jpayne@68: package sketch;
jpayne@68: 
jpayne@68: import java.util.ArrayList;
jpayne@68: import java.util.Collections;
jpayne@68: import java.util.Map.Entry;
jpayne@68: import java.util.concurrent.ConcurrentHashMap;
jpayne@68: 
jpayne@68: import fileIO.TextStreamWriter;
jpayne@68: import json.JsonObject;
jpayne@68: import shared.Shared;
jpayne@68: import shared.Tools;
jpayne@68: import structures.ByteBuilder;
jpayne@68: import structures.IntHashMap;
jpayne@68: import tax.TaxTree;
jpayne@68: 
jpayne@68: public class SketchResults extends SketchObject {
jpayne@68: 	
jpayne@68: 	SketchResults(Sketch s){
jpayne@68: 		sketch=s;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	SketchResults(Sketch s, ArrayList<Sketch> sketchList_, int[][] taxHits_){
jpayne@68: 		sketch=s;
jpayne@68: 		refSketchList=sketchList_;
jpayne@68: 		taxHits=taxHits_;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------            Methods           ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	
jpayne@68: 	public void addMap(ConcurrentHashMap<Integer, Comparison> map, DisplayParams params, CompareBuffer buffer) {
jpayne@68: 
jpayne@68: 		if(map.isEmpty()){return;}
jpayne@68: 		list=addToList(map, params, list);
jpayne@68: 		
jpayne@68: 		if((true || params.needContamCounts())){
jpayne@68: 			recompare(buffer, params);
jpayne@68: 		}
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public void recompare(CompareBuffer buffer, DisplayParams params){
jpayne@68: //		assert(makeIndex || !AUTOSIZE);
jpayne@68: 		
jpayne@68: 		assert(!sketch.merged());
jpayne@68: 		sketch.mergeBitSets();
jpayne@68: 		
jpayne@68: //		System.err.println(sketch.compareBitSet());
jpayne@68: //		assert(false) : sketch.compareBitSet().getClass();
jpayne@68: 		
jpayne@68: 		for(Comparison c : list){
jpayne@68: 			c.recompare(buffer, taxHits, params.contamLevel());
jpayne@68: 		}
jpayne@68: 		Collections.sort(list, params.comparator);
jpayne@68: 		Collections.reverse(list);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	private static ArrayList<Comparison> addToList(ConcurrentHashMap<Integer, Comparison> map, DisplayParams params, ArrayList<Comparison> old){
jpayne@68: 		
jpayne@68: //		System.err.println(map.size());
jpayne@68: //		System.err.println(map.keySet());
jpayne@68: 
jpayne@68: //		final TaxFilter white=params.taxFilterWhite;
jpayne@68: //		final TaxFilter black=params.taxFilterBlack;
jpayne@68: //		final boolean noFilter=(white==null && black==null);
jpayne@68: 		final int size=map.size();
jpayne@68: 		ArrayList<Comparison> al=(old==null ? new ArrayList<Comparison>(size) : old);
jpayne@68: 		for(Entry<Integer, Comparison> e : map.entrySet()){
jpayne@68: 			final Comparison c=e.getValue();
jpayne@68: 			al.add(c);
jpayne@68: //			if(noFilter || c.passesFilter(white, black)){
jpayne@68: //				al.add(c);
jpayne@68: //			}
jpayne@68: 		}
jpayne@68: 		Shared.sort(al, params.comparator);
jpayne@68: 		Collections.reverse(al);
jpayne@68: 		
jpayne@68: 		//Apply records per level filter
jpayne@68: 		if(params.recordsPerLevel>0 && al.size()>params.recordsPerLevel && al.get(0).hasQueryTaxID()){
jpayne@68: 			int[] count=new int[TaxTree.numTaxLevelNamesExtended];
jpayne@68: 			int removed=0;
jpayne@68: 			for(int i=0; i<al.size(); i++){
jpayne@68: 				Comparison c=al.get(i);
jpayne@68: 				int calevel=c.commonAncestorLevelInt();
jpayne@68: 				count[calevel]++;
jpayne@68: 				if(count[calevel]>params.recordsPerLevel){
jpayne@68: 					al.set(i, null);
jpayne@68: 					removed++;
jpayne@68: 				}
jpayne@68: 			}
jpayne@68: 			if(removed>0){Tools.condenseStrict(al);}
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		final long limit=(params.maxRecords*2+5);
jpayne@68: 		while(al.size()>limit){
jpayne@68: 			al.remove(al.size()-1);
jpayne@68: 		}
jpayne@68: 		return al;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public boolean isEmpty(){
jpayne@68: 		return list==null || list.isEmpty();
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------          Tax Methods         ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	
jpayne@68: 	public int primaryTax(int level){
jpayne@68: 		//I have no idea how to implement this...
jpayne@68: 		IntHashMap map=new IntHashMap();
jpayne@68: 		assert(false);
jpayne@68: 		return -1;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------         Print Methods        ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	
jpayne@68: 	private static String recordBreak="\n"; //"\n\n"
jpayne@68: 	
jpayne@68: 	void writeResults(DisplayParams params, TextStreamWriter tsw){
jpayne@68: 		ByteBuilder sb=toText(params);
jpayne@68: 		tsw.print(sb);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public ByteBuilder toText(DisplayParams params){
jpayne@68: 		assert(params.postParsed);
jpayne@68: 		if(sketch.hasSSU()){
jpayne@68: 			if(params.comparator==Comparison.SSUComparator){
jpayne@68: 				alignSSUs(params.maxRecords*4);//This should be enough...
jpayne@68: 				list.sort(params.comparator);
jpayne@68: 				Collections.reverse(list);
jpayne@68: 			}else if(params.printSSU()){
jpayne@68: 				alignSSUs(params.maxRecords);
jpayne@68: 			}
jpayne@68: 		}
jpayne@68: 		if(params.json()){
jpayne@68: 			JsonObject j=params.toJson(this);
jpayne@68: 			return j.toText();
jpayne@68: 		}
jpayne@68: 		final ByteBuilder sb=params.queryHeader(sketch);
jpayne@68: 		if(params.format==DisplayParams.FORMAT_QUERY_REF_ANI || params.format==DisplayParams.FORMAT_CONSTELLATION){
jpayne@68: 			if(list==null || list.isEmpty()){return sb;}
jpayne@68: 			int idx=0;
jpayne@68: 			int prevTaxID=0;
jpayne@68: 			for(Comparison c : list){
jpayne@68: 				assert(!params.printSSU() || !c.needsAlignment());
jpayne@68: 				params.formatComparison(c, sb, prevTaxID);
jpayne@68: 				prevTaxID=c.taxID();
jpayne@68: 				idx++;
jpayne@68: 				if(idx>=params.maxRecords){break;}
jpayne@68: 			}
jpayne@68: 		}else{
jpayne@68: 			sb.append(recordBreak);
jpayne@68: 
jpayne@68: 			if(list==null || list.isEmpty()){
jpayne@68: 				sb.append("No hits.\n");
jpayne@68: 			}else{
jpayne@68: 				if(params.format==DisplayParams.FORMAT_MULTICOLUMN){sb.append(params.header()).append('\n');}
jpayne@68: 				int idx=0;
jpayne@68: 				int prevTaxID=0;
jpayne@68: 				for(Comparison c : list){
jpayne@68: 					params.formatComparison(c, sb, prevTaxID);
jpayne@68: 					prevTaxID=c.taxID();
jpayne@68: 					idx++;
jpayne@68: 					if(idx>=params.maxRecords){break;}
jpayne@68: 				}
jpayne@68: 			}
jpayne@68: 		}
jpayne@68: 		return sb;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------          Alignment           ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	
jpayne@68: 	void alignSSUs(int maxRecords){
jpayne@68: 		if(!sketch.hasSSU()){return;}
jpayne@68: //		if(list!=null && list.size()>0){
jpayne@68: //			int idx=0;
jpayne@68: //			for(Comparison c : list){
jpayne@68: //				c.ssuIdentity();
jpayne@68: //				idx++;
jpayne@68: //				if(idx>=maxRecords){break;}
jpayne@68: //			}
jpayne@68: //		}
jpayne@68: 		assert(alignerPool!=null);
jpayne@68: 		alignerPool.addJobs(list, maxRecords);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------            Fields            ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	
jpayne@68: 	public final Sketch sketch;
jpayne@68: 	public ArrayList<Sketch> refSketchList;
jpayne@68: 	public int[][] taxHits;
jpayne@68: 	public ArrayList<Comparison> list;
jpayne@68: 	public int totalRecords=0;
jpayne@68: 	
jpayne@68: }