tools.min(maxGridDepth,
key.covLevel+matrixRange, Key.quantizeDepth(depth*maxDepthRatio));
final int minGCLevel=Tools.max(minGridGC, key.gcLevel-matrixRange, Key.quantizeGC(gc-maxGCDif));
final int maxGCLevel=Tools.min(maxGridGC, key.gcLevel+matrixRange, Key.quantizeGC(gc+maxGCDif));
int minDepthLevel2=0;
int maxDepthLevel2=0;
if(a.numDepths()>1) {
minDepthLevel2=Tools.max(minGridDepth, key.covLevel2-matrixRange, Key.quantizeDepth(depth2/maxDepthRatio));
maxDepthLevel2=Tools.min(maxGridDepth, key.covLevel2+matrixRange, Key.quantizeDepth(depth2*maxDepthRatio));
}
if(verbose) {
System.err.println("Using params minSizeToCompare="+minSizeToCompare+
", maxKmerDif="+oracle.maxKmerDif0+", maxDepthRatio="+maxDepthRatio+
", maxProduct="+oracle.maxProduct0+", maxGCDif="+maxGCDif+
", maxCovariance="+oracle.maxCovariance0+", matrixRange="+matrixRange);
}
for(int depthLevel2=minDepthLevel2; depthLevel2<=maxDepthLevel2; depthLevel2++) {
for(int depthLevel=minDepthLevel; depthLevel<=maxDepthLevel; depthLevel++) {
for(int gcLevel=minGCLevel; gcLevel<=maxGCLevel; gcLevel++) {
if(verbose) {System.err.println("Looking at depth "+depthLevel+", gc "+gcLevel);}
key.setLevel(gcLevel, depthLevel, depthLevel2);
ArrayList<Cluster> list=map.get(key);
if(list!=null) {
int idx=findBestBinIndex(a, list, minSizeToCompare, oracle);
if(verbose && idx>=0) {System.err.println("***Set best to "+oracle.best.id());}
}
}
}
}
return (Cluster)oracle.best;
}
private int findBestBinIndex(Bin a, ArrayList<? extends Bin> clusters,
int minSizeToCompare, Oracle oracle) {
int bestIdx=-1;
for(int i=0; i<clusters.size(); i++) {
Bin b=clusters.get(i);
if(b==null || a==b) {continue;}
if(b.size()<minSizeToCompare) {break;}
float f=oracle.similarity(a, b, 1f);
assert(f!=0) : b.id();
if(verbose) {
System.err.println("Comparing to "+b.id()+"; score="+oracle.score+"/"+oracle.topScore);
}
if(f>oracle.topScore) {
assert(f>0);//Actually, could be -1; or clear should set to -1
oracle.best=b;
oracle.bestIdx=bestIdx=i;
oracle.topScore=f;
}
}
return bestIdx;
}
ArrayList<Cluster> toList(boolean addResidue){
ArrayList<Cluster> list=new ArrayList<Cluster>();
for(Entry<Key, ArrayList<Cluster>> e : map.entrySet()) {
list.addAll(e.getValue());
}
if(addResidue) {
for(Bin b : residual) {
list.add(b.cluster()==null ? b.toCluster() : b.cluster());
}
}
return list;
}
@Override
public Iterator<Cluster> iterator() {
return toList(false).iterator();
}
public void clear(boolean clearResidual) {
map.clear();
if(clearResidual) {residual.clear();}
minGridGC=999999;
maxGridGC=0;
minGridDepth=999999;
maxGridDepth=0;
}
public boolean isValid() {
assert(isValid(contigList, true));
assert(isValid(residual, false));
for(ArrayList<Cluster> list : map.values()) {
assert(isValid(list, false));
}
return true;
}
public int countClusters() {
int sum=0;
for(ArrayList<Cluster> list : map.values()) {sum+=list.size();}
return sum;
}
public ConcurrentHashMap<Key, ArrayList<Cluster>> map=
new ConcurrentHashMap<Key, ArrayList<Cluster>>(2000, 0.6f, 32);
public ArrayList<Bin> residual=new ArrayList<Bin>();//Should really be contigs
public ArrayList<Contig> contigList;
private int minGridGC=999999;
private int maxGridGC=0;
private int minGridDepth=999999;
private int maxGridDepth=0;
// public AtomicLong fastComparisons=new AtomicLong(0);
// public AtomicLong slowComparisons=new AtomicLong(0);
}
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