SIGRS
Class LogWriter

java.lang.Object
  java.io.Writer
      java.io.PrintWriter
          SIGRS.LogWriter

All Implemented Interfaces:

java.io.Closeable, java.io.Flushable, java.lang.Appendable

public class LogWriter
extends java.io.PrintWriter

SIGRS is a collection of routines used in searching for regions of contrasting composition (CCRs) in sequence files using a partial sum process. Significance of segments is evaluated using Karlin-Altschul statistics and specifically an extension by Karlin-Dembo allowing for nucleotides to have a Markov-dependence (see e.g. Karlin & Altschul (1993) and Karlin & Dembo (1992)

The routines are provided as is and no guarantee regarding stability etc. is given so use at your own risk!

See publication Larsson, P., Hinas, A., Ardell, D.H., Kirsebom, L.A., Virtanen, A. and Söderbom, F. De novo search for non-coding RNA genes in the AT-rich genome of Dictyostelium discoideum: performance of Markov-dependent genome feature scoring

Questions and comments can be directed to Pontus.Larsson@icm.uu.se

Constructor Summary

LogWriter()

LogWriter(java.io.File logFile)

LogWriter(java.io.File logFile, boolean autoFlush)

LogWriter(java.io.OutputStream logStream)

LogWriter(java.io.OutputStream logStream, boolean autoFlush)

LogWriter(java.lang.String logFile)

LogWriter(java.lang.String logFile, boolean autoFlush)

LogWriter(java.io.Writer logWriter)

LogWriter(java.io.Writer logWriter, boolean autoFlush)

Method Summary

boolean	checkError()
void	close()
void	flush()
java.lang.String	getParent()
void	newLine()
void	print(boolean b)
void	print(char c)
void	print(char[] s)
void	print(double d)
void	print(float f)
void	print(int i)
void	print(long l)
void	print(java.lang.Object obj)
void	print(java.lang.String s)
void	println()
void	println(boolean b)
void	println(char c)
void	println(char[] s)
void	println(double d)
void	println(float f)
void	println(int i)
void	println(long l)
void	println(java.lang.Object obj)
void	println(java.lang.String s)
void	write(char[] buf)
void	write(char[] buf, int off, int len)
void	write(int i)
void	write(java.lang.String s)
void	write(java.lang.String s, int off, int len)

Methods inherited from class java.io.PrintWriter

append, append, append, format, format, printf, printf

Methods inherited from class java.lang.Object

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

Constructor Detail

LogWriter

public LogWriter()

LogWriter

public LogWriter(java.lang.String logFile)
          throws java.lang.Exception

Throws:

java.lang.Exception

LogWriter

public LogWriter(java.io.File logFile)
          throws java.lang.Exception

Throws:

java.lang.Exception

LogWriter

public LogWriter(java.io.File logFile,
                 boolean autoFlush)
          throws java.lang.Exception

Throws:

java.lang.Exception

LogWriter

public LogWriter(java.lang.String logFile,
                 boolean autoFlush)
          throws java.lang.Exception

Throws:

java.lang.Exception

LogWriter

public LogWriter(java.io.OutputStream logStream)

LogWriter

public LogWriter(java.io.OutputStream logStream,
                 boolean autoFlush)

LogWriter

public LogWriter(java.io.Writer logWriter)

LogWriter

public LogWriter(java.io.Writer logWriter,
                 boolean autoFlush)

Method Detail

checkError

public boolean checkError()

Overrides:

checkError in class java.io.PrintWriter

close

public void close()

Specified by:

close in interface java.io.Closeable

Overrides:

close in class java.io.PrintWriter

flush

public void flush()

Specified by:

flush in interface java.io.Flushable

Overrides:

flush in class java.io.PrintWriter

getParent

public java.lang.String getParent()

newLine

public void newLine()

print

public void print(boolean b)

Overrides:

print in class java.io.PrintWriter

print

public void print(char c)

Overrides:

print in class java.io.PrintWriter

print

public void print(char[] s)

Overrides:

print in class java.io.PrintWriter

print

public void print(double d)

Overrides:

print in class java.io.PrintWriter

print

public void print(float f)

Overrides:

print in class java.io.PrintWriter

print

public void print(int i)

Overrides:

print in class java.io.PrintWriter

print

public void print(long l)

Overrides:

print in class java.io.PrintWriter

print

public void print(java.lang.Object obj)

Overrides:

print in class java.io.PrintWriter

print

public void print(java.lang.String s)

Overrides:

print in class java.io.PrintWriter

println

public void println()

Overrides:

println in class java.io.PrintWriter

println

public void println(boolean b)

Overrides:

println in class java.io.PrintWriter

println

public void println(char c)

Overrides:

println in class java.io.PrintWriter

println

public void println(char[] s)

Overrides:

println in class java.io.PrintWriter

println

public void println(double d)

Overrides:

println in class java.io.PrintWriter

println

public void println(float f)

Overrides:

println in class java.io.PrintWriter

println

public void println(int i)

Overrides:

println in class java.io.PrintWriter

println

public void println(long l)

Overrides:

println in class java.io.PrintWriter

println

public void println(java.lang.Object obj)

Overrides:

println in class java.io.PrintWriter

println

public void println(java.lang.String s)

Overrides:

println in class java.io.PrintWriter

write

public void write(char[] buf)

Overrides:

write in class java.io.PrintWriter

write

public void write(char[] buf,
                  int off,
                  int len)

Overrides:

write in class java.io.PrintWriter

write

public void write(int i)

Overrides:

write in class java.io.PrintWriter

write

public void write(java.lang.String s)

Overrides:

write in class java.io.PrintWriter

write

public void write(java.lang.String s,
                  int off,
                  int len)

Overrides:

write in class java.io.PrintWriter