Mercurial > repos > rliterman > csp2

comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/fun/Calc.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 fun;
2
3 import java.io.PrintStream;
4 import java.util.Locale;
5
6 import shared.Parse;
7 import shared.Parser;
8 import shared.PreParser;
9 import shared.ReadStats;
10 import shared.Shared;
11 import shared.Timer;
12
13 public class Calc {
14
15 /*--------------------------------------------------------------*/
16 /*---------------- Initialization ----------------*/
17 /*--------------------------------------------------------------*/
18
19 /**
20 * Code entrance from the command line.
21 * @param args Command line arguments
22 */
23 public static void main(String[] args){
24 Timer t=new Timer();
25 Calc x=new Calc(args);
26 x.process(t);
27
28 //Close the print stream if it was redirected
29 Shared.closeStream(x.outstream);
30 }
31
32 /**
33 * Constructor.
34 * @param args Command line arguments
35 */
36 public Calc(String[] args){
37
38 {//Preparse block for help, config files, and outstream
39 PreParser pp=new PreParser(args, getClass(), false);
40 args=pp.args;
41 outstream=pp.outstream;
42 }
43
44 //Create a parser object
45 Parser parser=new Parser();
46
47 //Parse each argument
48 for(int i=0; i<args.length; i++){
49 String arg=args[i];
50
51 //Break arguments into their constituent parts, in the form of "a=b"
52 String[] split=arg.split("=");
53 String a=split[0].toLowerCase();
54 String b=split.length>1 ? split[1] : null;
55
56 if(a.equals("verbose")){
57 verbose=Parse.parseBoolean(b);
58 }else if(a.equals("parse_flag_goes_here")){
59 long fake_variable=Parse.parseKMG(b);
60 //Set a variable here
61 }else if(a.equals("num") || a.equals("numstats")){
62 numStats=Integer.parseInt(b);
63 }else if(parser.parse(arg, a, b)){//Parse standard flags in the parser
64 //do nothing
65 }else{
66 outstream.println("Unknown parameter "+args[i]);
67 assert(false) : "Unknown parameter "+args[i];
68 }
69 }
70
71 {//Process parser fields
72
73 overwrite=ReadStats.overwrite=parser.overwrite;
74 append=ReadStats.append=parser.append;
75
76 out1=parser.out1;
77 }
78 }
79
80
81 /*--------------------------------------------------------------*/
82 /*---------------- Outer Methods ----------------*/
83 /*--------------------------------------------------------------*/
84
85 /** Create read streams and process all data */
86 void process(Timer t){
87
88 //Process the read stream
89 processInner(numStats);
90
91 if(verbose){outstream.println("Finished; closing streams.");}
92
93 //Report timing and results
94 {
95 t.stop();
96 outstream.println("Time: \t"+t);
97 }
98
99 //Throw an exception of there was an error in a thread
100 if(errorState){
101 throw new RuntimeException(getClass().getName()+" terminated in an error state; the output may be corrupt.");
102 }
103 }
104
105 /** Iterate through the reads */
106 void processInner(int numStats){
107 int bits=numStats*5;
108 final int iters=1<<bits;
109 final int buckets=1+31*numStats;
110 int[] counts=new int[buckets];
111 for(int i=0; i<iters; i++){
112 counts[sum(i)]++;
113 }
114 int[] cumulative=new int[buckets];
115 cumulative[0]=counts[0];
116 for(int i=1; i<buckets; i++){
117 cumulative[i]=cumulative[i-1]+counts[i];
118 }
119 //StringBuilder sb=new StringBuilder();
120 final double mult=100.0/iters;
121 for(int i=0; i<buckets; i++){
122 String s=(String.format(Locale.ROOT, "%d\t%.4f%%\n", i, cumulative[i]*mult));
123 System.out.print(s);
124 }
125 }
126
127 int sum(int stats){
128 int sum=0;
129 while(stats>0){
130 sum+=(stats&0x1F);
131 stats>>>=5;
132 }
133 return sum;
134 }
135
136 /*--------------------------------------------------------------*/
137 /*---------------- Inner Methods ----------------*/
138 /*--------------------------------------------------------------*/
139
140 /*--------------------------------------------------------------*/
141 /*---------------- Fields ----------------*/
142 /*--------------------------------------------------------------*/
143
144 /** Primary output file path */
145 private String out1="stdout.txt";
146
147 private int numStats=6;
148
149 /*--------------------------------------------------------------*/
150 /*---------------- Common Fields ----------------*/
151 /*--------------------------------------------------------------*/
152
153 /** Print status messages to this output stream */
154 private PrintStream outstream=System.err;
155 /** Print verbose messages */
156 public static boolean verbose=false;
157 /** True if an error was encountered */
158 public boolean errorState=false;
159 /** Overwrite existing output files */
160 private boolean overwrite=false;
161 /** Append to existing output files */
162 private boolean append=false;
163
164 }