protected static String argumentExpression(ArgumentItem argItem) {
StringBuilder line = new StringBuilder();
Argument arg = argItem.getArgumentDescriptor();
String format;
if (arg.required()) format = argItem.takesMultipleArguments() ? "%s ..." : "%s";
else format = argItem.takesMultipleArguments() ? "[%s ...]" : "[%s]";
String name = StringUtil.varNameToNaturalName(argItem.getArgumentName());
line.append(String.format(format, name));
return line.toString();
}
@Test
public void performanceOfCSVSplit() throws Exception {
StopWatch s = new StopWatch();
String line = null;
final int N = 1;
Pattern p = Pattern.compile(",");
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> csv = StringUtil.splitCSV(line);
}
}
_logger.info("OpenCSV split:" + s.getElapsedTime());
}
public void printUsage(Writer out) {
Properties helpMessageTemplateValue = new Properties();
// argument list
Collections.sort(
argumentItemList,
new Comparator<ArgumentItem>() {
public int compare(ArgumentItem o1, ArgumentItem o2) {
return o1.getRange().compareTo(o2.getRange());
}
});
List<String> argExpressionList =
Algorithm.map(
argumentItemList,
new Mapper<ArgumentItem, String>() {
public String map(ArgumentItem input) {
return argumentExpression(input);
}
});
// usage information
if (usage != null) {
helpMessageTemplateValue.put(TemplateVariable.COMMAND.name(), usage.command());
if (usage.description() != null && usage.description().length() > 0)
helpMessageTemplateValue.put(TemplateVariable.DESCRIPTION.name(), usage.description());
}
helpMessageTemplateValue.put(
TemplateVariable.ARGUMENT_LIST.name(), StringUtil.join(argExpressionList, " "));
// option list
Collections.sort(
optionItemList,
new Comparator<OptionItem>() {
public int compare(OptionItem o1, OptionItem o2) {
Option opt1 = o1.getOption();
Option opt2 = o2.getOption();
// prefer options that have a short name
if (o1.hasSymbol()) {
if (!o2.hasSymbol()) return -1;
} else if (o2.hasSymbol()) return 1;
int diff = opt1.symbol().compareTo(opt2.symbol());
if (diff == 0) return opt1.longName().compareTo(opt2.longName());
else return diff;
}
});
List<String> descriptionList =
Algorithm.map(
optionItemList,
new Mapper<OptionItem, String>() {
public String map(OptionItem input) {
return optionDescription(input);
}
});
int maxDescriptionLength = 15;
for (String each : descriptionList)
if (each.length() > maxDescriptionLength) maxDescriptionLength = each.length();
String optionHelpFormat = String.format(" %%-%ds %%s", maxDescriptionLength);
StringWriter optionListHelpWriter = new StringWriter();
for (int i = 0; i < optionItemList.size(); ++i) {
OptionItem optionItem = optionItemList.get(i);
String optionHelp = descriptionList.get(i);
String line =
String.format(optionHelpFormat, optionHelp, optionItem.getOption().description());
optionListHelpWriter.append(line);
optionListHelpWriter.append(StringUtil.newline());
}
helpMessageTemplateValue.put(
TemplateVariable.OPTION_LIST.name(), optionListHelpWriter.toString());
// render help messages using template
ResourcePath rp =
new ResourcePath(usage != null ? usage.templatePath() : Usage.DEFAULT_TEMPLATE);
try {
Template helpMessageTemplate = new Template(rp.openBinaryStream());
String helpMessage = helpMessageTemplate.apply(helpMessageTemplateValue);
out.append(helpMessage);
out.flush();
} catch (IOException e) {
throw new XerialError(XerialErrorCode.OUTPUT_ERROR, e);
} catch (XerialException e) {
throw new XerialError(e);
}
}
@Override
public String toString() {
return String.format("function %s(%s)", name, StringUtil.join(argumentList, ", "));
}
@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());
}