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/*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see DF = new ThreadLocal() {
@Override
protected DecimalFormat initialValue() {
DecimalFormat df = new DecimalFormat();
DecimalFormatSymbols dfs = df.getDecimalFormatSymbols();
dfs.setDecimalSeparator('.');
dfs.setNaN("NaN");
dfs.setInfinity("Infinity");
df.setGroupingUsed(false);
df.setRoundingMode(RoundingMode.HALF_UP);
df.setDecimalFormatSymbols(dfs);
return df;
}
};
/**
* Tests if the given value codes "missing".
*
* @param val the value to be tested
* @return true if val codes "missing"
*/
public static boolean isMissingValue(double val) {
return Double.isNaN(val);
}
/**
* Returns the value used to code a missing value. Note that equality tests on
* this value will always return false, so use isMissingValue(double val) for
* testing..
*
* @return the value used as missing value.
*/
public static double missingValue() {
return Double.NaN;
}
/**
* Casting an object without "unchecked" compile-time warnings. Use only when
* absolutely necessary (e.g. when using clone()).
*/
@SuppressWarnings("unchecked")
public static T cast(Object x) {
return (T) x;
}
/**
* Reads properties that inherit from three locations. Properties are first
* defined in the system resource location (i.e. in the CLASSPATH). These
* default properties must exist. Properties optionally defined in the user
* properties location (WekaPackageManager.PROPERTIES_DIR) override default
* settings. Properties defined in the current directory (optional) override
* all these settings.
*
* @param resourceName the location of the resource that should be loaded.
* e.g.: "weka/core/Utils.props". (The use of hardcoded forward
* slashes here is OK - see jdk1.1/docs/guide/misc/resources.html)
* This routine will also look for the file (in this case)
* "Utils.props" in the users home directory and the current
* directory.
* @return the Properties
* @exception Exception if no default properties are defined, or if an error
* occurs reading the properties files.
*/
public static Properties readProperties(String resourceName) throws Exception {
Properties defaultProps = new Properties();
try {
// Apparently hardcoded slashes are OK here
// jdk1.1/docs/guide/misc/resources.html
Utils utils = new Utils();
Enumeration urls = utils.getClass().getClassLoader()
.getResources(resourceName);
boolean first = true;
while (urls.hasMoreElements()) {
URL url = urls.nextElement();
if (first) {
defaultProps.load(url.openStream());
first = false;
} else {
Properties props = new Properties(defaultProps);
props.load(url.openStream());
defaultProps = props;
}
}
} catch (Exception ex) {
System.err.println("Warning, unable to load properties file(s) from "
+ "system resource (Utils.java): " + resourceName);
}
// Hardcoded slash is OK here
// eg: see jdk1.1/docs/guide/misc/resources.html
int slInd = resourceName.lastIndexOf('/');
if (slInd != -1) {
resourceName = resourceName.substring(slInd + 1);
}
// Allow a properties file in the WekaPackageManager.PROPERTIES_DIR to
// override
Properties userProps = new Properties(defaultProps);
if (!WekaPackageManager.PROPERTIES_DIR.exists()) {
WekaPackageManager.PROPERTIES_DIR.mkdir();
}
File propFile = new File(WekaPackageManager.PROPERTIES_DIR.toString()
+ File.separator + resourceName);
if (propFile.exists()) {
try {
userProps.load(new FileInputStream(propFile));
} catch (Exception ex) {
throw new Exception("Problem reading user properties: " + propFile);
}
}
// Allow a properties file in the current directory to override
Properties localProps = new Properties(userProps);
propFile = new File(resourceName);
if (propFile.exists()) {
try {
localProps.load(new FileInputStream(propFile));
} catch (Exception ex) {
throw new Exception("Problem reading local properties: " + propFile);
}
}
return new EnvironmentProperties(localProps);
}
/**
* Returns the correlation coefficient of two double vectors.
*
* @param y1 double vector 1
* @param y2 double vector 2
* @param n the length of two double vectors
* @return the correlation coefficient
*/
public static final double correlation(double y1[], double y2[], int n) {
int i;
double av1 = 0.0, av2 = 0.0, y11 = 0.0, y22 = 0.0, y12 = 0.0, c;
if (n <= 1) {
return 1.0;
}
for (i = 0; i < n; i++) {
av1 += y1[i];
av2 += y2[i];
}
av1 /= n;
av2 /= n;
for (i = 0; i < n; i++) {
y11 += (y1[i] - av1) * (y1[i] - av1);
y22 += (y2[i] - av2) * (y2[i] - av2);
y12 += (y1[i] - av1) * (y2[i] - av2);
}
if (y11 * y22 == 0.0) {
c = 1.0;
} else {
c = y12 / Math.sqrt(Math.abs(y11 * y22));
}
return c;
}
/**
* Removes all occurrences of a string from another string.
*
* @param inString the string to remove substrings from.
* @param substring the substring to remove.
* @return the input string with occurrences of substring removed.
*/
public static String removeSubstring(String inString, String substring) {
StringBuffer result = new StringBuffer();
int oldLoc = 0, loc = 0;
while ((loc = inString.indexOf(substring, oldLoc)) != -1) {
result.append(inString.substring(oldLoc, loc));
oldLoc = loc + substring.length();
}
result.append(inString.substring(oldLoc));
return result.toString();
}
/**
* Replaces with a new string, all occurrences of a string from another
* string.
*
* @param inString the string to replace substrings in.
* @param subString the substring to replace.
* @param replaceString the replacement substring
* @return the input string with occurrences of substring replaced.
*/
public static String replaceSubstring(String inString, String subString,
String replaceString) {
StringBuffer result = new StringBuffer();
int oldLoc = 0, loc = 0;
while ((loc = inString.indexOf(subString, oldLoc)) != -1) {
result.append(inString.substring(oldLoc, loc));
result.append(replaceString);
oldLoc = loc + subString.length();
}
result.append(inString.substring(oldLoc));
return result.toString();
}
/**
* Pads a string to a specified length, inserting spaces on the left as
* required. If the string is too long, it is simply returned unchanged.
*
* @param inString the input string
* @param length the desired length of the output string
* @return the output string
*/
public static String padLeftAndAllowOverflow(String inString, int length) {
return String.format("%1$" + length + "s", inString);
}
/**
* Pads a string to a specified length, inserting spaces on the right as
* required. If the string is too long, it is simply returned unchanged.
*
* @param inString the input string
* @param length the desired length of the output string
* @return the output string
*/
public static String padRightAndAllowOverflow(String inString, int length) {
return String.format("%1$-" + length + "s", inString);
}
/**
* Pads a string to a specified length, inserting spaces on the left as
* required. If the string is too long, characters are removed (from the
* right).
*
* @param inString the input string
* @param length the desired length of the output string
* @return the output string
*/
public static String padLeft(String inString, int length) {
return String.format("%1$" + length + "." + length + "s", inString);
}
/**
* Pads a string to a specified length, inserting spaces on the right as
* required. If the string is too long, characters are removed (from the
* right).
*
* @param inString the input string
* @param length the desired length of the output string
* @return the output string
*/
public static String padRight(String inString, int length) {
return String.format("%1$-" + length + "." + length + "s", inString);
}
/**
* Rounds a double and converts it into String.
*
* @param value the double value
* @param afterDecimalPoint the (maximum) number of digits permitted after the
* decimal point
* @return the double as a formatted string
*/
public static/* @pure@ */String doubleToString(double value,
int afterDecimalPoint) {
DF.get().setMaximumFractionDigits(afterDecimalPoint);
return DF.get().format(value);
}
/**
* Rounds a double and converts it into a formatted decimal-justified String.
* Trailing 0's are replaced with spaces.
*
* @param value the double value
* @param width the width of the string
* @param afterDecimalPoint the number of digits after the decimal point
* @return the double as a formatted string
*/
public static/* @pure@ */String doubleToString(double value, int width,
int afterDecimalPoint) {
String tempString = doubleToString(value, afterDecimalPoint);
char[] result;
int dotPosition;
if (afterDecimalPoint >= width) {
return tempString;
}
// Initialize result
result = new char[width];
for (int i = 0; i < result.length; i++) {
result[i] = ' ';
}
if (afterDecimalPoint > 0) {
// Get position of decimal point and insert decimal point
dotPosition = tempString.indexOf('.');
if (dotPosition == -1) {
dotPosition = tempString.length();
} else {
result[width - afterDecimalPoint - 1] = '.';
}
} else {
dotPosition = tempString.length();
}
int offset = width - afterDecimalPoint - dotPosition;
if (afterDecimalPoint > 0) {
offset--;
}
// Not enough room to decimal align within the supplied width
if (offset < 0) {
return tempString;
}
// Copy characters before decimal point
for (int i = 0; i < dotPosition; i++) {
result[offset + i] = tempString.charAt(i);
}
// Copy characters after decimal point
for (int i = dotPosition + 1; i < tempString.length(); i++) {
result[offset + i] = tempString.charAt(i);
}
return new String(result);
}
/**
* Returns the basic class of an array class (handles multi-dimensional
* arrays).
*
* @param c the array to inspect
* @return the class of the innermost elements
*/
public static Class getArrayClass(Class c) {
if (c.getComponentType().isArray()) {
return getArrayClass(c.getComponentType());
} else {
return c.getComponentType();
}
}
/**
* Returns the dimensions of the given array. Even though the parameter is of
* type "Object" one can hand over primitve arrays, e.g. int[3] or
* double[2][4].
*
* @param array the array to determine the dimensions for
* @return the dimensions of the array
*/
public static int getArrayDimensions(Class array) {
if (array.getComponentType().isArray()) {
return 1 + getArrayDimensions(array.getComponentType());
} else {
return 1;
}
}
/**
* Returns the dimensions of the given array. Even though the parameter is of
* type "Object" one can hand over primitve arrays, e.g. int[3] or
* double[2][4].
*
* @param array the array to determine the dimensions for
* @return the dimensions of the array
*/
public static int getArrayDimensions(Object array) {
return getArrayDimensions(array.getClass());
}
/**
* Returns the given Array in a string representation. Even though the
* parameter is of type "Object" one can hand over primitve arrays, e.g.
* int[3] or double[2][4].
*
* @param array the array to return in a string representation
* @return the array as string
*/
public static String arrayToString(Object array) {
String result;
int dimensions;
int i;
result = "";
dimensions = getArrayDimensions(array);
if (dimensions == 0) {
result = "null";
} else if (dimensions == 1) {
for (i = 0; i < Array.getLength(array); i++) {
if (i > 0) {
result += ",";
}
if (Array.get(array, i) == null) {
result += "null";
} else {
result += Array.get(array, i).toString();
}
}
} else {
for (i = 0; i < Array.getLength(array); i++) {
if (i > 0) {
result += ",";
}
result += "[" + arrayToString(Array.get(array, i)) + "]";
}
}
return result;
}
/**
* Tests if a is equal to b.
*
* @param a a double
* @param b a double
*/
public static/* @pure@ */boolean eq(double a, double b) {
return (a == b) || ((a - b < SMALL) && (b - a < SMALL));
}
/**
* Checks if the given array contains any non-empty options.
*
* @param options an array of strings
* @exception Exception if there are any non-empty options
*/
public static void checkForRemainingOptions(String[] options)
throws Exception {
int illegalOptionsFound = 0;
StringBuffer text = new StringBuffer();
if (options == null) {
return;
}
for (String option : options) {
if (option.length() > 0) {
illegalOptionsFound++;
text.append(option + ' ');
}
}
if (illegalOptionsFound > 0) {
throw new Exception("Illegal options: " + text);
}
}
/**
* Checks if the given array contains the flag "-Char". Stops searching at the
* first marker "--". If the flag is found, it is replaced with the empty
* string.
*
* @param flag the character indicating the flag.
* @param options the array of strings containing all the options.
* @return true if the flag was found
* @exception Exception if an illegal option was found
*/
public static boolean getFlag(char flag, String[] options) throws Exception {
return getFlag("" + flag, options);
}
/**
* Checks if the given array contains the flag "-String". Stops searching at
* the first marker "--". If the flag is found, it is replaced with the empty
* string.
*
* @param flag the String indicating the flag.
* @param options the array of strings containing all the options.
* @return true if the flag was found
* @exception Exception if an illegal option was found
*/
public static boolean getFlag(String flag, String[] options) throws Exception {
int pos = getOptionPos(flag, options);
if (pos > -1) {
options[pos] = "";
}
return (pos > -1);
}
/**
* Gets an option indicated by a flag "-Char" from the given array of strings.
* Stops searching at the first marker "--". Replaces flag and option with
* empty strings.
*
* @param flag the character indicating the option.
* @param options the array of strings containing all the options.
* @return the indicated option or an empty string
* @exception Exception if the option indicated by the flag can't be found
*/
public static/* @non_null@ */String getOption(char flag, String[] options)
throws Exception {
return getOption("" + flag, options);
}
/**
* Gets an option indicated by a flag "-String" from the given array of
* strings. Stops searching at the first marker "--". Replaces flag and option
* with empty strings.
*
* @param flag the String indicating the option.
* @param options the array of strings containing all the options.
* @return the indicated option or an empty string
* @exception Exception if the option indicated by the flag can't be found
*/
public static/* @non_null@ */String getOption(String flag, String[] options)
throws Exception {
String newString;
int i = getOptionPos(flag, options);
if (i > -1) {
if (options[i].equals("-" + flag)) {
if (i + 1 == options.length) {
throw new Exception("No value given for -" + flag + " option.");
}
options[i] = "";
newString = new String(options[i + 1]);
options[i + 1] = "";
return newString;
}
if (options[i].charAt(1) == '-') {
return "";
}
}
return "";
}
/**
* Gets the index of an option or flag indicated by a flag "-Char" from the
* given array of strings. Stops searching at the first marker "--".
*
* @param flag the character indicating the option.
* @param options the array of strings containing all the options.
* @return the position if found, or -1 otherwise
*/
public static int getOptionPos(char flag, String[] options) {
return getOptionPos("" + flag, options);
}
/**
* Gets the index of an option or flag indicated by a flag "-String" from the
* given array of strings. Stops searching at the first marker "--".
*
* @param flag the String indicating the option.
* @param options the array of strings containing all the options.
* @return the position if found, or -1 otherwise
*/
public static int getOptionPos(String flag, String[] options) {
if (options == null) {
return -1;
}
for (int i = 0; i < options.length; i++) {
if ((options[i].length() > 0) && (options[i].charAt(0) == '-')) {
// Check if it is a negative number
try {
Double.valueOf(options[i]);
} catch (NumberFormatException e) {
// found?
if (options[i].equals("-" + flag)) {
return i;
}
// did we reach "--"?
if (options[i].charAt(1) == '-') {
return -1;
}
}
}
}
return -1;
}
/**
* Quotes a string if it contains special characters.
*
* The following rules are applied:
*
* A character is backquoted version of it is one of " ' % \ \n \r \t
* .
*
* A string is enclosed within single quotes if a character has been
* backquoted using the previous rule above or contains { } or is
* exactly equal to the strings , ? space or "" (empty string).
*
* A quoted question mark distinguishes it from the missing value which is
* represented as an unquoted question mark in arff files.
*
* @param string the string to be quoted
* @return the string (possibly quoted)
* @see #unquote(String)
*/
public static/* @pure@ */String quote(String string) {
boolean quote = false;
// backquote the following characters
if ((string.indexOf('\n') != -1) || (string.indexOf('\r') != -1)
|| (string.indexOf('\'') != -1) || (string.indexOf('"') != -1)
|| (string.indexOf('\\') != -1) || (string.indexOf('\t') != -1)
|| (string.indexOf('%') != -1) || (string.indexOf('\u001E') != -1)) {
string = backQuoteChars(string);
quote = true;
}
// Enclose the string in 's if the string contains a recently added
// backquote or contains one of the following characters.
if ((quote == true) || (string.indexOf('{') != -1)
|| (string.indexOf('}') != -1) || (string.indexOf(',') != -1)
|| (string.equals("?")) || (string.indexOf(' ') != -1)
|| (string.equals(""))) {
string = ("'".concat(string)).concat("'");
}
return string;
}
/**
* unquotes are previously quoted string (but only if necessary), i.e., it
* removes the single quotes around it. Inverse to quote(String).
*
* @param string the string to process
* @return the unquoted string
* @see #quote(String)
*/
public static String unquote(String string) {
if (string.startsWith("'") && string.endsWith("'")) {
string = string.substring(1, string.length() - 1);
if ((string.indexOf("\\n") != -1) || (string.indexOf("\\r") != -1)
|| (string.indexOf("\\'") != -1) || (string.indexOf("\\\"") != -1)
|| (string.indexOf("\\\\") != -1) || (string.indexOf("\\t") != -1)
|| (string.indexOf("\\%") != -1) || (string.indexOf("\\u001E") != -1)) {
string = unbackQuoteChars(string);
}
}
return string;
}
/**
* Converts carriage returns and new lines in a string into \r and \n.
* Backquotes the following characters: ` " \ \t and %
*
* @param string the string
* @return the converted string
* @see #unbackQuoteChars(String)
*/
public static/* @pure@ */String backQuoteChars(String string) {
int index;
StringBuffer newStringBuffer;
// replace each of the following characters with the backquoted version
char charsFind[] = { '\\', '\'', '\t', '\n', '\r', '"', '%', '\u001E' };
String charsReplace[] = { "\\\\", "\\'", "\\t", "\\n", "\\r", "\\\"",
"\\%", "\\u001E" };
for (int i = 0; i < charsFind.length; i++) {
if (string.indexOf(charsFind[i]) != -1) {
newStringBuffer = new StringBuffer();
while ((index = string.indexOf(charsFind[i])) != -1) {
if (index > 0) {
newStringBuffer.append(string.substring(0, index));
}
newStringBuffer.append(charsReplace[i]);
if ((index + 1) < string.length()) {
string = string.substring(index + 1);
} else {
string = "";
}
}
newStringBuffer.append(string);
string = newStringBuffer.toString();
}
}
return string;
}
/**
* Converts carriage returns and new lines in a string into \r and \n.
*
* @param string the string
* @return the converted string
*/
public static String convertNewLines(String string) {
int index;
// Replace with \n
StringBuffer newStringBuffer = new StringBuffer();
while ((index = string.indexOf('\n')) != -1) {
if (index > 0) {
newStringBuffer.append(string.substring(0, index));
}
newStringBuffer.append('\\');
newStringBuffer.append('n');
if ((index + 1) < string.length()) {
string = string.substring(index + 1);
} else {
string = "";
}
}
newStringBuffer.append(string);
string = newStringBuffer.toString();
// Replace with \r
newStringBuffer = new StringBuffer();
while ((index = string.indexOf('\r')) != -1) {
if (index > 0) {
newStringBuffer.append(string.substring(0, index));
}
newStringBuffer.append('\\');
newStringBuffer.append('r');
if ((index + 1) < string.length()) {
string = string.substring(index + 1);
} else {
string = "";
}
}
newStringBuffer.append(string);
return newStringBuffer.toString();
}
/**
* Reverts \r and \n in a string into carriage returns and new lines.
*
* @param string the string
* @return the converted string
*/
public static String revertNewLines(String string) {
int index;
// Replace with \n
StringBuffer newStringBuffer = new StringBuffer();
while ((index = string.indexOf("\\n")) != -1) {
if (index > 0) {
newStringBuffer.append(string.substring(0, index));
}
newStringBuffer.append('\n');
if ((index + 2) < string.length()) {
string = string.substring(index + 2);
} else {
string = "";
}
}
newStringBuffer.append(string);
string = newStringBuffer.toString();
// Replace with \r
newStringBuffer = new StringBuffer();
while ((index = string.indexOf("\\r")) != -1) {
if (index > 0) {
newStringBuffer.append(string.substring(0, index));
}
newStringBuffer.append('\r');
if ((index + 2) < string.length()) {
string = string.substring(index + 2);
} else {
string = "";
}
}
newStringBuffer.append(string);
return newStringBuffer.toString();
}
/**
* Returns the secondary set of options (if any) contained in the supplied
* options array. The secondary set is defined to be any options after the
* first "--". These options are removed from the original options array.
*
* @param options the input array of options
* @return the array of secondary options
*/
public static String[] partitionOptions(String[] options) {
for (int i = 0; i < options.length; i++) {
if (options[i].equals("--")) {
options[i++] = "";
String[] result = new String[options.length - i];
for (int j = i; j < options.length; j++) {
result[j - i] = options[j];
options[j] = "";
}
return result;
}
}
return new String[0];
}
/**
* The inverse operation of backQuoteChars(). Converts back-quoted carriage
* returns and new lines in a string to the corresponding character ('\r' and
* '\n'). Also "un"-back-quotes the following characters: ` " \ \t and %
*
* @param string the string
* @return the converted string
* @see #backQuoteChars(String)
*/
public static String unbackQuoteChars(String string) {
int index;
StringBuffer newStringBuffer;
// replace each of the following characters with the backquoted version
String charsFind[] = { "\\\\", "\\'", "\\t", "\\n", "\\r", "\\\"", "\\%",
"\\u001E" };
char charsReplace[] = { '\\', '\'', '\t', '\n', '\r', '"', '%', '\u001E' };
int pos[] = new int[charsFind.length];
int curPos;
String str = new String(string);
newStringBuffer = new StringBuffer();
while (str.length() > 0) {
// get positions and closest character to replace
curPos = str.length();
index = -1;
for (int i = 0; i < pos.length; i++) {
pos[i] = str.indexOf(charsFind[i]);
if ((pos[i] > -1) && (pos[i] < curPos)) {
index = i;
curPos = pos[i];
}
}
// replace character if found, otherwise finished
if (index == -1) {
newStringBuffer.append(str);
str = "";
} else {
newStringBuffer.append(str.substring(0, pos[index]));
newStringBuffer.append(charsReplace[index]);
str = str.substring(pos[index] + charsFind[index].length());
}
}
return newStringBuffer.toString();
}
/**
* Split up a string containing options into an array of strings, one for each
* option.
*
* @param quotedOptionString the string containing the options
* @return the array of options
* @throws Exception in case of an unterminated string, unknown character or a
* parse error
*/
public static String[] splitOptions(String quotedOptionString)
throws Exception {
Vector optionsVec = new Vector();
String str = new String(quotedOptionString);
int i;
while (true) {
// trimLeft
i = 0;
while ((i < str.length()) && (Character.isWhitespace(str.charAt(i)))) {
i++;
}
str = str.substring(i);
// stop when str is empty
if (str.length() == 0) {
break;
}
// if str start with a double quote
if (str.charAt(0) == '"') {
// find the first not anti-slached double quote
i = 1;
while (i < str.length()) {
if (str.charAt(i) == str.charAt(0)) {
break;
}
if (str.charAt(i) == '\\') {
i += 1;
if (i >= str.length()) {
throw new Exception("String should not finish with \\");
}
}
i += 1;
}
if (i >= str.length()) {
throw new Exception("Quote parse error.");
}
// add the founded string to the option vector (without quotes)
String optStr = str.substring(1, i);
optStr = unbackQuoteChars(optStr);
optionsVec.addElement(optStr);
str = str.substring(i + 1);
} else {
// find first whiteSpace
i = 0;
while ((i < str.length()) && (!Character.isWhitespace(str.charAt(i)))) {
i++;
}
// add the founded string to the option vector
String optStr = str.substring(0, i);
optionsVec.addElement(optStr);
str = str.substring(i);
}
}
// convert optionsVec to an array of String
String[] options = new String[optionsVec.size()];
for (i = 0; i < optionsVec.size(); i++) {
options[i] = optionsVec.elementAt(i);
}
return options;
}
/**
* Joins all the options in an option array into a single string, as might be
* used on the command line.
*
* @param optionArray the array of options
* @return the string containing all options.
*/
public static String joinOptions(String[] optionArray) {
String optionString = "";
for (String element : optionArray) {
if (element.equals("")) {
continue;
}
boolean escape = false;
for (int n = 0; n < element.length(); n++) {
if (Character.isWhitespace(element.charAt(n))) {
escape = true;
break;
}
}
if (escape) {
optionString += '"' + backQuoteChars(element) + '"';
} else {
optionString += element;
}
optionString += " ";
}
return optionString.trim();
}
/**
* Creates a new instance of an object given it's class name and (optional)
* arguments to pass to it's setOptions method. If the object implements
* OptionHandler and the options parameter is non-null, the object will have
* it's options set. Example use:
*
*
*
* String classifierName = Utils.getOption('W', options);
* Classifier c = (Classifier)Utils.forName(Classifier.class,
* classifierName,
* options);
* setClassifier(c);
*
*
* @param classType the class that the instantiated object should be
* assignable to -- an exception is thrown if this is not the case
* @param className the fully qualified class name of the object
* @param options an array of options suitable for passing to setOptions. May
* be null. Any options accepted by the object will be removed from
* the array.
* @return the newly created object, ready for use.
* @exception Exception if the class name is invalid, or if the class is not
* assignable to the desired class type, or the options supplied
* are not acceptable to the object
*/
public static Object forName(Class classType, String className,
String[] options) throws Exception {
if (System.getProperty("weka.test.maventest", "").equalsIgnoreCase("true")) {
return forNameNoSchemeMatch(classType, className, options);
}
List matches = Run.findSchemeMatch(classType, className, false,
true);
if (matches.size() == 0) {
throw new Exception("Can't find class called: " + className);
}
if (matches.size() > 1) {
StringBuffer sb = new StringBuffer("More than one possibility matched '"
+ className + "':\n");
for (String s : matches) {
sb.append(" " + s + '\n');
}
throw new Exception(sb.toString());
}
className = matches.get(0);
Class c = null;
try {
c = Class.forName(className);
} catch (Exception ex) {
throw new Exception("Can't find class called: " + className);
}
Object o = c.newInstance();
if ((o instanceof OptionHandler) && (options != null)) {
((OptionHandler) o).setOptions(options);
Utils.checkForRemainingOptions(options);
}
return o;
}
/**
* Creates a new instance of an object given it's class name and (optional)
* arguments to pass to it's setOptions method. If the object implements
* OptionHandler and the options parameter is non-null, the object will have
* it's options set. Example use:
*
*
*
* String classifierName = Utils.getOption('W', options);
* Classifier c = (Classifier)Utils.forName(Classifier.class,
* classifierName,
* options);
* setClassifier(c);
*
*
* @param classType the class that the instantiated object should be
* assignable to -- an exception is thrown if this is not the case
* @param className the fully qualified class name of the object
* @param options an array of options suitable for passing to setOptions. May
* be null. Any options accepted by the object will be removed from
* the array.
* @return the newly created object, ready for use.
* @exception Exception if the class name is invalid, or if the class is not
* assignable to the desired class type, or the options supplied
* are not acceptable to the object
*/
@SuppressWarnings("unchecked")
protected static Object forNameNoSchemeMatch(Class classType,
String className,
String[] options) throws Exception {
Class c = null;
try {
c = Class.forName(className);
} catch (Exception ex) {
throw new Exception("Can't find class called: " + className);
}
if (classType != null && !classType.isAssignableFrom(c)) {
throw new Exception(classType.getName() + " is not assignable from "
+ className);
}
Object o = c.newInstance();
if ((o instanceof OptionHandler) && (options != null)) {
((OptionHandler) o).setOptions(options);
Utils.checkForRemainingOptions(options);
}
return o;
}
/**
* Generates a commandline of the given object. If the object is not
* implementing OptionHandler, then it will only return the classname,
* otherwise also the options.
*
* @param obj the object to turn into a commandline
* @return the commandline
*/
public static String toCommandLine(Object obj) {
StringBuffer result;
result = new StringBuffer();
if (obj != null) {
result.append(obj.getClass().getName());
if (obj instanceof OptionHandler) {
result.append(" " + joinOptions(((OptionHandler) obj).getOptions()));
}
}
return result.toString().trim();
}
/**
* Computes entropy for an array of integers.
*
* @param counts array of counts
* @return - a log2 a - b log2 b - c log2 c + (a+b+c) log2 (a+b+c) when given
* array [a b c]
*/
public static/* @pure@ */double info(int counts[]) {
int total = 0;
double x = 0;
for (int count : counts) {
x -= xlogx(count);
total += count;
}
return x + xlogx(total);
}
/**
* Tests if a is smaller or equal to b.
*
* @param a a double
* @param b a double
*/
public static/* @pure@ */boolean smOrEq(double a, double b) {
return (a - b < SMALL) || (a <= b);
}
/**
* Tests if a is greater or equal to b.
*
* @param a a double
* @param b a double
*/
public static/* @pure@ */boolean grOrEq(double a, double b) {
return (b - a < SMALL) || (a >= b);
}
/**
* Tests if a is smaller than b.
*
* @param a a double
* @param b a double
*/
public static/* @pure@ */boolean sm(double a, double b) {
return (b - a > SMALL);
}
/**
* Tests if a is greater than b.
*
* @param a a double
* @param b a double
*/
public static/* @pure@ */boolean gr(double a, double b) {
return (a - b > SMALL);
}
/**
* Returns the kth-smallest value in the array.
*
* @param array the array of integers
* @param k the value of k
* @return the kth-smallest value
*/
public static int kthSmallestValue(int[] array, int k) {
int[] index = initialIndex(array.length);
return array[index[select(array, index, 0, array.length - 1, k)]];
}
/**
* Returns the kth-smallest value in the array
*
* @param array the array of double
* @param k the value of k
* @return the kth-smallest value
*/
public static double kthSmallestValue(double[] array, int k) {
int[] index = initialIndex(array.length);
return array[index[select(array, index, 0, array.length - 1, k)]];
}
/**
* Returns the logarithm of a for base 2.
*
* @param a a double
* @return the logarithm for base 2
*/
public static/* @pure@ */double log2(double a) {
return Math.log(a) / log2;
}
/**
* Returns index of maximum element in a given array of doubles. First maximum
* is returned.
*
* @param doubles the array of doubles
* @return the index of the maximum element
*/
public static/* @pure@ */int maxIndex(double[] doubles) {
double maximum = 0;
int maxIndex = 0;
for (int i = 0; i < doubles.length; i++) {
if ((i == 0) || (doubles[i] > maximum)) {
maxIndex = i;
maximum = doubles[i];
}
}
return maxIndex;
}
/**
* Returns index of maximum element in a given array of integers. First
* maximum is returned.
*
* @param ints the array of integers
* @return the index of the maximum element
*/
public static/* @pure@ */int maxIndex(int[] ints) {
int maximum = 0;
int maxIndex = 0;
for (int i = 0; i < ints.length; i++) {
if ((i == 0) || (ints[i] > maximum)) {
maxIndex = i;
maximum = ints[i];
}
}
return maxIndex;
}
/**
* Computes the mean for an array of doubles.
*
* @param vector the array
* @return the mean
*/
public static/* @pure@ */double mean(double[] vector) {
double sum = 0;
if (vector.length == 0) {
return 0;
}
for (double element : vector) {
sum += element;
}
return sum / vector.length;
}
/**
* Returns index of minimum element in a given array of integers. First
* minimum is returned.
*
* @param ints the array of integers
* @return the index of the minimum element
*/
public static/* @pure@ */int minIndex(int[] ints) {
int minimum = 0;
int minIndex = 0;
for (int i = 0; i < ints.length; i++) {
if ((i == 0) || (ints[i] < minimum)) {
minIndex = i;
minimum = ints[i];
}
}
return minIndex;
}
/**
* Returns index of minimum element in a given array of doubles. First minimum
* is returned.
*
* @param doubles the array of doubles
* @return the index of the minimum element
*/
public static/* @pure@ */int minIndex(double[] doubles) {
double minimum = 0;
int minIndex = 0;
for (int i = 0; i < doubles.length; i++) {
if ((i == 0) || (doubles[i] < minimum)) {
minIndex = i;
minimum = doubles[i];
}
}
return minIndex;
}
/**
* Normalizes the doubles in the array by their sum.
*
* @param doubles the array of double
* @exception IllegalArgumentException if sum is Zero or NaN
*/
public static void normalize(double[] doubles) {
double sum = 0;
for (double d : doubles) {
sum += d;
}
normalize(doubles, sum);
}
/**
* Normalizes the doubles in the array using the given value.
*
* @param doubles the array of double
* @param sum the value by which the doubles are to be normalized
* @exception IllegalArgumentException if sum is zero or NaN
*/
public static void normalize(double[] doubles, double sum) {
if (Double.isNaN(sum)) {
throw new IllegalArgumentException("Can't normalize array. Sum is NaN.");
}
if (sum == 0) {
// Maybe this should just be a return.
throw new IllegalArgumentException("Can't normalize array. Sum is zero.");
}
for (int i = 0; i < doubles.length; i++) {
doubles[i] /= sum;
}
}
/**
* Converts an array containing the natural logarithms of probabilities stored
* in a vector back into probabilities. The probabilities are assumed to sum
* to one.
*
* @param a an array holding the natural logarithms of the probabilities
* @return the converted array
*/
public static double[] logs2probs(double[] a) {
double max = a[maxIndex(a)];
double sum = 0.0;
double[] result = new double[a.length];
for (int i = 0; i < a.length; i++) {
result[i] = Math.exp(a[i] - max);
sum += result[i];
}
normalize(result, sum);
return result;
}
/**
* Returns the log-odds for a given probabilitiy.
*
* @param prob the probabilitiy
*
* @return the log-odds after the probability has been mapped to [Utils.SMALL,
* 1-Utils.SMALL]
*/
public static/* @pure@ */double probToLogOdds(double prob) {
if (gr(prob, 1) || (sm(prob, 0))) {
throw new IllegalArgumentException("probToLogOdds: probability must "
+ "be in [0,1] " + prob);
}
double p = SMALL + (1.0 - 2 * SMALL) * prob;
return Math.log(p / (1 - p));
}
/**
* Rounds a double to the next nearest integer value. The JDK version of it
* doesn't work properly.
*
* @param value the double value
* @return the resulting integer value
*/
public static/* @pure@ */int round(double value) {
int roundedValue = value > 0 ? (int) (value + 0.5) : -(int) (Math
.abs(value) + 0.5);
return roundedValue;
}
/**
* Rounds a double to the next nearest integer value in a probabilistic
* fashion (e.g. 0.8 has a 20% chance of being rounded down to 0 and a 80%
* chance of being rounded up to 1). In the limit, the average of the rounded
* numbers generated by this procedure should converge to the original double.
*
* @param value the double value
* @param rand the random number generator
* @return the resulting integer value
*/
public static int probRound(double value, Random rand) {
if (value >= 0) {
double lower = Math.floor(value);
double prob = value - lower;
if (rand.nextDouble() < prob) {
return (int) lower + 1;
} else {
return (int) lower;
}
} else {
double lower = Math.floor(Math.abs(value));
double prob = Math.abs(value) - lower;
if (rand.nextDouble() < prob) {
return -((int) lower + 1);
} else {
return -(int) lower;
}
}
}
/**
* Replaces all "missing values" in the given array of double values with
* MAX_VALUE.
*
* @param array the array to be modified.
*/
public static void replaceMissingWithMAX_VALUE(double[] array) {
for (int i = 0; i < array.length; i++) {
if (isMissingValue(array[i])) {
array[i] = Double.MAX_VALUE;
}
}
}
/**
* Rounds a double to the given number of decimal places.
*
* @param value the double value
* @param afterDecimalPoint the number of digits after the decimal point
* @return the double rounded to the given precision
*/
public static/* @pure@ */double roundDouble(double value,
int afterDecimalPoint) {
double mask = Math.pow(10.0, afterDecimalPoint);
return (Math.round(value * mask)) / mask;
}
/**
* Sorts a given array of integers in ascending order and returns an array of
* integers with the positions of the elements of the original array in the
* sorted array. The sort is stable. (Equal elements remain in their original
* order.)
*
* @param array this array is not changed by the method!
* @return an array of integers with the positions in the sorted array.
*/
public static/* @pure@ */int[] sort(int[] array) {
int[] index = initialIndex(array.length);
int[] newIndex = new int[array.length];
int[] helpIndex;
int numEqual;
quickSort(array, index, 0, array.length - 1);
// Make sort stable
int i = 0;
while (i < index.length) {
numEqual = 1;
for (int j = i + 1; ((j < index.length) && (array[index[i]] == array[index[j]])); j++) {
numEqual++;
}
if (numEqual > 1) {
helpIndex = new int[numEqual];
for (int j = 0; j < numEqual; j++) {
helpIndex[j] = i + j;
}
quickSort(index, helpIndex, 0, numEqual - 1);
for (int j = 0; j < numEqual; j++) {
newIndex[i + j] = index[helpIndex[j]];
}
i += numEqual;
} else {
newIndex[i] = index[i];
i++;
}
}
return newIndex;
}
/**
* Sorts a given array of doubles in ascending order and returns an array of
* integers with the positions of the elements of the original array in the
* sorted array. NOTE THESE CHANGES: the sort is no longer stable and it
* doesn't use safe floating-point comparisons anymore. Occurrences of
* Double.NaN are treated as Double.MAX_VALUE.
*
* @param array this array is not changed by the method!
* @return an array of integers with the positions in the sorted array.
*/
public static/* @pure@ */int[] sort(/* @non_null@ */double[] array) {
int[] index = initialIndex(array.length);
if (array.length > 1) {
array = array.clone();
replaceMissingWithMAX_VALUE(array);
quickSort(array, index, 0, array.length - 1);
}
return index;
}
/**
* Sorts a given array of doubles in ascending order and returns an array of
* integers with the positions of the elements of the original array in the
* sorted array. Missing values in the given array are replaced by
* Double.MAX_VALUE, so the array is modified in that case!
*
* @param array the array to be sorted, which is modified if it has missing
* values
* @return an array of integers with the positions in the sorted array.
*/
public static/* @pure@ */int[] sortWithNoMissingValues(
/* @non_null@ */double[] array) {
int[] index = initialIndex(array.length);
if (array.length > 1) {
quickSort(array, index, 0, array.length - 1);
}
return index;
}
/**
* Sorts a given array of doubles in ascending order and returns an array of
* integers with the positions of the elements of the original array in the
* sorted array. The sort is stable (Equal elements remain in their original
* order.) Occurrences of Double.NaN are treated as Double.MAX_VALUE
*
* @param array this array is not changed by the method!
* @return an array of integers with the positions in the sorted array.
*/
public static/* @pure@ */int[] stableSort(double[] array) {
int[] index = initialIndex(array.length);
if (array.length > 1) {
int[] newIndex = new int[array.length];
int[] helpIndex;
int numEqual;
array = array.clone();
replaceMissingWithMAX_VALUE(array);
quickSort(array, index, 0, array.length - 1);
// Make sort stable
int i = 0;
while (i < index.length) {
numEqual = 1;
for (int j = i + 1; ((j < index.length) && Utils.eq(array[index[i]],
array[index[j]])); j++) {
numEqual++;
}
if (numEqual > 1) {
helpIndex = new int[numEqual];
for (int j = 0; j < numEqual; j++) {
helpIndex[j] = i + j;
}
quickSort(index, helpIndex, 0, numEqual - 1);
for (int j = 0; j < numEqual; j++) {
newIndex[i + j] = index[helpIndex[j]];
}
i += numEqual;
} else {
newIndex[i] = index[i];
i++;
}
}
return newIndex;
} else {
return index;
}
}
/**
* Computes the variance for an array of doubles.
*
* @param vector the array
* @return the variance
*/
public static/* @pure@ */double variance(double[] vector) {
if (vector.length <= 1)
return Double.NaN;
double mean = 0;
double var = 0;
for (int i = 0; i < vector.length; i++) {
double delta = vector[i] - mean;
mean += delta/(i + 1);
var += (vector[i] - mean)*delta;
}
var /= vector.length - 1;
// We don't like negative variance
if (var < 0) {
return 0;
} else {
return var;
}
}
/**
* Computes the sum of the elements of an array of doubles.
*
* @param doubles the array of double
* @return the sum of the elements
*/
public static/* @pure@ */double sum(double[] doubles) {
double sum = 0;
for (double d : doubles) {
sum += d;
}
return sum;
}
/**
* Computes the sum of the elements of an array of integers.
*
* @param ints the array of integers
* @return the sum of the elements
*/
public static/* @pure@ */int sum(int[] ints) {
int sum = 0;
for (int j : ints) {
sum += j;
}
return sum;
}
/**
* Returns c*log2(c) for a given integer value c.
*
* @param c an integer value
* @return c*log2(c) (but is careful to return 0 if c is 0)
*/
public static/* @pure@ */double xlogx(int c) {
if (c == 0) {
return 0.0;
}
return c * Utils.log2(c);
}
/**
* Initial index, filled with values from 0 to size - 1.
*/
private static int[] initialIndex(int size) {
int[] index = new int[size];
for (int i = 0; i < size; i++) {
index[i] = i;
}
return index;
}
/**
* Sorts left, right, and center elements only, returns resulting center as
* pivot.
*/
private static int sortLeftRightAndCenter(double[] array, int[] index, int l,
int r) {
int c = (l + r) / 2;
conditionalSwap(array, index, l, c);
conditionalSwap(array, index, l, r);
conditionalSwap(array, index, c, r);
return c;
}
/**
* Swaps two elements in the given integer array.
*/
private static void swap(int[] index, int l, int r) {
int help = index[l];
index[l] = index[r];
index[r] = help;
}
/**
* Conditional swap for quick sort.
*/
private static void conditionalSwap(double[] array, int[] index, int left,
int right) {
if (array[index[left]] > array[index[right]]) {
int help = index[left];
index[left] = index[right];
index[right] = help;
}
}
/**
* Partitions the instances around a pivot. Used by quicksort and
* kthSmallestValue.
*
* @param array the array of doubles to be sorted
* @param index the index into the array of doubles
* @param l the first index of the subset
* @param r the last index of the subset
*
* @return the index of the middle element
*/
private static int partition(double[] array, int[] index, int l, int r,
double pivot) {
r--;
while (true) {
while ((array[index[++l]] < pivot)) {
;
}
while ((array[index[--r]] > pivot)) {
;
}
if (l >= r) {
return l;
}
swap(index, l, r);
}
}
/**
* Partitions the instances around a pivot. Used by quicksort and
* kthSmallestValue.
*
* @param array the array of integers to be sorted
* @param index the index into the array of integers
* @param l the first index of the subset
* @param r the last index of the subset
*
* @return the index of the middle element
*/
private static int partition(int[] array, int[] index, int l, int r) {
double pivot = array[index[(l + r) / 2]];
int help;
while (l < r) {
while ((array[index[l]] < pivot) && (l < r)) {
l++;
}
while ((array[index[r]] > pivot) && (l < r)) {
r--;
}
if (l < r) {
help = index[l];
index[l] = index[r];
index[r] = help;
l++;
r--;
}
}
if ((l == r) && (array[index[r]] > pivot)) {
r--;
}
return r;
}
/**
* Implements quicksort with median-of-three method and explicit sort for
* problems of size three or less.
*
* @param array the array of doubles to be sorted
* @param index the index into the array of doubles
* @param left the first index of the subset to be sorted
* @param right the last index of the subset to be sorted
*/
// @ requires 0 <= first && first <= right && right < array.length;
// @ requires (\forall int i; 0 <= i && i < index.length; 0 <= index[i] &&
// index[i] < array.length);
// @ requires array != index;
// assignable index;
private static void quickSort(/* @non_null@ */double[] array, /* @non_null@ */
int[] index, int left, int right) {
int diff = right - left;
switch (diff) {
case 0:
// No need to do anything
return;
case 1:
// Swap two elements if necessary
conditionalSwap(array, index, left, right);
return;
case 2:
// Just need to sort three elements
conditionalSwap(array, index, left, left + 1);
conditionalSwap(array, index, left, right);
conditionalSwap(array, index, left + 1, right);
return;
default:
// Establish pivot
int pivotLocation = sortLeftRightAndCenter(array, index, left, right);
// Move pivot to the right, partition, and restore pivot
swap(index, pivotLocation, right - 1);
int center =
partition(array, index, left, right, array[index[right - 1]]);
swap(index, center, right - 1);
// Sort recursively
quickSort(array, index, left, center - 1);
quickSort(array, index, center + 1, right);
}
}
/**
* Implements quicksort according to Manber's "Introduction to Algorithms".
*
* @param array the array of integers to be sorted
* @param index the index into the array of integers
* @param left the first index of the subset to be sorted
* @param right the last index of the subset to be sorted
*/
// @ requires 0 <= first && first <= right && right < array.length;
// @ requires (\forall int i; 0 <= i && i < index.length; 0 <= index[i] &&
// index[i] < array.length);
// @ requires array != index;
// assignable index;
private static void quickSort(/* @non_null@ */int[] array, /* @non_null@ */
int[] index, int left, int right) {
if (left < right) {
int middle = partition(array, index, left, right);
quickSort(array, index, left, middle);
quickSort(array, index, middle + 1, right);
}
}
/**
* Implements computation of the kth-smallest element according to Manber's
* "Introduction to Algorithms".
*
* @param array the array of double
* @param index the index into the array of doubles
* @param left the first index of the subset
* @param right the last index of the subset
* @param k the value of k
*
* @return the index of the kth-smallest element
*/
// @ requires 0 <= first && first <= right && right < array.length;
private static int select(/* @non_null@ */double[] array, /* @non_null@ */
int[] index, int left, int right, int k) {
int diff = right - left;
switch (diff) {
case 0:
// Nothing to be done
return left;
case 1:
// Swap two elements if necessary
conditionalSwap(array, index, left, right);
return left + k - 1;
case 2:
// Just need to sort three elements
conditionalSwap(array, index, left, left + 1);
conditionalSwap(array, index, left, right);
conditionalSwap(array, index, left + 1, right);
return left + k - 1;
default:
// Establish pivot
int pivotLocation = sortLeftRightAndCenter(array, index, left, right);
// Move pivot to the right, partition, and restore pivot
swap(index, pivotLocation, right - 1);
int center =
partition(array, index, left, right, array[index[right - 1]]);
swap(index, center, right - 1);
// Proceed recursively
if ((center - left + 1) >= k) {
return select(array, index, left, center, k);
} else {
return select(array, index, center + 1, right, k - (center - left + 1));
}
}
}
/**
* Converts a File's absolute path to a path relative to the user (ie start)
* directory. Includes an additional workaround for Cygwin, which doesn't like
* upper case drive letters.
*
* @param absolute the File to convert to relative path
* @return a File with a path that is relative to the user's directory
* @exception Exception if the path cannot be constructed
*/
public static File convertToRelativePath(File absolute) throws Exception {
File result;
String fileStr;
result = null;
// if we're running windows, it could be Cygwin
if (File.separator.equals("\\")) {
// Cygwin doesn't like upper case drives -> try lower case drive
try {
fileStr = absolute.getPath();
fileStr = fileStr.substring(0, 1).toLowerCase() + fileStr.substring(1);
result = createRelativePath(new File(fileStr));
} catch (Exception e) {
// no luck with Cygwin workaround, convert it like it is
result = createRelativePath(absolute);
}
} else {
result = createRelativePath(absolute);
}
return result;
}
/**
* Converts a File's absolute path to a path relative to the user (ie start)
* directory.
*
* @param absolute the File to convert to relative path
* @return a File with a path that is relative to the user's directory
* @exception Exception if the path cannot be constructed
*/
protected static File createRelativePath(File absolute) throws Exception {
File userDir = new File(System.getProperty("user.dir"));
String userPath = userDir.getAbsolutePath() + File.separator;
String targetPath = (new File(absolute.getParent())).getPath()
+ File.separator;
String fileName = absolute.getName();
StringBuffer relativePath = new StringBuffer();
// relativePath.append("."+File.separator);
// System.err.println("User dir "+userPath);
// System.err.println("Target path "+targetPath);
// file is in user dir (or subdir)
int subdir = targetPath.indexOf(userPath);
if (subdir == 0) {
if (userPath.length() == targetPath.length()) {
relativePath.append(fileName);
} else {
int ll = userPath.length();
relativePath.append(targetPath.substring(ll));
relativePath.append(fileName);
}
} else {
int sepCount = 0;
String temp = new String(userPath);
while (temp.indexOf(File.separator) != -1) {
int ind = temp.indexOf(File.separator);
sepCount++;
temp = temp.substring(ind + 1, temp.length());
}
String targetTemp = new String(targetPath);
String userTemp = new String(userPath);
int tcount = 0;
while (targetTemp.indexOf(File.separator) != -1) {
int ind = targetTemp.indexOf(File.separator);
int ind2 = userTemp.indexOf(File.separator);
String tpart = targetTemp.substring(0, ind + 1);
String upart = userTemp.substring(0, ind2 + 1);
if (tpart.compareTo(upart) != 0) {
if (tcount == 0) {
tcount = -1;
}
break;
}
tcount++;
targetTemp = targetTemp.substring(ind + 1, targetTemp.length());
userTemp = userTemp.substring(ind2 + 1, userTemp.length());
}
if (tcount == -1) {
// then target file is probably on another drive (under windows)
throw new Exception("Can't construct a path to file relative to user "
+ "dir.");
}
if (targetTemp.indexOf(File.separator) == -1) {
targetTemp = "";
}
for (int i = 0; i < sepCount - tcount; i++) {
relativePath.append(".." + File.separator);
}
relativePath.append(targetTemp + fileName);
}
// System.err.println("new path : "+relativePath.toString());
return new File(relativePath.toString());
}
/**
* Implements computation of the kth-smallest element according to Manber's
* "Introduction to Algorithms".
*
* @param array the array of integers
* @param index the index into the array of integers
* @param left the first index of the subset
* @param right the last index of the subset
* @param k the value of k
*
* @return the index of the kth-smallest element
*/
// @ requires 0 <= first && first <= right && right < array.length;
private static int select(/* @non_null@ */int[] array, /* @non_null@ */
int[] index, int left, int right, int k) {
if (left == right) {
return left;
} else {
int middle = partition(array, index, left, right);
if ((middle - left + 1) >= k) {
return select(array, index, left, middle, k);
} else {
return select(array, index, middle + 1, right, k - (middle - left + 1));
}
}
}
/**
* For a named dialog, returns true if the user has opted not to view it again
* in the future.
*
* @param dialogName the name of the dialog to check (e.g.
* weka.gui.GUICHooser.HowToFindPackageManager).
* @return true if the user has opted not to view the named dialog in the
* future.
*/
public static boolean getDontShowDialog(String dialogName) {
File wekaHome = WekaPackageManager.WEKA_HOME;
if (!wekaHome.exists()) {
return false;
}
File dialogSubDir = new File(wekaHome.toString() + File.separator
+ "systemDialogs");
if (!dialogSubDir.exists()) {
return false;
}
File dialogFile = new File(dialogSubDir.toString() + File.separator
+ dialogName);
return dialogFile.exists();
}
/**
* Specify that the named dialog is not to be displayed in the future.
*
* @param dialogName the name of the dialog not to show again (e.g.
* weka.gui.GUIChooser.HowToFindPackageManager).
* @throws Exception if the marker file that is used to indicate that a named
* dialog is not to be shown can't be created. This file lives in
* $WEKA_HOME/systemDialogs
*/
public static void setDontShowDialog(String dialogName) throws Exception {
File wekaHome = WekaPackageManager.WEKA_HOME;
if (!wekaHome.exists()) {
return;
}
File dialogSubDir = new File(wekaHome.toString() + File.separator
+ "systemDialogs");
if (!dialogSubDir.exists()) {
if (!dialogSubDir.mkdir()) {
return;
}
}
File dialogFile = new File(dialogSubDir.toString() + File.separator
+ dialogName);
dialogFile.createNewFile();
}
/**
* For a named dialog, if the user has opted not to view it again, returns the
* answer the answer the user supplied when they closed the dialog. Returns
* null if the user did opt to view the dialog again.
*
* @param dialogName the name of the dialog to check (e.g.
* weka.gui.GUICHooser.HowToFindPackageManager).
* @return the answer the user supplied the last time they viewed the named
* dialog (if they opted not to view it again in the future) or null
* if the user opted to view the dialog again in the future.
*/
public static String getDontShowDialogResponse(String dialogName)
throws Exception {
if (!getDontShowDialog(dialogName)) {
return null; // This must be the first time - no file recorded yet.
}
File wekaHome = WekaPackageManager.WEKA_HOME;
File dialogSubDir = new File(wekaHome.toString() + File.separator
+ "systemDialogs" + File.separator + dialogName);
BufferedReader br = new BufferedReader(new FileReader(dialogSubDir));
String response = br.readLine();
br.close();
return response;
}
/**
* Specify that the named dialog is not to be shown again in the future. Also
* records the answer that the user chose when closing the dialog.
*
* @param dialogName the name of the dialog to no longer display
* @param response the user selected response when they closed the dialog
* @throws Exception if there is a problem saving the information
*/
public static void setDontShowDialogResponse(String dialogName,
String response) throws Exception {
File wekaHome = WekaPackageManager.WEKA_HOME;
if (!wekaHome.exists()) {
return;
}
File dialogSubDir = new File(wekaHome.toString() + File.separator
+ "systemDialogs");
if (!dialogSubDir.exists()) {
if (!dialogSubDir.mkdir()) {
return;
}
}
File dialogFile = new File(dialogSubDir.toString() + File.separator
+ dialogName);
BufferedWriter br = new BufferedWriter(new FileWriter(dialogFile));
br.write(response + "\n");
br.flush();
br.close();
}
/**
* Breaks up the string, if wider than "columns" characters.
*
* @param s the string to process
* @param columns the width in columns
* @return the processed string
*/
public static String[] breakUp(String s, int columns) {
Vector result;
String line;
BreakIterator boundary;
int boundaryStart;
int boundaryEnd;
String word;
String punctuation;
int i;
String[] lines;
result = new Vector();
punctuation = " .,;:!?'\"";
lines = s.split("\n");
for (i = 0; i < lines.length; i++) {
boundary = BreakIterator.getWordInstance();
boundary.setText(lines[i]);
boundaryStart = boundary.first();
boundaryEnd = boundary.next();
line = "";
while (boundaryEnd != BreakIterator.DONE) {
word = lines[i].substring(boundaryStart, boundaryEnd);
if (line.length() >= columns) {
if (word.length() == 1) {
if (punctuation.indexOf(word.charAt(0)) > -1) {
line += word;
word = "";
}
}
result.add(line);
line = "";
}
line += word;
boundaryStart = boundaryEnd;
boundaryEnd = boundary.next();
}
if (line.length() > 0) {
result.add(line);
}
}
return result.toArray(new String[result.size()]);
}
/**
* Utility method for grabbing the global info help (if it exists) from an
* arbitrary object. Can also append capabilities information if the object is
* a CapabilitiesHandler.
*
* @param object the object to grab global info from
* @param addCapabilities true if capabilities information is to be added to
* the result
* @return the global help info or null if global info does not exist
*/
public static String getGlobalInfo(Object object, boolean addCapabilities) {
// set tool tip text from global info if supplied
String gi = null;
StringBuilder result = new StringBuilder();
try {
BeanInfo bi = Introspector.getBeanInfo(object.getClass());
MethodDescriptor[] methods = bi.getMethodDescriptors();
for (MethodDescriptor method : methods) {
String name = method.getDisplayName();
Method meth = method.getMethod();
if (name.equals("globalInfo")) {
if (meth.getReturnType().equals(String.class)) {
Object args[] = {};
String globalInfo = (String) (meth.invoke(object, args));
gi = globalInfo;
break;
}
}
}
} catch (Exception ex) {
}
// Max. number of characters per line (may overflow)
int lineWidth = 180;
result.append("");
if (gi != null && gi.length() > 0) {
StringBuilder firstLine = new StringBuilder();
firstLine.append("");
boolean addFirstBreaks = true;
int indexOfDot = gi.indexOf(".");
if (indexOfDot > 0) {
firstLine.append(gi.substring(0, gi.indexOf(".")));
if (gi.length() - indexOfDot < 3) {
addFirstBreaks = false;
}
gi = gi.substring(indexOfDot + 1, gi.length());
} else {
firstLine.append(gi);
gi = "";
}
firstLine.append("");
if ((addFirstBreaks) && !(gi.startsWith("\n\n"))) {
if (!gi.startsWith("\n")) {
firstLine.append("
");
}
firstLine.append("
");
}
result.append(Utils.lineWrap(firstLine.toString(), lineWidth));
result.append(Utils.lineWrap(gi, lineWidth).replace("\n", "
"));
result.append("
");
}
if (addCapabilities) {
if (object instanceof CapabilitiesHandler) {
if (!result.toString().endsWith("
")) {
result.append("
");
}
String caps = PropertySheetPanel.addCapabilities(
"CAPABILITIES",
((CapabilitiesHandler) object).getCapabilities());
caps = Utils.lineWrap(caps, lineWidth).replace("\n", "
");
result.append(caps);
}
if (object instanceof MultiInstanceCapabilitiesHandler) {
result.append("
");
String caps = PropertySheetPanel.addCapabilities(
"MI CAPABILITIES",
((MultiInstanceCapabilitiesHandler) object)
.getMultiInstanceCapabilities());
caps = Utils.lineWrap(caps, lineWidth).replace("\n", "
");
result.append(caps);
}
}
result.append("");
if (result.toString().equals("")) {
return null;
}
return result.toString();
}
/**
* Implements simple line breaking. Reformats the given string by introducing
* line breaks so that, ideally, no line exceeds the given number of
* characters. Line breaks are assumed to be indicated by newline characters.
* Existing line breaks are left in the input text.
*
* @param input the string to line wrap
* @param maxLineWidth the maximum permitted number of characters in a line
* @return the processed string
*/
public static String lineWrap(String input, int maxLineWidth) {
StringBuffer sb = new StringBuffer();
BreakIterator biterator = BreakIterator.getLineInstance();
biterator.setText(input);
int linestart = 0;
int previous = 0;
while (true) {
int next = biterator.next();
String toAdd = input.substring(linestart, previous);
if (next == BreakIterator.DONE) {
sb.append(toAdd);
break;
}
if (next - linestart > maxLineWidth) {
sb.append(toAdd + '\n');
linestart = previous;
} else {
int newLineIndex = toAdd.lastIndexOf('\n');
if (newLineIndex != -1) {
sb.append(toAdd.substring(0, newLineIndex + 1));
linestart += newLineIndex + 1;
}
}
previous = next;
}
return sb.toString();
}
/**
* Returns the revision string.
*
* @return the revision
*/
@Override
public String getRevision() {
return RevisionUtils.extract("$Revision: 12251 $");
}
/**
* Main method for testing this class.
*
* @param ops some dummy options
*/
public static void main(String[] ops) {
double[] doublesWithNaN = { 4.5, 6.7, Double.NaN, 3.4, 4.8, 1.2, 3.4 };
double[] doubles = { 4.5, 6.7, 6.7, 3.4, 4.8, 1.2, 3.4, 6.7, 6.7, 3.4 };
int[] ints = { 12, 6, 2, 18, 16, 6, 7, 5, 18, 18, 17 };
try {
// Option handling
System.out.println("First option split up:");
if (ops.length > 0) {
String[] firstOptionSplitUp = Utils.splitOptions(ops[0]);
for (String element : firstOptionSplitUp) {
System.out.println(element);
}
}
System.out.println("Partitioned options: ");
String[] partitionedOptions = Utils.partitionOptions(ops);
for (String partitionedOption : partitionedOptions) {
System.out.println(partitionedOption);
}
System.out.println("Get position of flag -f: "
+ Utils.getOptionPos('f', ops));
System.out.println("Get flag -f: " + Utils.getFlag('f', ops));
System.out.println("Get position of option -o: "
+ Utils.getOptionPos('o', ops));
System.out.println("Get option -o: " + Utils.getOption('o', ops));
System.out.println("Checking for remaining options... ");
Utils.checkForRemainingOptions(ops);
// Statistics
System.out.println("Original array with NaN (doubles): ");
for (double element : doublesWithNaN) {
System.out.print(element + " ");
}
System.out.println();
System.out.println("Original array (doubles): ");
for (double d : doubles) {
System.out.print(d + " ");
}
System.out.println();
System.out.println("Original array (ints): ");
for (int j : ints) {
System.out.print(j + " ");
}
System.out.println();
System.out.println("Correlation: "
+ Utils.correlation(doubles, doubles, doubles.length));
System.out.println("Mean: " + Utils.mean(doubles));
System.out.println("Variance: " + Utils.variance(doubles));
System.out.println("Sum (doubles): " + Utils.sum(doubles));
System.out.println("Sum (ints): " + Utils.sum(ints));
System.out.println("Max index (doubles): " + Utils.maxIndex(doubles));
System.out.println("Max index (ints): " + Utils.maxIndex(ints));
System.out.println("Min index (doubles): " + Utils.minIndex(doubles));
System.out.println("Min index (ints): " + Utils.minIndex(ints));
System.out.println("Median (doubles): "
+ Utils.kthSmallestValue(doubles, doubles.length / 2));
System.out.println("Median (ints): "
+ Utils.kthSmallestValue(ints, ints.length / 2));
// Sorting and normalizing
System.out.println("Sorted array with NaN (doubles): ");
int[] sorted = Utils.sort(doublesWithNaN);
for (int i = 0; i < doublesWithNaN.length; i++) {
System.out.print(doublesWithNaN[sorted[i]] + " ");
}
System.out.println();
System.out.println("Sorted array (doubles): ");
sorted = Utils.sort(doubles);
for (int i = 0; i < doubles.length; i++) {
System.out.print(doubles[sorted[i]] + " ");
}
System.out.println();
System.out.println("Sorted array (ints): ");
sorted = Utils.sort(ints);
for (int i = 0; i < ints.length; i++) {
System.out.print(ints[sorted[i]] + " ");
}
System.out.println();
System.out.println("Indices from stable sort (doubles): ");
sorted = Utils.stableSort(doubles);
for (int i = 0; i < doubles.length; i++) {
System.out.print(sorted[i] + " ");
}
System.out.println();
System.out.println("Indices from sort (ints): ");
sorted = Utils.sort(ints);
for (int i = 0; i < ints.length; i++) {
System.out.print(sorted[i] + " ");
}
System.out.println();
System.out.println("Normalized array (doubles): ");
Utils.normalize(doubles);
for (double d : doubles) {
System.out.print(d + " ");
}
System.out.println();
System.out.println("Normalized again (doubles): ");
Utils.normalize(doubles, Utils.sum(doubles));
for (double d : doubles) {
System.out.print(d + " ");
}
System.out.println();
// Pretty-printing
System.out.println("-4.58: " + Utils.doubleToString(-4.57826535, 2));
System.out.println("-6.78: " + Utils.doubleToString(-6.78214234, 6, 2));
// Comparisons
System.out.println("5.70001 == 5.7 ? " + Utils.eq(5.70001, 5.7));
System.out.println("5.70001 > 5.7 ? " + Utils.gr(5.70001, 5.7));
System.out.println("5.70001 >= 5.7 ? " + Utils.grOrEq(5.70001, 5.7));
System.out.println("5.7 < 5.70001 ? " + Utils.sm(5.7, 5.70001));
System.out.println("5.7 <= 5.70001 ? " + Utils.smOrEq(5.7, 5.70001));
// Math
System.out.println("Info (ints): " + Utils.info(ints));
System.out.println("log2(4.6): " + Utils.log2(4.6));
System.out.println("5 * log(5): " + Utils.xlogx(5));
System.out.println("5.5 rounded: " + Utils.round(5.5));
System.out.println("5.55555 rounded to 2 decimal places: "
+ Utils.roundDouble(5.55555, 2));
// Arrays
System.out.println("Array-Dimensions of 'new int[][]': "
+ Utils.getArrayDimensions(new int[][] {}));
System.out.println("Array-Dimensions of 'new int[][]{{1,2,3},{4,5,6}}': "
+ Utils.getArrayDimensions(new int[][] { { 1, 2, 3 }, { 4, 5, 6 } }));
String[][][] s = new String[3][4][];
System.out.println("Array-Dimensions of 'new String[3][4][]': "
+ Utils.getArrayDimensions(s));
} catch (Exception e) {
e.printStackTrace();
}
}
}