1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
|
package tax;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.HashMap;
import fileIO.ReadWrite;
import fileIO.TextFile;
import shared.Timer;
import shared.Tools;
public class ImgRecord2 implements Serializable {
private static final long serialVersionUID = 8596055205924485293L;
public static void main(String[] args){
String in=args[0];
String out=args.length>1 ? args[1] : null;
if(!Tools.testInputFiles(false, true, in)){
throw new RuntimeException("\nCan't read some input files.\n");
}
if(!Tools.testOutputFiles(true, false, false, out)){
throw new RuntimeException("\nCan't write to some output files.\n");
}
Timer t=new Timer();
HashMap<Long, ImgRecord2> map=toMap(in);
t.stop();
System.err.println(map.size()+"; "+t);
if(out!=null){ReadWrite.writeObjectInThread(map, out, false);}
}
public static HashMap<Long, ImgRecord2> toMap(String fname){
ImgRecord2[] array=toArray(fname);
HashMap<Long, ImgRecord2> map=new HashMap<Long, ImgRecord2>((3+array.length*4)/3);
for(ImgRecord2 ir : array){
map.put(ir.imgID, ir);
}
return map;
}
public static ImgRecord2[] toArray(String fname){
TextFile tf=new TextFile(fname, false);
ArrayList<ImgRecord2> list=new ArrayList<ImgRecord2>();
for(String line=tf.nextLine(); line!=null; line=tf.nextLine()){
if(line.length()<1 || !Tools.isDigit(line.charAt(0))){
//do nothing
}else{
ImgRecord2 record=new ImgRecord2(line);
list.add(record);
}
}
tf.close();
return list.toArray(new ImgRecord2[0]);
}
public ImgRecord2(String line){
String[] split=line.split("\t");
imgID=Long.parseLong(split[0]);
taxID=(split[1]==null || split[1].length()<1 ? 0 : Integer.parseInt(split[1]));
name=(storeName ? split[2] : null);
}
public static final long parseImgId(String header, boolean doAssertions){
final char delimiter=TaxTree.ncbiHeaderDelimiter(header);
assert(!doAssertions || delimiter!=' ') : header;
// System.err.println("A: '"+delimiter+"'");
if(delimiter==' '){return -1;}
final int idx=header.indexOf("img"+delimiter);
// System.err.println("B: "+idx);
assert(!doAssertions || idx>=0) : "Could not img id number from "+header;
if(idx<0){return -1;}
long img=0;
for(int i=idx+4; i<header.length(); i++){
final char c=header.charAt(i);
if(c==delimiter || c==' '){break;}
assert(Tools.isDigit(c)) : c+", '"+header+"'";
img=img*10+(c-'0');
}
assert(!doAssertions || img>0) : "Could not img id number from "+header;
return img>0 ? img : -1;
}
public static boolean storeName=true;
public final long imgID;
public final int taxID;
public final String name;
}
|
