trans.tpmap
Class TPMapDuplicateFilter

java.lang.Object
  trans.tpmap.TPMapDuplicateFilter

public class TPMapDuplicateFilter

extends java.lang.Object

For extracting duplicate oligo/ features from Affy's bpmap file, can be used as a stand alone but better to use TPMapProcessor. The TPMapDuplicateFilter first creates a hashMap of unique oligo sequences paired with an ArrayList of chip coordinates where a particular oligo was spotted. In most cases, each oligo was spotted only once. In some cases the same oligo was placed on the array many times. This repeat information will be used by the CelMapper program to average the intensities of all the repeats, for a particular oligo, and assign this value to each spot. This repeat information is saved as an unordered array of TPMapFeature[] to disk. The TPMapDuplicate Filter then reads line by line thru the bpmap txt file and removes any adjacent repeated sequences. (After averaging they all will have the same value.) It then removes any oligo that maps more than once to the genome. This "dupFree" bpmap text file is written to disk. Recommend rewriting this to use first hashMap to eliminate dups and skip the second step.

Constructor Summary

TPMapDuplicateFilter(java.io.File bpmapFile, java.io.File saveDirectory, java.lang.String newFileName)
For running in combination with TPMapProcessor

TPMapDuplicateFilter(java.lang.String fileName)
For running this alone.

Method Summary

void	filterTPMap()
int	getLineNumber()
void	loadBPHashMap(int initialValue, java.io.File file)
static void	main(java.lang.String[] args)
static boolean	matches(TPMapFeature a, TPMapFeature b) Only checks coordinates!
void	removeAdjacentDuplicates() Throws out data lines that are immediately adjacent and have the same sequence.
void	removeDuplicateMappingOligos(java.io.File bpmap) Removes any oligo that is found more than once in the bpmap file.

Methods inherited from class java.lang.Object

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

Constructor Detail

TPMapDuplicateFilter

public TPMapDuplicateFilter(java.lang.String fileName)

For running this alone.

TPMapDuplicateFilter

public TPMapDuplicateFilter(java.io.File bpmapFile,
                            java.io.File saveDirectory,
                            java.lang.String newFileName)

For running in combination with TPMapProcessor

Method Detail

filterTPMap

public void filterTPMap()

removeDuplicateMappingOligos

public void removeDuplicateMappingOligos(java.io.File bpmap)

Removes any oligo that is found more than once in the bpmap file. Run removeAdjacentDuplicates() first!

removeAdjacentDuplicates

public void removeAdjacentDuplicates()

Throws out data lines that are immediately adjacent and have the same sequence.

loadBPHashMap

public void loadBPHashMap(int initialValue,
                          java.io.File file)

matches

public static boolean matches(TPMapFeature a,
                              TPMapFeature b)

Only checks coordinates!

main

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

getLineNumber

public int getLineNumber()