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package sketch;
import java.util.HashMap;
class Record implements Cloneable, Comparable<Record> {
Record(ResultLineParser parser){
qTaxID=parser.qTaxID;
rTaxID=parser.rTaxID;
qBases=parser.qBases;
rBases=parser.rBases;
qSize=parser.qSize;
rSize=parser.rSize;
ani=parser.ani;
ssu=parser.ssu;
taxLevelExtended=parser.taxLevelExtended;
text=parser.text;
}
Record copy(){
try {
return (Record) this.clone();
} catch (CloneNotSupportedException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
return null;
}
public void processSSU(){
if(verbose){System.err.println("Record.processSSU(): qTaxID="+qTaxID+", rTaxID="+rTaxID+", ssu="+(float)ssu);}
final HashMap<Integer, byte[]> map=SSUMap.r16SMap;
if(ssu<=0 && map!=null){
byte[] qssu=map.get(qTaxID);
byte[] rssu=map.get(rTaxID);
if(qssu!=null && rssu!=null){
ssu=SketchObject.align(qssu, rssu);
if(verbose){System.err.println("Aligned; ssu="+(float)ssu);}
}else{
if(verbose){System.err.println("Missing: "+qTaxID+"="+qssu+", "+rTaxID+"="+rssu);}
}
}else{
if(verbose){System.err.println("Skipping: ssu="+(float)ssu+", map="+(map==null ? "null" : map.size()));}
}
}
@Override
public int compareTo(Record o) {
return ani>o.ani ? -1 : ani<o.ani ? 1 : 0;
}
public double ssu(){return ssu<=0 ? 0 : ssu;}
final int qTaxID;
final int rTaxID;
final long qBases;
final long rBases;
final long qSize;
final long rSize;
final double ani;
private double ssu=-1;
int taxLevelExtended;
int correctNCBI;//0 is false, 1 is true
int correctSSU;//0 is false, 1 is true
boolean missingSSU;
byte[] text;
//All records are correctNCBI there is no later record with a lower taxLevel.
//Records are correctSSU if:
//Their SSUID is >= that of all subsequent records, and the next record (if present) has a SSUID
static boolean verbose;
}
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