Mercurial > repos > rliterman > csp2

comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/icecream/PBHeader.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 icecream;
2
3 import shared.Parse;
4
5 public class PBHeader {
6
7 public PBHeader(String s){
8 setFrom(s);
9 }
10
11 //m64021_190821_100154/102/32038_35649
12 //m64021_190821_100154 is run id
13 //102 is zmw id
14 //32038_35649 are movie coordinates
15 //This function allows extra stuff like whitespace after the end of the formal header.
16 public void setFrom(final String header){
17 original=header;
18 int slash1=header.indexOf('/');
19 assert(slash1>=0) : "Misformatted PBHeader: "+header;
20 int slash2=header.indexOf('/', slash1+1);
21 assert(slash2>=0) : "Misformatted PBHeader: "+header;
22 int under3=header.indexOf('_', slash2+1);
23 assert(under3>=0) : "Misformatted PBHeader: "+header;
24 int terminator=under3+1;
25 while(terminator<header.length() && Character.isDigit(header.charAt(terminator))){terminator++;}
26 runID=header.substring(0, slash1);
27 // System.err.println("\n"+header+"\n"+slash1+","+slash2);
28 zmwID=Parse.parseInt(header, slash1+1, slash2);
29 start=Parse.parseInt(header, slash2+1, under3);
30 stop=Parse.parseInt(header, under3+1, terminator);
31 }
32
33 public static int parseZMW(final String header){
34 int slash1=header.indexOf('/');
35 assert(slash1>=0) : "Misformatted PBHeader: "+header;
36 int slash2=header.indexOf('/', slash1+1);
37 assert(slash2>=0) : "Misformatted PBHeader: "+header;
38 int zmwID=Parse.parseInt(header, slash1+1, slash2);
39 return zmwID;
40 }
41
42 public String original;
43 public String runID;
44 public int zmwID;
45 public int start;
46 public int stop;
47
48 }