net.maizegenetics.util.Utils Maven / Gradle / Ivy
/*
* Utils.java
*
* Created on May 27, 2003, 2:03 AM
*/
package net.maizegenetics.util;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import java.io.*;
import java.net.URL;
import java.nio.file.Path;
import java.util.*;
import java.util.stream.Stream;
import java.util.zip.GZIPInputStream;
import java.util.zip.GZIPOutputStream;
import java.util.zip.ZipEntry;
import java.util.zip.ZipFile;
/**
* @author terryc
*/
public final class Utils {
private static final Logger myLogger = LogManager.getLogger(Utils.class);
private static Collection myJavaPackages = null;
private Utils() {
// Utility Class
}
/**
* Returns the base name of a string delimited with periods (i.e. Java
* Class).
*
* @param str string to parse
*
* @return base name
*/
public static String getBasename(String str) {
int index = str.lastIndexOf('.');
index++;
return str.substring(index);
}
/**
* This returns the filename only. Preceding directories are removed and
* everything after last . is removed.
*
* @param str original filename
*
* @return trimmed filename
*/
public static String getFilename(String str) {
int indexForwardSlash = str.lastIndexOf('/');
int indexBackwardSlash = str.lastIndexOf('\\');
int index = 0;
if ((indexForwardSlash == -1) && (indexBackwardSlash == -1)) {
index = 0;
} else if (indexForwardSlash > indexBackwardSlash) {
index = indexForwardSlash + 1;
} else {
index = indexBackwardSlash + 1;
}
String result = str.substring(index);
if (result.indexOf('.') > 0) {
result = result.substring(0, result.indexOf('.'));
}
return result;
}
/**
* This returns the filename only. Preceding directories are removed and
* suffix. If suffix not found, then everything after last . is removed.
*
* @param str original filename
* @param suffix suffix
*
* @return trimmed filename
*/
public static String getFilename(String str, String suffix) {
int indexForwardSlash = str.lastIndexOf('/');
int indexBackwardSlash = str.lastIndexOf('\\');
int index = 0;
if ((indexForwardSlash == -1) && (indexBackwardSlash == -1)) {
index = 0;
} else if (indexForwardSlash > indexBackwardSlash) {
index = indexForwardSlash + 1;
} else {
index = indexBackwardSlash + 1;
}
String result = str.substring(index);
if ((suffix != null) && (result.lastIndexOf(suffix) > 0)) {
result = result.substring(0, result.lastIndexOf(suffix));
}
if (result.endsWith(".gz")) {
result = result.substring(0, result.lastIndexOf(".gz"));
}
if (result.lastIndexOf('.') > 0) {
result = result.substring(0, result.lastIndexOf('.'));
}
return result;
}
/**
* Returns just the directory with the filename removed.
*
* @param str original filename
*
* @return directory
*/
public static String getDirectory(String str) {
int indexForwardSlash = str.lastIndexOf('/');
int indexBackwardSlash = str.lastIndexOf('\\');
int index = 0;
if ((indexForwardSlash == -1) && (indexBackwardSlash == -1)) {
index = -1;
} else if (indexForwardSlash > indexBackwardSlash) {
index = indexForwardSlash;
} else {
index = indexBackwardSlash;
}
if (index == -1) {
return ".";
} else {
return str.substring(0, index);
}
}
/**
* This returns a set of fully qualified resource names that match the
* specified filename.
*
* @param filename filename
*
* @return set of resource names
*/
public static Set getFullyQualifiedResourceNames(String filename) {
Set result = new LinkedHashSet<>();
String classpath = System.getProperty("java.class.path");
String[] paths = classpath.split(File.pathSeparator);
for (String path : paths) {
if (path.trim().length() != 0) {
File file = new File(path);
if (file.exists()) {
try (ZipFile zFile = new ZipFile(file.getAbsolutePath());) {
Enumeration entries = zFile.entries();
while (entries.hasMoreElements()) {
ZipEntry entry = entries.nextElement();
if (!entry.isDirectory()) {
String name = entry.getName();
if (name.endsWith(filename)) {
result.add("/" + name);
}
}
}
} catch (Exception e) {
myLogger.debug(e.getMessage(), e);
}
}
}
}
return result;
}
public static List getFullyQualifiedClassNames(String simpleName) {
if (myJavaPackages == null) {
myJavaPackages = getJavaPackages();
}
List fqns = new ArrayList();
for (String aPackage : myJavaPackages) {
try {
String fqn = aPackage + "." + simpleName;
Class.forName(fqn);
fqns.add(fqn);
} catch (Throwable e) {
// Do Nothing
}
}
return fqns;
}
public static Collection getJavaPackages() {
String classpath = System.getProperty("java.class.path");
return getPackagesFromClassPath(classpath);
}
public static Set getPackagesFromClassPath(String classpath) {
Set packages = new HashSet();
String[] paths = classpath.split(File.pathSeparator);
for (String path : paths) {
if (path.trim().length() == 0) {
continue;
} else {
File file = new File(path);
if (file.exists()) {
String childPath = file.getAbsolutePath();
if (childPath.endsWith(".jar")) {
packages.addAll(readZipFile(childPath));
} else {
packages.addAll(readDirectory(childPath));
}
}
}
}
return packages;
}
public static Set getTasselClasses() {
String classpath = System.getProperty("java.class.path");
String[] paths = classpath.split(File.pathSeparator);
String tasselPath = null;
for (String path : paths) {
if (path.trim().length() != 0) {
File file = new File(path);
if (file.exists()) {
tasselPath = file.getAbsolutePath();
if (tasselPath.endsWith("sTASSEL.jar")) {
break;
}
}
}
}
Set classes = new LinkedHashSet<>();
try (ZipFile zFile = new ZipFile(tasselPath);) {
Enumeration entries = zFile.entries();
while (entries.hasMoreElements()) {
ZipEntry entry = entries.nextElement();
if (!entry.isDirectory()) {
String name = entry.getName().replace(File.separator, ".");
if ((name.endsWith(".class")) && (!name.contains("$"))) {
name = name.substring(0, name.lastIndexOf(".class"));
classes.add(name);
}
}
}
} catch (Exception e) {
e.printStackTrace();
}
return classes;
}
public static Set readDirectory(String path) {
Set packages = new HashSet();
File file = new File(path);
int startIndex = path.length() + 1;
for (File child : file.listFiles()) {
recursiveRead(child, startIndex, packages);
}
return packages;
}
public static void recursiveRead(File file, int startIndex, Set packages) {
if (!file.isFile()) {
packages.add(file.getAbsolutePath().substring(startIndex).replace(File.separator, "."));
for (File child : file.listFiles()) {
recursiveRead(child, startIndex, packages);
}
}
}
public static Set readZipFile(String path) {
Set packages = new HashSet();
try {
ZipFile zFile = new ZipFile(path);
Enumeration entries = zFile.entries();
while (entries.hasMoreElements()) {
ZipEntry entry = entries.nextElement();
if (!entry.isDirectory()) {
String dirName = new File(entry.getName()).getParent();
if (dirName != null) {
String name = dirName.replace(File.separator, ".");
if (name.endsWith(".")) {
name = name.substring(0, name.length() - 1);
}
packages.add(name);
}
}
}
} catch (Exception e) {
e.printStackTrace();
}
return packages;
}
public static String shortenStrLineLen(String str, int preferredLen) {
return shortenStrLineLen(str, preferredLen, -1);
}
/**
*
*/
public static String shortenStrLineLen(String str, int preferredLen, int preferredLines) {
StringBuilder buffer = new StringBuilder();
int startIndex = 0;
int endIndex = preferredLen;
int strLen = str.length();
int numLines = 0;
while (startIndex < strLen - 1) {
int place = str.indexOf(' ', endIndex);
int newLine = str.indexOf('\n', startIndex);
if ((newLine != -1) && (newLine < place)) {
place = newLine;
}
String part = null;
if (place == -1) {
part = str.substring(startIndex);
buffer.append(part);
buffer.append("\n");
break;
} else {
place++;
part = str.substring(startIndex, place);
buffer.append(part);
buffer.append("\n");
startIndex = place;
endIndex = place + preferredLen;
}
numLines++;
if ((preferredLines > 0) && (numLines >= preferredLines)) {
return buffer.toString();
}
}
return buffer.toString();
}
/**
* Adds suffix (i.e. .txt) to end of filename if it's not already there.
*
* @param filename filename
* @param suffix suffix
*
* @return filename with suffix
*/
public static String addSuffixIfNeeded(String filename, String suffix) {
String temp = filename.toLowerCase();
if (suffix.charAt(0) != '.') {
suffix = '.' + suffix;
}
if (temp.endsWith(suffix)) {
return filename;
} else {
return filename + suffix;
}
}
public static String addGzSuffixIfNeeded(String filename, String suffix) {
String gzipSuffix = suffix + ".gz";
String result = addSuffixIfNeeded(filename, gzipSuffix, new String[]{suffix, gzipSuffix});
return addSuffixIfNeeded(result, ".gz");
}
/**
* Adds default suffix if not already one of the possible suffixes.
*
* @param filename filename
* @param defaultSuffix default suffix
* @param possible possible suffixes
*
* @return filename with suffix
*/
public static String addSuffixIfNeeded(String filename, String defaultSuffix, String[] possible) {
String temp = filename.toLowerCase();
for (String possible1 : possible) {
String current = possible1.toLowerCase();
if (current.charAt(0) != '.') {
current = '.' + current;
}
if (temp.endsWith(current)) {
return filename;
}
}
if (defaultSuffix.charAt(0) != '.') {
return filename + '.' + defaultSuffix;
} else {
return filename + defaultSuffix;
}
}
public static BufferedReader getBufferedReader(String inSourceName) {
return getBufferedReader(inSourceName, 8192);
}
public static BufferedReader getBufferedReader(String inSourceName, int bufSize) {
try {
if (bufSize < 1) {
return getBufferedReader(inSourceName);
} else if (inSourceName.startsWith("http")) {
if (inSourceName.endsWith(".gz")) {
return new BufferedReader(new InputStreamReader(new GZIPInputStream((new URL(inSourceName)).openStream(), bufSize)), bufSize);
} else {
return new BufferedReader(new InputStreamReader((new URL(inSourceName)).openStream()), bufSize);
}
} else if (inSourceName.endsWith(".gz")) {
return new BufferedReader(new InputStreamReader(new GZIPInputStream(new FileInputStream(inSourceName), bufSize)), bufSize);
} else {
return new BufferedReader(new InputStreamReader(new FileInputStream(inSourceName)), bufSize);
}
} catch (Exception e) {
myLogger.error("getBufferedReader: Error getting reader for: " + inSourceName);
e.printStackTrace();
}
return null;
}
public static BufferedReader getBufferedReader(File file, int bufSize) {
return getBufferedReader(file.getAbsolutePath(), bufSize);
}
/**
* Read all lines from a file as a {@code Stream}. Unlike Path.readAllLines,
* this method does not read all lines into a {@code List}, but instead
* populates lazily as the stream is consumed.
*
*
* Bytes from the file are decoded into characters using the specified
* charset and the same line terminators as specified by {@code
* readAllLines} are supported.
*
*
* After this method returns, then any subsequent I/O exception that occurs
* while reading from the file or when a malformed or unmappable byte
* sequence is read, is wrapped in an {@link java.io.UncheckedIOException}
* that will be thrown from the {@link java.util.stream.Stream} method that
* caused the read to take place. In case an {@code IOException} is thrown
* when closing the file, it is also wrapped as an
* {@code UncheckedIOException}.
*
*
* The returned stream encapsulates a {@link java.io.Reader}. If timely
* disposal of file system resources is required, the try-with-resources
* construct should be used to ensure that the stream's
* {@link java.util.stream.Stream#close close} method is invoked after the
* stream operations are completed.
*
* @param path the path to the file
*
* @return the lines from the file as a {@code Stream}
* @throws IOException if an I/O error occurs opening the file
* @throws SecurityException In the case of the default provider, and a
* security manager is installed, the
* {@link SecurityManager#checkRead(String) checkRead} method is invoked to
* check read access to the file
* @see java.io.BufferedReader#lines()
* @since 1.8
*/
public static Stream lines(Path path, int bufSize) throws IOException {
BufferedReader br = getBufferedReader(path.toString(), bufSize);
try {
return br.lines().onClose(asUncheckedRunnable(br));
} catch (Error | RuntimeException e) {
try {
br.close();
} catch (IOException ex) {
try {
e.addSuppressed(ex);
} catch (Throwable ignore) {
}
}
throw e;
}
}
/**
* Convert a Closeable to a Runnable by converting checked IOException to
* UncheckedIOException
*/
private static Runnable asUncheckedRunnable(Closeable c) {
return () -> {
try {
c.close();
} catch (IOException e) {
throw new UncheckedIOException(e);
}
};
}
public static BufferedWriter getBufferedWriter(String filename) {
return getBufferedWriter(filename, false);
}
public static BufferedWriter getBufferedWriter(String filename, boolean append) {
return getBufferedWriter(new File(filename), append);
}
public static BufferedWriter getBufferedWriter(File file) {
return getBufferedWriter(file, false);
}
public static BufferedWriter getBufferedWriter(File file, boolean append) {
String filename = null;
try {
filename = file.getCanonicalPath();
if (filename.endsWith(".gz")) {
return new BufferedWriter(new OutputStreamWriter(new GZIPOutputStream(new FileOutputStream(file, append))));
} else {
return new BufferedWriter(new OutputStreamWriter(new FileOutputStream(file, append)));
}
} catch (Exception e) {
myLogger.debug(e.getMessage(), e);
throw new IllegalStateException("getBufferedReader: Error getting reader for: " + filename + "\n" + e.getMessage());
}
}
public static DataOutputStream getDataOutputStream(String filename, int bufSize) {
try {
if (filename.endsWith(".gz")) {
return new DataOutputStream(new BufferedOutputStream(new GZIPOutputStream(new FileOutputStream(filename), bufSize)));
} else {
return new DataOutputStream(new BufferedOutputStream(new FileOutputStream(filename), bufSize));
}
} catch (Exception e) {
myLogger.error("getDataOutputStream: Error getting reader for: " + filename);
e.printStackTrace();
}
return null;
}
/**
* Finds index of Nth occurrence of character in string.
*
* @param str string
* @param match character to match
* @param n Nth occurrence
*
* @return index
*/
public static int findNthOccurrenceInString(String str, char match, int n) {
int result = str.indexOf(match);
while (--n > 0 && result != -1) {
result = str.indexOf(match, result + 1);
}
return result;
}
/**
* Returns max heap size in MB.
*
* @return max heap size
*/
public static long getMaxHeapSizeMB() {
return Runtime.getRuntime().maxMemory() / 1048576l;
}
/**
* Gets input stream for given file.
*
* @param filename file name
*
* @return input stream
*/
public static InputStream getInputStream(String filename) {
try {
if (filename.startsWith("http")) {
if (filename.endsWith(".gz")) {
return new GZIPInputStream((new URL(filename)).openStream());
} else {
return (new URL(filename)).openStream();
}
} else if (filename.endsWith(".gz")) {
return new GZIPInputStream(new FileInputStream(filename));
} else {
return new FileInputStream(filename);
}
} catch (Exception e) {
myLogger.error("getInputStream: Error getting reader for: " + filename);
e.printStackTrace();
}
return null;
}
public static BufferedOutputStream getBufferedOutputStream(String filename) {
try {
if (filename.endsWith(".gz")) {
return new BufferedOutputStream(new GZIPOutputStream(new FileOutputStream(filename)));
} else {
return new BufferedOutputStream(new FileOutputStream(filename));
}
} catch (Exception e) {
myLogger.error("getOutputStream: Error getting output stream for: " + filename);
myLogger.debug(e.getMessage(), e);
}
return null;
}
/**
* Return number of lines in given file.
*
* @param filename file name
*
* @return number of lines
*/
public static int getNumberLines(String filename) {
InputStream input = getInputStream(filename);
try {
byte[] buffer = new byte[1024];
int result = 0;
int numChrsRead = 0;
while ((numChrsRead = input.read(buffer)) != -1) {
for (int i = 0; i < numChrsRead; ++i) {
if (buffer[i] == '\n') {
++result;
}
}
}
return result;
} catch (Exception e) {
e.printStackTrace();
throw new IllegalStateException("Utils: getNumberLines: Problem getting number lines: " + filename);
} finally {
try {
input.close();
} catch (Exception e) {
// do nothing
}
}
}
/**
* Return number of lines in given file that doesn't begin with Hash (#) and
* isn't blank.
*
* @param filename file name
*
* @return number of lines
*/
public static int getNumberLinesNotHashOrBlank(String filename) {
InputStream input = getInputStream(filename);
try {
byte[] buffer = new byte[1024];
int result = 0;
boolean isHash = false;
boolean isBlank = true;
int numChrsRead = input.read(buffer);
// Check if first char of file is #
if (numChrsRead > 0) {
isHash = buffer[0] == '#';
}
while (numChrsRead > 0) {
for (int i = 0; i < numChrsRead - 1; ++i) {
if (buffer[i] == '\n') {
if (isHash) {
isHash = false;
} else if (!isBlank) {
++result;
}
if (buffer[i + 1] == '#') {
isHash = true;
}
isBlank = true;
} else {
isBlank = false;
}
}
if (buffer[numChrsRead - 1] == '\n') {
if (isHash) {
isHash = false;
} else if (!isBlank) {
++result;
}
numChrsRead = input.read(buffer);
if (numChrsRead > 0) {
isHash = buffer[0] == '#';
}
isBlank = true;
} else {
numChrsRead = input.read(buffer);
}
}
return result;
} catch (Exception e) {
e.printStackTrace();
throw new IllegalStateException("Utils: getNumberLinesNotHashOrBlank: Problem getting number lines: " + filename);
} finally {
try {
input.close();
} catch (Exception e) {
// do nothing
}
}
}
public static String readLineSkipComments(BufferedReader br) throws IOException {
String s = br.readLine();
while ((s.startsWith("#"))) {
s = br.readLine();
}
return s;
}
}