Mercurial > repos > rliterman > csp2

comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/fileIO/MatrixFile.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 fileIO;
2 import dna.Matrix;
3
4
5
6 public class MatrixFile extends TextFile{
7
8 public static void main(String[] args){
9
10 try {
11 //Name of mat file
12 String name=args[0];
13
14 MatrixFile mat=new MatrixFile(name);
15
16 String s=null;
17
18 for(s=mat.readLine(); s!=null; s=mat.readLine()){
19 System.out.println(s);
20 }
21 } catch (Exception e) {
22 throw new RuntimeException(e);
23 }
24
25 }
26
27
28 public MatrixFile(String name){super(name, false);}
29
30 @Override
31 public String nextLine(){
32 String line=readLine();
33
34 while(line!=null && line.charAt(0)!='{' && line.charAt(0)!='/'){
35 line=readLine();
36 }
37 return line;
38 }
39
40 public Matrix nextMatrix(){
41 String line;
42 String[] split;
43
44 line=nextLine();
45 if(line==null || line.startsWith("//end")){return null;}
46
47 assert(line.startsWith("//name: ")) : line;
48 String name=line.replace("//name: ","").trim();
49
50 line=nextLine();
51 assert(line.startsWith("//size: ")) : line;
52 line=line.replace("//size: ","");
53 split=line.split("x");
54 int length=Integer.parseInt(split[0]);
55 int width=Integer.parseInt(split[1]);
56
57 line=nextLine();
58 assert(line.startsWith("//prefix: ")) : line;
59 line=line.replace("//prefix: ","");
60 int prefix=Integer.parseInt(line);
61
62 line=nextLine();
63 assert(line.startsWith("//count: ")) : line;
64 line=line.replace("//count: ","");
65 int count=Integer.parseInt(line);
66
67
68 float[][] grid=new float[length][width];
69 for(int i=0; i<length; i++){
70 line=nextLine();
71
72 while(line.startsWith("//")){line=nextLine();}
73
74 assert(line.startsWith("{"));
75 if(line.endsWith(",")){line=line.substring(0, line.length()-1);}
76 assert(line.endsWith("}"));
77 line=line.replace("{", "").replace("}", "").replace(" ", "");
78 split=line.split(",");
79 assert(split.length==width);
80 for(int j=0; j<split.length; j++){
81 grid[i][j]=Float.parseFloat(split[j]);
82 }
83 }
84
85 return new Matrix(grid, prefix, name);
86 }
87
88 }