charite.christo.protein
Class ReferenceSequence

java.lang.Object
  java.lang.Thread
      charite.christo.protein.ReferenceSequence

All Implemented Interfaces:

java.lang.Runnable

public class ReferenceSequence
extends java.lang.Thread

Nested Class Summary

Nested classes/interfaces inherited from class java.lang.Thread

java.lang.Thread.State, java.lang.Thread.UncaughtExceptionHandler

Field Summary

Fields inherited from class java.lang.Thread

MAX_PRIORITY, MIN_PRIORITY, NORM_PRIORITY

Constructor Summary

ReferenceSequence(java.lang.String otherId, Protein p, BA log, boolean background, java.lang.Runnable runWhenInitialized)

Method Summary

int	countMismatch(int fromIdx, int toIdx, int[] colFromTo)
float	getAlignmentScore()
java.lang.String	getLinkForAlignment()
BA	getLocalAlignment(int aFrom, int aTo, BA sb)
Protein	getReferenceProtein()
boolean	getSuccess()
short[]	getUniprotIdx2Idx()
void	run()
boolean[]	uniprotIdx2Idx(boolean[] uniprot, int offset, int[] returnMinIdx)

Methods inherited from class java.lang.Thread

activeCount, checkAccess, countStackFrames, currentThread, destroy, dumpStack, enumerate, getAllStackTraces, getContextClassLoader, getDefaultUncaughtExceptionHandler, getId, getName, getPriority, getStackTrace, getState, getThreadGroup, getUncaughtExceptionHandler, holdsLock, interrupt, interrupted, isAlive, isDaemon, isInterrupted, join, join, join, resume, setContextClassLoader, setDaemon, setDefaultUncaughtExceptionHandler, setName, setPriority, setUncaughtExceptionHandler, sleep, sleep, start, stop, stop, suspend, toString, yield

Methods inherited from class java.lang.Object

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

Constructor Detail

ReferenceSequence

public ReferenceSequence(java.lang.String otherId,
                         Protein p,
                         BA log,
                         boolean background,
                         java.lang.Runnable runWhenInitialized)

Method Detail

run

public void run()

Specified by:

run in interface java.lang.Runnable

Overrides:

run in class java.lang.Thread

getSuccess

public boolean getSuccess()

getLinkForAlignment

public java.lang.String getLinkForAlignment()

getUniprotIdx2Idx

public short[] getUniprotIdx2Idx()

getReferenceProtein

public Protein getReferenceProtein()

uniprotIdx2Idx

public boolean[] uniprotIdx2Idx(boolean[] uniprot,
                                int offset,
                                int[] returnMinIdx)

getAlignmentScore

public float getAlignmentScore()

getLocalAlignment

public BA getLocalAlignment(int aFrom,
                            int aTo,
                            BA sb)

countMismatch

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