Package util.apps

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

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          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...