tools.progressbar
Class Utils

java.lang.Object
  extended by tools.progressbar.Utils

public class Utils
extends java.lang.Object

Various utils, which I need quite often.

Author:
wrzodek

Constructor Summary
Utils()
           
 
Method Summary
static boolean ArrayContains(java.lang.String[][] arr, java.lang.String s)
           
static double average(double[] d)
          Mittelwertberechnung.
static double[] average(double[][] d)
          Spaltenweise mittelwertberechnung.
static double average1(double[] d)
           
static double[] average1(double[][] d)
           
static double average2(double[] d)
           
static double[] average2(double[][] d)
           
static java.lang.String complement(java.lang.String s)
           
static double computeCorrelation(double[] y, double[] x, double mean_y, double mean_x)
          Empirical Correlation Coefficient computes the correlation coefficient between y (lables) and x (predictions)
static boolean containsWord(java.lang.String containingLine, java.lang.String containedString)
          Same as isWord !!!
static boolean copyFile(java.io.File in, java.io.File out)
          Copies a file.
static int[] countNucleotides(java.lang.String sequence, int xMeres)
           
static java.lang.String cut(double d)
          Cut at dot.
static double[][] divide(double[][] arr1, double[][] arr2)
           
static double[][] divide(int[][] arr1, int[][] arr2)
           
static int DNA2Num(char a)
           
static int DNA2Num(java.lang.String a)
          Example: AA: 0 AC: 1 AG: 2 AT: 3 CA: 4 TA: 12 TT: 15
static java.lang.String ensureSlash(java.lang.String path)
          Ensures that path ends with a slash (for folder processing).
static java.lang.String firstUppercase(java.lang.String s)
           
static int getNumberFromString(int startAtPos, java.lang.String toParse)
           
static int getNumberFromString(java.lang.String behindLastIndexOfString, java.lang.String toParse)
          Funzt nur f�r positive, nat�rliche Zahlen!
static java.lang.String getTimeString(long miliseconds)
          Given the miliseconds elapsed, returns a formatted time string up to a max deph of 3. e.g. "16h 4m 4s" or "2d 16h 4m" or "4s 126dms"
static boolean isNumber(java.lang.String s, boolean onlyDigits)
          Nicht ganz korrekt da auch 4.345,2.1 als nummer erkannt wird, aber das reicht mir so.
static boolean isWord(java.lang.String containingLine, java.lang.String containedString)
          Kann auch als Synonym f�r "containsWord" gebraucht werden.
static boolean isWord(java.lang.String containingLine, java.lang.String containedString, boolean ignoreDigits)
           
static java.lang.Object loadObject(java.io.File file)
           
static java.lang.Object loadObject(java.io.InputStream inn)
           
static java.lang.Object loadObject(java.lang.String filename)
           
static char Num2DNA(int a)
           
static java.lang.String Num2DNA(int n, int xMeres)
           
static java.lang.String parseCommandLine(java.lang.String[] args, java.lang.String searchForCommand, boolean hasArgument)
          Usefull for parsing command line arguments.
static void printMinMaxInfNaN(double[] arr)
           
static java.lang.StringBuffer replicateCharacter(char c, int times)
           
static java.lang.String replicateCharacter(java.lang.String ch, int times)
           
static java.lang.String reverse(java.lang.String s)
           
static double round(double zahl, int stellen)
           
static boolean saveObject(java.lang.String filename, java.lang.Object obj)
           
static boolean shutdownSystem()
           
static double variance(double[] d)
          Calculates and returns the variance of the given list of double values
static double variance(double[] d, double mean)
          Calculates and returns the variance of the given list of double values.
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

Utils

public Utils()
Method Detail

ArrayContains

public static boolean ArrayContains(java.lang.String[][] arr,
                                    java.lang.String s)
Parameters:
arr -
s -
Returns:

average

public static double average(double[] d)
Mittelwertberechnung. Versuchts erst schneller und nimmt sonst den langsameren, aber sicheren Algorithmus.


average

public static double[] average(double[][] d)
Spaltenweise mittelwertberechnung. Versuchts erst schneller und nimmt sonst den langsameren, aber sicheren Algorithmus.


average1

public static double average1(double[] d)
Parameters:
d -
Returns:

average1

public static double[] average1(double[][] d)
Parameters:
d -
Returns:

average2

public static double average2(double[] d)
Parameters:
d -
Returns:

average2

public static double[] average2(double[][] d)
Parameters:
d -
Returns:

complement

public static java.lang.String complement(java.lang.String s)
Parameters:
s -
Returns:

computeCorrelation

public static double computeCorrelation(double[] y,
                                        double[] x,
                                        double mean_y,
                                        double mean_x)
Empirical Correlation Coefficient computes the correlation coefficient between y (lables) and x (predictions)

Parameters:
y -
x -
mean_y -
mean_x -
Returns:

containsWord

public static boolean containsWord(java.lang.String containingLine,
                                   java.lang.String containedString)
Same as isWord !!!


copyFile

public static boolean copyFile(java.io.File in,
                               java.io.File out)
Copies a file. Does NOT check if out already exists. Will overwrite out if it already exists.

Parameters:
in -
out -
Returns:
success.

countNucleotides

public static int[] countNucleotides(java.lang.String sequence,
                                     int xMeres)
Parameters:
sequence -
xMeres -
Returns:

cut

public static java.lang.String cut(double d)
Cut at dot. E.g. 1.68 => 1 In contrary, decimal format "#" would return 2!

Parameters:
d -
Returns:

divide

public static double[][] divide(double[][] arr1,
                                double[][] arr2)
Parameters:
arr1 -
arr2 -
Returns:

divide

public static double[][] divide(int[][] arr1,
                                int[][] arr2)
Parameters:
arr1 -
arr2 -
Returns:

DNA2Num

public static int DNA2Num(char a)
Parameters:
a -
Returns:

DNA2Num

public static int DNA2Num(java.lang.String a)
Example: AA: 0 AC: 1 AG: 2 AT: 3 CA: 4 TA: 12 TT: 15


ensureSlash

public static java.lang.String ensureSlash(java.lang.String path)
Ensures that path ends with a slash (for folder processing).

Parameters:
path -

firstUppercase

public static java.lang.String firstUppercase(java.lang.String s)
Parameters:
s -
Returns:

getNumberFromString

public static int getNumberFromString(int startAtPos,
                                      java.lang.String toParse)
Parameters:
startAtPos -
toParse -
Returns:

getNumberFromString

public static int getNumberFromString(java.lang.String behindLastIndexOfString,
                                      java.lang.String toParse)
Funzt nur f�r positive, nat�rliche Zahlen!


getTimeString

public static java.lang.String getTimeString(long miliseconds)
Given the miliseconds elapsed, returns a formatted time string up to a max deph of 3. e.g. "16h 4m 4s" or "2d 16h 4m" or "4s 126dms"

Parameters:
miliseconds -
Returns:

isNumber

public static boolean isNumber(java.lang.String s,
                               boolean onlyDigits)
Nicht ganz korrekt da auch 4.345,2.1 als nummer erkannt wird, aber das reicht mir so.


isWord

public static boolean isWord(java.lang.String containingLine,
                             java.lang.String containedString)
Kann auch als Synonym f�r "containsWord" gebraucht werden.

Parameters:
containingLine -
containedString -
Returns:

isWord

public static boolean isWord(java.lang.String containingLine,
                             java.lang.String containedString,
                             boolean ignoreDigits)
Parameters:
containingLine -
containedString -
ignoreDigits -
Returns:

loadObject

public static java.lang.Object loadObject(java.io.File file)
Parameters:
file -
Returns:

loadObject

public static java.lang.Object loadObject(java.io.InputStream inn)
Parameters:
inn -
Returns:

loadObject

public static java.lang.Object loadObject(java.lang.String filename)
Parameters:
filename -
Returns:

Num2DNA

public static char Num2DNA(int a)
Parameters:
a -
Returns:

Num2DNA

public static java.lang.String Num2DNA(int n,
                                       int xMeres)
Parameters:
n -
xMeres -
Returns:

variance

public static double variance(double[] d)
Calculates and returns the variance of the given list of double values

Parameters:
d - the list of double values
Returns:

variance

public static double variance(double[] d,
                              double mean)
Calculates and returns the variance of the given list of double values. This version of the method also takes the precalculated mean of the values as parameter to prevent redundant calculations.

Parameters:
d - the list of double values
mean - the mean of the double values
Returns:

parseCommandLine

public static java.lang.String parseCommandLine(java.lang.String[] args,
                                                java.lang.String searchForCommand,
                                                boolean hasArgument)
                                         throws java.lang.Exception
Usefull for parsing command line arguments.

Parameters:
args - - Command line arguments.
searchForCommand - - Command to search for
hasArgument - - Has the command an argument? If yes, the Argument will be returned.
Returns:
The Argument, if hasArgument is set. Otherwise: "true" if command is available. "false" if not.
Throws:
java.lang.Exception - "Missing argument.". If that's the case.

printMinMaxInfNaN

public static void printMinMaxInfNaN(double[] arr)
Parameters:
arr -

replicateCharacter

public static java.lang.StringBuffer replicateCharacter(char c,
                                                        int times)
Parameters:
c -
times -
Returns:

replicateCharacter

public static java.lang.String replicateCharacter(java.lang.String ch,
                                                  int times)
Parameters:
ch -
times -
Returns:

reverse

public static java.lang.String reverse(java.lang.String s)
Parameters:
s -
Returns:

round

public static double round(double zahl,
                           int stellen)
Parameters:
zahl -
stellen -
Returns:

saveObject

public static boolean saveObject(java.lang.String filename,
                                 java.lang.Object obj)
Parameters:
filename -
obj -
Returns:

shutdownSystem

public static boolean shutdownSystem()
Returns: