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java.lang.Objectmappingmicroarrayprobestotheratgenomeviaapersistentindex.ProcessProbes
public class ProcessProbes
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 | |
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ProcessProbes()
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Method Summary | |
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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)
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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 |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public ProcessProbes()
Method Detail |
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public static void processProbes(java.lang.String probesLocation, java.lang.String filesDestination, java.lang.String genome) throws java.io.IOException
java.io.IOException
public static java.lang.String complement(java.lang.String line)
line
- the DNA sequence
public static java.lang.String reverse(java.lang.String line)
line
- the string
public static long processSeq(java.lang.String line)
line
- the DNA sequence
private static boolean isFastaProbeFile(java.io.File f)
f
- the file to be checked
true
if file f is a fasta probe file, false
otherwiseprivate static java.lang.String strip(java.lang.String f)
f
- the file
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