edu.mssm.crover.tools.tissue
Class getCuratedTissue

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

public class getCuratedTissue

extends java.lang.Object

Reads a file of raw tissues and checks whether a CuratedTissue exists for that raw tissue. If the "-cancer" option is given on the command line, prints out the raw tissue for all tissues annotated as coming from tumor, otherwise it prints out the list of tissues in each raw tissue. If the "-all" option is given on the command line, two levels of parents interfaces of the curated tissues are also given.

Field Summary

static java.lang.String	hierarchy_package
static boolean	stdout
static java.io.Writer	writer

Constructor Summary

getCuratedTissue()

Method Summary

static boolean	findCancer(java.lang.String[] args) Returns whether to print out all the tissues which come from tumor tissue.
static void	findCuratedTissues(java.lang.String tissueFile, boolean cancer, boolean getParents, java.lang.String outfile)
static boolean	findParents(java.lang.String[] args) Returns whether to print out two levels of parent interfaces of the curated tissues.
static java.lang.String	getOutFile(java.lang.String[] args) Returns the name of the output file.
static java.lang.String	getTissueFile(java.lang.String[] args) Returns the name of the input file.
static void	main(java.lang.String[] args)
static void	printout(java.lang.String output)

Methods inherited from class java.lang.Object

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

Field Detail

hierarchy_package

public static final java.lang.String hierarchy_package

See Also:

Constant Field Values

writer

public static java.io.Writer writer

stdout

public static boolean stdout

Constructor Detail

getCuratedTissue

public getCuratedTissue()

Method Detail

getTissueFile

public static java.lang.String getTissueFile(java.lang.String[] args)

Returns the name of the input file. Read from the command line, after "-i" flag. There should be one raw tissue per line. This is a necessary parameter.

getOutFile

public static java.lang.String getOutFile(java.lang.String[] args)

Returns the name of the output file. Read from the command line, after "-o" flag.

findCancer

public static boolean findCancer(java.lang.String[] args)

Returns whether to print out all the tissues which come from tumor tissue. If the "-cancer" flag is present on the command line, then TRUE.

findParents

public static boolean findParents(java.lang.String[] args)

Returns whether to print out two levels of parent interfaces of the curated tissues. If the "-all" flag is present on the command line, then TRUE.

findCuratedTissues

public static void findCuratedTissues(java.lang.String tissueFile,
                                      boolean cancer,
                                      boolean getParents,
                                      java.lang.String outfile)

printout

public static void printout(java.lang.String output)

main

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