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this.motif.
readers vector.
MultiMotif.
MultiMotif.
ResetableReader to the vector of
subsequence readers.
Reader to the underlying storage container.
OutputStream.
MotifList and adds all the motifs in
there into this tree view by calling addMotif(Motif, -1).
cols columns and rows
rows and fills it with the given array.
this.motif.
methodToCall.
Readers stored in this class.
OutputStreams.
ICommunicator for this class.
this class to another one of the same type.
clusters.
toString() text as text.
toString()) and some informations,
like motif type (class name), description, motif consensus sequence
as children.
MotifList and the MultiMotif's
motifs and counts the motifs matching the given name.
read(char[], int, int), skip(int) and
read().
distanceMode got from the
ICommunicator-interface and then creates
the DoubleMotifs with the distances.
DoubleMotifs from the single motifs
of the given MotifList.
JMenu for this panel which may be added to
any frame or dialog, preferably to the parent of this panel.
PSPMotif from a SequenceMotif
or a RegularExpressionMotif, respectively.
MultiMotif is reversed and
also the motifs stored are reversed and complemented.
DoubleMotifs from the default single motifs
and assigns them a weight (which is got from running the jPREdictor
with the 'new_pre.fasta' as model and the 'non_pre.fasta' as
background).
MultiMotif.
JComponent using the graphics
settings.
DoubleMotifs from the extended single motifs
and assigns them a weight (which is got from running the jPREdictor
with the 'new_pre.fasta' as model and the 'non_pre.fasta' as
background).
SequenceReader.Files into one string.
w with the new
weights for the motifs.
w with the new
weights for the motifs.
readFiltered()-method.
readFiltered()-method.
MotifList and the MultiMotifs
motifs for the given name.
Double.NaN.
OutputStreams.
formatTime( msec, -1, true ).
MultiMotif.
MultiMotif.
this(0, start, end).
null.
this.motif.
Component given.
this.getMaximum(int).
this.getMaximum(int).
MotifList as was given the constructor,
or as was given to the setMotifList(MotifList)-method,
respectively.
MotifList.
MultiMotif is built upon.
MultiMotif from the motifs and distances
in the tree.
index.
MultiFileReader or a
ResetableReader from the filenames comprised in
names.
SequenceEnumerator
from the object given.
MultiMotifs given to this class.
this list the single motifs
and stores them in a new MotifList.
JTree from the headline (root) and all
motifs (children).
Double.NaN.
OutputStream is designed to reroute all output
written to it to a JTextArea.append(String).
MotifList, this class was created with.
LOOKANDFEEL.
initSearch for all motifs stored in this Vector.
MultiMotif.
coll to this
MotifList.
MultiMotif.
Integer.MAX_VALUE is
returned.
localOp.
Reader.
Reader and the size of the internal buffer.
mark(int) and
used by reset() to read ahead to this position.
mark(int) and
used by reset() to read ahead to this position.
Markable
interface.Readers through one of the
add-methods.
BufferedReader if necessary.
Doubles is cutted or pumped up to the
new Dimension.
doubles from a matrix of
Doubles.
Doubles from a matrix of
doubles.
JTree) within a
JScrollPane.Vector.MultiMotif was not designed completely.null.
JTree) within a
JScrollPane.MultiFileReader represents the logical concatenation of
other Readers.MultiMotif with a name and a description.
MultiMotifs.OutputStream is designed to multiply the output data
and send it to all registered output streams.add(OutputStream).
add(OutputStream).
DoubleMotifs for the prediction made
in 2006/04 by Fiedler, 2006, NAR web server issue.
SequenceReader
class.Sequence
to return.
OutputStream is designed to absorb all
output as if it would be send to /dev/null.SequenceEnumeration
interfaceObject parameter in some methods
is a String containing a filename.
Object parameter in some methods
is a String containing the name of a FASTA file.
Object parameter in some methods
is an arbitrary Reader containing a readable stream.
Object parameter in some methods
is an arbitrary Reader containing a readable stream
delivering data in FASTA format.
Object parameter in some methods
is a Sequence or a MappedCharSequence.
Object parameter in some methods
is a String containing the sequence.
Object parameter in some methods
is a String containing one or more sequences, which
are in FASTA-format.
MotifList and either a
CharSequence or a SequenceReader (from which
the CharSequences are obtained) and which searches the
motifs in the list in all sequences by calling for every motif the
searchAll-method.
RelationMeasure.
String from this struct:
seqNumber:seqStart-seqEnd:score
adjustmentValueChanged to give the
start of the score vector, from which the plot is started to
be painted.
adjustmentValueChanged to give the
start of the string to be printed.
null, if this queue is empty.
comm.out().print(), if verify is
true.
- print(PrintStream) -
Method in class de.unibi.techfak.jpredictor.motifs.Motif
- Prints the motif to the given stream, e.g.
- print() -
Method in class de.unibi.techfak.jpredictor.motifs.Motif
- Prints the motif to
System.out.
- print(PrintStream) -
Method in class de.unibi.techfak.jpredictor.motifs.MultiMotif
- Prints this
MultiMotif via a PrintStream.
- print(PrintStream) -
Method in class de.unibi.techfak.jpredictor.motifs.PSPMotif
-
- print(PrintStream) -
Method in class de.unibi.techfak.jpredictor.motifs.RegularExpressionMotif
-
- probArrayMinus -
Variable in class de.unibi.techfak.jpredictor.motifs.MotifSearchAdapter.SearchFields
- The two arrays where the probabilities of occurrences of motif
characters are stored.
- probArrayPlus -
Variable in class de.unibi.techfak.jpredictor.motifs.MotifSearchAdapter.SearchFields
- The two arrays where the probabilities of occurrences of motif
characters are stored.
- processScore(ScoredSequenceStruct) -
Static method in class de.unibi.techfak.jpredictor.operator.ScoringFactory
-
Process a given score, that is, joins the score to the results
of previous calculations.
- processScores() -
Static method in class de.unibi.techfak.jpredictor.jPREdictor
- Takes the file given by option '-f' and comprises the scores in it
to bands for many cutoffs.
- progInfo -
Static variable in class de.unibi.techfak.jpredictor.jPREdictor
- Informations on and description of the program.
- propertyChange(PropertyChangeEvent) -
Method in class de.unibi.techfak.jpredictor.gui.TextInsertDialog
- Reacts on pressing the two buttons.
- PSPMotif - Class in de.unibi.techfak.jpredictor.motifs
- Contains a motif represented by probabilities for every base in every
position (PSPM = position specific probability matrix).
- PSPMotif(String, String) -
Constructor for class de.unibi.techfak.jpredictor.motifs.PSPMotif
- Creates a motif with name and description, but empty position
specific probabilty matrix.
- PSSMotif - Class in de.unibi.techfak.jpredictor.motifs
- Contains a motif represented by scores for every base in every
position (PSSM = position specific score matrix).
- PSSMotif(String, String) -
Constructor for class de.unibi.techfak.jpredictor.motifs.PSSMotif
- Inits the name and the description.
- putCommunicatorToForms() -
Method in class de.unibi.techfak.jpredictor.gui.MainPanel
- Stores all information from the static communicator associated with
this class in the main windows input forms.
- putFormsToCommunicator(boolean) -
Method in class de.unibi.techfak.jpredictor.gui.MainPanel
- Stores all information from the main windows input forms in the
static communicator associated with this class.
LinkedList.SequenceReader
and, if wished, discarding of new line characters, too.BufferedReader.
BufferedReader and writes them into the buffer.
readFiltered().
readFiltered() and writes them into the buffer.
readers.
len characters from the line and stores them
in a new string.
this.reader.read().
getNextResult().
null.
OutputStream from the list of
receivers.
MultiMotif with the given one.
seqNumber, seqStart and
seqEnd to -1, score to
Double.NaN.
Reader fails the file is
tried to be reopened, if the file was constructed via a filename.
Reader is re-set and all
SequenceInformationBlocks lying beyond the
mark are deleted.
new BufferedReader(new FileReader( filename ))
Readers.scoreProbability.
JComponent, in which the score plot
is drawn.JComponent, in which the sequence
together with the motifs is drawn.methodToCall.
initSearch and matches the motif on this
CharSequence with respect to the search mode and the
search window determined by the two parameters seqStart
and seqWidth.
initSearch and matches the motif on that
CharSequence with respect to the search mode and the
sequence window.
MotifList, until a Motif was found,
that matches the given name.
MotifList and the MultiMotifs
motifs for the given name.
MotifList for the given Motif by comparing
references.
methodToCall.
methodToCall.
searchSequence, set by the method search
from the Interface MotifSearcher
ScorePlotArea.
null, it is returned and
the seqReader variable is not used.
Reader, which must not be
null and the name and description of that sequence.
null
and a SequenceInformationBlock.
SequenceInformationBlocks.
SequenceEnumeration-interface.RegularExpressionMotif.SequenceEnumeration-object usable for going
through all sequences in this Reader sequentially.
initSearchWindow.
initSearchWindow.
cutoff.
PrintStream as new error message
output stream.
JStatusBar object the number of labels
that are wished to be shown.
MotifList.
TextArea.
PrintStream as new output stream.
CharSequence, filename or stream) to
perform searching and scoring on.
PrintStream as new verbose message
output stream.
MultiFileReader
.
StatusBar object with the amount of labels.
this.motif.
start(int) method.
type says.
[rows][columns].
TextArea to insert text into.coordLabel label.
adjustmentValueChanged to give the
start on the y-axis in dots.OutputStreams.
OutputStreams.
OutputStreams.
MultiMotif.
true, if the user has not clicked on one of the
buttons for x-zoom .
true, if the user has not clicked on one of the
buttons for y-zoom .
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