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'STRAP:multiple sequence alignments ' | ||||||||
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java.lang.Object charite.christo.strap.ReferenceSequence
public class ReferenceSequence
Field Summary |
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Fields inherited from interface charite.christo.interfaces.ChRunnable |
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APPEND, DOWNLOAD_FINISHED, INTERPRET_LINE, LOG, SET_ICON_IMAGE |
Constructor Summary | |
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ReferenceSequence(String otherId,
StrapProtein protein,
ChRunnable log,
boolean background,
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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String |
getLinkForAlignment()
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ByteArray |
getLocalAlignment(int iAa_from,
int iAa_to,
ByteArray sb)
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StrapProtein |
getReferenceProtein()
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short[] |
getUniprotIdx2Idx()
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Object |
run(String id,
Object arg)
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boolean[] |
uniprotIdx2Idx(boolean[] uniprot)
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Methods inherited from class java.lang.Object |
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equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public ReferenceSequence(String otherId, StrapProtein protein, ChRunnable log, boolean background, Runnable runWhenInitialized)
Method Detail |
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public StrapProtein getReferenceProtein()
public Object run(String id, Object arg)
run
in interface ChRunnable
public String getLinkForAlignment()
public short[] getUniprotIdx2Idx()
public boolean[] uniprotIdx2Idx(boolean[] uniprot)
public float getAlignmentScore()
public ByteArray getLocalAlignment(int iAa_from, int iAa_to, ByteArray sb)
public int countMismatch(int fromIdx, int toIdx, int[] colFromTo)
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