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package sketch;
import java.util.ArrayList;
import java.util.Collections;
import fileIO.ByteStreamWriter;
import shared.Tools;
class RecordSet {
RecordSet(int qID_){
qID=qID_;
}
public void sortAndSweep() {
if(verbose){System.err.println("RecordSet.sortAndSweep(): qID="+qID+", sorted="+sorted+", swept="+swept+", ssuProcessed="+ssuProcessed);}
if(sorted && swept){return;}
Collections.sort(records);
sorted=true;
long seen=0;
int removed=0;
for(int i=0; i<records.size(); i++){
Record r=records.get(i);
long mask=1L<<r.taxLevelExtended;
if((seen&mask)!=0){
records.set(i, null);
removed++;
}
seen|=mask;
}
if(removed>0){
Tools.condenseStrict(records);
}
swept=true;
}
public void processSSU(){
if(verbose){System.err.println("RecordSet.processSSU(): qID="+qID+", sorted="+sorted+", swept="+swept+", ssuProcessed="+ssuProcessed);}
if(ssuProcessed || SSUMap.r16SMap==null){return;}//TODO
for(Record r : records){
r.processSSU();
}
ssuProcessed=true;
}
int[] test(ByteStreamWriter bswBad){
if(verbose){System.err.println("RecordSet.test(): qID="+qID+", sorted="+sorted+", swept="+swept+", ssuProcessed="+ssuProcessed);}
boolean failed=false;
int[] status=new int[AnalyzeSketchResults.taxLevels];
for(int level=1; level<AnalyzeSketchResults.taxLevels; level++){
Record first=null;
boolean correctTax=true;
boolean correctSSU=true;
boolean missingSSU=false;
for(Record r : records){
if(r.taxLevelExtended<level){
//Ignore
}else{
if(first==null){
first=r;
correctTax=true;
correctSSU=true;
missingSSU=first.ssu()<=0;
}else{
if(r.taxLevelExtended>=first.taxLevelExtended){
//OK
}else{
//Incorrect NCBI
correctTax=false;
if(r.ssu()<=0 || first.ssu()<=0){
//Missing SSU
missingSSU=true;
}else if(first.ssu()>=r.ssu()){
//Correct SSU
}else{
//Incorrect SSU
correctSSU=false;
failed=true;
}
}
}
}
}
int x;
if(first==null){
//No hit
x=AnalyzeSketchResults.NOHIT;
}else if(correctTax){
x=AnalyzeSketchResults.CORRECT;
}else{
x=AnalyzeSketchResults.INCORRECT_TAX;
if(!correctSSU){x|=AnalyzeSketchResults.INCORRECT_SSU;}
else if(missingSSU){x|=AnalyzeSketchResults.MISSING_SSU;}
}
status[level]=x;
if(first==null){break;}//array is initialized to zero anyway
}
if(failed && bswBad!=null){
bswBad.println();
for(Record r : records){
bswBad.println(r.text);
}
}
return status;
}
ArrayList<Record> records=new ArrayList<Record>(8);
void addLevel(int level){
long mask=1L<<level;
assert((levels&mask)==0);
levels|=mask;
}
boolean hasLevel(int level){
long mask=1L<<level;
return (levels&mask)==mask;
}
long levels;
final int qID;
boolean sorted=false;
boolean swept=false;
boolean ssuProcessed=false;
static boolean verbose;
}
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