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package bin;
import java.util.ArrayList;
import java.util.Iterator;
import dna.AminoAcid;
import shared.Shared;
import shared.Tools;
import sketch.Sketch;
import sketch.SketchMakerMini;
import stream.Read;
import structures.ByteBuilder;
public class Contig extends Bin {
public Contig(String name_, byte[] bases_, int id_) {
name=name_;
shortName=ContigRenamer.toShortName(name);
bases=bases_;
id=id_;
}
// public Contig(String name_, byte[] bases_, int id_) {
// name=name_;
// shortName=ContigRenamer.toShortName(name);
// bases=bases_;
// setID(id_);
// }
@Override
public String name() {return name;}
@Override
public boolean isCluster() {return false;}
@Override
public Cluster toCluster() {
assert(cluster==null);
return new Cluster(this);
}
boolean sameCluster(Bin b) {
return cluster!=null && cluster.contigSet.contains(b.id());
}
// @Override
// public int clusterID() {return clusterID;}
@Override
public Cluster cluster() {return cluster;}
@Override
public void setID(int id_) {
// assert(id==-1 && id_>-1);
id=id_;
}
@Override
public int id() {
// assert(id>=0);
return id;
}
@Override
public boolean isValid() {
if(numDepths()<1) {
assert(false) : numDepths()+", "+name+"\n"+this;
return false;
}
if(tetramers==null) {
assert(false) : name;
return false;
}
// assert(gcSum>0) : gcSum+", "+new String(bases);
if(cluster!=null) {
if(!cluster.contigSet.contains(id())) {
assert(false) : id()+", "+cluster.id+", "+cluster.contigSet;
return false;
}
// if(pairMap!=null && !pairMap.isEmpty()) {
// for(KeyValue kv : KeyValue.toList(pairMap)) {
// int value2=cluster.pairMap.get(kv.key);
// assert(value2>=kv.value) : pairMap+"\n"+cluster.pairMap;
// }
// }
}
return true;
}
public void loadCounts() {
assert(numTetramers==0);
tetramers=new int[canonicalKmers[4]];
numTetramers=countKmers(bases, tetramers, 4);
// invKmers=1f/Tools.max(1, numTetramers);
for(byte b : bases) {
int x=AminoAcid.baseToNumber[b];
gcSum+=(x==1 || x==2) ? 1 : 0;
}
if(countPentamers && size()>=minPentamerSizeCount) {
pentamers=new int[canonicalKmers[5]];
numPentamers=countKmers(bases, pentamers, 5);
}
}
/** In fasta format */
public void appendTo(ByteBuilder bb, int cluster) {
bb.append('>').append(name);
if(cluster>=0) {bb.tab().append("cluster_").append(cluster);}
bb.nl();
final int wrap=Shared.FASTA_WRAP;
for(int i=0; i<bases.length; i+=wrap) {
//Now with modified append I can just append(bases, wrap)
bb.append(bases, i, wrap).nl();
}
}
@Override
public long size() {return bases.length;}
@Override
public Sketch toSketch(SketchMakerMini smm, Read r) {
String name=Long.toString(id());
if(r==null) {r=new Read(null, null, name, id());}
r.id=name;
r.numericID=id();
r.bases=bases;
smm.processReadNucleotide(r);
return smm.toSketch(0);
}
public final ByteBuilder toCov(ByteBuilder bb) {
if(bb==null) {bb=new ByteBuilder();}
bb.append(shortName);
bb.tab().append(id());
bb.tab().append(size());
for(int i=0, max=numDepths(); i<max; i++) {
bb.tab().append(depth(i), 2);
}
ArrayList<KeyValue> list=KeyValue.toList(pairMap);
if(list!=null) {
for(int i=0; i<list.size() && i<DataLoader.MAX_EDGES_TO_PRINT; i++) {
KeyValue ip=list.get(i);
bb.tab().append(ip.key).tab().append(ip.value);
}
}
return bb;
}
@Override
public int numContigs() {return 1;}
@Override
public Iterator<Contig> iterator() {
return new ContigIterator();
}
private class ContigIterator implements Iterator<Contig> {
@Override
public boolean hasNext() {
return hasMore;
}
@Override
public Contig next() {
if(!hasMore) {return null;}
hasMore=false;
return Contig.this;
}
boolean hasMore=true;
}
private int id=-1;
public Cluster cluster=null;
public final String name;
public final String shortName;
public final byte[] bases;
}
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