de.unibi.techfak.jpredictor.operator
Class States

java.lang.Object
  de.unibi.techfak.jpredictor.operator.States

Direct Known Subclasses:

DefaultCommunicator

 class States
extends java.lang.Object

Class to use for the communicator as option holder. Here are all fields stored used by the operator inclusive their default values. receiver.

Nested Class Summary

(package private) class

States.SequenceStore This class is a wrapper class for holding a sequence object and the type information about it.

Field Summary

protected boolean	allowThreadRunning The flag that decides whether a thread needs to break as soon as possible.
protected java.lang.String	distanceMode Sets the distance mode, that defines the distance between two motifs combined in a DoubleMotif.
protected java.io.PrintStream	err The output stream to which the error messages should be directed.
protected double	fixedCutoff The cutoff for scoring a sequence using weighted motifs.
static double	fixedCutoffDefault The default for the cutoff is Double.NaN.
protected double[]	globalBackground The DNA/RNA character distribution.
static double[]	globalCharacterDistributionDefault The default character distribution for the valid DNA/RNA characters.
protected boolean	graphicalOutput The parameter which controlls whether the user wants to have a graphical output or not.
protected MotifList	motifList The list of motifs that are searched in the window on a sequence.
protected java.util.Vector	motifOccurrenceVector If the graphical output is activated this vector holds all data to show the occurrences of motifs.Initially it is null.
protected java.io.PrintStream	out The standard output stream to which all output should be directed.
protected java.util.Random	rand The random number generator that comes with this class.
protected java.util.Vector	scorePlotVector If the graphical output is activated this vector holds all data to draw a score plot.
protected long	seed The seed of the number generator.
protected boolean	sequenceLengthNormalization Sets, whether the occurrences of motifs on sequences are normalized (divided) by the corresponding sequence' length.
static boolean	sequenceLengthNormalizationDefault The default value whether normalization is wished or not.
protected States.SequenceStore[]	sequenceStore The array to store the sequence informations for the search sequence, the positive and the negativ training set.
protected static int	STORE_NEGATIVE_TRAINING_SET The number of the negative training set in the sequenceStore-Array
protected static int	STORE_POSITIVE_TRAINING_SET The number of the positive training set in the sequenceStore-Array
protected static int	STORE_SEQUENCE The number of the search sequence in the sequenceStore-Array
protected java.io.PrintStream	ver The output stream to which verify messages should be directed.
protected int	windowShift The window for searching and scoring in is shifted on the sequence by this value.
static int	windowShiftDefault The default for shifting the window on a sequence is 10.
protected int	windowWidth The width of the window on a sequence.
static int	windowWidthDefault The default for the width of the window on a sequence is 500.

Constructor Summary

States()
The simple constructor.

Method Summary

Methods inherited from class java.lang.Object

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

Field Detail

STORE_SEQUENCE

protected static final int STORE_SEQUENCE

The number of the search sequence in the sequenceStore-Array

See Also:

Constant Field Values

STORE_POSITIVE_TRAINING_SET

protected static final int STORE_POSITIVE_TRAINING_SET

The number of the positive training set in the sequenceStore-Array

See Also:

Constant Field Values

STORE_NEGATIVE_TRAINING_SET

protected static final int STORE_NEGATIVE_TRAINING_SET

The number of the negative training set in the sequenceStore-Array

See Also:

Constant Field Values

sequenceStore

protected States.SequenceStore[] sequenceStore

The array to store the sequence informations for the search sequence, the positive and the negativ training set.

windowWidthDefault

public static final int windowWidthDefault

The default for the width of the window on a sequence is 500.

See Also:

Constant Field Values

windowWidth

protected int windowWidth

The width of the window on a sequence. Within this window is searching and scoring performed.

windowShiftDefault

public static final int windowShiftDefault

The default for shifting the window on a sequence is 10.

See Also:

Constant Field Values

windowShift

protected int windowShift

The window for searching and scoring in is shifted on the sequence by this value.

motifList

protected MotifList motifList

The list of motifs that are searched in the window on a sequence.

sequenceLengthNormalizationDefault

public static final boolean sequenceLengthNormalizationDefault

The default value whether normalization is wished or not. It is set to 'true'.

See Also:

Constant Field Values

sequenceLengthNormalization

protected boolean sequenceLengthNormalization

Sets, whether the occurrences of motifs on sequences are normalized (divided) by the corresponding sequence' length.

See Also:

ICommunicator.setSequenceLengthNormalization(boolean)

distanceMode

protected java.lang.String distanceMode

Sets the distance mode, that defines the distance between two motifs combined in a DoubleMotif. There is no default value for this field, but it is preset to DISTANCE_BELOW220.

allowThreadRunning

protected boolean allowThreadRunning

The flag that decides whether a thread needs to break as soon as possible. When the operator starts a thread to perform search or score tasks this flag should be set to true. By calling the method stopRunning() defined in the interface ICommunicator this flag is set to false and all running threads should break regulary as soon as possible. Regulary means, that the thread should send their defined finishing result to the communicator.

out

protected java.io.PrintStream out

The standard output stream to which all output should be directed. By default it is set to System.out.

err

protected java.io.PrintStream err

The output stream to which the error messages should be directed. By default it is set to System.err.

ver

protected java.io.PrintStream ver

The output stream to which verify messages should be directed. It is set to PrintStream( new NilOutputStream() ) per default.

graphicalOutput

protected boolean graphicalOutput

The parameter which controlls whether the user wants to have a graphical output or not.

scorePlotVector

protected java.util.Vector scorePlotVector

If the graphical output is activated this vector holds all data to draw a score plot. Initially it is null.

motifOccurrenceVector

protected java.util.Vector motifOccurrenceVector

If the graphical output is activated this vector holds all data to show the occurrences of motifs.Initially it is null.

fixedCutoffDefault

public static final double fixedCutoffDefault

The default for the cutoff is Double.NaN. This means that no cutoff is set and when scoring a sequence the single scores are output.

See Also:

Constant Field Values

fixedCutoff

protected double fixedCutoff

The cutoff for scoring a sequence using weighted motifs. If such a cutoff is set other than the default and a sequence is scored the scores are comprised to bands and every band above the set cutoff is output. Otherwise scoring would yield the single scores for every sequence window.

globalCharacterDistributionDefault

public static final double[] globalCharacterDistributionDefault

The default character distribution for the valid DNA/RNA characters. It is messured in the Drosophila melanogaster genome. The probabilities for single nucleotides to occur are f(A)=f(T)=0.283 and f(C)=f(G)=0.217.

globalBackground

protected double[] globalBackground

The DNA/RNA character distribution. Normally, it is set to default. It is used for building PSSMs from PSPMs or for cutoff calculation, where the random sequence is built from that distribution (only if the user does not give its own distribution). Also, it is used for

See Also:

globalCharacterDistributionDefault

rand

protected java.util.Random rand

The random number generator that comes with this class. Might be useful, if the seed has to be known or has to be set twice. Initialized as in Java version 1.4.2 with the System.currentTimeMillis().

seed

protected long seed

The seed of the number generator. It is set when the number generator is initialized.

Constructor Detail

States

States()

The simple constructor. Sets the SequenceStore array and the output streams: out to System.out, err to System.err, and ver to NilOutputStream

See Also:

NilOutputStream