Package util.apps

Scripts for printing arrays, manipulating files, scatter plots...

See:
Description

Class Summary

ArrayPrinter	Prints serialized arrays to screen.
ConvertFasta2GCBoolean	Converts fasta file(s) into serialized boolean[]s where every base g or c is true all others false.
Correlate	Calculates a Pearson correlation coefficient between all pairs of serializae float[].
Delme2
FileJoiner	Joins text files into a single file, avoiding line concatenations.
FileSplitter	Application for splitting a large text file into smaller files given a maximum number of lines.
FileTrimmer	Removes empty lines from text files in a given directory.
Flash
GeneNameCounter	Counts the frequency of words in the master list, then assigns these frequencies to words in the test list.
HouseBean
IntersectLists	Compares two lists of words for intersection.
JQSub	Fires command lines on clusters through qsub.
MakeBioTools	Utility app to pull classes into folders and extract menus to html.
ParseMLSHTML
PrintSelectColumns	Prints out select columns from a tab delimited file, skips lines, appends words, etc.
RenameRWSResults	Takes the output of RocWindowScanner from the cluster and renames the file
ScatterDrawFrame	Helper class for ScatterPlot, the frame.
ScatterDrawPanel	Helper class for ScatterPlot, the guts of drawing the scatter plot.
ScatterPlot	Draws a simple scatter plot and calculates a Pearson correlation coefficient for two serialized int[] or float[] arrays.
ScoreChromosomes	Scores chromosomes for the presence of transcription factor binding sites.
ScoreSequences	Scores sequences for the presence of transcription factor binding sites.
SubtractOneFromLastColumn	Subtracts 1 from the last column assuming it's an integer.
TASSignalChromFileSplitter
TextParser	For parsing a text file into a tab delimited file, working template.
WindowScoreSmoother	Slides a window across an array of numbers averaging the scores.

Package util.apps Description

Scripts for printing arrays, manipulating files, scatter plots...