edu.mssm.crover.tools.tissue
Class tiquery

java.lang.Object
  |
  +--edu.mssm.crover.tools.tissue.tiquery

public class tiquery
extends java.lang.Object


Constructor Summary
tiquery()
           
 
Method Summary
static java.lang.String[] getAcc(java.lang.String[] args)
          Returns an accession number.
static java.lang.String getAccsFile(java.lang.String[] args)
          Returns the name of the file with the list of accession numbers.
static java.lang.String getCacheFile(java.lang.String[] args)
          Returns the name of the file into which the cache is to be serialized.
static java.lang.String getIEIFile(java.lang.String[] args)
          Returns the name of the file with the list of tissues that the gene expression is to be tested against.
static java.lang.String getISTFile(java.lang.String[] args)
          Returns the name of the file with the list of tissues that the gene expression specificity is to be tested against.
static java.lang.String getOutFile(java.lang.String[] args)
          Sets the prefix for the result files.
static double getPurity(java.lang.String[] args)
          Returns the sequencing error rate.
static java.lang.String getTiacFile(java.lang.String[] args)
          Returns the name of the query sequence input file.
static java.lang.String getTiacsFile(java.lang.String[] args)
          Returns the name of the file which lists the tiac files to be queried.
static void main(java.lang.String[] args)
           
static void printHelpFile()
           
static void runTIQuery(java.lang.String[] args)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

tiquery

public tiquery()
Method Detail

getTiacFile

public static java.lang.String getTiacFile(java.lang.String[] args)
Returns the name of the query sequence input file. Read from the command line, after "-tiac" flag. This, or -tiacs, is a necessary parameter.


getTiacsFile

public static java.lang.String getTiacsFile(java.lang.String[] args)
Returns the name of the file which lists the tiac files to be queried. Read from the command line, after "-tiacs" flag. This, or -tiac, is a necessary parameter.


getOutFile

public static java.lang.String getOutFile(java.lang.String[] args)
Sets the prefix for the result files. If no output file name is specified, the default prefix is "tiquery".


getPurity

public static double getPurity(java.lang.String[] args)
Returns the sequencing error rate. If there is no error rate specified on the command line, a default of 95% is used.


getAccsFile

public static java.lang.String getAccsFile(java.lang.String[] args)
Returns the name of the file with the list of accession numbers. Read from the command line, after "-accs" flag.


getAcc

public static java.lang.String[] getAcc(java.lang.String[] args)
Returns an accession number. Read from the command line, after "-acc" flag.


getISTFile

public static java.lang.String getISTFile(java.lang.String[] args)
Returns the name of the file with the list of tissues that the gene expression specificity is to be tested against. Read from the command line, after "-isSpecificToFile" flag.


getIEIFile

public static java.lang.String getIEIFile(java.lang.String[] args)
Returns the name of the file with the list of tissues that the gene expression is to be tested against. Read from the command line, after "-isExpressedInFile" flag.


getCacheFile

public static java.lang.String getCacheFile(java.lang.String[] args)
Returns the name of the file into which the cache is to be serialized. Read from the command line, after "-ser" flag.


printHelpFile

public static void printHelpFile()

main

public static void main(java.lang.String[] args)

runTIQuery

public static void runTIQuery(java.lang.String[] args)


Copyright @ 2003 Mount Sinai School of Medicine. All Rights Reserved.