Mercurial > repos > rliterman > csp2

comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/sketch/SketchResults.java @ 68:5028fdace37b

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
author jpayne
date Tue, 18 Mar 2025 16:23:26 -0400
parents
children
comparison
equal deleted inserted replaced
67:0e9998148a16 68:5028fdace37b
1 package sketch;
2
3 import java.util.ArrayList;
4 import java.util.Collections;
5 import java.util.Map.Entry;
6 import java.util.concurrent.ConcurrentHashMap;
7
8 import fileIO.TextStreamWriter;
9 import json.JsonObject;
10 import shared.Shared;
11 import shared.Tools;
12 import structures.ByteBuilder;
13 import structures.IntHashMap;
14 import tax.TaxTree;
15
16 public class SketchResults extends SketchObject {
17
18 SketchResults(Sketch s){
19 sketch=s;
20 }
21
22 SketchResults(Sketch s, ArrayList<Sketch> sketchList_, int[][] taxHits_){
23 sketch=s;
24 refSketchList=sketchList_;
25 taxHits=taxHits_;
26 }
27
28 /*--------------------------------------------------------------*/
29 /*---------------- Methods ----------------*/
30 /*--------------------------------------------------------------*/
31
32 public void addMap(ConcurrentHashMap<Integer, Comparison> map, DisplayParams params, CompareBuffer buffer) {
33
34 if(map.isEmpty()){return;}
35 list=addToList(map, params, list);
36
37 if((true || params.needContamCounts())){
38 recompare(buffer, params);
39 }
40 }
41
42 public void recompare(CompareBuffer buffer, DisplayParams params){
43 // assert(makeIndex || !AUTOSIZE);
44
45 assert(!sketch.merged());
46 sketch.mergeBitSets();
47
48 // System.err.println(sketch.compareBitSet());
49 // assert(false) : sketch.compareBitSet().getClass();
50
51 for(Comparison c : list){
52 c.recompare(buffer, taxHits, params.contamLevel());
53 }
54 Collections.sort(list, params.comparator);
55 Collections.reverse(list);
56 }
57
58 private static ArrayList<Comparison> addToList(ConcurrentHashMap<Integer, Comparison> map, DisplayParams params, ArrayList<Comparison> old){
59
60 // System.err.println(map.size());
61 // System.err.println(map.keySet());
62
63 // final TaxFilter white=params.taxFilterWhite;
64 // final TaxFilter black=params.taxFilterBlack;
65 // final boolean noFilter=(white==null && black==null);
66 final int size=map.size();
67 ArrayList<Comparison> al=(old==null ? new ArrayList<Comparison>(size) : old);
68 for(Entry<Integer, Comparison> e : map.entrySet()){
69 final Comparison c=e.getValue();
70 al.add(c);
71 // if(noFilter || c.passesFilter(white, black)){
72 // al.add(c);
73 // }
74 }
75 Shared.sort(al, params.comparator);
76 Collections.reverse(al);
77
78 //Apply records per level filter
79 if(params.recordsPerLevel>0 && al.size()>params.recordsPerLevel && al.get(0).hasQueryTaxID()){
80 int[] count=new int[TaxTree.numTaxLevelNamesExtended];
81 int removed=0;
82 for(int i=0; i<al.size(); i++){
83 Comparison c=al.get(i);
84 int calevel=c.commonAncestorLevelInt();
85 count[calevel]++;
86 if(count[calevel]>params.recordsPerLevel){
87 al.set(i, null);
88 removed++;
89 }
90 }
91 if(removed>0){Tools.condenseStrict(al);}
92 }
93
94 final long limit=(params.maxRecords*2+5);
95 while(al.size()>limit){
96 al.remove(al.size()-1);
97 }
98 return al;
99 }
100
101 public boolean isEmpty(){
102 return list==null || list.isEmpty();
103 }
104
105 /*--------------------------------------------------------------*/
106 /*---------------- Tax Methods ----------------*/
107 /*--------------------------------------------------------------*/
108
109 public int primaryTax(int level){
110 //I have no idea how to implement this...
111 IntHashMap map=new IntHashMap();
112 assert(false);
113 return -1;
114 }
115
116 /*--------------------------------------------------------------*/
117 /*---------------- Print Methods ----------------*/
118 /*--------------------------------------------------------------*/
119
120 private static String recordBreak="\n"; //"\n\n"
121
122 void writeResults(DisplayParams params, TextStreamWriter tsw){
123 ByteBuilder sb=toText(params);
124 tsw.print(sb);
125 }
126
127 public ByteBuilder toText(DisplayParams params){
128 assert(params.postParsed);
129 if(sketch.hasSSU()){
130 if(params.comparator==Comparison.SSUComparator){
131 alignSSUs(params.maxRecords*4);//This should be enough...
132 list.sort(params.comparator);
133 Collections.reverse(list);
134 }else if(params.printSSU()){
135 alignSSUs(params.maxRecords);
136 }
137 }
138 if(params.json()){
139 JsonObject j=params.toJson(this);
140 return j.toText();
141 }
142 final ByteBuilder sb=params.queryHeader(sketch);
143 if(params.format==DisplayParams.FORMAT_QUERY_REF_ANI || params.format==DisplayParams.FORMAT_CONSTELLATION){
144 if(list==null || list.isEmpty()){return sb;}
145 int idx=0;
146 int prevTaxID=0;
147 for(Comparison c : list){
148 assert(!params.printSSU() || !c.needsAlignment());
149 params.formatComparison(c, sb, prevTaxID);
150 prevTaxID=c.taxID();
151 idx++;
152 if(idx>=params.maxRecords){break;}
153 }
154 }else{
155 sb.append(recordBreak);
156
157 if(list==null || list.isEmpty()){
158 sb.append("No hits.\n");
159 }else{
160 if(params.format==DisplayParams.FORMAT_MULTICOLUMN){sb.append(params.header()).append('\n');}
161 int idx=0;
162 int prevTaxID=0;
163 for(Comparison c : list){
164 params.formatComparison(c, sb, prevTaxID);
165 prevTaxID=c.taxID();
166 idx++;
167 if(idx>=params.maxRecords){break;}
168 }
169 }
170 }
171 return sb;
172 }
173
174 /*--------------------------------------------------------------*/
175 /*---------------- Alignment ----------------*/
176 /*--------------------------------------------------------------*/
177
178 void alignSSUs(int maxRecords){
179 if(!sketch.hasSSU()){return;}
180 // if(list!=null && list.size()>0){
181 // int idx=0;
182 // for(Comparison c : list){
183 // c.ssuIdentity();
184 // idx++;
185 // if(idx>=maxRecords){break;}
186 // }
187 // }
188 assert(alignerPool!=null);
189 alignerPool.addJobs(list, maxRecords);
190 }
191
192 /*--------------------------------------------------------------*/
193 /*---------------- Fields ----------------*/
194 /*--------------------------------------------------------------*/
195
196 public final Sketch sketch;
197 public ArrayList<Sketch> refSketchList;
198 public int[][] taxHits;
199 public ArrayList<Comparison> list;
200 public int totalRecords=0;
201
202 }