Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
DigestUtils	18	66	20	0.074468087.4%	Show methods

Class DigestUtils

Class DigestUtils	Line # 18	Total Statements 66	Complexity 20	TOTAL Coverage 0.074468087.4%
<clinit>, line 38()   <clinit>, line 38()	3838	2.02	2.02	1.0 1.0100%
computeMD5(byte[]) : byte[]   computeMD5(byte[]) : byte[]	4444	59.059	15.015	0.0 0.00%
toHexString(byte[]) : String   toHexString(byte[]) : String	130130	4.04	2.02	0.0 0.00%
computeSHA256(byte[]) : byte[]   computeSHA256(byte[]) : byte[]	144144	1.01	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.021276595	jalview.util.StringUtilsTest.testGetHashedBytesjalview.util.StringUtilsTest.testGetHashedBytes	1PASS
	0.021276595	jalview.project.Jalview2xmlTests.testSaveAndLoadAnnotationBasedTreejalview.project.Jalview2xmlTests.testSaveAndLoadAnnotationBasedTree	1PASS
	0.021276595	jalview.util.StringUtilsTest.testGetHashedBytesjalview.util.StringUtilsTest.testGetHashedBytes	1PASS
	0.021276595	jalview.bin.CommandsTest.structureImageOutputTestjalview.bin.CommandsTest.structureImageOutputTest	1PASS
	0.021276595	jalview.util.StringUtilsTest.testGetHashedBytesjalview.util.StringUtilsTest.testGetHashedBytes	1PASS
	0.021276595	jalview.project.Jalview2xmlTests.testRNAStructureRecoveryjalview.project.Jalview2xmlTests.testRNAStructureRecovery	1PASS
	0.021276595	jalview.util.StringUtilsTest.testGetHashedBytesjalview.util.StringUtilsTest.testGetHashedBytes	1PASS

 

Source view

1		package jalview.util;
2
3		import java.nio.charset.Charset;
4		import java.nio.charset.StandardCharsets;
5
6		import net.meyfa.sha256.Sha256;
7
8		/**
9		* This code copied from Rosetta Code. See
10		* https://rosettacode.org/wiki/MD5/Implementation#Java
11		* https://rosettacode.org/wiki/SHA-256#Implementation_2 Licensed under GNU Free
12		* Document License 1.3 (see end of web page).
13		* https://github.com/meyfa/java-sha256/blob/main/src/main/java/net/meyfa/sha256/Sha256.java
14		* Licensed under MIT. We need a native implementation of MD5 and SHA256 for
15		* JalviewJS which doesn't play well with java.security.MessageDigest or
16		* sun.security.utils.*.
17		*/
		7.4% Uncovered Elements: 87 (94) Complexity: 20 Complexity Density: 0.3
18		public class DigestUtils
19		{
20
21		static final Charset enc = StandardCharsets.UTF_8;
22
23		/**
24		* MD5 implementation -- https://rosettacode.org/wiki/MD5/Implementation
25		*/
26		private static final int INIT_A = 0x67452301;
27
28		private static final int INIT_B = (int) 0xEFCDAB89L;
29
30		private static final int INIT_C = (int) 0x98BADCFEL;
31
32		private static final int INIT_D = 0x10325476;
33
34		private static final int[] SHIFT_AMTS = { 7, 12, 17, 22, 5, 9, 14, 20, 4,
35		11, 16, 23, 6, 10, 15, 21 };
36
37		private static final int[] TABLE_T = new int[64];
		100% Uncovered Elements: 0 (4) Complexity: 2 Complexity Density: 1
38	50	static...
39		{
40	3250	for (int i = 0; i < 64; i++)
41	3200	TABLE_T[i] = (int) (long) ((1L << 32) * Math.abs(Math.sin(i + 1)));
42		}
43
		0% Uncovered Elements: 79 (79) Complexity: 15 Complexity Density: 0.25
44	0	public static byte[] computeMD5(byte[] message)...
45		{
46	0	int messageLenBytes = message.length;
47	0	int numBlocks = ((messageLenBytes + 8) >>> 6) + 1;
48	0	int totalLen = numBlocks << 6;
49	0	byte[] paddingBytes = new byte[totalLen - messageLenBytes];
50	0	paddingBytes[0] = (byte) 0x80;
51
52	0	long messageLenBits = (long) messageLenBytes << 3;
53	0	for (int i = 0; i < 8; i++)
54		{
55	0	paddingBytes[paddingBytes.length - 8 + i] = (byte) messageLenBits;
56	0	messageLenBits >>>= 8;
57		}
58
59	0	int a = INIT_A;
60	0	int b = INIT_B;
61	0	int c = INIT_C;
62	0	int d = INIT_D;
63	0	int[] buffer = new int[16];
64	0	for (int i = 0; i < numBlocks; i++)
65		{
66	0	int index = i << 6;
67	0	for (int j = 0; j < 64; j++, index++)
68	0	buffer[j >>> 2] = ((int) ((index < messageLenBytes) ? message[index]
69		: paddingBytes[index - messageLenBytes]) << 24)
70		| (buffer[j >>> 2] >>> 8);
71	0	int originalA = a;
72	0	int originalB = b;
73	0	int originalC = c;
74	0	int originalD = d;
75	0	for (int j = 0; j < 64; j++)
76		{
77	0	int div16 = j >>> 4;
78	0	int f = 0;
79	0	int bufferIndex = j;
80	0	switch (div16)
81		{
82	0	case 0:
83	0	f = (b & c) | (~b & d);
84	0	break;
85
86	0	case 1:
87	0	f = (b & d) | (c & ~d);
88	0	bufferIndex = (bufferIndex * 5 + 1) & 0x0F;
89	0	break;
90
91	0	case 2:
92	0	f = b ^ c ^ d;
93	0	bufferIndex = (bufferIndex * 3 + 5) & 0x0F;
94	0	break;
95
96	0	case 3:
97	0	f = c ^ (b | ~d);
98	0	bufferIndex = (bufferIndex * 7) & 0x0F;
99	0	break;
100		}
101	0	int temp = b + Integer.rotateLeft(
102		a + f + buffer[bufferIndex] + TABLE_T[j],
103		SHIFT_AMTS[(div16 << 2) | (j & 3)]);
104	0	a = d;
105	0	d = c;
106	0	c = b;
107	0	b = temp;
108		}
109
110	0	a += originalA;
111	0	b += originalB;
112	0	c += originalC;
113	0	d += originalD;
114		}
115
116	0	byte[] md5 = new byte[16];
117	0	int count = 0;
118	0	for (int i = 0; i < 4; i++)
119		{
120	0	int n = (i == 0) ? a : ((i == 1) ? b : ((i == 2) ? c : d));
121	0	for (int j = 0; j < 4; j++)
122		{
123	0	md5[count++] = (byte) n;
124	0	n >>>= 8;
125		}
126		}
127	0	return md5;
128		}
129
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.5
130	0	public static String toHexString(byte[] b)...
131		{
132	0	StringBuilder sb = new StringBuilder();
133	0	for (int i = 0; i < b.length; i++)
134		{
135	0	sb.append(String.format("%02X", b[i] & 0xFF));
136		}
137	0	return sb.toString();
138		}
139
140		/**
141		* SHA256 implementation --
142		* https://github.com/meyfa/java-sha256/blob/main/src/main/java/net/meyfa/sha256/Sha256.java
143		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
144	63	public static byte[] computeSHA256(byte[] message)...
145		{
146	63	return Sha256.hash(message);
147		}
148		}