// TODO: write tests.
// create target directory, if it does not exist.
public static void copyDirectory(String sourceDirectoryPath, String targetDirectoryPath) {
File sourceDirectory = new File(sourceDirectoryPath);
File targetDirectory = new File(targetDirectoryPath);
try {
if (sourceDirectory.isDirectory()) {
// do recursion
if (!targetDirectory.exists()) {
targetDirectory.mkdir();
}
String[] children = sourceDirectory.list();
for (int i = 0; i < children.length; i++) {
copyDirectory(
sourceDirectoryPath + "\\" + children[i], targetDirectory + "\\" + children[i]);
}
} else {
// copy the file
copyFile(sourceDirectory.getAbsolutePath(), targetDirectory.getAbsolutePath());
}
} catch (Exception e) {
e.printStackTrace();
}
}
/**
* reads in data from a file.
*
* @param numberOfRows
* @param numberOfColumns
* @param ignoreFirstLine
* @return
*/
public static double[][] readMatrix(
int numberOfRows, int numberOfColumns, boolean ignoreFirstLine, String fileName) {
double[][] matrix = new double[numberOfRows][numberOfColumns];
try {
FileReader fr = new FileReader(fileName);
BufferedReader br = new BufferedReader(fr);
String line;
StringTokenizer tokenizer;
String token;
if (ignoreFirstLine) {
br.readLine();
}
line = br.readLine();
int rowId = 0;
while (line != null) {
tokenizer = new StringTokenizer(line);
for (int i = 0; i < numberOfColumns; i++) {
token = tokenizer.nextToken();
double parsedNumber = Double.parseDouble(token);
matrix[rowId][i] = parsedNumber;
}
if (tokenizer.hasMoreTokens()) {
// if there are more columns than expected, throw an
// exception
throw new RuntimeException("the number of columns is wrong");
}
line = br.readLine();
rowId++;
}
if (rowId != numberOfRows) {
throw new RuntimeException("the number of rows is wrong");
}
} catch (RuntimeException e) {
// just forward the runtime exception
throw e;
} catch (Exception e) {
e.printStackTrace();
throw new RuntimeException("Error reading the matrix from the file");
}
return matrix;
}
public static Matrix<String> readStringMatrix(
String fileName, String delim, StringMatrixFilter filter) {
Matrix<String> matrix = new Matrix<String>();
try {
// FileReader fr = new FileReader(fileName);
FileInputStream fis = new FileInputStream(fileName);
InputStreamReader isr = new InputStreamReader(fis, "ISO-8859-1");
BufferedReader br = null;
if (fileName.toLowerCase(Locale.ROOT).endsWith(".gz")) {
br = IOUtils.getBufferedReader(fileName);
} else {
br = new BufferedReader(isr);
}
String line;
StringTokenizer tokenizer;
line = br.readLine();
while (line != null) {
ArrayList<String> row = new ArrayList<String>();
if (delim == null) {
tokenizer = new StringTokenizer(line);
} else {
tokenizer = new StringTokenizer(line, delim);
}
while (tokenizer.hasMoreTokens()) {
row.add(tokenizer.nextToken());
}
if (filter != null && filter.removeLine(line)) {
} else {
matrix.addRow(row);
}
line = br.readLine();
}
} catch (Exception e) {
e.printStackTrace();
throw new Error("Error reading the file: " + fileName);
}
return matrix;
}
/**
* TODO: write test.
*
* @param sourceFilePath
* @param targetFilePath
*/
public static void copyFile(String sourceFilePath, String targetFilePath) {
File sourceFile = new File(sourceFilePath);
File targetFile = new File(targetFilePath);
try {
// copy the file
InputStream in = new FileInputStream(sourceFile);
OutputStream out = new FileOutputStream(targetFile);
byte[] buf = new byte[1024];
int len;
while ((len = in.read(buf)) > 0) {
out.write(buf, 0, len);
}
in.close();
out.close();
} catch (Exception e) {
e.printStackTrace();
}
}
/**
* Write out a list of Strings
*
* <p>after each String in the list a "\n" is added.
*
* @param list
* @param fileName
*/
public static void writeList(ArrayList<String> list, String fileName) {
Writer writer = null;
if (fileName.toLowerCase(Locale.ROOT).endsWith(".gz")) {
writer = IOUtils.getBufferedWriter(fileName);
}
try {
if (writer == null) {
FileOutputStream fos = new FileOutputStream(fileName);
writer = new OutputStreamWriter(fos);
}
char[] charArray = Lists.getCharsOfAllArrayItemsWithNewLineCharacterInbetween(list);
writer.write(charArray);
writer.flush();
writer.close();
} catch (Exception e) {
e.printStackTrace();
}
}
public static LinkedList<String> readFileRows(String fileName) {
LinkedList<String> list = new LinkedList<String>();
try {
FileInputStream fis = new FileInputStream(fileName);
InputStreamReader isr = new InputStreamReader(fis, "ISO-8859-1");
BufferedReader br = new BufferedReader(isr);
String line;
line = br.readLine();
while (line != null) {
list.add(line);
line = br.readLine();
}
} catch (Exception e) {
e.printStackTrace();
DebugLib.stopSystemAndReportInconsistency();
}
return list;
}