Class TPMapDuplicateFilter

  extended bytrans.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( bpmapFile, 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, 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( 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


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


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

Method Detail


public void filterTPMap()


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


public void removeAdjacentDuplicates()
Throws out data lines that are immediately adjacent and have the same sequence.


public void loadBPHashMap(int initialValue,


public static boolean matches(TPMapFeature a,
                              TPMapFeature b)
Only checks coordinates!


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


public int getLineNumber()