charite.christo.strap
Class AbstractAligner

java.lang.Object
  charite.christo.strap.AbstractAligner

All Implemented Interfaces:

CanBeStopped, Disposable, HasControlPanel, HasNativeExec, HasPropertyMap, IsEnabled

Direct Known Subclasses:

Aligner3D_Mapsci, Aligner3D_Matt, Aligner3D_Mustang, Aligner3D_Smolign, MultipleAligner_SPEM, MultipleAlignerAlign_m, MultipleAlignerAmap, MultipleAlignerClustalW, MultipleAlignerDialign, MultipleAlignerDialignT, MultipleAlignerKalign, MultipleAlignerMafft, MultipleAlignerMuscle, MultipleAlignerProbcons2, MultipleAlignerT_Coffee, PairAlignerJAligner, PairAlignerNeoBio, Superimpose_CE, Superimpose_GangstaPlus, Superimpose_LajollaProtein, Superimpose_native_CE, Superimpose_TM_align

public abstract class AbstractAligner
extends java.lang.Object
implements Disposable, HasControlPanel, HasPropertyMap, HasNativeExec, IsEnabled, CanBeStopped

Field Summary

static java.lang.String	MFA_FILE
static java.lang.String	PFX_DPKG
static java.lang.String	RPLC_WIN_DOT_EXE

Fields inherited from interface charite.christo.Disposable

NONE

Fields inherited from interface charite.christo.CanBeStopped

vALIGNMENTS

Constructor Summary

AbstractAligner()

Method Summary

void	addProfile(byte[][] ss)
static java.lang.Object	cbCommutative(boolean create)
void	compute()
abstract Superimpose3D.Result	computeResult(byte[][] sequences, Protein[] proteins)
void	defineParameters(long opt, java.lang.String s)
java.io.File	dirTemp()
void	dispose()
byte[][]	getAlignedSequences()
javax.swing.JComponent	getControlPanel(boolean real)
int[]	getIndicesOfSequences()
int	getMaxNumberOfProfiles()
BasicExecutable	getNativeExec(boolean createNew)
long	getOptions()
PrgParas	getPrgParas()
byte[][][]	getProfiles()
long	getPropertyFlags()
java.util.Map	getPropertyMap(boolean create)
Protein[]	getProteins()
Superimpose3D.Result	getResult()
float	getRmsd()
float	getScore()
byte[][]	getSequences()
java.lang.Object	getSharedInstance()
BasicExecutable	initX(java.lang.String name, java.lang.String srcUrls, java.lang.String instScript)
static byte[][]	insertWhereNoCoordinates(int startR, byte[] ggR, int startM, byte[] ggM, Protein pR, Protein pM)
boolean	isEnabled(java.lang.Object p)
java.io.File	mfaInFile(byte[][] ss)
static Superimpose3D.Result	parse(int numSeq, BA txt, Superimpose3D.Result result0, long options)
java.io.File	pdbFile(Protein p, int i, boolean[] res, long protWriterOptions)
void	setOptions(long optionFlags)
void	setPropertyFlags(long flags)
void	setProteins(Protein... pp)
void	setSequences(byte[]... ss)
void	setSharedInstance(java.lang.Object shared)
void	stop()

Methods inherited from class java.lang.Object

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

Field Detail

MFA_FILE

public static final java.lang.String MFA_FILE

See Also:

Constant Field Values

PFX_DPKG

public static final java.lang.String PFX_DPKG

See Also:

Constant Field Values

RPLC_WIN_DOT_EXE

public static final java.lang.String RPLC_WIN_DOT_EXE

See Also:

Constant Field Values

Constructor Detail

AbstractAligner

public AbstractAligner()

Method Detail

setSequences

public void setSequences(byte[]... ss)

getSequences

public byte[][] getSequences()

setOptions

public final void setOptions(long optionFlags)

getOptions

public final long getOptions()

getPropertyFlags

public final long getPropertyFlags()

setPropertyFlags

public void setPropertyFlags(long flags)

setProteins

public final void setProteins(Protein... pp)

getProteins

public final Protein[] getProteins()

getNativeExec

public BasicExecutable getNativeExec(boolean createNew)

Specified by:

getNativeExec in interface HasNativeExec

initX

public BasicExecutable initX(java.lang.String name,
                             java.lang.String srcUrls,
                             java.lang.String instScript)

stop

public void stop()

Specified by:

stop in interface CanBeStopped

getPrgParas

public final PrgParas getPrgParas()

setSharedInstance

public final void setSharedInstance(java.lang.Object shared)

getSharedInstance

public final java.lang.Object getSharedInstance()

defineParameters

public void defineParameters(long opt,
                             java.lang.String s)

dispose

public void dispose()

Specified by:

dispose in interface Disposable

getControlPanel

public javax.swing.JComponent getControlPanel(boolean real)

Specified by:

getControlPanel in interface HasControlPanel

cbCommutative

public static java.lang.Object cbCommutative(boolean create)

getPropertyMap

public java.util.Map getPropertyMap(boolean create)

Specified by:

getPropertyMap in interface HasPropertyMap

computeResult

public abstract Superimpose3D.Result computeResult(byte[][] sequences,
                                                   Protein[] proteins)

compute

public void compute()

getResult

public Superimpose3D.Result getResult()

getScore

public final float getScore()

getRmsd

public final float getRmsd()

getAlignedSequences

public byte[][] getAlignedSequences()

getIndicesOfSequences

public int[] getIndicesOfSequences()

addProfile

public void addProfile(byte[][] ss)

getProfiles

public byte[][][] getProfiles()

getMaxNumberOfProfiles

public int getMaxNumberOfProfiles()

isEnabled

public boolean isEnabled(java.lang.Object p)

Specified by:

isEnabled in interface IsEnabled

dirTemp

public final java.io.File dirTemp()

mfaInFile

public final java.io.File mfaInFile(byte[][] ss)

pdbFile

public final java.io.File pdbFile(Protein p,
                                  int i,
                                  boolean[] res,
                                  long protWriterOptions)

insertWhereNoCoordinates

public static byte[][] insertWhereNoCoordinates(int startR,
                                                byte[] ggR,
                                                int startM,
                                                byte[] ggM,
                                                Protein pR,
                                                Protein pM)

parse

public static Superimpose3D.Result parse(int numSeq,
                                         BA txt,
                                         Superimpose3D.Result result0,
                                         long options)