Static Public Member Functions
static Map	loadData (File file) throws IOException

static Map< String, String >	loadPIDName (File file) throws IOException

static Map< String, ArrayList >	parseCDT (File file) throws IOException

static Map< String, String >	parseChipFile (File file) throws IOException

static ArrayList< String >	getOrderedListCDT (File file) throws IOException

static void	writeGCT (String save, Map< String, ArrayList > gct) throws IOException

static ArrayList	parseCLS (File file) throws IOException

static String	getControlClass (File file) throws IOException

static Set	parseCLSGroups (File file) throws IOException

static Map	getGroupIndexes (ArrayList< String > groups)

static Map< String, ArrayList >	getGroupIndexes (File clsFile) throws IOException

static Map< Integer, String >	getIndexGroup (ArrayList< String > groups)

static void	writeGMTFile (String save, Map< String, Collection< String >> gmtFile) throws IOException

static MatrixWithHeaders	parseNumericCls (File file, List< String > header) throws NumberFormatException, IOException

static Collection< String >	parseGeneList (File file) throws IOException

static Map< String, ArrayList < Double > >	logTransform (Map< String, ArrayList< Double >> data, double addFactor)

Member Function Documentation

static String broad.core.util.ParseGCTFile.getControlClass ( File file ) throws IOException

static

static Map broad.core.util.ParseGCTFile.getGroupIndexes ( ArrayList< String > groups )

static

static Map<String, ArrayList> broad.core.util.ParseGCTFile.getGroupIndexes ( File clsFile ) throws IOException

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static Map<Integer, String> broad.core.util.ParseGCTFile.getIndexGroup ( ArrayList< String > groups )

static

static ArrayList<String> broad.core.util.ParseGCTFile.getOrderedListCDT ( File file ) throws IOException

static

static Map broad.core.util.ParseGCTFile.loadData ( File file ) throws IOException

static

static Map<String, String> broad.core.util.ParseGCTFile.loadPIDName ( File file ) throws IOException

static

static Map<String, ArrayList<Double> > broad.core.util.ParseGCTFile.logTransform	(	Map< String, ArrayList< Double >>	data,
		double	addFactor
	)

static

static Map<String, ArrayList> broad.core.util.ParseGCTFile.parseCDT ( File file ) throws IOException

static

static Map<String, String> broad.core.util.ParseGCTFile.parseChipFile ( File file ) throws IOException

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static ArrayList broad.core.util.ParseGCTFile.parseCLS ( File file ) throws IOException

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static Set broad.core.util.ParseGCTFile.parseCLSGroups ( File file ) throws IOException

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static Collection<String> broad.core.util.ParseGCTFile.parseGeneList ( File file ) throws IOException

static

static MatrixWithHeaders broad.core.util.ParseGCTFile.parseNumericCls	(	File	file,
		List< String >	header
	)		throws NumberFormatException, IOException

static

static void broad.core.util.ParseGCTFile.writeGCT	(	String	save,
		Map< String, ArrayList >	gct
	)		throws IOException

static

static void broad.core.util.ParseGCTFile.writeGMTFile	(	String	save,
		Map< String, Collection< String >>	gmtFile
	)		throws IOException

static

The documentation for this class was generated from the following file:

Static Public Member Functions