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P

PackedIntegerArrayList - Class in info.bioinfweb.commons.collections

Implements a list of packed integer values which can occupy a space between 1 and 63 bits per value depending on the specified constructor parameter.

PackedIntegerArrayList(int, long, long) - Constructor for class info.bioinfweb.commons.collections.PackedIntegerArrayList

Creates a new instance of this class.

packedList - Variable in class info.bioinfweb.commons.collections.PackedPrimitiveWrapperArrayList

PackedObjectArrayList<E> - Class in info.bioinfweb.commons.collections

Implements a packed list of objects which uses an underlying instance of PackedIntegerArrayList.

PackedObjectArrayList(int, int) - Constructor for class info.bioinfweb.commons.collections.PackedObjectArrayList

Creates a new instance of this class.

PackedPrimitiveWrapperArrayList<E extends java.lang.Number> - Class in info.bioinfweb.commons.collections

An adapter class providing access to an instance if PackedIntegerArrayList using the List interface where the element type can be any numeric primitive wrapper class of the Java API, namely Byte, Short, Integer or Long.

PackedPrimitiveWrapperArrayList(int, long, int) - Constructor for class info.bioinfweb.commons.collections.PackedPrimitiveWrapperArrayList

paint(Graphics) - Method in class info.bioinfweb.commons.applet.DoubleBufferedApplet

paintComponent(Graphics) - Method in class info.bioinfweb.commons.swing.scrollpaneselector.ExtendedScrollPaneSelector

paintComponent(Graphics) - Method in class org.jdesktop.swingx.scrollpaneselector.ScrollPaneBidule

paintComponent(Graphics) - Method in class org.jdesktop.swingx.scrollpaneselector.ScrollPaneSelector

paintOffscreen(Graphics) - Method in class info.bioinfweb.commons.applet.DoubleBufferedApplet

paintPreview(Graphics2D, double) - Method in interface info.bioinfweb.commons.swing.scrollpaneselector.ScrollPaneSelectable

This method is called by ExetededScrollPaneSelector to paint its preview field.

PairwiseAligner - Interface in info.bioinfweb.commons.bio.alignment.pairwise

PARAM_OUTPUT_JSP - Static variable in class info.bioinfweb.commons.servlet.Model2Servlet

PARAM_TARGET_URL - Static variable in class info.bioinfweb.commons.servlet.HTTPIncludeServlet

ParameterMap - Class in info.bioinfweb.commons.collections

Class that stores different objects by string keys.

ParameterMap() - Constructor for class info.bioinfweb.commons.collections.ParameterMap

parse(String) - Method in class info.bioinfweb.commons.tokenizer.StrTokenizer

parseDouble(String) - Static method in class info.bioinfweb.commons.Math2

Parses a double value which can have either "," or "." as its decimal separator.

parseDouble() - Method in class info.bioinfweb.commons.swing.DecimalInput

Parses the current value of the text field.

parseFloat(String) - Static method in class info.bioinfweb.commons.Math2

Parses a float value which can have either "," or "." as its decimal separator.

parseFloat() - Method in class info.bioinfweb.commons.swing.DecimalInput

Parses the current value of the text field.

parseFormatVersion(String) - Static method in class info.bioinfweb.commons.io.FormatVersion

parseHeader(HttpServletRequest) - Static method in class info.bioinfweb.commons.servlet.acceptlanguage.AcceptLanguageParser

parseHeader(String) - Static method in class info.bioinfweb.commons.servlet.acceptlanguage.AcceptLanguageParser

parseInt() - Method in class info.bioinfweb.commons.swing.DecimalInput

Parses the current value as an int.

parseLong() - Method in class info.bioinfweb.commons.swing.DecimalInput

Parses the current value as an long.

parseToken(String) - Method in class info.bioinfweb.commons.bio.biojavax.bio.phylo.io.nexus.SetsBlockParser

parseType(String) - Static method in enum info.bioinfweb.commons.appversion.ApplicationType

Parses a text representation of an application type.

peek(char[]) - Method in class info.bioinfweb.commons.io.PeekReader

peek(char[], int, int) - Method in class info.bioinfweb.commons.io.PeekReader

Copies the specified number of positions from the peek buffer to the specified array.

peek() - Method in class info.bioinfweb.commons.io.PeekReader

Returns integer representation of the character at the current position of this reader without moving forward in the stream.

peek(int) - Method in class info.bioinfweb.commons.io.PeekReader

Returns the integer representation of the character that would be returned after offset calls of Reader.read().

peekChar() - Method in class info.bioinfweb.commons.io.PeekReader

Returns the character at the current position of this reader without moving forward in the stream.

peekChar(int) - Method in class info.bioinfweb.commons.io.PeekReader

Returns the character that would be returned after offset calls of Reader.read().

peekLine() - Method in class info.bioinfweb.commons.io.PeekReader

peekNextID() - Method in class info.bioinfweb.commons.IntegerIDManager

Peeks the value that would be returned by the next call of IntegerIDManager.createNewID().

peekNextID() - Method in class info.bioinfweb.commons.LongIDManager

Peeks the value that would be returned by the next call of LongIDManager.createNewID().

PeekReader - Class in info.bioinfweb.commons.io

Reader implementation that allows to peek upcoming characters from the underlying reader.

PeekReader(Reader, int) - Constructor for class info.bioinfweb.commons.io.PeekReader

Creates a new instance of this class and fills the initial peek buffer.

PeekReader(Reader) - Constructor for class info.bioinfweb.commons.io.PeekReader

Creates a new instance of this class with the default peek buffer size (PeekReader.DEFAULT_PEEK_BUFFER_SIZE) and fills the initial peek buffer.

PeekReader.ReadResult - Class in info.bioinfweb.commons.io

Stores information about the result of a read operation, as it is returned by some methods of PeekReader.

peekString(int) - Method in class info.bioinfweb.commons.io.PeekReader

Previews the specified number of characters and returns them as a string.

PhylipWriter<S extends org.biojava3.core.sequence.template.Sequence<C>,C extends org.biojava3.core.sequence.template.Compound> - Class in info.bioinfweb.commons.bio.biojava3.alignment.io.phylip

Writes an alignment to a file in PHYLIP format.

PhylipWriter() - Constructor for class info.bioinfweb.commons.bio.biojava3.alignment.io.phylip.PhylipWriter

PhylipWriter(boolean) - Constructor for class info.bioinfweb.commons.bio.biojava3.alignment.io.phylip.PhylipWriter

PhylipWriter(boolean, int) - Constructor for class info.bioinfweb.commons.bio.biojava3.alignment.io.phylip.PhylipWriter

PhylipWriter(UniqueNameMap) - Constructor for class info.bioinfweb.commons.bio.biojava3.alignment.io.phylip.PhylipWriter

Note that certain parameter sets for the specified name map might lead to an invalid output of this class.

preferredLayoutSize(Container) - Method in class info.bioinfweb.commons.swing.WrapLayout

Returns the preferred dimensions for this layout given the visible components in the specified target container.

previous() - Method in class info.bioinfweb.commons.collections.ListIteratorDecorator

previousIndex() - Method in class info.bioinfweb.commons.collections.ListIteratorDecorator

printLog(PrintStream, String) - Method in class info.bioinfweb.commons.testing.TestLogger

printLog(String) - Method in class info.bioinfweb.commons.testing.TestLogger

printLogToErr(String) - Method in class info.bioinfweb.commons.testing.TestLogger

ProgramMainClass - Class in info.bioinfweb.commons

Main classes of applications providing a global Preferences and ApplicationVersion object can be inherited from this class.

ProgramMainClass(ApplicationVersion) - Constructor for class info.bioinfweb.commons.ProgramMainClass

Creates a new instance of this class.

ProgressDialog - Class in info.bioinfweb.commons.swing

A modal dialog displaying a progress bar that can be updated using the methods of ProgressMonitor.

ProgressDialog(Window, String) - Constructor for class info.bioinfweb.commons.swing.ProgressDialog

Creates a new instance of this class with the default cancel button and an updatable progress text which uses ProgressDialog.DEFAULT_PROGRESS_FORMAT to display the progrss value.

ProgressDialog(Window, String, DecimalFormat) - Constructor for class info.bioinfweb.commons.swing.ProgressDialog

Creates a new instance of this class with the default cancel button and an updatable progress text.

ProgressDialog(Window, String, DecimalFormat, boolean) - Constructor for class info.bioinfweb.commons.swing.ProgressDialog

Creates a new instance of this class with the default cancel button.

ProgressDialog(Window, String, DecimalFormat, boolean, String) - Constructor for class info.bioinfweb.commons.swing.ProgressDialog

Creates a new instance of this class.

ProgressMonitor - Interface in info.bioinfweb.commons.progress

This interface is used by the repeat finders to report their progress.

propertyChange(PropertyChangeEvent) - Method in class info.bioinfweb.commons.beans.PropertyChangeEventForwarder

propertyChange(PropertyChangeEvent) - Method in class info.bioinfweb.commons.changemonitor.PropertyChangeMonitor

PropertyChangeEventForwarder - Class in info.bioinfweb.commons.beans

Delegates PropertyChangeEvents to a collection of other PropertyChangeListeners and optionally adds a prefix to the property name.

PropertyChangeEventForwarder(String, Collection<PropertyChangeListener>) - Constructor for class info.bioinfweb.commons.beans.PropertyChangeEventForwarder

Creates a new instance of this class.

PropertyChangeEventForwarder(String, PropertyChangeListener) - Constructor for class info.bioinfweb.commons.beans.PropertyChangeEventForwarder

Creates a new instance of this class.

PropertyChangeMonitor - Class in info.bioinfweb.commons.changemonitor

This class can be used to assign a ChangeMonitor to an object that accepts PropertyChangeListeners.

PropertyChangeMonitor(String) - Constructor for class info.bioinfweb.commons.changemonitor.PropertyChangeMonitor

Creates a new instance of this class.

put(String, Action) - Method in class info.bioinfweb.commons.swing.ActionMap

putApplicationLogger(ApplicationLogger) - Method in class info.bioinfweb.commons.log.ApplicationLoggerParameterMap

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