charite.christo.protein
Class Bl2seq

java.lang.Object
  charite.christo.protein.Bl2seq

All Implemented Interfaces:

HasNativeExec

public class Bl2seq
extends java.lang.Object
implements HasNativeExec

HELP Given is an amino acid sequence and one (or several) nucleotide sequences of unknown frame shift. This dialog finds the coding strand and the coding nucleotides to produce an amino acids sequence similar to the given one.

Example Input:

   aa=VVLATEKKQKSILYDERSVHKVEPITKHIGLVYSGMGPDYRVLVHRARKLAQQYYLVYQEPIPTAQLVQRVASVMQE
   nt=GcgGcgAacGgcGtgGtgCtgGcgAccGaaAaaAaaCagAaaAgcAttCtgTatGatGaaCgcAgcGtgCatAaaGtgGaaCcgAttAccAaaCatAttGgcCtgG
   

As a result the nt sequence is translated into:

   VWXSVPLYARCVHHTECFSVFFRSPAPRRSP
   

Nested Class Summary

static class

Bl2seq.Hit

Field Summary

static long	ALIGNMENT
static java.lang.String	BLASTN
static java.lang.String	blastp
static java.lang.String	BLASTX
static long	OUTPUT_LONG
static long	OUTPUT_SHORT
static long	TRANS_3

Constructor Summary

Bl2seq(long opt, byte[] seqI, byte[] seqJ, java.lang.String prg, BA log)

Method Summary

void	compute()
Bl2seq.Hit[]	getHits()
BasicExecutable	getNativeExec(boolean createNew)
java.lang.String	getProgram()
BA	getResultText()
byte[]	getSequence(int i)
static boolean[]	getTranslatedNucleotides(byte[] nt, byte[] aa, Bl2seq.Hit h0, Bl2seq.Hit[] hh, long options)
static java.lang.String	toText(Bl2seq.Hit h, long options)

Methods inherited from class java.lang.Object

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

Field Detail

BLASTN

public static final java.lang.String BLASTN

See Also:

Constant Field Values

BLASTX

public static final java.lang.String BLASTX

See Also:

Constant Field Values

blastp

public static final java.lang.String blastp

See Also:

Constant Field Values

OUTPUT_SHORT

public static final long OUTPUT_SHORT

See Also:

Constant Field Values

OUTPUT_LONG

public static final long OUTPUT_LONG

See Also:

Constant Field Values

ALIGNMENT

public static final long ALIGNMENT

See Also:

Constant Field Values

TRANS_3

public static final long TRANS_3

See Also:

Constant Field Values

Constructor Detail

Bl2seq

public Bl2seq(long opt,
              byte[] seqI,
              byte[] seqJ,
              java.lang.String prg,
              BA log)

Method Detail

getSequence

public byte[] getSequence(int i)

getNativeExec

public BasicExecutable getNativeExec(boolean createNew)

Specified by:

getNativeExec in interface HasNativeExec

compute

public void compute()

getResultText

public BA getResultText()

getHits

public Bl2seq.Hit[] getHits()

getProgram

public java.lang.String getProgram()

toText

public static java.lang.String toText(Bl2seq.Hit h,
                                      long options)

getTranslatedNucleotides

public static boolean[] getTranslatedNucleotides(byte[] nt,
                                                 byte[] aa,
                                                 Bl2seq.Hit h0,
                                                 Bl2seq.Hit[] hh,
                                                 long options)