mappingmicroarrayprobestotheratgenomeviaapersistentindex
Class ProcessProbes

java.lang.Object
  extended by mappingmicroarrayprobestotheratgenomeviaapersistentindex.ProcessProbes

public class ProcessProbes
extends java.lang.Object

Processes probe data into control files for loading into the database. It takes as arguments the location of the probe data and the location where the control files and .dat have to be saved to.


Constructor Summary
ProcessProbes()
           
 
Method Summary
static java.lang.String complement(java.lang.String line)
          Returns the complement of the given DNA sequence
private static boolean isFastaProbeFile(java.io.File f)
          Checks to see if file f is a fasta probe file
static void processProbes(java.lang.String probesLocation, java.lang.String filesDestination, java.lang.String genome)
           
static long processSeq(java.lang.String line)
          Converts the DNA sequence into an integer
static java.lang.String reverse(java.lang.String line)
          Reverses a string
private static java.lang.String strip(java.lang.String f)
          Returns the name of the file f after removing the file extension
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

ProcessProbes

public ProcessProbes()
Method Detail

processProbes

public static void processProbes(java.lang.String probesLocation,
                                 java.lang.String filesDestination,
                                 java.lang.String genome)
                          throws java.io.IOException
Throws:
java.io.IOException

complement

public static java.lang.String complement(java.lang.String line)
Returns the complement of the given DNA sequence

Parameters:
line - the DNA sequence
Returns:
the complement of the DNA sequence

reverse

public static java.lang.String reverse(java.lang.String line)
Reverses a string

Parameters:
line - the string
Returns:
the reversed string

processSeq

public static long processSeq(java.lang.String line)
Converts the DNA sequence into an integer

Parameters:
line - the DNA sequence
Returns:
the integer representing the DNA sequence

isFastaProbeFile

private static boolean isFastaProbeFile(java.io.File f)
Checks to see if file f is a fasta probe file

Parameters:
f - the file to be checked
Returns:
true if file f is a fasta probe file, false otherwise

strip

private static java.lang.String strip(java.lang.String f)
Returns the name of the file f after removing the file extension

Parameters:
f - the file
Returns:
the name of the file after removing the file extension