@Test
public void performanceOfTabSplit() throws Exception {
StopWatch s = new StopWatch();
String line = null;
final int N = 1;
Pattern p = Pattern.compile("\t");
s.reset();
for (int i = 0; i < N; i++) {
BufferedReader br =
new BufferedReader(
new InputStreamReader(
FileResource.find(SilkWalkerTest.class, "scaffold1.silk").openStream()));
while ((line = br.readLine()) != null) {
String[] tab = p.split(line);
}
}
_logger.info("default tab split:" + s.getElapsedTime());
s.reset();
for (int i = 0; i < N; i++) {
BufferedReader br =
new BufferedReader(
new InputStreamReader(
FileResource.find(SilkWalkerTest.class, "scaffold1.silk").openStream()));
while ((line = br.readLine()) != null) {
ArrayList<String> tokens = StringUtil.splitAtTab(line);
}
}
_logger.info("my tab split:" + s.getElapsedTime());
s.reset();
for (int i = 0; i < N; i++) {
BufferedReader br =
new BufferedReader(
new InputStreamReader(
FileResource.find(SilkWalkerTest.class, "scaffold1.silk").openStream()));
while ((line = br.readLine()) != null) {
StringTokenizer t = new StringTokenizer(line, "\t");
ArrayList<String> tokens = new ArrayList<String>();
while (t.hasMoreTokens()) {
tokens.add(t.nextToken());
}
}
}
_logger.info("tokenizer tab split:" + s.getElapsedTime());
s.reset();
for (int i = 0; i < N; i++) {
FastBufferedReader fb =
new FastBufferedReader(
new InputStreamReader(
FileResource.find(SilkWalkerTest.class, "scaffold1.silk").openStream()));
while ((line = fb.readLine()) != null) {
ArrayList<String> tab = StringUtil.splitAtTab(line);
}
}
_logger.info("fast reader:" + s.getElapsedTime());
}
@Test
public void perfTest() throws Exception {
StopWatch s = new StopWatch();
File in = FileResource.copyToTemp(SilkWalkerTest.class, "scaffold1.silk", new File("target"));
final int N = 2;
{
s.reset();
int lineCount = 0;
char[] buf = new char[8192];
for (int i = 0; i < N; i++) {
BufferedReader fb = new BufferedReader(new FileReader(in));
for (int readSize = 0; (readSize = fb.read(buf)) != -1; ) {
for (int c = 0; c < readSize; c++) {
if (buf[c] == '\r') {
lineCount++;
if (c + 1 < readSize && buf[c + 1] == '\n') {
c++;
}
} else if (buf[c] == '\n') {
lineCount++;
}
}
}
}
_logger.info(String.format("BufferedReader: %.2f", s.getElapsedTime()));
}
{
s.reset();
int lineCount = 0;
for (int i = 0; i < N; i++) {
BufferedScanner fb = new BufferedScanner(new FileInputStream(in));
for (CharSequence line; (line = fb.nextLine()) != null; lineCount++) {}
}
_logger.info(
String.format("BufferedScanner nextLine: %.2f, line:%d", s.getElapsedTime(), lineCount));
}
{
s.reset();
int lineCount = 0;
for (int i = 0; i < N; i++) {
BufferedReader fb = new BufferedReader(new FileReader(in));
for (String line; (line = fb.readLine()) != null; lineCount++) {}
}
_logger.info(
String.format("BufferedReader readLine: %.2f, line:%d", s.getElapsedTime(), lineCount));
}
{
s.reset();
int lineCount = 0;
for (int i = 0; i < N; i++) {
BufferedScanner fb = new BufferedScanner(new FileInputStream(in));
for (CharSequence line; (line = fb.nextLine()) != null; lineCount++) {
String st = line.toString();
}
}
_logger.info(
String.format(
"BufferedScanner nextLine (with String conversion): %.2f, line:%d",
s.getElapsedTime(), lineCount));
}
{
s.reset();
int lineCount = 0;
for (int i = 0; i < N; i++) {
BufferedScanner fb = new BufferedScanner(new FileReader(in));
for (CharSequence line; (line = fb.nextLine()) != null; lineCount++) {}
}
_logger.info(
String.format(
"BufferedScanner nextLine with Reader input: %.2f, line:%d",
s.getElapsedTime(), lineCount));
}
{
s.reset();
int lineCount = 0;
char[] buf = new char[8192];
for (int i = 0; i < N; i++) {
FastBufferedReader fb = new FastBufferedReader(new FileReader(in));
for (int readSize = 0; (readSize = fb.read(buf)) != -1; ) {
for (int c = 0; c < readSize; c++) {
if (buf[c] == '\r') {
lineCount++;
if (c + 1 < readSize && buf[c + 1] == '\n') {
c++;
}
} else if (buf[c] == '\n') {
lineCount++;
}
}
}
}
_logger.info(String.format("FastBufferedReader: %.2f", s.getElapsedTime()));
}
{
s.reset();
int lineCount = 0;
byte[] buf = new byte[8192];
for (int i = 0; i < N; i++) {
FastBufferedInputStream fb = new FastBufferedInputStream(new FileInputStream(in));
for (int readSize = 0; (readSize = fb.read(buf)) != -1; ) {
for (int c = 0; c < readSize; c++) {
if (buf[c] == '\r') {
lineCount++;
if (c + 1 < readSize && buf[c + 1] == '\n') {
c++;
}
} else if (buf[c] == '\n') {
lineCount++;
}
}
}
}
_logger.info(String.format("FastBufferedInputStream: %.2f", s.getElapsedTime()));
}
{
s.reset();
int lineCount = 0;
byte[] buf = new byte[8192];
for (int i = 0; i < N; i++) {
BufferedInputStream fb = new BufferedInputStream(new FileInputStream(in));
for (int readSize = 0; (readSize = fb.read(buf)) != -1; ) {
for (int c = 0; c < readSize; c++) {
if (buf[c] == '\r') {
lineCount++;
if (c + 1 < readSize && buf[c + 1] == '\n') {
c++;
}
} else if (buf[c] == '\n') {
lineCount++;
}
}
}
}
_logger.info(String.format("BufferedInputStream: %.2f", s.getElapsedTime()));
}
}
