A B C D E F G H I J K L M N O P Q R S T U V W X Z

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idExists(Connection, String, String, long) - Static method in class info.bioinfweb.commons.sql.IDGenerator

Returns whether an ID already exists is the specified column of the specified table.

idExists(Connection, String, String, String) - Static method in class info.bioinfweb.commons.sql.IDGenerator

IDGenerator - Class in info.bioinfweb.commons.sql

IDGenerator() - Constructor for class info.bioinfweb.commons.sql.IDGenerator

ImageRescaler - Class in info.bioinfweb.commons.graphics

ImageRescaler() - Constructor for class info.bioinfweb.commons.graphics.ImageRescaler

indexByName(String) - Method in class info.bioinfweb.commons.bio.biojava3.alignment.SimpleAlignment

indexByName(String) - Method in interface info.bioinfweb.commons.bio.biojava3.alignment.template.Alignment

indexOf(Object) - Method in class info.bioinfweb.commons.collections.ListDecorator

indexOfWhiteSpace(CharSequence) - Static method in class info.bioinfweb.commons.text.StringUtils

Returns the first index of any whitespace character.

indexOfWhiteSpace(CharSequence, int) - Static method in class info.bioinfweb.commons.text.StringUtils

Returns the first index of any whitespace character.

info.bioinfweb.commons - package info.bioinfweb.commons

info.bioinfweb.commons.applet - package info.bioinfweb.commons.applet

info.bioinfweb.commons.appversion - package info.bioinfweb.commons.appversion

info.bioinfweb.commons.beans - package info.bioinfweb.commons.beans

info.bioinfweb.commons.bio - package info.bioinfweb.commons.bio

info.bioinfweb.commons.bio.alignment.pairwise - package info.bioinfweb.commons.bio.alignment.pairwise

info.bioinfweb.commons.bio.biojava3.alignment - package info.bioinfweb.commons.bio.biojava3.alignment

info.bioinfweb.commons.bio.biojava3.alignment.io - package info.bioinfweb.commons.bio.biojava3.alignment.io

info.bioinfweb.commons.bio.biojava3.alignment.io.fasta - package info.bioinfweb.commons.bio.biojava3.alignment.io.fasta

info.bioinfweb.commons.bio.biojava3.alignment.io.hennig86 - package info.bioinfweb.commons.bio.biojava3.alignment.io.hennig86

info.bioinfweb.commons.bio.biojava3.alignment.io.mega - package info.bioinfweb.commons.bio.biojava3.alignment.io.mega

info.bioinfweb.commons.bio.biojava3.alignment.io.nexus - package info.bioinfweb.commons.bio.biojava3.alignment.io.nexus

info.bioinfweb.commons.bio.biojava3.alignment.io.phylip - package info.bioinfweb.commons.bio.biojava3.alignment.io.phylip

info.bioinfweb.commons.bio.biojava3.alignment.template - package info.bioinfweb.commons.bio.biojava3.alignment.template

info.bioinfweb.commons.bio.biojava3.core.sequence - package info.bioinfweb.commons.bio.biojava3.core.sequence

info.bioinfweb.commons.bio.biojava3.core.sequence.compound - package info.bioinfweb.commons.bio.biojava3.core.sequence.compound

info.bioinfweb.commons.bio.biojava3.core.sequence.io - package info.bioinfweb.commons.bio.biojava3.core.sequence.io

info.bioinfweb.commons.bio.biojava3.core.sequence.template - package info.bioinfweb.commons.bio.biojava3.core.sequence.template

info.bioinfweb.commons.bio.biojava3.core.sequence.views - package info.bioinfweb.commons.bio.biojava3.core.sequence.views

info.bioinfweb.commons.bio.biojavax.bio.phylo.io.nexus - package info.bioinfweb.commons.bio.biojavax.bio.phylo.io.nexus

info.bioinfweb.commons.changemonitor - package info.bioinfweb.commons.changemonitor

info.bioinfweb.commons.collections - package info.bioinfweb.commons.collections

Contains extensions to the Java Collections API made for bioinfweb projects that can be of general use.

info.bioinfweb.commons.collections.bitstorage - package info.bioinfweb.commons.collections.bitstorage

info.bioinfweb.commons.collections.bitstorage.exception - package info.bioinfweb.commons.collections.bitstorage.exception

Contains exceptions associated with the bit storage classes in bioinfweb.commons.collections.

info.bioinfweb.commons.collections.observable - package info.bioinfweb.commons.collections.observable

Contains implementation related to observable collections (e.g.

info.bioinfweb.commons.events - package info.bioinfweb.commons.events

Contains event object implementations of general use.

info.bioinfweb.commons.graphics - package info.bioinfweb.commons.graphics

info.bioinfweb.commons.io - package info.bioinfweb.commons.io

info.bioinfweb.commons.io.streammessage - package info.bioinfweb.commons.io.streammessage

info.bioinfweb.commons.log - package info.bioinfweb.commons.log

Classes in this package implement a simple logging API for messages of different types that an application can output to the user.

info.bioinfweb.commons.progress - package info.bioinfweb.commons.progress

info.bioinfweb.commons.servlet - package info.bioinfweb.commons.servlet

info.bioinfweb.commons.servlet.acceptlanguage - package info.bioinfweb.commons.servlet.acceptlanguage

info.bioinfweb.commons.sql - package info.bioinfweb.commons.sql

info.bioinfweb.commons.sql.sqlproperties - package info.bioinfweb.commons.sql.sqlproperties

info.bioinfweb.commons.swing - package info.bioinfweb.commons.swing

info.bioinfweb.commons.swing.actions - package info.bioinfweb.commons.swing.actions

info.bioinfweb.commons.swing.scrollpaneselector - package info.bioinfweb.commons.swing.scrollpaneselector

info.bioinfweb.commons.swt - package info.bioinfweb.commons.swt

info.bioinfweb.commons.testing - package info.bioinfweb.commons.testing

info.bioinfweb.commons.text - package info.bioinfweb.commons.text

info.bioinfweb.commons.tokenizer - package info.bioinfweb.commons.tokenizer

insertBits(long, long) - Method in interface info.bioinfweb.commons.collections.bitstorage.BitField

Inserts the specified number of bits at the specified position of the bit field and moves all bits with indices >= start to the right.

insertIntoDB(String, Object[]) - Method in class info.bioinfweb.commons.servlet.SQLManipulator

Inserts a new entry in a databse table.

insertIntoDB(String, String[], Object[]) - Method in class info.bioinfweb.commons.servlet.SQLManipulator

Inserts a new entry in a database table

insertRange(long, long) - Method in class info.bioinfweb.commons.collections.PackedIntegerArrayList

Reserves space for the specified number of elements at the specified position.

insertUpdate(DocumentEvent) - Method in class info.bioinfweb.commons.swing.SwingChangeMonitor

installScrollPaneSelector(JScrollPane) - Static method in class info.bioinfweb.commons.swing.scrollpaneselector.ExtendedScrollPaneSelector

Installs a ScrollPaneSelector to the given JScrollPane instance.

installScrollPaneSelector(JScrollPane) - Static method in class org.jdesktop.swingx.scrollpaneselector.ScrollPaneSelector

Installs a ScrollPaneSelector to the given JScrollPane instance.

INT_PATTERN - Static variable in class info.bioinfweb.commons.Math2

INTEGER_FORMAT - Static variable in class info.bioinfweb.commons.swing.DecimalInput

INTEGER_FORMAT - Static variable in class info.bioinfweb.commons.text.StringUtils

IntegerIDManager - Class in info.bioinfweb.commons

A tool class that creates unique int IDs.

IntegerIDManager() - Constructor for class info.bioinfweb.commons.IntegerIDManager

InternationalFileFilter - Class in info.bioinfweb.commons.io

InternationalFileFilter() - Constructor for class info.bioinfweb.commons.io.InternationalFileFilter

IntervalInformation(int, Comparator<E>) - Constructor for class info.bioinfweb.commons.collections.SequenceIntervalList.IntervalInformation

intPow(int, int) - Static method in class info.bioinfweb.commons.Math2

InvalidBitNumberForPrimitiveException - Exception in info.bioinfweb.commons.collections.bitstorage.exception

InvalidBitNumberForPrimitiveException(String, BitField, long, int) - Constructor for exception info.bioinfweb.commons.collections.bitstorage.exception.InvalidBitNumberForPrimitiveException

Creates a new instance of this class.

InvalidXSDPathException - Exception in info.bioinfweb.commons.io

This exception is thrown by XMLUtils.extractXSDFileName(javax.xml.stream.events.StartElement) if the value of the xsi:schemaLocation attribute is not a valid path.

InvalidXSDPathException() - Constructor for exception info.bioinfweb.commons.io.InvalidXSDPathException

InvalidXSDPathException(String, Throwable) - Constructor for exception info.bioinfweb.commons.io.InvalidXSDPathException

InvalidXSDPathException(String) - Constructor for exception info.bioinfweb.commons.io.InvalidXSDPathException

InvalidXSDPathException(Throwable) - Constructor for exception info.bioinfweb.commons.io.InvalidXSDPathException

invert(CharSequence) - Static method in class info.bioinfweb.commons.text.StringUtils

invertColor(Color) - Static method in class info.bioinfweb.commons.graphics.GraphicsUtils

ioFinished() - Method in interface info.bioinfweb.commons.io.IOProgressListener

This method is called when a reading or writing of data has been finished.

ioFinished() - Method in class info.bioinfweb.commons.io.IOProgressListenerAdapter

ioFinished() - Method in class info.bioinfweb.commons.io.IOProgressListenerVector

ioProgress(long) - Method in interface info.bioinfweb.commons.io.IOProgressListener

This method is called when a progress in reading or writing data has been made.

ioProgress(long) - Method in class info.bioinfweb.commons.io.IOProgressListenerAdapter

ioProgress(long) - Method in class info.bioinfweb.commons.io.IOProgressListenerVector

IOProgressListener - Interface in info.bioinfweb.commons.io

Classes that implement this interface can be informed about the progress of reading and writing data.

IOProgressListenerAdapter - Class in info.bioinfweb.commons.io

An abstract adapter class for receiving IO progress events.

IOProgressListenerAdapter() - Constructor for class info.bioinfweb.commons.io.IOProgressListenerAdapter

IOProgressListenerVector - Class in info.bioinfweb.commons.io

This class can be used if several profress listeners should be informed about the same process.

IOProgressListenerVector() - Constructor for class info.bioinfweb.commons.io.IOProgressListenerVector

ioStarts() - Method in interface info.bioinfweb.commons.io.IOProgressListener

This method is called when a reading or writing of data is about to begin.

ioStarts() - Method in class info.bioinfweb.commons.io.IOProgressListenerAdapter

ioStarts() - Method in class info.bioinfweb.commons.io.IOProgressListenerVector

IOUtils - Class in info.bioinfweb.commons.io

This class provides general tools for reading and writing data.

IOUtils() - Constructor for class info.bioinfweb.commons.io.IOUtils

IS_64_BIT_ARCHITECTURE - Static variable in class info.bioinfweb.commons.SystemUtils

isAcceptFilesWithExceptions() - Method in class info.bioinfweb.commons.io.ContentExtensionFileFilter

Determines whether this filter accepts files where IOExceptions were thrown while they were tested with ContentExtensionFileFilter.acceptContent(File).

isAllowClose() - Method in class info.bioinfweb.commons.io.LimitedInputStream

Determines whether closing this input stream shall currently be prevented.

isAllowClose() - Method in class info.bioinfweb.commons.io.LimitedReader

Determines whether closing this reader shall currently be prevented.

isAminoAcidAmbiguityCode(String) - Static method in class info.bioinfweb.commons.bio.SequenceUtils

Determines whether the specified character is an amino acid ambiguity code.

isBetween(byte, byte, byte) - Static method in class info.bioinfweb.commons.Math2

Checks if the specified value is greater or equal to the specified minimum and lower or equal to the specified maximum.

isBetween(int, int, int) - Static method in class info.bioinfweb.commons.Math2

Checks if the specified value is greater or equal to the specified minimum and lower or equal to the specified maximum.

isBetween(long, long, long) - Static method in class info.bioinfweb.commons.Math2

Checks if the specified value is greater or equal to the specified minimum and lower or equal to the specified maximum.

isBetween(float, float, float) - Static method in class info.bioinfweb.commons.Math2

Checks if the specified value is greater or equal to the specified minimum and lower or equal to the specified maximum.

isBetween(double, double, double) - Static method in class info.bioinfweb.commons.Math2

Checks if the specified value is greater or equal to the specified minimum and lower or equal to the specified maximum.

isBetweenNE(byte, byte, byte) - Static method in class info.bioinfweb.commons.Math2

Checks if the specified value is greater then the specified minimum and lower than the specified maximum.

isBetweenNE(int, int, int) - Static method in class info.bioinfweb.commons.Math2

Checks if the specified value is greater then the specified minimum and lower than the specified maximum.

isBetweenNE(long, long, long) - Static method in class info.bioinfweb.commons.Math2

Checks if the specified value is greater then the specified minimum and lower than the specified maximum.

isBetweenNE(float, float, float) - Static method in class info.bioinfweb.commons.Math2

Checks if the specified value is greater then the specified minimum and lower than the specified maximum.

isBetweenNE(double, double, double) - Static method in class info.bioinfweb.commons.Math2

Checks if the specified value is greater then the specified minimum and lower than the specified maximum.

isCanceled() - Method in interface info.bioinfweb.commons.progress.ProgressMonitor

isCanceled() - Method in class info.bioinfweb.commons.progress.VoidProgressMonitor

This method always returns false.

isCanceled() - Method in class info.bioinfweb.commons.swing.ProgressDialog

isCharacterType(int) - Static method in class info.bioinfweb.commons.io.XMLUtils

isChildComponent(Component, Component) - Static method in class info.bioinfweb.commons.swing.SwingUtils

isChildComponent(Composite, Control) - Static method in class info.bioinfweb.commons.swt.SWTUtils

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

Allows to determine whether the specified maximum number of characters were read or all characters were read as intended.

isConntected() - Method in class info.bioinfweb.commons.servlet.SQLManipulator

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

Returns the whether the given string can be parsed to a double or a float.

isDiscrete() - Method in enum info.bioinfweb.commons.bio.CharacterStateSetType

Tests whether this token set type describes a set of discrete tokens.

isDNAChar(char) - Static method in class info.bioinfweb.commons.bio.SequenceUtils

isEmpty() - Method in class info.bioinfweb.commons.bio.biojava3.alignment.SimpleAlignment

isEmpty() - Method in interface info.bioinfweb.commons.bio.biojava3.alignment.template.Alignment

isEmpty() - Method in class info.bioinfweb.commons.collections.ListDecorator

isEmpty() - Method in class info.bioinfweb.commons.collections.NonStoringCollection

Since no objects are stored in this collection this method will always return true.

isEmpty() - Method in class info.bioinfweb.commons.collections.SequenceIntervalList

isEmpty() - Method in class info.bioinfweb.commons.swing.ActionMap

isEmpty() - Method in class info.bioinfweb.commons.text.UniqueNameMap

isFillUp() - Method in class info.bioinfweb.commons.text.UniqueNameMapParameters

isHorizontal() - Method in class info.bioinfweb.commons.swt.ScrolledCompositeSyncListener

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

Checks if the specified value is the string representation of a mathematical integer.

isInt(double) - Static method in class info.bioinfweb.commons.Math2

Checks if the specified value is a mathematical integer.

isInt(float) - Static method in class info.bioinfweb.commons.Math2

Checks if the specified value is a mathematical integer.

isInTokenSet(char, String) - Static method in class info.bioinfweb.commons.bio.SequenceUtils

isLimitReached() - Method in class info.bioinfweb.commons.io.LimitedInputStream

Checks whether the specified maximum number of bytes has been read from the decorated input stream.

isLimitReached() - Method in class info.bioinfweb.commons.io.LimitedReader

Checks whether the specified maximum number of characters has been read from the underlying reader.

isNewLineChar(char) - Static method in class info.bioinfweb.commons.text.StringUtils

Checks if the specified character is a new line character

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

Tests of the character that will be returned by the next call of e.g.

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

Tests of the specified string is contained in the underlying character stream at the current position.

isNext(String[]) - Method in class info.bioinfweb.commons.io.PeekReader

Tests if one of the specified strings is contained in the underlying character stream at the current position.

isNonAmbiguityAminoAcid(String) - Static method in class info.bioinfweb.commons.bio.SequenceUtils

isNonAmbiguityNucleotide(char) - Static method in class info.bioinfweb.commons.bio.SequenceUtils

isNucleotide() - Method in enum info.bioinfweb.commons.bio.CharacterStateSetType

Tests whether this token set type describes a set of nucleotide tokens.

isNucleotideAmbuguityCode(char) - Static method in class info.bioinfweb.commons.bio.SequenceUtils

Determines whether the specified character is an IUPAC ambiguity code.

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

isRNAChar(char) - Static method in class info.bioinfweb.commons.bio.SequenceUtils

isSaveCanceled() - Method in class info.bioinfweb.commons.swing.FileChooserDirModel

isSignificant() - Method in class info.bioinfweb.commons.swing.AbstractDocumentEdit

isUnlimitedLength() - Method in class info.bioinfweb.commons.text.UniqueNameMapParameters

isUseErrorStream() - Method in class info.bioinfweb.commons.log.ConsoleApplicationLogger

Determines whether error messages received by this logger should be written to System.err or System.out.

isVertical() - Method in class info.bioinfweb.commons.swt.ScrolledCompositeSyncListener

itemStateChanged(ItemEvent) - Method in class info.bioinfweb.commons.swing.SwingChangeMonitor

iterator() - Method in class info.bioinfweb.commons.bio.biojava3.core.sequence.views.ConcatenatedSequenceView

iterator() - Method in class info.bioinfweb.commons.collections.ListDecorator

iterator() - Method in class info.bioinfweb.commons.collections.NonStoringCollection

Since no objects are stored in this collection this method will always return an empty iterator.

iterator() - Method in class info.bioinfweb.commons.collections.SequenceIntervalList

Returns an iterator over the list.

A B C D E F G H I J K L M N O P Q R S T U V W X Z