util.bio.seq
Class FetchIndexedSequence

java.lang.Object
  util.bio.seq.FetchIndexedSequence

public class FetchIndexedSequence

extends java.lang.Object

Constructor Summary

FetchIndexedSequence(java.io.File indexDirectory)

Method Summary

java.lang.String	fetchSequence(java.lang.String chromosome, int start, int stop) Returns null if chromsome doesn't exist or the start or stop indexedSequence out of range.
java.lang.String[]	fetchSequences(int[][] startStop) Assumes startStop[index][0 start, 1 stop] is sorted by starts.
java.lang.String[]	fetchSequences(java.lang.String chromosome, int[][] startStop) Returns null if chromsome doesn't exist or the start or stop indexedSequence out of range.
static void	main(java.lang.String[] args)
void	makeIndexedSequences()
void	nullIndexedSequences() Good to call after each call to fetchSequences() unless you'll be fetching more from the same chromosome.
boolean	setIndexedSequence(java.lang.String chromosome)

Methods inherited from class java.lang.Object

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

Constructor Detail

FetchIndexedSequence

public FetchIndexedSequence(java.io.File indexDirectory)

Method Detail

setIndexedSequence

public boolean setIndexedSequence(java.lang.String chromosome)

fetchSequences

public java.lang.String[] fetchSequences(int[][] startStop)

Assumes startStop[index][0 start, 1 stop] is sorted by starts. Assumes indexedSequence is set! Must call setIndexedSequence(chromosome) prior to calling.

fetchSequence

public java.lang.String fetchSequence(java.lang.String chromosome,
                                      int start,
                                      int stop)

Returns null if chromsome doesn't exist or the start or stop indexedSequence out of range. For multiple fetches use the fetchSequences() method.

fetchSequences

public java.lang.String[] fetchSequences(java.lang.String chromosome,
                                         int[][] startStop)

Returns null if chromsome doesn't exist or the start or stop indexedSequence out of range. Assumes the startStop int[index][0 start, 1 stop] is sorted by starts.

makeIndexedSequences

public void makeIndexedSequences()

nullIndexedSequences

public void nullIndexedSequences()

Good to call after each call to fetchSequences() unless you'll be fetching more from the same chromosome.

main

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