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'STRAP:multiple sequence alignments ' | ||||||||
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java.lang.Object charite.christo.strap.AbstractAligner charite.christo.strap.extensions.MultipleAlignerMuscle
public final class MultipleAlignerMuscle
HELP
HOME: HOME:MultipleAlignerMuscle
Windows (cygwin):
Building the program fails
Publication: PUBMED:15318951
MS_Windows: To build the package successfully please change the file intmath.cpp:
Move the definition of the method log2(double) to the top and rename it e.g. to Log2 (upper case).
Field Summary |
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Fields inherited from class charite.christo.strap.AbstractAligner |
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MFA_FILE, PFX_DPKG, RPLC_WIN_DOT_EXE |
Fields inherited from interface charite.christo.HasPrgParas |
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FURTHER_PARAMETERS |
Fields inherited from interface charite.christo.protein.SequenceAligner |
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OPTION_CHECK_PERFECT_MATCH, OPTION_NOT_TO_SECURITY_LIST, OPTION_USE_SECONDARY_STRUCTURE, PROPERTY_LOCAL_ALIGNMENT, PROPERTY_ONLY_TWO_SEQUENCES, SCORE_FOR_PERFECT_MATCH |
Fields inherited from interface charite.christo.Disposable |
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NONE |
Fields inherited from interface charite.christo.CanBeStopped |
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vALIGNMENTS |
Constructor Summary | |
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MultipleAlignerMuscle()
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Method Summary | |
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Superimpose3D.Result |
computeResult(byte[][] seqs,
Protein[] proteinsNotNeeded)
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Methods inherited from class charite.christo.strap.AbstractAligner |
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addProfile, cbCommutative, compute, defineParameters, dirTemp, dispose, getAlignedSequences, getControlPanel, getIndicesOfSequences, getMaxNumberOfProfiles, getNativeExec, getOptions, getPrgParas, getProfiles, getPropertyFlags, getPropertyMap, getProteins, getResult, getRmsd, getScore, getSequences, getSharedInstance, initX, insertWhereNoCoordinates, isEnabled, mfaInFile, parse, pdbFile, setOptions, setPropertyFlags, setProteins, setSequences, setSharedInstance, stop |
Methods inherited from class java.lang.Object |
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equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Methods inherited from interface charite.christo.HasPrgParas |
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defineParameters, getPrgParas |
Methods inherited from interface charite.christo.NeedsSharedInstance |
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getSharedInstance, setSharedInstance |
Methods inherited from interface charite.christo.protein.SequenceAlignerSorting |
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getIndicesOfSequences |
Methods inherited from interface charite.christo.protein.SequenceAligner |
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compute, getAlignedSequences, getOptions, getPropertyFlags, getSequences, setOptions, setSequences |
Constructor Detail |
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public MultipleAlignerMuscle()
Method Detail |
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public Superimpose3D.Result computeResult(byte[][] seqs, Protein[] proteinsNotNeeded)
computeResult
in class AbstractAligner
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