util.bio.xamer
Class XamerCounter

java.lang.Object
  util.bio.xamer.XamerCounter

public class XamerCounter

extends java.lang.Object

Counts the frequency of random words in a list of sequences.

Constructor Summary

XamerCounter()

Method Summary

int[]	calculateTotalNumberOfOligosPerRound(java.lang.String[][] seqs)
static java.lang.String[][]	fetchSequences(java.lang.String[] files) Fetch all sequences from each multi-FASTA file
static java.util.ArrayList	findSequenceHits(java.lang.String[] seqs, java.lang.String oligo) Looks for an exact match of the oligo to each of the seqs, returning the seqs that contain the oligo
static java.lang.String[]	hexamerGenerator()
static void	main(java.lang.String[] args)
static java.lang.String[]	pentamerGenerator()
static java.lang.String	reverseCompDNA(java.lang.String seq)
static java.util.ArrayList	searchForXamers(java.lang.String[] xamers, java.lang.String[][] seqs) Creates an ArrayList of Xamer objects, where each Xamer contains all the seqs, by round that were found to match a particular xamers[i]
void	setRevCompRefs(java.util.ArrayList xamers) Set refs to reverse comp xamer

Methods inherited from class java.lang.Object

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

Constructor Detail

XamerCounter

public XamerCounter()

Method Detail

setRevCompRefs

public void setRevCompRefs(java.util.ArrayList xamers)

Set refs to reverse comp xamer

reverseCompDNA

public static java.lang.String reverseCompDNA(java.lang.String seq)

searchForXamers

public static java.util.ArrayList searchForXamers(java.lang.String[] xamers,
                                                  java.lang.String[][] seqs)

Creates an ArrayList of Xamer objects, where each Xamer contains all the seqs, by round that were found to match a particular xamers[i]

calculateTotalNumberOfOligosPerRound

public int[] calculateTotalNumberOfOligosPerRound(java.lang.String[][] seqs)

findSequenceHits

public static java.util.ArrayList findSequenceHits(java.lang.String[] seqs,
                                                   java.lang.String oligo)

Looks for an exact match of the oligo to each of the seqs, returning the seqs that contain the oligo

fetchSequences

public static java.lang.String[][] fetchSequences(java.lang.String[] files)

Fetch all sequences from each multi-FASTA file

main

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

hexamerGenerator

public static java.lang.String[] hexamerGenerator()

pentamerGenerator

public static java.lang.String[] pentamerGenerator()