Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
RandomAccessFileWrap	23	49	28	0.00%	Show methods

Class RandomAccessFileWrap

Class RandomAccessFileWrap	Line # 23	Total Statements 49	Complexity 28	TOTAL Coverage 0.00%
setOffset(long) : void   setOffset(long) : void	2828	2.02	1.01	0.0 0.00%
getOffset() : long   getOffset() : long	3434	1.01	1.01	0.0 0.00%
getBufferSize() : int   getBufferSize() : int	4545	1.01	1.01	0.0 0.00%
setBufferSize(int) : void   setBufferSize(int) : void	5050	2.02	1.01	0.0 0.00%
RandomAccessFileWrap(String)   RandomAccessFileWrap(String)	5656	1.01	1.01	0.0 0.00%
RandomAccessFileWrap(RandomAccessFile)   RandomAccessFileWrap(RandomAccessFile)	6161	1.01	1.01	0.0 0.00%
charAt(int) : char   charAt(int) : char	6666	11.011	7.07	0.0 0.00%
toString() : String   toString() : String	9999	1.01	1.01	0.0 0.00%
length() : int   length() : int	105105	6.06	3.03	0.0 0.00%
substring(int,int) : String   substring(int,int) : String	122122	4.04	2.02	0.0 0.00%
unwrap() : Object   unwrap() : Object	133133	1.01	1.01	0.0 0.00%
main(String[]) : void   main(String[]) : void	145145	13.013	4.04	0.0 0.00%
newStringBufferLike() : BasicStringBufferLike   newStringBufferLike() : BasicStringBufferLike	172172	1.01	1.01	0.0 0.00%
indexOf(char) : int   indexOf(char) : int	178178	4.04	3.03	0.0 0.00%

 

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1		//
2		// This software is now distributed according to
3		// the Lesser Gnu Public License. Please see
4		// http://www.gnu.org/copyleft/lesser.txt for
5		// the details.
6		// -- Happy Computing!
7		//
8		package com.stevesoft.pat.wrap;
9
10		import jalview.util.MessageManager;
11
12		import java.io.IOException;
13		import java.io.RandomAccessFile;
14
15		import com.stevesoft.pat.BasicStringBufferLike;
16		import com.stevesoft.pat.Regex;
17		import com.stevesoft.pat.StringLike;
18
19		/**
20		* Provides a wrapper for a RandomAccessFile so that it can be searched by
21		* Regex.
22		*/
		0% Uncovered Elements: 83 (83) Complexity: 28 Complexity Density: 0.57
23		public class RandomAccessFileWrap implements StringLike
24		{
25
26		long offset = 0;
27
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
28	0	public void setOffset(long o)...
29		{
30	0	offset = o;
31	0	i0 = iend = 0;
32		}
33
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
34	0	public long getOffset()...
35		{
36	0	return offset;
37		}
38
39		RandomAccessFile raf;
40
41		int i0 = 0, iend = 0;
42
43		byte[] buf = new byte[1024];
44
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
45	0	public int getBufferSize()...
46		{
47	0	return buf.length;
48		}
49
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
50	0	public void setBufferSize(int bs)...
51		{
52	0	buf = new byte[bs];
53	0	i0 = iend = 0;
54		}
55
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
56	0	public RandomAccessFileWrap(String file) throws IOException...
57		{
58	0	this.raf = new RandomAccessFile(file, "r");
59		}
60
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
61	0	public RandomAccessFileWrap(RandomAccessFile raf)...
62		{
63	0	this.raf = raf;
64		}
65
		0% Uncovered Elements: 17 (17) Complexity: 7 Complexity Density: 0.64
66	0	@Override...
67		public char charAt(int i)
68		{
69	0	if (i >= i0 && i < iend)
70		{
71	0	return (char) buf[i - i0];
72		}
73
74	0	try
75		{
76	0	i0 = i - 5;
77		// if(i0+offset<0) i0=(int)(-offset);
78	0	if (i0 < 0)
79		{
80	0	i0 = 0;
81		}
82	0	raf.seek(i0 + offset);
83	0	iend = i0 + raf.read(buf, 0, buf.length);
84
85	0	if (i >= i0 && i < iend)
86		{
87	0	return (char) buf[i - i0];
88		}
89		} catch (Throwable t)
90		{
91		}
92
93	0	throw new ArrayIndexOutOfBoundsException(MessageManager
94		.formatMessage("exception.out_of_bounds_for_file", new String[]
95		{ Integer.valueOf(i).toString(), Integer.valueOf(i0).toString(),
96		Integer.valueOf(iend).toString() }));
97		}
98
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
99	0	@Override...
100		public String toString()
101		{
102	0	throw new Error(MessageManager.getString("error.not_implemented"));
103		}
104
		0% Uncovered Elements: 8 (8) Complexity: 3 Complexity Density: 0.5
105	0	@Override...
106		public int length()
107		{
108	0	try
109		{
110	0	long len = raf.length() - offset;
111	0	if (len > Integer.MAX_VALUE)
112		{
113	0	return Integer.MAX_VALUE;
114		}
115	0	return (int) len;
116		} catch (IOException ioe)
117		{
118	0	return 0;
119		}
120		}
121
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.5
122	0	@Override...
123		public String substring(int i1, int i2)
124		{
125	0	StringBuffer sb = new StringBuffer();
126	0	for (int i = i1; i < i2; i++)
127		{
128	0	sb.append(charAt(i));
129		}
130	0	return sb.toString();
131		}
132
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
133	0	@Override...
134		public Object unwrap()
135		{
136	0	return raf;
137		}
138
139		/**
140		* @j2sIgnore
141		*
142		* @param files
143		* @throws IOException
144		*/
		0% Uncovered Elements: 19 (19) Complexity: 4 Complexity Density: 0.31
145	0	public static void main(String[] files) throws IOException...
146		{
147	0	for (int i = 0; i < files.length; i++)
148		{
149	0	RandomAccessFileWrap fw = new RandomAccessFileWrap(
150		new RandomAccessFile(files[i], "r"));
151	0	Regex r = new Regex("toString\\(\\) *(?@{})");
152	0	r.setGFlag(true);
153	0	r.optimize();
154	0	System.out.print(files[i] + " ");
155	0	int j = 0;
156	0	do
157		{
158	0	if (r.searchFrom(fw, j))
159		{
160	0	System.out.println("Matched at index: " + r.matchedFrom());
161	0	j = r.matchedTo();
162		}
163		else
164		{
165	0	System.out.println("not found");
166		}
167	0	System.out.println(r.stringMatched());
168	0	} while (r.didMatch());
169		}
170		}
171
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
172	0	@Override...
173		public BasicStringBufferLike newStringBufferLike()
174		{
175	0	return new StringBufferWrap();
176		}
177
		0% Uncovered Elements: 8 (8) Complexity: 3 Complexity Density: 0.75
178	0	@Override...
179		public int indexOf(char c)
180		{
181	0	for (int i = 0; i < length(); i++)
182		{
183	0	if (charAt(i) == c)
184		{
185	0	return i;
186		}
187		}
188	0	return -1;
189		}
190		}