我目前正在处理字符串形式的DNA序列，其中内含子是小写字母，外显子是大写字母。该方法的目的是尽可能快地以String的形式检索外显子。
序列示例：
ATGGATGACAGgtgagaggacactcgggtcccagccccaggctctgccctcaggaagggggtcagctctcaggggcatctccctctcacagcccagccctggggatgatgtgggagccccatttatacacggtgcctccttctctcctagAGCCTACATAG
我的第一个版本是使用String replaceAll（）方法，但它特别慢：
public String getExons(String sequence) {
return sequence.replaceAll("[atgc]", "");
}
所以我尝试了一个新版本，它提高了性能，但仍然很慢：
public String getExons(String sequence) {
StringBuilder exonBuilder = new StringBuilder();
for (int i = 0; i < sequence.length(); i++) {
char c = sequence.charAt(i);
if (c == 'A' || c == 'T' || c == 'G' || c == 'C') exonBuilder.append(c);
}
return exonBuilder.toString();
还有另一种方法可以提高性能吗？
答案 0 :(得分：9)
你需要使用带有双指针技巧的char数组。我在我的机器上得到了这个结果：
编辑：使用预热阶段进行更新。 Java是来自Ubuntu 14 LTS的OpenJDK 8
Edit2：哈希表是最快的边距。
Edit3：我的代码中有一个错误。双指针技巧是最快的。
GTCtgACgGT
getExons1: 1068
getExons2: 377
getExons3: 313
getExons3b: 251
getExons4: 586
getExons5: 189
getExons6: 671
Edit4：使用带有1M DNA String的JMH运行基准测试。结果与我之前关于“x优于y”的基准一致，最差的是正则表达式，最好的是双指针，第二个最好的是天真的3B：
Benchmark Mode Cnt Score Error Units
MyBenchmark.benchExons1 thrpt 200 33.659 ± 1.036 ops/s
MyBenchmark.benchExons2 thrpt 200 107.095 ± 4.074 ops/s
MyBenchmark.benchExons3a thrpt 200 118.543 ± 3.779 ops/s
MyBenchmark.benchExons3b thrpt 200 163.717 ± 4.602 ops/s
MyBenchmark.benchExons4 thrpt 200 69.942 ± 2.019 ops/s
MyBenchmark.benchExons5 thrpt 200 191.142 ± 5.307 ops/s
MyBenchmark.benchExons6 thrpt 200 57.654 ± 1.963 ops/s
Edit5：使用10 MB字符串：
Benchmark Mode Cnt Score Error Units
MyBenchmark.benchExons1 thrpt 200 4.640 ± 0.068 ops/s
MyBenchmark.benchExons2 thrpt 200 13.451 ± 0.161 ops/s
MyBenchmark.benchExons3a thrpt 200 15.379 ± 0.232 ops/s
MyBenchmark.benchExons3b thrpt 200 19.550 ± 0.181 ops/s
MyBenchmark.benchExons4 thrpt 200 8.510 ± 0.147 ops/s
MyBenchmark.benchExons5 thrpt 200 24.343 ± 0.331 ops/s
MyBenchmark.benchExons6 thrpt 200 7.339 ± 0.074 ops/s
代码：
package org.sample;
import org.openjdk.jmh.annotations.Benchmark;
import org.openjdk.jmh.annotations.Scope;
import org.openjdk.jmh.annotations.State;
import java.util.HashMap;
import java.util.Random;
@State(Scope.Thread)
public class MyBenchmark {
String DNA;
public MyBenchmark() {
DNA = buildRandomDNA(1000000);
}
static String letters = "ATGCatgc";
public static String buildRandomDNA(int size) {
StringBuilder builder = new StringBuilder(size);
Random r = new Random();
for (int i = 0; i < size; ++i) {
builder.append(letters.charAt(r.nextInt(letters.length())));
}
return builder.toString();
}
@Benchmark
public void benchExons1() {
getExons1(DNA);
}
@Benchmark
public void benchExons2() {
getExons2(DNA);
}
@Benchmark
public void benchExons3a() {
getExons3a(DNA);
}
@Benchmark
public void benchExons3b() {
getExons3b(DNA);
}
@Benchmark
public void benchExons4() {
getExons4(DNA);
}
@Benchmark
public void benchExons5() {
getExons5(DNA);
}
@Benchmark
public void benchExons6() {
getExons6(DNA);
}
public static String getExons1(String sequence) {
return sequence.replaceAll("[atgc]", "");
}
public static String getExons2(String sequence) {
StringBuilder exonBuilder = new StringBuilder();
for (int i = 0; i < sequence.length(); i++) {
char c = sequence.charAt(i);
if (c == 'A' || c == 'T' || c == 'G' || c == 'C')
exonBuilder.append(c);
}
return exonBuilder.toString();
}
public static String getExons3a(String sequence) {
StringBuilder exonBuilder = new StringBuilder();
for (int i = 0; i < sequence.length(); i++) {
char c = sequence.charAt(i);
if (c <= 'Z') {
exonBuilder.append((char) c);
}
}
return exonBuilder.toString();
}
public static String getExons3b(String sequence1) {
char[] sequence = sequence1.toCharArray();
StringBuilder exonBuilder = new StringBuilder();
for (int i = 0; i < sequence.length; i++) {
if (sequence[i] <= 'Z') {
exonBuilder.append(sequence[i]);
}
}
return exonBuilder.toString();
}
public static HashMap<String, String> M = new HashMap<String, String>();
public static void buildTable() {
for (int a = 0; a < letters.length(); ++a) {
for (int b = 0; b < letters.length(); ++b) {
for (int c = 0; c < letters.length(); ++c) {
for (int d = 0; d < letters.length(); ++d) {
String key = "" + letters.charAt(a) + letters.charAt(b) + letters.charAt(c) + letters.charAt(d);
M.put(key, getExons1(key));
}
}
}
}
}
public static String getExons4(String sequence1) {
char[] sequence = sequence1.toCharArray();
StringBuilder exonBuilder = new StringBuilder();
for (int i = 0; i < sequence.length; i += 4) {
exonBuilder.append(M.get(new String(sequence, i, 4)));
}
return exonBuilder.toString();
}
public static String getExons5(String sequence1) {
char[] sequence = sequence1.toCharArray();
int p = 0;
for (int i = 0; i < sequence.length; i++) {
if (sequence[i] <= 'Z') {
sequence[p] = sequence[i];
++p;
}
}
return new String(sequence, 0, p);
}
public static int dnatoint(char[] s, int start, int len) {
int key = 0;
for (; len > 0; len--, start++) {
switch (s[start]) {
case 'A': key = (key << 3) | 0; break;
case 'C': key = (key << 3) | 1; break;
case 'G': key = (key << 3) | 2; break;
case 'T': key = (key << 3) | 3; break;
case 'a': key = (key << 3) | 4; break;
case 'c': key = (key << 3) | 5; break;
case 'g': key = (key << 3) | 6; break;
case 't': key = (key << 3) | 7; break;
}
}
return key;
}
public static String[] M2 = new String[8*8*8*8];
public static void buildTable2() {
for (int a = 0; a < letters.length(); ++a) {
for (int b = 0; b < letters.length(); ++b) {
for (int c = 0; c < letters.length(); ++c) {
for (int d = 0; d < letters.length(); ++d) {
String key = "" + letters.charAt(a) + letters.charAt(b) + letters.charAt(c) + letters.charAt(d);
M2[dnatoint(key.toCharArray(), 0, 4)] = getExons1(key);
}
}
}
}
}
public static String getExons6(String sequence1) {
char[] sequence = sequence1.toCharArray();
StringBuilder exonBuilder = new StringBuilder();
assert (sequence.length % 4) == 0;
for (int i = 0; i < sequence.length; i += 4) {
exonBuilder.append(M2[dnatoint(sequence, i, 4)]);
}
return exonBuilder.toString();
}
static {
buildTable();
buildTable2();
}
//@Benchmark
public void testMethod() {
// This is a demo/sample template for building your JMH benchmarks. Edit as needed.
// Put your benchmark code here.
}
}
答案 1 :(得分：5)
使用以下：
$((function(_this) {
return function() {
return rest_api_login(function(login_ok, userName, userRoles) {
console.log("login_ok " + login_ok + ", userName " + userName + ", roles [" + (userRoles.join(", ")) + "]");
vcm.app.userName = userName;
vcm.app.userRoles = userRoles;
vcm.app.defaultClassifications = [];
return initialize_templates(function(loaded_templates) {
console.log("loaded_templates", loaded_templates);
return vcm.app.main_application();
});
});
};
})(this));
答案 2 :(得分：5)
这里有一个替代方案，在我看来更简洁，并且和其他人一样快。
sequence.chars()
.filter(c -> c >= 65 && c <= 90)
.collect(StringBuilder::new,
(StringBuilder sb, int c) -> sb.append((char) c),
StringBuilder::append);
答案 3 :(得分：1)
public static void main(String[] args) {
String str = "ATGGATGACAGgtgagaggacactcgggtcccagccccaggctctgccctcaggaagggggtcagctctcaggggcatctccctctcacagcccagccctggggatgatgtgggagccccatttatacacggtgcctccttctctcctagAGCCTACATAG";
byte[] bytes = str.getBytes();
for(int i=0; i<str.length(); i++) {
if (str.charAt(i) >= 90) {
bytes[i] = (byte) (str.charAt(i) - 32);
}
}
System.out.println(new String(bytes));
}