Package org.snpeff.util

Class Gpr

  • public class Gpr
extends java.lang.Object
    General pupose rutines
    Author:
    root

    • Field Summary

      Fields 
      Modifier and Type Field Description
      static long GB  
      static java.lang.String[] GZIP_EXTENTIONS  
      static java.lang.String HOME  
      static long KB  
      static long MB  
      static int NUM_CORES  
      static long TB  

    • Constructor Summary

      Constructors 
      Constructor Description
      Gpr()  

    • Method Summary

      All Methods Static Methods Concrete Methods 
      Modifier and Type Method Description
      static java.lang.String baseName​(java.lang.String file)
      Return file's name (without the path)
      static java.lang.String baseName​(java.lang.String file, java.lang.String ext)
      Return file's name (without the path)
      static java.lang.String bin64​(long l)
      Show a long as a 64 bit binary number
      static boolean canRead​(java.lang.String fileName)
      Can we read this file (either exact name or append a '.gz'
      static int compareNull​(java.lang.Comparable c1, java.lang.Comparable c2)  
      static java.lang.String compileDate​(java.lang.Class<?> cl)  
      static java.lang.String compileTimeStamp()  
      static java.lang.String compileTimeStamp​(java.lang.Class<?> cl)
      Return a time-stamp showing When was the JAR file created OR when was a class compiled
      static java.lang.String compileTimeStamp​(java.lang.Class<?> cl, java.text.SimpleDateFormat dateFormat)
      Return a time-stamp showing When was the JAR file created OR when was a class compiled
      static int countColumns​(java.lang.String file)
      Count number of column in a file
      static int countLines​(java.lang.String file)
      Count lines in a file (same as 'wc -l file' in unix)
      static java.lang.String dirName​(java.lang.String file)
      Return file's dir
      static boolean exists​(java.lang.String file)
      Does 'file' exist?
      static java.lang.String extName​(java.lang.String file)
      Get a file's extension (all letters after the last '.'
      static java.lang.String head​(java.lang.Object o)  
      static java.lang.StringBuffer inputStream2StringBuffer​(java.io.InputStream inputStream)  
      static boolean isStdin​(java.lang.String fileName)
      Empty or '-' means STDIN
      static boolean isValidIp​(java.lang.String ip)  
      static boolean isValidRid​(int i)
      Is this a valid Rid
      static java.lang.String noSpaces​(java.lang.String str)
      Remove spaces and tabs from string.
      static boolean parseBoolSafe​(java.lang.String s)
      Equivalent to Boolean.parseBoolean, except it returns 0 on invalid integer (NumberFormatException)
      static double parseDoubleSafe​(java.lang.String s)
      Equivalent to Double.parseDouble(), except it returns 0 on invalid double (NumberFormatException)
      static float parseFloatSafe​(java.lang.String s)
      Equivalent to Float.parseFloat(), except it returns 0 on invalid double (NumberFormatException)
      static int parseIntSafe​(java.lang.String s)
      Equivalent to Integer.parseInt, except it returns 0 on invalid integer (NumberFormatException)
      static long parseLongSafe​(java.lang.String s)
      Equivalent to Integer.parseInt, except it returns 0 on invalid integer (NumberFormatException)
      static java.lang.String prependEachLine​(java.lang.String prepend, java.lang.Object lines)
      Prepend a message to each line
      static java.lang.String read​(java.io.InputStream is)
      Read an input stream
      static java.io.BufferedReader reader​(java.lang.String fileName)
      Try to open a file (BufferedReader) using either the file or a gzip file (appending '.gz' to fileName)
      static java.io.BufferedReader reader​(java.lang.String fileName, boolean gzip)
      Try to open a file (BufferedReader) using either the file or a gzip file (appending '.gz' to fileName)
      static java.lang.String readFile​(java.lang.String fileName)
      Read a file as a String.
      static java.lang.String readFile​(java.lang.String fileName, boolean gzipped)
      Read a file as a String.
      static java.lang.Object readFileSerialized​(java.lang.String fileName)
      Read an object from a file (supposing an object was previously serialized to that file)
      static java.lang.Object readFileSerializedGz​(java.lang.String fileName)
      Read an object from a file (supposing an object was previously serialized to that file) Note: The file is compressed using GZIP
      static java.lang.Object readFileSerializedGzThrow​(java.lang.String fileName)
      Read an object from a file (supposing an object was previously serialized to that file) Note: Same as 'readFileSerializedGz' but it throws all the exceptions
      static java.lang.String removeBackslashR​(java.lang.String line)
      Remove trailing '\r'
      static java.lang.String removeExt​(java.lang.String file)  
      static java.lang.String removeExt​(java.lang.String file, java.lang.String[] fileExtensions)
      Remove extension from a file (if matches one of 'fileExtensions[]')
      static java.lang.String repeat​(char c, int n)
      Create a string of n time 'c'
      static java.lang.String sanityzeFileName​(java.lang.String fileName)  
      static java.lang.String sanityzeName​(java.lang.String fileName)  
      static void showMark​(int i, int showEvery)
      Show a mark
      static void showMark​(int i, int showEvery, java.lang.String newLineStr)
      Show a mark
      static void showMarkStderr​(int i, int showEvery)
      Show a mark (on STDERR)
      static void showStackTrace​(int steps)  
      static void showStackTrace​(int steps, int offset)
      Prints a stack trace for a number of steps
      static java.lang.String[] split​(java.lang.String value, char delim)
      Splits a separated string into an array of String tokens.
      static java.lang.String tabs​(int tabs)  
      static java.lang.String tail​(java.lang.Object o)  
      static java.lang.String toByteSize​(long l)  
      static void toFile​(java.lang.String fileName, java.lang.Object obj)
      Write an object to a file
      static void toFile​(java.lang.String fileName, java.lang.Object obj, boolean append)
      Write an object to a file
      static void toFileGz​(java.lang.String fileName, java.lang.Object obj)
      Write an object to a file (as a string) Note: The file is compressed using GZIP
      static void toFileSerialize​(java.lang.String fileName, java.lang.Object obj)
      Write an object to a file by invoking Serialization methods
      static void toFileSerializeGz​(java.lang.String fileName, java.lang.Object obj)
      Write an object to a file by invoking Serialization methods Note: The file is compressed using GZIP
      static java.lang.String toString​(boolean[] vals)  
      static java.lang.String toString​(double val)  
      static java.lang.String toString​(double[] vals)  
      static java.lang.String toString​(double[][] vals)  
      static java.lang.String toString​(int[] vals)  
      static java.lang.String toStringHead​(double[] vals)  

      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

    • Constructor Detail

      • Gpr

        public Gpr()

    • Method Detail

      • baseName

        public static java.lang.String baseName​(java.lang.String file)
        Return file's name (without the path)

      • baseName

        public static java.lang.String baseName​(java.lang.String file,
                                        java.lang.String ext)
        Return file's name (without the path)

      • bin64

        public static java.lang.String bin64​(long l)
        Show a long as a 64 bit binary number

      • canRead

        public static boolean canRead​(java.lang.String fileName)
        Can we read this file (either exact name or append a '.gz'

      • compareNull

        public static int compareNull​(java.lang.Comparable c1,
                              java.lang.Comparable c2)

      • compileDate

        public static java.lang.String compileDate​(java.lang.Class<?> cl)

      • compileTimeStamp

        public static java.lang.String compileTimeStamp()

      • compileTimeStamp

        public static java.lang.String compileTimeStamp​(java.lang.Class<?> cl)
        Return a time-stamp showing When was the JAR file created OR when was a class compiled

      • compileTimeStamp

        public static java.lang.String compileTimeStamp​(java.lang.Class<?> cl,
                                                java.text.SimpleDateFormat dateFormat)
        Return a time-stamp showing When was the JAR file created OR when was a class compiled

      • countColumns

        public static int countColumns​(java.lang.String file)
        Count number of column in a file

      • countLines

        public static int countLines​(java.lang.String file)
        Count lines in a file (same as 'wc -l file' in unix)
        Parameters:
        file -
        Returns:

      • dirName

        public static java.lang.String dirName​(java.lang.String file)
        Return file's dir

      • exists

        public static boolean exists​(java.lang.String file)
        Does 'file' exist?

      • extName

        public static java.lang.String extName​(java.lang.String file)
        Get a file's extension (all letters after the last '.'

      • head

        public static java.lang.String head​(java.lang.Object o)

      • inputStream2StringBuffer

        public static java.lang.StringBuffer inputStream2StringBuffer​(java.io.InputStream inputStream)
                                                       throws java.io.IOException
        Throws:
        java.io.IOException

      • isStdin

        public static boolean isStdin​(java.lang.String fileName)
        Empty or '-' means STDIN

      • isValidIp

        public static boolean isValidIp​(java.lang.String ip)

      • isValidRid

        public static boolean isValidRid​(int i)
        Is this a valid Rid

      • noSpaces

        public static java.lang.String noSpaces​(java.lang.String str)
        Remove spaces and tabs from string.

      • parseBoolSafe

        public static boolean parseBoolSafe​(java.lang.String s)
        Equivalent to Boolean.parseBoolean, except it returns 0 on invalid integer (NumberFormatException)

      • parseDoubleSafe

        public static double parseDoubleSafe​(java.lang.String s)
        Equivalent to Double.parseDouble(), except it returns 0 on invalid double (NumberFormatException)

      • parseFloatSafe

        public static float parseFloatSafe​(java.lang.String s)
        Equivalent to Float.parseFloat(), except it returns 0 on invalid double (NumberFormatException)
        Parameters:
        s -
        Returns:
        int

      • parseIntSafe

        public static int parseIntSafe​(java.lang.String s)
        Equivalent to Integer.parseInt, except it returns 0 on invalid integer (NumberFormatException)
        Parameters:
        s -
        Returns:
        int

      • parseLongSafe

        public static long parseLongSafe​(java.lang.String s)
        Equivalent to Integer.parseInt, except it returns 0 on invalid integer (NumberFormatException)
        Parameters:
        s -
        Returns:
        int

      • prependEachLine

        public static java.lang.String prependEachLine​(java.lang.String prepend,
                                               java.lang.Object lines)
        Prepend a message to each line

      • read

        public static java.lang.String read​(java.io.InputStream is)
        Read an input stream
        Parameters:
        is -
        Returns:

      • reader

        public static java.io.BufferedReader reader​(java.lang.String fileName)
        Try to open a file (BufferedReader) using either the file or a gzip file (appending '.gz' to fileName)

      • reader

        public static java.io.BufferedReader reader​(java.lang.String fileName,
                                            boolean gzip)
        Try to open a file (BufferedReader) using either the file or a gzip file (appending '.gz' to fileName)
        Parameters:
        gzip - : If true, file is assumed to be gzipped

      • readFile

        public static java.lang.String readFile​(java.lang.String fileName)
        Read a file as a String. Note: the file can be compressed using gzip (file name must have a ".gz" extension).
        Parameters:
        fileName - : File to read (null on error)
        showExceptions - : show exceptions if true

      • readFile

        public static java.lang.String readFile​(java.lang.String fileName,
                                        boolean gzipped)
        Read a file as a String. Note: the file can be compressed using gzip (file name must have a ".gz" extension).
        Parameters:
        fileName - : File to read (null on error)
        showExceptions - : show exceptions if true

      • readFileSerialized

        public static java.lang.Object readFileSerialized​(java.lang.String fileName)
        Read an object from a file (supposing an object was previously serialized to that file)
        Parameters:
        fileName -
        Returns:
        An object from that file

      • readFileSerializedGz

        public static java.lang.Object readFileSerializedGz​(java.lang.String fileName)
        Read an object from a file (supposing an object was previously serialized to that file) Note: The file is compressed using GZIP
        Parameters:
        fileName -
        Returns:
        An object from that file

      • readFileSerializedGzThrow

        public static java.lang.Object readFileSerializedGzThrow​(java.lang.String fileName)
                                                  throws java.io.FileNotFoundException,
                                                         java.io.IOException,
                                                         java.lang.ClassNotFoundException
        Read an object from a file (supposing an object was previously serialized to that file) Note: Same as 'readFileSerializedGz' but it throws all the exceptions
        Parameters:
        fileName -
        Returns:
        An object from that file
        Throws:
        java.io.IOException
        java.io.FileNotFoundException
        java.lang.ClassNotFoundException

      • removeBackslashR

        public static java.lang.String removeBackslashR​(java.lang.String line)
        Remove trailing '\r'

      • removeExt

        public static java.lang.String removeExt​(java.lang.String file)

      • removeExt

        public static java.lang.String removeExt​(java.lang.String file,
                                         java.lang.String[] fileExtensions)
        Remove extension from a file (if matches one of 'fileExtensions[]')

      • repeat

        public static java.lang.String repeat​(char c,
                                      int n)
        Create a string of n time 'c'

      • sanityzeFileName

        public static java.lang.String sanityzeFileName​(java.lang.String fileName)

      • sanityzeName

        public static java.lang.String sanityzeName​(java.lang.String fileName)

      • showMark

        public static void showMark​(int i,
                            int showEvery)
        Show a mark

      • showMark

        public static void showMark​(int i,
                            int showEvery,
                            java.lang.String newLineStr)
        Show a mark

      • showMarkStderr

        public static void showMarkStderr​(int i,
                                  int showEvery)
        Show a mark (on STDERR)

      • showStackTrace

        public static void showStackTrace​(int steps)

      • showStackTrace

        public static void showStackTrace​(int steps,
                                  int offset)
        Prints a stack trace for a number of steps
        Parameters:
        count -

      • split

        public static java.lang.String[] split​(java.lang.String value,
                                       char delim)
        Splits a separated string into an array of String tokens. If the input string is null, this method returns null.

        Implementation note: for performance reasons, this implementation uses neither StringTokenizer nor String.split(). StringTokenizer does not return all tokens for strings of the form "1,2,,3," unless you use an instance that returns the separator. By doing so, our code would need to modify the token string which would create another temporary object and would make this method very slow.
        String.split does not return all tokens for strings of the form "1,2,3,,,". We simply cannot use this method.

        The result is a custom String splitter algorithm which performs well for large Strings.

        Parameters:
        value - the string value to split into tokens
        Returns:
        an array of String Objects or null if the string value is null

      • tabs

        public static java.lang.String tabs​(int tabs)

      • tail

        public static java.lang.String tail​(java.lang.Object o)

      • toByteSize

        public static java.lang.String toByteSize​(long l)

      • toFile

        public static void toFile​(java.lang.String fileName,
                          java.lang.Object obj)
        Write an object to a file

      • toFile

        public static void toFile​(java.lang.String fileName,
                          java.lang.Object obj,
                          boolean append)
        Write an object to a file

      • toFileGz

        public static void toFileGz​(java.lang.String fileName,
                            java.lang.Object obj)
        Write an object to a file (as a string) Note: The file is compressed using GZIP
        Parameters:
        fileName - : File to write
        obj - : Object

      • toFileSerialize

        public static void toFileSerialize​(java.lang.String fileName,
                                   java.lang.Object obj)
        Write an object to a file by invoking Serialization methods
        Parameters:
        fileName - : File to write
        obj - : Object

      • toFileSerializeGz

        public static void toFileSerializeGz​(java.lang.String fileName,
                                     java.lang.Object obj)
        Write an object to a file by invoking Serialization methods Note: The file is compressed using GZIP
        Parameters:
        fileName - : File to write
        obj - : Object

      • toString

        public static java.lang.String toString​(boolean[] vals)

      • toString

        public static java.lang.String toString​(double[] vals)

      • toString

        public static java.lang.String toString​(double[][] vals)

      • toString

        public static java.lang.String toString​(double val)

      • toString

        public static java.lang.String toString​(int[] vals)

      • toStringHead

        public static java.lang.String toStringHead​(double[] vals)