charite.christo.protein
Interface SequenceAligner

All Known Subinterfaces:

SequenceAligner3D, SequenceAlignerSorting, SequenceAlignerTakesProfile

All Known Implementing Classes:

Aligner3D, Aligner3D_Mapsci, Aligner3D_Matt, Aligner3D_Mustang, Aligner3D_Smolign, MultiFromPairAligner, MultipleAligner_SPEM, MultipleAlignerAlign_m, MultipleAlignerAmap, MultipleAlignerClustalW, MultipleAlignerDialign, MultipleAlignerDialignT, MultipleAlignerKalign, MultipleAlignerMafft, MultipleAlignerMuscle, MultipleAlignerProbcons2, MultipleAlignerT_Coffee, PairAlignerJAligner, PairAlignerJAlignerPROXY, PairAlignerNeoBio, PairAlignerNeoBioPROXY, Superimpose_CE, Superimpose_CEPROXY, Superimpose_native_CE, Superimpose_TM_align

public interface SequenceAligner

Classes that provide a calculation of sequence alignments. PACKAGE: PACKAGE:charite.christo. With JAVADOC:SequenceAligner#setSequences(String[]) the amino acid sequences of the proteins are set. Alignment starts on invoking JAVADOC:SequenceAligner#compute() STRAP retrieves the result by calling JAVADOC:SequenceAligner#getAlignedSequences(). JAVADOC:SequenceAligner#getOptions()may rcontain the flag PROPERTY_ONLY_TWO_SEQUENCES if the procedure is capable of aligning only pairs of sequences. A container of GUI elements for the user is provided on pressing ICON:IC_CONTROLPANEL when the class implements JAVADOC:HasControlPanel. The GUI elements may be used to select gap-panalties or BLOSUM matrices.

Field Summary

static long	OPTION_CHECK_PERFECT_MATCH
static long	OPTION_NOT_TO_SECURITY_LIST
static long	OPTION_USE_SECONDARY_STRUCTURE
static long	PROPERTY_LOCAL_ALIGNMENT
static long	PROPERTY_ONLY_TWO_SEQUENCES
static float	SCORE_FOR_PERFECT_MATCH

Method Summary

void	compute() The time consuming computation.
byte[][]	getAlignedSequences()
long	getOptions()
long	getPropertyFlags()
byte[][]	getSequences() Return the sequences that have been set with setSequences(String[])
void	setOptions(long optionFlags) Multiple aligners are usually not limited in the number of sequences.
void	setSequences(byte[]... ss)

Field Detail

OPTION_USE_SECONDARY_STRUCTURE

static final long OPTION_USE_SECONDARY_STRUCTURE

See Also:

Constant Field Values

OPTION_CHECK_PERFECT_MATCH

static final long OPTION_CHECK_PERFECT_MATCH

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Constant Field Values

OPTION_NOT_TO_SECURITY_LIST

static final long OPTION_NOT_TO_SECURITY_LIST

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Constant Field Values

PROPERTY_LOCAL_ALIGNMENT

static final long PROPERTY_LOCAL_ALIGNMENT

See Also:

Constant Field Values

PROPERTY_ONLY_TWO_SEQUENCES

static final long PROPERTY_ONLY_TWO_SEQUENCES

See Also:

Constant Field Values

SCORE_FOR_PERFECT_MATCH

static final float SCORE_FOR_PERFECT_MATCH

See Also:

Constant Field Values

Method Detail

setSequences

void setSequences(byte[]... ss)

getSequences

byte[][] getSequences()

Return the sequences that have been set with setSequences(String[])

compute

void compute()

The time consuming computation.

getPropertyFlags

long getPropertyFlags()

getAlignedSequences

byte[][] getAlignedSequences()

setOptions

void setOptions(long optionFlags)

Multiple aligners are usually not limited in the number of sequences. Pair aligners should return "2". See JAVADOC:charite.christo.strap.extensions.MultiFromPairAligner

getOptions

long getOptions()