我的 Java 程序需要使用大矩阵中所有元素对的参数启动 agrep.exe，并获取两个字符串的匹配错误数。我写了一段代码，但运行速度很慢。我可以加快这部分代码的速度吗？或者，也许，你可以建议我一些 agrep 函数的 java 实现？
public static double getSignatureDistance(String one, String two) throws IOException, InterruptedException {
String strReprOne = one.replace(".*","").replace("\\.",".");
String strReprTwo = two.replace(".*","").replace("\\.",".");
PrintWriter writer = new PrintWriter("tmp.txt", "UTF-8");
writer.print(strReprTwo);
writer.close();
List<String> cmd = new ArrayList<>();
cmd.add("agrep.exe");
cmd.add("-B");
cmd.add(one);
cmd.add("tmp.txt");
ProcessBuilder pb = new ProcessBuilder(cmd);
pb.redirectErrorStream(true);
Process proc = pb.start();
BufferedReader in = new BufferedReader(new InputStreamReader(proc.getInputStream()));
StringBuilder lineBuilder = new StringBuilder();
String line = "";
char[] buf = new char[2];
while (in.read(buf) == 2) {
lineBuilder.append(buf);
}
line = lineBuilder.toString();
Pattern p = Pattern.compile("(\\d+)\\serror");
Matcher m = p.matcher(line);
double agrep = 0;
if(m.find()) {
agrep = Double.valueOf(m.group(1));
}
in.close();
proc.destroy();
double length = strReprOne.length();
return agrep/length;
}
我可以为此目的使用 FREJ 库吗？例如，执行字符串匹配，得到匹配结果并乘以匹配区域的长度？