|
0
|
1 package middlewares;
|
|
|
2
|
|
|
3 import java.io.File;
|
|
|
4 import java.io.FileNotFoundException;
|
|
|
5 import java.io.FileWriter;
|
|
|
6 import java.io.IOException;
|
|
|
7 import java.net.URL;
|
|
|
8 import java.util.ArrayList;
|
|
|
9 import java.util.Scanner;
|
|
|
10
|
|
|
11 import datastructures.ReducedReadLine;
|
|
|
12 import datastructures.TargetLine;
|
|
|
13 import exceptions.ChromosomeFormatException;
|
|
|
14 import exceptions.ChromosomeNotFoundException;
|
|
|
15 import exceptions.NullOrNegativeRangeException;
|
|
|
16 import exceptions.RangeFormatException;
|
|
|
17 import exceptions.RangeLimitNotFoundException;
|
|
|
18
|
|
|
19 /**
|
|
|
20 * Miscellaneous methods for different uses.
|
|
|
21 *
|
|
|
22 * @author Ali Abdallah
|
|
|
23 * @version 01.2011
|
|
|
24 * @since jdk 1.6.0
|
|
|
25 */
|
|
|
26 public class Misc {
|
|
|
27
|
|
|
28 /**
|
|
|
29 * Make the first letter big, if possible. nGSrich -> NGSrich.
|
|
|
30 *
|
|
|
31 * @param s the string
|
|
|
32 * @return the same string with the first letter big.
|
|
|
33 */
|
|
|
34 public static String bigFirst(String s) {
|
|
|
35 return s.substring(0, 1).toUpperCase() + s.substring(1);
|
|
|
36 }
|
|
|
37
|
|
|
38 /**
|
|
|
39 * Creates a shortcut for the file with a different file extension.
|
|
|
40 *
|
|
|
41 * @param fName the original file name.
|
|
|
42 * @param newExt the new extension of the file.
|
|
|
43 * @param dir the directory of the mad link.
|
|
|
44 * @return a link to the file fName with a different extension.
|
|
|
45 */
|
|
|
46 public static File rename(String fName, String newExt, String dir) {
|
|
|
47
|
|
|
48 String inDirShortCut = dir + Misc.slash(dir);
|
|
|
49 String fShortcutName = inDirShortCut + Misc.prefix(fName) + "."
|
|
|
50 + newExt;
|
|
|
51 Runtime r = Runtime.getRuntime();
|
|
|
52 try {
|
|
|
53 r.exec("ln -s " + fName + " " + fShortcutName);
|
|
|
54 } catch (IOException e) {
|
|
|
55 e.printStackTrace();
|
|
|
56 }
|
|
|
57 try {
|
|
|
58 Thread.sleep(100);
|
|
|
59 } catch (InterruptedException e) {
|
|
|
60 e.printStackTrace();
|
|
|
61 }
|
|
|
62 return new File(fShortcutName);
|
|
|
63 }
|
|
|
64
|
|
|
65 /**
|
|
|
66 * @return the path of the bin directory of this software.
|
|
|
67 */
|
|
|
68 public static String binDir() {
|
|
|
69 URL url = new Misc().getClass().getResource("Misc.class");
|
|
|
70 String path = url.toString().substring(url.toString().indexOf(":") + 1);
|
|
|
71 path = path.substring(0, path.lastIndexOf("/"));
|
|
|
72
|
|
|
73 return path.substring(0, path.lastIndexOf("/"));
|
|
|
74
|
|
|
75 }
|
|
|
76
|
|
|
77 /**
|
|
|
78 * @return the path of this software.
|
|
|
79 */
|
|
|
80 public static String scriptDir() {
|
|
|
81 URL url = new Misc().getClass().getResource("../NGSrich.class");
|
|
|
82 String path = url.toString().substring(url.toString().indexOf(":") + 1);
|
|
|
83 path = path.substring(0, path.lastIndexOf("/"));
|
|
|
84 return path.substring(0, path.lastIndexOf("/")+1);
|
|
|
85
|
|
|
86 }
|
|
|
87
|
|
|
88 public static void main(String[] args) {
|
|
|
89 System.out.println(scriptDir());
|
|
|
90 }
|
|
|
91
|
|
|
92 /**
|
|
|
93 * @param path
|
|
|
94 * @return extends the path by a slash at the end, in the case it don't
|
|
|
95 * exists.
|
|
|
96 */
|
|
|
97 public static String slash(String path) {
|
|
|
98 return (path.endsWith("/") ? "" : "/");
|
|
|
99 }
|
|
|
100
|
|
|
101 /**
|
|
|
102 * @return the name of the host.
|
|
|
103 */
|
|
|
104 public static String getHostName() {
|
|
|
105 Runtime rt = Runtime.getRuntime();
|
|
|
106 String erg = "";
|
|
|
107 try {
|
|
|
108 File f = new File("hostname.sh");
|
|
|
109 FileWriter fw = new FileWriter(f);
|
|
|
110
|
|
|
111 fw.write("#!/bin/bash\r\nproc=$(hostname -s).$$\r\necho $proc");
|
|
|
112 fw.close();
|
|
|
113 Process p = rt.exec("chmod 700 " + f.getAbsolutePath());
|
|
|
114 p = rt.exec("sh " + f.getAbsolutePath());
|
|
|
115
|
|
|
116 Scanner s = new Scanner(p.getInputStream());
|
|
|
117
|
|
|
118 while (s.hasNextLine()) {
|
|
|
119 erg += (s.nextLine());
|
|
|
120 }
|
|
|
121 s.close();
|
|
|
122
|
|
|
123 f.delete();
|
|
|
124 } catch (IOException e) {
|
|
|
125 e.printStackTrace();
|
|
|
126 }
|
|
|
127 return erg;
|
|
|
128 }
|
|
|
129
|
|
|
130 /**
|
|
|
131 * @param fileName
|
|
|
132 * @return the extension of the file.
|
|
|
133 */
|
|
|
134 public static String suffix(String fileName) {
|
|
|
135 return fileName.substring(fileName.lastIndexOf(".") + 1);
|
|
|
136 }
|
|
|
137
|
|
|
138 /**
|
|
|
139 * @param fileName
|
|
|
140 * @return the name of the file without the extension.
|
|
|
141 */
|
|
|
142 public static String prefix(String fileName) {
|
|
|
143 return fileName.substring(fileName.lastIndexOf("/") + 1,
|
|
|
144 fileName.lastIndexOf("."));
|
|
|
145 }
|
|
|
146
|
|
|
147 /**
|
|
|
148 * @param fileName
|
|
|
149 * @return the directory of the specified file.
|
|
|
150 */
|
|
|
151 public static String path(String fileName) {
|
|
|
152 String absolutePath =
|
|
|
153 new File(fileName).getParentFile().getAbsolutePath();
|
|
|
154 return absolutePath+slash(absolutePath);
|
|
|
155 }
|
|
|
156
|
|
|
157 /**
|
|
|
158 * Check if the chromosome names in the target file are a subset of the
|
|
|
159 * chromosome name in the alignment file.
|
|
|
160 *
|
|
|
161 * @param alignment the alignment file.
|
|
|
162 * @param target the target file.
|
|
|
163 * @return true if target chromosomes are a subset of alignment chromosome
|
|
|
164 * and false otherwise.
|
|
|
165 */
|
|
|
166 public static boolean areChromosomeCompatible(File alignment, File target){
|
|
|
167 Scanner aScan = null, tScan = null;
|
|
|
168 try {
|
|
|
169 aScan = new Scanner(alignment);
|
|
|
170 tScan = new Scanner(target);
|
|
|
171
|
|
|
172 ArrayList<String> alist = new ArrayList<String>();
|
|
|
173 ArrayList<String> tlist = new ArrayList<String>();
|
|
|
174 while(aScan.hasNextLine()){
|
|
|
175 ReducedReadLine rl = new ReducedReadLine(aScan.nextLine());
|
|
|
176 if(alist.indexOf(rl.chrom())==-1)
|
|
|
177 alist.add(rl.chrom());
|
|
|
178 }
|
|
|
179 while(tScan.hasNextLine()){
|
|
|
180 TargetLine tl = new TargetLine(tScan.nextLine());
|
|
|
181 if(tlist.indexOf(tl.chrom())==-1)
|
|
|
182 tlist.add(tl.chrom());
|
|
|
183 }
|
|
|
184 for(int i = 0; i < tlist.size(); i++){
|
|
|
185 if(alist.indexOf(tlist.get(i))!=-1)
|
|
|
186 return true;
|
|
|
187 }
|
|
|
188 } catch (FileNotFoundException e) {
|
|
|
189 e.printStackTrace();
|
|
|
190 } catch (ChromosomeFormatException e) {
|
|
|
191 e.printStackTrace();
|
|
|
192 } catch (ChromosomeNotFoundException e) {
|
|
|
193 e.printStackTrace();
|
|
|
194 } catch (RangeFormatException e) {
|
|
|
195 e.printStackTrace();
|
|
|
196 } catch (RangeLimitNotFoundException e) {
|
|
|
197 e.printStackTrace();
|
|
|
198 } catch (NullOrNegativeRangeException e) {
|
|
|
199 e.printStackTrace();
|
|
|
200 }
|
|
|
201
|
|
|
202
|
|
|
203 return false;
|
|
|
204 }
|
|
|
205
|
|
|
206 }
|
