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java.lang.Objectmappingmicroarrayprobestotheratgenomeviaapersistentindex.CreateArr1
public class CreateArr1
This code processes the provided chromosome file into a control file and .dat files for loading into the database. It takes as arguments the location of the chromosome, ** the number of the chromosome (1-22) and the location where the control and .dat files have to be saved to.
Field Summary | |
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(package private) static int |
alphabet
|
(package private) static int |
binNum
|
(package private) static int[] |
bins
|
(package private) static long |
binSize
|
(package private) static java.io.DataOutputStream[] |
files
|
(package private) static int |
maxLength
|
(package private) static java.lang.String |
path
|
(package private) static int |
sequenceCount
|
(package private) static long |
totalIndexSize
|
(package private) static byte[] |
values
|
(package private) static int |
windowLen
|
Constructor Summary | |
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CreateArr1()
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Method Summary | |
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static void |
createControlAndDATFiles(java.lang.String chromosomesLocation,
java.lang.String filesDestination,
java.lang.String genome,
javax.swing.JTextArea area)
Creates the control and .dat files |
static void |
getAA(java.io.FileInputStream in,
java.io.PrintWriter cpw,
int chrom,
javax.swing.JTextArea area)
Processes chromosome and writes output to the control file and .dat files to be loaded into a database |
static byte |
getLetterCode(byte let)
Takes the byte version of the letter and returns the number associated with it. |
private static boolean |
isFastaFile(java.io.File f)
Checks to see if file f is a fasta file |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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static byte[] values
static java.io.DataOutputStream[] files
static java.lang.String path
static int sequenceCount
static int maxLength
static int[] bins
static int binNum
static long binSize
static int alphabet
static long totalIndexSize
static int windowLen
Constructor Detail |
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public CreateArr1()
Method Detail |
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public static byte getLetterCode(byte let)
let
- the byte version of the letter
public static void getAA(java.io.FileInputStream in, java.io.PrintWriter cpw, int chrom, javax.swing.JTextArea area) throws java.lang.Exception
in
- the chromosome filecpw
- the PrintWriter for the control filechrom
- the chromosome number
java.lang.Exception
public static void createControlAndDATFiles(java.lang.String chromosomesLocation, java.lang.String filesDestination, java.lang.String genome, javax.swing.JTextArea area) throws java.io.IOException
chromosomesLocation
- the location of the chromosome filesfilesDestination
- the destination of the control and .dat filesgenome
- the genome
java.io.IOException
- if there is a problem with the filesprivate static boolean isFastaFile(java.io.File f)
f
- the file to be checked
true
if file f is a fasta file, false
otherwise
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