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package sort;
import stream.Read;
import tax.TaxNode;
import tax.TaxTree;
/**
* @author Brian Bushnell
* @date Oct 27, 2014
*
*/
public final class ReadComparatorTaxa extends ReadComparator {
private ReadComparatorTaxa(){}
@Override
public int compare(Read r1, Read r2) {
int x=compareInner(r1, r2);
return ascending*x;
}
private static int compareInner(Read r1, Read r2) {
final TaxNode a0=tree.parseNodeFromHeader(r1.id, true);
final TaxNode b0=tree.parseNodeFromHeader(r2.id, true);
TaxNode a=a0, b=b0;
// if(a==null){a=tree.getNode(1);}
// if(b==null){b=tree.getNode(1);}
if(a==null || b==null){
// System.err.println("null for "+r1.id+", "+r2.id);
if(a==null && b==null){return ReadComparatorName.comparator.compare(r1, r2);}
return (a==null ? 1 : -1);
}
if(a==b){
return ReadComparatorName.comparator.compare(r1, r2);
}
// final TaxNode c=tree.commonAncestor(a, b);
// if(c==null){
// assert(false) : r1.id+", "+r2.id+", "+a;
// return compareSimple(tree.highestAncestor(a), tree.highestAncestor(b));
// }
//
// while(a.id!=c.id && a.pid!=c.id){a=tree.getNode(a.pid);}
// while(b.id!=c.id && c.pid!=c.id){b=tree.getNode(b.pid);}
while(a.id!=a.pid && a.levelExtended<TaxTree.FAMILY_E){
TaxNode x=tree.getNode(a.pid);
if(x.levelExtended>TaxTree.FAMILY_E){break;}
a=x;
}
while(b.id!=b.pid && b.levelExtended<TaxTree.FAMILY_E){
TaxNode x=tree.getNode(b.pid);
if(x.levelExtended>TaxTree.FAMILY_E){break;}
b=x;
}
if(a==b){
while(a.id!=a.pid && a.levelExtended<TaxTree.GENUS_E){
TaxNode x=tree.getNode(a.pid);
if(x.levelExtended>TaxTree.GENUS_E){break;}
a=x;
}
while(b.id!=b.pid && b.levelExtended<TaxTree.GENUS_E){
TaxNode x=tree.getNode(b.pid);
if(x.levelExtended>TaxTree.GENUS_E){break;}
b=x;
}
if(a==b){
a=a0;
b=b0;
while(a.id!=a.pid && a.levelExtended<TaxTree.SPECIES_E){
TaxNode x=tree.getNode(a.pid);
if(x.levelExtended>TaxTree.SPECIES_E){break;}
a=x;
}
while(b.id!=b.pid && b.levelExtended<TaxTree.SPECIES_E){
TaxNode x=tree.getNode(b.pid);
if(x.levelExtended>TaxTree.SPECIES_E){break;}
b=x;
}
if(a==b){
return compareSimple(a0, b0);
}
}
}
return compareSimple(a, b);
}
private static int compareSimple(final TaxNode a, final TaxNode b){
if(a.levelExtended!=b.levelExtended){return a.levelExtended-b.levelExtended;}
return a.id-b.id;
}
private int ascending=1;
@Override
public void setAscending(boolean asc){
ascending=(asc ? 1 : -1);
}
public static TaxTree tree;
public static final ReadComparatorTaxa comparator=new ReadComparatorTaxa();
}
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