gata.plotter
Class ConservedSeqs

java.lang.Object
  gata.plotter.ConservedSeqs

public class ConservedSeqs

extends java.lang.Object

Author:

Nix Takes an array of Alignments and converts it into two conserved text sequences

Constructor Summary

ConservedSeqs(GATAParams params)

Method Summary

static int[][]	convertToBlocks(StartStop[] ss)
void	fetchNewRegions(int leftBaseRef, int rightBaseRef, int leftBaseComp, int rightBaseComp)
static java.lang.String[]	fetchSeq(java.lang.String file)
boolean	fetchSequences()
void	generateConservedSeqs()
Console	getConsole()
static int[][]	growIntArrays(int[][] ints)
void	printSeqsToConsole()
void	printTruncatedSeqsToConsole(int leftBaseRef, int rightBaseRef, int leftBaseComp, int rightBaseComp)
static java.lang.String	reformatSeq(int[][] blocks, java.lang.String seq, java.lang.String format) Reformats a sequence given and int[][] containing start stops

Methods inherited from class java.lang.Object

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

Constructor Detail

ConservedSeqs

public ConservedSeqs(GATAParams params)

Method Detail

fetchSequences

public boolean fetchSequences()

fetchNewRegions

public void fetchNewRegions(int leftBaseRef,
                            int rightBaseRef,
                            int leftBaseComp,
                            int rightBaseComp)

generateConservedSeqs

public void generateConservedSeqs()

printSeqsToConsole

public void printSeqsToConsole()

printTruncatedSeqsToConsole

public void printTruncatedSeqsToConsole(int leftBaseRef,
                                        int rightBaseRef,
                                        int leftBaseComp,
                                        int rightBaseComp)

reformatSeq

public static java.lang.String reformatSeq(int[][] blocks,
                                           java.lang.String seq,
                                           java.lang.String format)

Reformats a sequence given and int[][] containing start stops

fetchSeq

public static java.lang.String[] fetchSeq(java.lang.String file)

convertToBlocks

public static int[][] convertToBlocks(StartStop[] ss)

growIntArrays

public static int[][] growIntArrays(int[][] ints)

getConsole

public Console getConsole()