charite.christo.strap
Class ReferenceSequence

java.lang.Object
  charite.christo.strap.ReferenceSequence

All Implemented Interfaces:

ChRunnable

public class ReferenceSequence
extends Object
implements ChRunnable

Field Summary

Fields inherited from interface charite.christo.interfaces.ChRunnable

APPEND, DOWNLOAD_FINISHED, INTERPRET_LINE, LOG, SET_ICON_IMAGE

Constructor Summary

ReferenceSequence(String otherId, StrapProtein protein, ChRunnable log, boolean background, Runnable runWhenInitialized)

Method Summary

int	countMismatch(int fromIdx, int toIdx, int[] colFromTo)
float	getAlignmentScore()
String	getLinkForAlignment()
ByteArray	getLocalAlignment(int iAa_from, int iAa_to, ByteArray sb)
StrapProtein	getReferenceProtein()
short[]	getUniprotIdx2Idx()
Object	run(String id, Object arg)
boolean[]	uniprotIdx2Idx(boolean[] uniprot)

Methods inherited from class java.lang.Object

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

Constructor Detail

ReferenceSequence

public ReferenceSequence(String otherId,
                         StrapProtein protein,
                         ChRunnable log,
                         boolean background,
                         Runnable runWhenInitialized)

Method Detail

getReferenceProtein

public StrapProtein getReferenceProtein()

run

public Object run(String id,
                  Object arg)

Specified by:

run in interface ChRunnable

getLinkForAlignment

public String getLinkForAlignment()

getUniprotIdx2Idx

public short[] getUniprotIdx2Idx()

uniprotIdx2Idx

public boolean[] uniprotIdx2Idx(boolean[] uniprot)

getAlignmentScore

public float getAlignmentScore()

getLocalAlignment

public ByteArray getLocalAlignment(int iAa_from,
                                   int iAa_to,
                                   ByteArray sb)

countMismatch

public int countMismatch(int fromIdx,
                         int toIdx,
                         int[] colFromTo)