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package sketch;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Map.Entry;
import java.util.concurrent.ConcurrentHashMap;
import fileIO.TextStreamWriter;
import json.JsonObject;
import shared.Shared;
import shared.Tools;
import structures.ByteBuilder;
import structures.IntHashMap;
import tax.TaxTree;
public class SketchResults extends SketchObject {
SketchResults(Sketch s){
sketch=s;
}
SketchResults(Sketch s, ArrayList<Sketch> sketchList_, int[][] taxHits_){
sketch=s;
refSketchList=sketchList_;
taxHits=taxHits_;
}
/*--------------------------------------------------------------*/
/*---------------- Methods ----------------*/
/*--------------------------------------------------------------*/
public void addMap(ConcurrentHashMap<Integer, Comparison> map, DisplayParams params, CompareBuffer buffer) {
if(map.isEmpty()){return;}
list=addToList(map, params, list);
if((true || params.needContamCounts())){
recompare(buffer, params);
}
}
public void recompare(CompareBuffer buffer, DisplayParams params){
// assert(makeIndex || !AUTOSIZE);
assert(!sketch.merged());
sketch.mergeBitSets();
// System.err.println(sketch.compareBitSet());
// assert(false) : sketch.compareBitSet().getClass();
for(Comparison c : list){
c.recompare(buffer, taxHits, params.contamLevel());
}
Collections.sort(list, params.comparator);
Collections.reverse(list);
}
private static ArrayList<Comparison> addToList(ConcurrentHashMap<Integer, Comparison> map, DisplayParams params, ArrayList<Comparison> old){
// System.err.println(map.size());
// System.err.println(map.keySet());
// final TaxFilter white=params.taxFilterWhite;
// final TaxFilter black=params.taxFilterBlack;
// final boolean noFilter=(white==null && black==null);
final int size=map.size();
ArrayList<Comparison> al=(old==null ? new ArrayList<Comparison>(size) : old);
for(Entry<Integer, Comparison> e : map.entrySet()){
final Comparison c=e.getValue();
al.add(c);
// if(noFilter || c.passesFilter(white, black)){
// al.add(c);
// }
}
Shared.sort(al, params.comparator);
Collections.reverse(al);
//Apply records per level filter
if(params.recordsPerLevel>0 && al.size()>params.recordsPerLevel && al.get(0).hasQueryTaxID()){
int[] count=new int[TaxTree.numTaxLevelNamesExtended];
int removed=0;
for(int i=0; i<al.size(); i++){
Comparison c=al.get(i);
int calevel=c.commonAncestorLevelInt();
count[calevel]++;
if(count[calevel]>params.recordsPerLevel){
al.set(i, null);
removed++;
}
}
if(removed>0){Tools.condenseStrict(al);}
}
final long limit=(params.maxRecords*2+5);
while(al.size()>limit){
al.remove(al.size()-1);
}
return al;
}
public boolean isEmpty(){
return list==null || list.isEmpty();
}
/*--------------------------------------------------------------*/
/*---------------- Tax Methods ----------------*/
/*--------------------------------------------------------------*/
public int primaryTax(int level){
//I have no idea how to implement this...
IntHashMap map=new IntHashMap();
assert(false);
return -1;
}
/*--------------------------------------------------------------*/
/*---------------- Print Methods ----------------*/
/*--------------------------------------------------------------*/
private static String recordBreak="\n"; //"\n\n"
void writeResults(DisplayParams params, TextStreamWriter tsw){
ByteBuilder sb=toText(params);
tsw.print(sb);
}
public ByteBuilder toText(DisplayParams params){
assert(params.postParsed);
if(sketch.hasSSU()){
if(params.comparator==Comparison.SSUComparator){
alignSSUs(params.maxRecords*4);//This should be enough...
list.sort(params.comparator);
Collections.reverse(list);
}else if(params.printSSU()){
alignSSUs(params.maxRecords);
}
}
if(params.json()){
JsonObject j=params.toJson(this);
return j.toText();
}
final ByteBuilder sb=params.queryHeader(sketch);
if(params.format==DisplayParams.FORMAT_QUERY_REF_ANI || params.format==DisplayParams.FORMAT_CONSTELLATION){
if(list==null || list.isEmpty()){return sb;}
int idx=0;
int prevTaxID=0;
for(Comparison c : list){
assert(!params.printSSU() || !c.needsAlignment());
params.formatComparison(c, sb, prevTaxID);
prevTaxID=c.taxID();
idx++;
if(idx>=params.maxRecords){break;}
}
}else{
sb.append(recordBreak);
if(list==null || list.isEmpty()){
sb.append("No hits.\n");
}else{
if(params.format==DisplayParams.FORMAT_MULTICOLUMN){sb.append(params.header()).append('\n');}
int idx=0;
int prevTaxID=0;
for(Comparison c : list){
params.formatComparison(c, sb, prevTaxID);
prevTaxID=c.taxID();
idx++;
if(idx>=params.maxRecords){break;}
}
}
}
return sb;
}
/*--------------------------------------------------------------*/
/*---------------- Alignment ----------------*/
/*--------------------------------------------------------------*/
void alignSSUs(int maxRecords){
if(!sketch.hasSSU()){return;}
// if(list!=null && list.size()>0){
// int idx=0;
// for(Comparison c : list){
// c.ssuIdentity();
// idx++;
// if(idx>=maxRecords){break;}
// }
// }
assert(alignerPool!=null);
alignerPool.addJobs(list, maxRecords);
}
/*--------------------------------------------------------------*/
/*---------------- Fields ----------------*/
/*--------------------------------------------------------------*/
public final Sketch sketch;
public ArrayList<Sketch> refSketchList;
public int[][] taxHits;
public ArrayList<Comparison> list;
public int totalRecords=0;
}
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