Mercurial > repos > rliterman > csp2

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