Mercurial > repos > rliterman > csp2

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

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planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
author jpayne
date Tue, 18 Mar 2025 16:23:26 -0400
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67:0e9998148a16 68:5028fdace37b
1 package prok;
2
3 import java.util.Arrays;
4
5 import shared.Tools;
6 import stream.Read;
7 import structures.ByteBuilder;
8 import structures.LongHashSet;
9
10 class StatsContainer {
11
12 /*--------------------------------------------------------------*/
13 /*---------------- Initialization ----------------*/
14 /*--------------------------------------------------------------*/
15
16 StatsContainer(int type_, int kInner, int framesInner, int kStart, int framesStart, int offsetStart, int kStop, int framesStop, int offsetStop){
17 type=type_;
18 name=ProkObject.typeStrings[type];
19 setInner(kInner, framesInner);
20 setStart(kStart, framesStart, offsetStart);
21 setStop(kStop, framesStop, offsetStop);
22 }
23
24 StatsContainer(int type_){
25 type=type_;
26 name=ProkObject.typeStrings[type];
27 }
28
29 void setInner(int kInner, int framesInner){
30 assert(inner==null);
31 statsArray[0]=inner=new FrameStats(name+" inner", kInner, framesInner, 0);
32 }
33
34 void setStart(int kStart, int framesStart, int offsetStart){
35 assert(start==null);
36 statsArray[1]=start=new FrameStats(name+" start", kStart, framesStart, offsetStart);
37 }
38
39 void setStop(int kStop, int framesStop, int offsetStop){
40 assert(stop==null);
41 statsArray[2]=stop=new FrameStats(name+" stop", kStop, framesStop, offsetStop);
42 }
43
44 void setInner(FrameStats fs){
45 assert(inner==null);
46 assert(fs!=null);
47 statsArray[0]=inner=fs;
48 }
49
50 void setStart(FrameStats fs){
51 assert(start==null);
52 statsArray[1]=start=fs;
53 }
54
55 void setStop(FrameStats fs){
56 assert(stop==null);
57 statsArray[2]=stop=fs;
58 }
59
60 /*--------------------------------------------------------------*/
61 /*---------------- Methods ----------------*/
62 /*--------------------------------------------------------------*/
63
64 @Override
65 public String toString(){
66 return appendTo(new ByteBuilder()).toString();
67 }
68
69 public ByteBuilder appendTo(ByteBuilder bb) {
70 bb.append("#name\t").append(name).nl();
71 bb.append("#type\t").append(type).nl();
72 bb.append("#count\t").append(lengthCount).nl();
73 bb.append("#lengthSum\t").append(lengthSum).nl();
74 //lengths
75 bb.append("#contains\t").append(3).nl();
76 if(ProkObject.processType(type)) {
77 for(FrameStats fs : statsArray){
78 fs.appendTo(bb);
79 }
80 }else{
81 for(FrameStats fs : statsArray){
82 fs.append0(bb);
83 }
84 }
85 return bb;
86 }
87
88 public void clear(){
89 for(int i=0; i<statsArray.length; i++){
90 if(statsArray[i]!=null){
91 statsArray[i].clear();
92 }
93 }
94
95 assert(inner==statsArray[0]);
96 assert(start==statsArray[1]);
97 assert(stop==statsArray[2]);
98
99 Arrays.fill(lengths, 0);
100 lengthSum=0;
101 lengthCount=0;
102 calculate();
103 }
104
105 public void setFrom(StatsContainer sc){
106 assert(sc.name.equals(name));
107 for(int i=0; i<statsArray.length; i++){
108 FrameStats fs=sc.statsArray[i];
109 if(statsArray[i]==null){
110 statsArray[i]=new FrameStats(fs.name, fs.k, fs.frames, fs.leftOffset);
111 statsArray[i].add(fs);
112 }else{
113 statsArray[i].setFrom(fs);
114 }
115 }
116 inner=statsArray[0];
117 start=statsArray[1];
118 stop=statsArray[2];
119
120 for(int i=0; i<lengths.length; i++){lengths[i]=sc.lengths[i];}
121 lengthSum=sc.lengthSum;
122 lengthCount=sc.lengthCount;
123 calculate();
124 }
125
126 public void add(StatsContainer sc){
127 assert(sc.name.equals(name));
128 for(int i=0; i<statsArray.length; i++){
129 FrameStats fs=sc.statsArray[i];
130 if(statsArray[i]==null){
131 statsArray[i]=new FrameStats(fs.name, fs.k, fs.frames, fs.leftOffset);
132 }
133 statsArray[i].add(fs);
134 }
135
136 inner=statsArray[0];
137 start=statsArray[1];
138 stop=statsArray[2];
139
140 Tools.add(lengths, sc.lengths);
141 lengthSum+=sc.lengthSum;
142 lengthCount+=sc.lengthCount;
143 calculate();
144 }
145
146 public void multiplyBy(double mult) {
147 for(int i=0; i<statsArray.length; i++){
148 FrameStats fs=statsArray[i];
149 fs.multiplyBy(mult);
150 }
151
152 Tools.multiplyBy(lengths, mult);
153 lengthSum=Math.round(lengthSum*mult);
154 lengthCount=Math.round(lengthCount*mult);
155 calculate();
156 }
157
158 public void calculate(){
159 for(int i=0; i<statsArray.length; i++){
160 statsArray[i].calculate();
161 }
162 lengthAvg=(int)(lengthSum/Tools.max(1.0, lengthCount));
163 invLengthAvg=1f/Tools.max(1, lengthAvg);
164 }
165
166 public void addLength(int x){
167 lengthSum+=x;
168 lengthCount++;
169 lengths[Tools.min(x, lengths.length-1)]++;
170 }
171
172 /*--------------------------------------------------------------*/
173 /*---------------- Fields ----------------*/
174 /*--------------------------------------------------------------*/
175
176 FrameStats inner;
177 FrameStats start;
178 FrameStats stop;
179 final FrameStats[] statsArray=new FrameStats[3];
180
181 int kLongLen(){return ProkObject.kLongLen(type);}
182 LongHashSet kmerSet(){return ProkObject.kmerSet(type);}
183 Read[] consensusSequence(){return ProkObject.consensusReads(type);}
184 float minIdentity(){return ProkObject.minID(type);}
185
186 public int startSlop(){return ProkObject.startSlop(type);}
187 public int stopSlop(){return ProkObject.stopSlop(type);}
188
189 final String name;
190 long lengthSum=0;
191 long lengthCount=0;
192 int lengthAvg=-1;
193 float invLengthAvg;
194
195 int[] lengths=new int[5000];
196 public final int type;
197
198 }