Class Gpr

java.lang.Object
org.snpeff.util.Gpr

public class Gpr extends Object
General pupose rutines
Author:
root
  • Field Details

  • Constructor Details

    • Gpr

      public Gpr()
  • Method Details

    • baseName

      public static String baseName(String file)
      Return file's name (without the path)
    • baseName

      public static String baseName(String file, String ext)
      Return file's name (without the path)
    • bin64

      public static String bin64(long l)
      Show a long as a 64 bit binary number
    • canRead

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

      public static int compareNull(Comparable c1, Comparable c2)
    • compileDate

      public static String compileDate(Class<?> cl)
    • compileTimeStamp

      public static String compileTimeStamp()
    • compileTimeStamp

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

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

      public static int countColumns(String file)
      Count number of column in a file
    • countLines

      public static int countLines(String file)
      Count lines in a file (same as 'wc -l file' in unix)
      Parameters:
      file -
      Returns:
    • dirName

      public static String dirName(String file)
      Return file's dir
    • exists

      public static boolean exists(String file)
      Does 'file' exist?
    • extName

      public static String extName(String file)
      Get a file's extension (all letters after the last '.'
    • head

      public static String head(Object o)
    • inputStream2StringBuffer

      public static StringBuffer inputStream2StringBuffer(InputStream inputStream) throws IOException
      Throws:
      IOException
    • isStdin

      public static boolean isStdin(String fileName)
      Empty or '-' means STDIN
    • isValidIp

      public static boolean isValidIp(String ip)
    • isValidRid

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

      public static String noSpaces(String str)
      Remove spaces and tabs from string.
    • parseBoolSafe

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

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

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

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

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

      public static String prependEachLine(String prepend, Object lines)
      Prepend a message to each line
    • read

      public static String read(InputStream is)
      Read an input stream
      Parameters:
      is -
      Returns:
    • reader

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

      public static BufferedReader reader(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 String readFile(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 String readFile(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 Object readFileSerialized(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 Object readFileSerializedGz(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 Object readFileSerializedGzThrow(String fileName) throws FileNotFoundException, IOException, 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:
      IOException
      FileNotFoundException
      ClassNotFoundException
    • removeBackslashR

      public static String removeBackslashR(String line)
      Remove trailing '\r'
    • removeExt

      public static String removeExt(String file)
    • removeExt

      public static String removeExt(String file, String[] fileExtensions)
      Remove extension from a file (if matches one of 'fileExtensions[]')
    • repeat

      public static String repeat(char c, int n)
      Create a string of n time 'c'
    • sanityzeFileName

      public static String sanityzeFileName(String fileName)
    • sanityzeName

      public static String sanityzeName(String fileName)
    • showMark

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

      public static void showMark(int i, int showEvery, 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 String[] split(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 String tabs(int tabs)
    • tail

      public static String tail(Object o)
    • toByteSize

      public static String toByteSize(long l)
    • toFile

      public static void toFile(String fileName, Object obj)
      Write an object to a file
    • toFile

      public static void toFile(String fileName, Object obj, boolean append)
      Write an object to a file
    • toFileGz

      public static void toFileGz(String fileName, 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(String fileName, Object obj)
      Write an object to a file by invoking Serialization methods
      Parameters:
      fileName - : File to write
      obj - : Object
    • toFileSerializeGz

      public static void toFileSerializeGz(String fileName, 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 String toString(boolean[] vals)
    • toString

      public static String toString(double[] vals)
    • toString

      public static String toString(double[][] vals)
    • toString

      public static String toString(double val)
    • toString

      public static String toString(int[] vals)
    • toStringHead

      public static String toStringHead(double[] vals)