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'STRAP:multiple sequence alignments ' | ||||||||
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java.lang.Object java.lang.Thread charite.christo.protein.ReferenceSequence
public class ReferenceSequence
Nested Class Summary |
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Nested classes/interfaces inherited from class java.lang.Thread |
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java.lang.Thread.State, java.lang.Thread.UncaughtExceptionHandler |
Field Summary |
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Fields inherited from class java.lang.Thread |
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MAX_PRIORITY, MIN_PRIORITY, NORM_PRIORITY |
Constructor Summary | |
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ReferenceSequence(java.lang.String otherId,
Protein p,
BA log,
boolean background,
java.lang.Runnable runWhenInitialized)
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Method Summary | |
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int |
countMismatch(int fromIdx,
int toIdx,
int[] colFromTo)
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float |
getAlignmentScore()
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java.lang.String |
getLinkForAlignment()
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BA |
getLocalAlignment(int aFrom,
int aTo,
BA sb)
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Protein |
getReferenceProtein()
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boolean |
getSuccess()
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short[] |
getUniprotIdx2Idx()
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void |
run()
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boolean[] |
uniprotIdx2Idx(boolean[] uniprot,
int offset,
int[] returnMinIdx)
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Methods inherited from class java.lang.Thread |
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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 |
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equals, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Constructor Detail |
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public ReferenceSequence(java.lang.String otherId, Protein p, BA log, boolean background, java.lang.Runnable runWhenInitialized)
Method Detail |
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public void run()
run
in interface java.lang.Runnable
run
in class java.lang.Thread
public boolean getSuccess()
public java.lang.String getLinkForAlignment()
public short[] getUniprotIdx2Idx()
public Protein getReferenceProtein()
public boolean[] uniprotIdx2Idx(boolean[] uniprot, int offset, int[] returnMinIdx)
public float getAlignmentScore()
public BA getLocalAlignment(int aFrom, int aTo, BA sb)
public int countMismatch(int fromIdx, int toIdx, int[] colFromTo)
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