- AboutDialog - Class in info.bioinfweb.commons.swing
-
A customizable about dialog that contains information in mutliple tabs.
- AboutDialog(Dialog, boolean) - Constructor for class info.bioinfweb.commons.swing.AboutDialog
-
- AboutDialog(Dialog, String, boolean, GraphicsConfiguration) - Constructor for class info.bioinfweb.commons.swing.AboutDialog
-
- AboutDialog(Dialog, String, boolean) - Constructor for class info.bioinfweb.commons.swing.AboutDialog
-
- AboutDialog(Dialog, String) - Constructor for class info.bioinfweb.commons.swing.AboutDialog
-
- AboutDialog(Dialog) - Constructor for class info.bioinfweb.commons.swing.AboutDialog
-
- AboutDialog(Frame, boolean) - Constructor for class info.bioinfweb.commons.swing.AboutDialog
-
- AboutDialog(Frame, String, boolean, GraphicsConfiguration) - Constructor for class info.bioinfweb.commons.swing.AboutDialog
-
- AboutDialog(Frame, String, boolean) - Constructor for class info.bioinfweb.commons.swing.AboutDialog
-
- AboutDialog(Frame, String) - Constructor for class info.bioinfweb.commons.swing.AboutDialog
-
- AboutDialog(Frame) - Constructor for class info.bioinfweb.commons.swing.AboutDialog
-
- AboutDialog(Window, Dialog.ModalityType) - Constructor for class info.bioinfweb.commons.swing.AboutDialog
-
- AboutDialog(Window, String, Dialog.ModalityType, GraphicsConfiguration) - Constructor for class info.bioinfweb.commons.swing.AboutDialog
-
- AboutDialog(Window, String, Dialog.ModalityType) - Constructor for class info.bioinfweb.commons.swing.AboutDialog
-
- AboutDialog(Window, String) - Constructor for class info.bioinfweb.commons.swing.AboutDialog
-
- AboutDialog(Window) - Constructor for class info.bioinfweb.commons.swing.AboutDialog
-
- absoluteFilePath(File, File) - Static method in class info.bioinfweb.commons.io.IOUtils
-
Returns an absolute version of path.
- AbstractAlignmentReader<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
-
- AbstractAlignmentReader(SequenceCreatorInterface<C>) - Constructor for class info.bioinfweb.commons.bio.biojava3.alignment.io.AbstractAlignmentReader
-
- AbstractAlignmentWriter<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
-
- AbstractAlignmentWriter(UniqueNameMap) - Constructor for class info.bioinfweb.commons.bio.biojava3.alignment.io.AbstractAlignmentWriter
-
- AbstractAlignmentWriter() - Constructor for class info.bioinfweb.commons.bio.biojava3.alignment.io.AbstractAlignmentWriter
-
- AbstractApplicationLogger - Class in info.bioinfweb.commons.log
-
Implements basic functionality (especially method delegation) of a application logger.
- AbstractApplicationLogger() - Constructor for class info.bioinfweb.commons.log.AbstractApplicationLogger
-
- AbstractDocumentEdit - Class in info.bioinfweb.commons.swing
-
Implements basic functionality for edits on a document that takes track of changes.
- AbstractDocumentEdit() - Constructor for class info.bioinfweb.commons.swing.AbstractDocumentEdit
-
- AbstractIntegerBitList<N extends java.lang.Number> - Class in info.bioinfweb.commons.collections.bitstorage
-
- AbstractIntegerBitList(int) - Constructor for class info.bioinfweb.commons.collections.bitstorage.AbstractIntegerBitList
-
- AbstractNucleotideCompoundSet2 - Class in info.bioinfweb.commons.bio.biojava3.core.sequence.template
-
Ancestor of the nucleotide compound sets in info.bioinfweb.biojavax.
- AbstractNucleotideCompoundSet2() - Constructor for class info.bioinfweb.commons.bio.biojava3.core.sequence.template.AbstractNucleotideCompoundSet2
-
- AbstractProgressMonitor - Class in info.bioinfweb.commons.progress
-
- AbstractProgressMonitor() - Constructor for class info.bioinfweb.commons.progress.AbstractProgressMonitor
-
- AbstractSaver - Class in info.bioinfweb.commons.io
-
- AbstractSaver() - Constructor for class info.bioinfweb.commons.io.AbstractSaver
-
- AbstractUndoActionManagement - Class in info.bioinfweb.commons.swing
-
Implements basic functionality for applications using an
AccessibleUndoManager to display undoable (and
redoable) edits in swing submenus.
- AbstractUndoActionManagement() - Constructor for class info.bioinfweb.commons.swing.AbstractUndoActionManagement
-
- accept(File) - Method in class info.bioinfweb.commons.io.ContentExtensionFileFilter
-
- accept(File) - Method in class info.bioinfweb.commons.io.ExtensionFileFilter
-
This default implementation accepts all files that are directories or that end with one of the defined extensions.
- accept(File, String) - Method in class info.bioinfweb.commons.io.ExtensionFileFilter
-
- ACCEPT_LANG_PATTERN_ALL - Static variable in class info.bioinfweb.commons.servlet.acceptlanguage.AcceptLanguageParser
-
- ACCEPT_LANG_PATTERN_NO_COUNTRY - Static variable in class info.bioinfweb.commons.servlet.acceptlanguage.AcceptLanguageParser
-
- ACCEPT_LANG_PATTERN_NO_QUALITY - Static variable in class info.bioinfweb.commons.servlet.acceptlanguage.AcceptLanguageParser
-
- acceptContent(File) - Method in class info.bioinfweb.commons.io.ContentExtensionFileFilter
-
Tests the contents of the specified file.
- acceptContent(FileInputStream) - Method in class info.bioinfweb.commons.io.ContentExtensionFileFilter
-
Inherited classes must implement this method to test the content of a file.
- AcceptLanguageEntry - Class in info.bioinfweb.commons.servlet.acceptlanguage
-
Represents one entry in the list of accepted languages in the Accept-Language HTTP header.
- AcceptLanguageEntry() - Constructor for class info.bioinfweb.commons.servlet.acceptlanguage.AcceptLanguageEntry
-
- AcceptLanguageEntry(String, String, double) - Constructor for class info.bioinfweb.commons.servlet.acceptlanguage.AcceptLanguageEntry
-
- AcceptLanguageEntry(String, String) - Constructor for class info.bioinfweb.commons.servlet.acceptlanguage.AcceptLanguageEntry
-
- AcceptLanguageParser - Class in info.bioinfweb.commons.servlet.acceptlanguage
-
Class that parses the accept-language HTTP header including its quality scores.
- AcceptLanguageParser() - Constructor for class info.bioinfweb.commons.servlet.acceptlanguage.AcceptLanguageParser
-
- AcceptLanguageRedirectServlet - Class in info.bioinfweb.commons.servlet.acceptlanguage
-
This servlet redirects the client to the URL associated with its accepted language.
- AcceptLanguageRedirectServlet() - Constructor for class info.bioinfweb.commons.servlet.acceptlanguage.AcceptLanguageRedirectServlet
-
- AcceptLanguageRedirectServlet(String) - Constructor for class info.bioinfweb.commons.servlet.acceptlanguage.AcceptLanguageRedirectServlet
-
- AccessibleUndoManager - Class in info.bioinfweb.commons.swing
-
An extension of UndoManager that allows to access all edit objects contained in the underlying list.
- AccessibleUndoManager() - Constructor for class info.bioinfweb.commons.swing.AccessibleUndoManager
-
- ActionMap - Class in info.bioinfweb.commons.swing
-
This class allows to store various Action objects in a Map
and access them with a unique String.
- ActionMap() - Constructor for class info.bioinfweb.commons.swing.ActionMap
-
- actionPerformed(ActionEvent) - Method in class info.bioinfweb.commons.swing.actions.OpenWebsiteAction
-
- add(AmbiguityBaseScore) - Method in class info.bioinfweb.commons.bio.AmbiguityBaseScore
-
- add(String, S) - Method in class info.bioinfweb.commons.bio.biojava3.alignment.SimpleAlignment
-
- add(int, String, S) - Method in class info.bioinfweb.commons.bio.biojava3.alignment.SimpleAlignment
-
- add(String, S) - Method in interface info.bioinfweb.commons.bio.biojava3.alignment.template.Alignment
-
- add(int, String, S) - Method in interface info.bioinfweb.commons.bio.biojava3.alignment.template.Alignment
-
- add(E) - Method in class info.bioinfweb.commons.collections.ListDecorator
-
- add(int, E) - Method in class info.bioinfweb.commons.collections.ListDecorator
-
- add(E) - Method in class info.bioinfweb.commons.collections.ListIteratorDecorator
-
- add(SimpleSequenceInterval) - Method in class info.bioinfweb.commons.collections.NonOverlappingIntervalList
-
- add(int) - Method in class info.bioinfweb.commons.collections.NonOverlappingIntervalList
-
- add(int, int) - Method in class info.bioinfweb.commons.collections.NonOverlappingIntervalList
-
- add(Object) - Method in class info.bioinfweb.commons.collections.NonStoringCollection
-
Always returns false.
- add(long, long) - Method in class info.bioinfweb.commons.collections.PackedIntegerArrayList
-
Adds the specified element to this list and moves other elements to the right if necessary.
- add(long) - Method in class info.bioinfweb.commons.collections.PackedIntegerArrayList
-
Adds the specified element to the end of this list.
- add(E) - Method in class info.bioinfweb.commons.collections.PackedObjectArrayList
-
- add(int, E) - Method in class info.bioinfweb.commons.collections.PackedObjectArrayList
-
- add(int, E) - Method in class info.bioinfweb.commons.collections.PackedPrimitiveWrapperArrayList
-
- add(E) - Method in class info.bioinfweb.commons.collections.SequenceIntervalList
-
- add(E) - Method in class info.bioinfweb.commons.collections.SequenceIntervalList.IntervalInformation
-
- add(IOProgressListener) - Method in class info.bioinfweb.commons.io.IOProgressListenerVector
-
- add(E) - Method in class info.bioinfweb.commons.swing.ListBackedListModel
-
- add(int, E) - Method in class info.bioinfweb.commons.swing.ListBackedListModel
-
- add(String) - Method in class info.bioinfweb.commons.tokenizer.StrTokenizer
-
- addAll(Collection<? extends E>) - Method in class info.bioinfweb.commons.collections.ListDecorator
-
- addAll(int, Collection<? extends E>) - Method in class info.bioinfweb.commons.collections.ListDecorator
-
- addAll(NonOverlappingIntervalList, int, int, boolean) - Method in class info.bioinfweb.commons.collections.NonOverlappingIntervalList
-
Adds all or a part of the intervals contained in another list to this list.
- addAll(NonOverlappingIntervalList) - Method in class info.bioinfweb.commons.collections.NonOverlappingIntervalList
-
Adds all of the intervals contained in another list to this list.
- addAll(Collection<? extends E>) - Method in class info.bioinfweb.commons.collections.NonStoringCollection
-
Always returns false.
- addAll(Collection<? extends E>) - Method in class info.bioinfweb.commons.collections.SequenceIntervalList
-
- addAllCharSets(Collection<CharSet>) - Method in class info.bioinfweb.commons.bio.biojava3.alignment.SimpleAlignment
-
- addAllCharSets(Collection<CharSet>) - Method in interface info.bioinfweb.commons.bio.biojava3.alignment.template.Alignment
-
- addAmbiguityDNACompounds() - Method in class info.bioinfweb.commons.bio.biojava3.core.sequence.template.AbstractNucleotideCompoundSet2
-
- addAmbiguityDNARNACompounds() - Method in class info.bioinfweb.commons.bio.biojava3.core.sequence.template.AbstractNucleotideCompoundSet2
-
- addAmbiguityRNACompounds() - Method in class info.bioinfweb.commons.bio.biojava3.core.sequence.template.AbstractNucleotideCompoundSet2
-
- addCharSet(CharSet) - Method in class info.bioinfweb.commons.bio.biojava3.alignment.SimpleAlignment
-
- addCharSet(CharSet) - Method in interface info.bioinfweb.commons.bio.biojava3.alignment.template.Alignment
-
- addCharSet(String) - Method in class info.bioinfweb.commons.bio.biojavax.bio.phylo.io.nexus.SetsBlock
-
Adds a new character set with the specified name, if not already present.
- addCharSet(String) - Method in class info.bioinfweb.commons.bio.biojavax.bio.phylo.io.nexus.SetsBlockBuilder
-
- addCharSet(String) - Method in interface info.bioinfweb.commons.bio.biojavax.bio.phylo.io.nexus.SetsBlockListener
-
Adds a new character set with the specified name, if not already present.
- addCharSetInterval(String, int, int) - Method in class info.bioinfweb.commons.bio.biojavax.bio.phylo.io.nexus.SetsBlock
-
Adds the specified interval to the specified character set.
- addCharSetInterval(String, int, int) - Method in class info.bioinfweb.commons.bio.biojavax.bio.phylo.io.nexus.SetsBlockBuilder
-
- addCharSetInterval(String, int, int) - Method in interface info.bioinfweb.commons.bio.biojavax.bio.phylo.io.nexus.SetsBlockListener
-
Adds the specified interval to the specified character set.
- addComment(NexusComment) - Method in class info.bioinfweb.commons.bio.biojavax.bio.phylo.io.nexus.SetsBlockBuilder
-
The implementation of this method is currently empty since HIR Finder does not process
any information included in Nexus comments.
- addEdit(UndoableEdit) - Method in class info.bioinfweb.commons.swing.AbstractDocumentEdit
-
- addEntry(String, CharSequence) - Method in class info.bioinfweb.commons.testing.TestLogger
-
- addEntry(String, Object...) - Method in class info.bioinfweb.commons.testing.TestLogger
-
- addError(String, int) - Method in class info.bioinfweb.commons.log.AbstractApplicationLogger
-
- addError(String) - Method in class info.bioinfweb.commons.log.AbstractApplicationLogger
-
- addError(Throwable, boolean) - Method in class info.bioinfweb.commons.log.AbstractApplicationLogger
-
- addError(Throwable, boolean, int) - Method in class info.bioinfweb.commons.log.AbstractApplicationLogger
-
- addError(String) - Method in interface info.bioinfweb.commons.log.ApplicationLogger
-
Outputs an error message to the user.
- addError(String, int) - Method in interface info.bioinfweb.commons.log.ApplicationLogger
-
Outputs an error message to the user.
- addError(Throwable, boolean) - Method in interface info.bioinfweb.commons.log.ApplicationLogger
-
Outputs an error message to the user.
- addError(Throwable, boolean, int) - Method in interface info.bioinfweb.commons.log.ApplicationLogger
-
Outputs an error message to the user.
- addError(String) - Method in class info.bioinfweb.commons.log.ApplicationLoggerDialog
-
- addError(String, int) - Method in class info.bioinfweb.commons.log.ApplicationLoggerDialog
-
- addError(Throwable, boolean) - Method in class info.bioinfweb.commons.log.ApplicationLoggerDialog
-
- addError(Throwable, boolean, int) - Method in class info.bioinfweb.commons.log.ApplicationLoggerDialog
-
- addError(String) - Method in class info.bioinfweb.commons.log.MultipleApplicationLoggersAdapter
-
- addError(String, int) - Method in class info.bioinfweb.commons.log.MultipleApplicationLoggersAdapter
-
- addError(Throwable, boolean) - Method in class info.bioinfweb.commons.log.MultipleApplicationLoggersAdapter
-
- addError(Throwable, boolean, int) - Method in class info.bioinfweb.commons.log.MultipleApplicationLoggersAdapter
-
- addError(String) - Method in class info.bioinfweb.commons.log.VoidApplicationLogger
-
- addError(String, int) - Method in class info.bioinfweb.commons.log.VoidApplicationLogger
-
- addError(Throwable, boolean) - Method in class info.bioinfweb.commons.log.VoidApplicationLogger
-
- addError(Throwable, boolean, int) - Method in class info.bioinfweb.commons.log.VoidApplicationLogger
-
- addFileChooser(JFileChooser) - Method in class info.bioinfweb.commons.swing.FileChooserDirModel
-
- addFileExtension(String) - Method in class info.bioinfweb.commons.io.AbstractSaver
-
- addFileExtension(String) - Method in interface info.bioinfweb.commons.io.Savable
-
Adds an file extension to the list of the allowed file extensions which can be entered
by the user in the save as dialog.
- addLeadingKeyword(String, String) - Static method in class info.bioinfweb.commons.sql.SQLUtils
-
- addListChangeListener(ListChangeListener<E>) - Method in class info.bioinfweb.commons.collections.observable.ObservableList
-
Adds a change listener to track changes of the underlying list.
- addListToLogger(ApplicationLogger) - Method in class info.bioinfweb.commons.log.MessageListApplicationLogger
-
Adds all messages stored in this list to the other logger.
- addMessage(String, int) - Method in class info.bioinfweb.commons.log.AbstractApplicationLogger
-
- addMessage(String) - Method in class info.bioinfweb.commons.log.AbstractApplicationLogger
-
- addMessage(ApplicationLoggerMessage) - Method in interface info.bioinfweb.commons.log.ApplicationLogger
-
Outputs a usual message to the user.
- addMessage(String) - Method in interface info.bioinfweb.commons.log.ApplicationLogger
-
Outputs a usual message to the user.
- addMessage(String, int) - Method in interface info.bioinfweb.commons.log.ApplicationLogger
-
Outputs a usual message to the user.
- addMessage(ApplicationLoggerMessage) - Method in class info.bioinfweb.commons.log.ApplicationLoggerDialog
-
- addMessage(String, int) - Method in class info.bioinfweb.commons.log.ApplicationLoggerDialog
-
- addMessage(String) - Method in class info.bioinfweb.commons.log.ApplicationLoggerDialog
-
- addMessage(ApplicationLoggerMessage) - Method in class info.bioinfweb.commons.log.ConsoleApplicationLogger
-
- addMessage(ApplicationLoggerMessage) - Method in class info.bioinfweb.commons.log.JTextAreaApplicationLogger
-
- addMessage(ApplicationLoggerMessage) - Method in class info.bioinfweb.commons.log.MessageListApplicationLogger
-
- addMessage(ApplicationLoggerMessage) - Method in class info.bioinfweb.commons.log.MultipleApplicationLoggersAdapter
-
- addMessage(String) - Method in class info.bioinfweb.commons.log.MultipleApplicationLoggersAdapter
-
- addMessage(String, int) - Method in class info.bioinfweb.commons.log.MultipleApplicationLoggersAdapter
-
- addMessage(ApplicationLoggerMessage) - Method in class info.bioinfweb.commons.log.SwingDocumentApplicationLogger
-
- addMessage(ApplicationLoggerMessage) - Method in class info.bioinfweb.commons.log.TextFileApplicationLogger
-
- addMessage(ApplicationLoggerMessage) - Method in class info.bioinfweb.commons.log.VoidApplicationLogger
-
- addMessage(String) - Method in class info.bioinfweb.commons.log.VoidApplicationLogger
-
- addMessage(String, int) - Method in class info.bioinfweb.commons.log.VoidApplicationLogger
-
- addMoreButtons(JPanel) - Method in class info.bioinfweb.commons.swing.OkCancelApplyDialog
-
- addMoreButtons(JPanel) - Method in class info.bioinfweb.commons.swing.OkCancelApplyHelpDialog
-
- addName(String) - Method in class info.bioinfweb.commons.text.UniqueNameMap
-
Adds an original name as the key and its processed version as the values to the map.
- addNames(Collection<String>) - Method in class info.bioinfweb.commons.text.UniqueNameMap
-
- addPropertyChangeListener(PropertyChangeListener) - Method in class info.bioinfweb.commons.graphics.ZoomableFont
-
- addPropertyChangeListener(String, PropertyChangeListener) - Method in class info.bioinfweb.commons.graphics.ZoomableFont
-
- addScrolledTab(String, Icon, Component, String) - Method in class info.bioinfweb.commons.swing.AboutDialog
-
- addTab(String, Icon, Component, String) - Method in class info.bioinfweb.commons.swing.AboutDialog
-
- addTab(String, Icon, String, String, String) - Method in class info.bioinfweb.commons.swing.AboutDialog
-
- addTimeDiff(String, String) - Method in class info.bioinfweb.commons.testing.TestLogger
-
Adds the time span that has passed between the call of this method and the time stored in
sourceName to the value in targetName.
- addTo(Container) - Method in class info.bioinfweb.commons.changemonitor.PropertyChangeMonitor
-
- addToColorChannels(Color, int) - Static method in class info.bioinfweb.commons.graphics.GraphicsUtils
-
Adds a constant value to all color channels of the specified color.
- addToNumericValue(String, long) - Method in class info.bioinfweb.commons.testing.TestLogger
-
- addToProgressValue(double) - Method in class info.bioinfweb.commons.progress.AbstractProgressMonitor
-
- addToProgressValue(double, String) - Method in class info.bioinfweb.commons.progress.AbstractProgressMonitor
-
- addToProgressValue(double) - Method in interface info.bioinfweb.commons.progress.ProgressMonitor
-
- addToProgressValue(double, String) - Method in interface info.bioinfweb.commons.progress.ProgressMonitor
-
- addToProgressValue(double) - Method in class info.bioinfweb.commons.swing.ProgressDialog
-
- addToProgressValue(double, String) - Method in class info.bioinfweb.commons.swing.ProgressDialog
-
- addTrailingKeyword(String, String) - Static method in class info.bioinfweb.commons.sql.SQLUtils
-
- addWarning(String, int) - Method in class info.bioinfweb.commons.log.AbstractApplicationLogger
-
- addWarning(String) - Method in class info.bioinfweb.commons.log.AbstractApplicationLogger
-
- addWarning(String) - Method in interface info.bioinfweb.commons.log.ApplicationLogger
-
Outputs a warning message to the user.
- addWarning(String, int) - Method in interface info.bioinfweb.commons.log.ApplicationLogger
-
Outputs a warning message to the user.
- addWarning(String, int) - Method in class info.bioinfweb.commons.log.ApplicationLoggerDialog
-
- addWarning(String) - Method in class info.bioinfweb.commons.log.ApplicationLoggerDialog
-
- addWarning(String) - Method in class info.bioinfweb.commons.log.MultipleApplicationLoggersAdapter
-
- addWarning(String, int) - Method in class info.bioinfweb.commons.log.MultipleApplicationLoggersAdapter
-
- addWarning(String) - Method in class info.bioinfweb.commons.log.VoidApplicationLogger
-
- addWarning(String, int) - Method in class info.bioinfweb.commons.log.VoidApplicationLogger
-
- ADENINE_INDEX - Static variable in class info.bioinfweb.commons.bio.AmbiguityBaseScore
-
- adjustFromFont(Font) - Method in class info.bioinfweb.commons.graphics.ZoomableFont
-
- afterAdd(int, Collection<? extends E>) - Method in class info.bioinfweb.commons.collections.ListDecorator
-
This method is called at the end of all methods of this list that add elements to it, including
methods called on the results of
or iterators.
- afterAdd(int, E) - Method in class info.bioinfweb.commons.collections.ListIteratorDecorator
-
- afterAdd(int, Collection<? extends E>) - Method in class info.bioinfweb.commons.collections.observable.ObservableList
-
- afterElementReplaced(ListReplaceEvent<E>) - Method in class info.bioinfweb.commons.collections.observable.ListChangeAdapter
-
Empty implementation to be overwritten if necessary.
- afterElementReplaced(ListReplaceEvent<E>) - Method in interface info.bioinfweb.commons.collections.observable.ListChangeListener
-
Called after an element in the monitored list has been replaced by another one.
- afterElementsAdded(ListAddEvent<E>) - Method in class info.bioinfweb.commons.collections.observable.ListChangeAdapter
-
Empty implementation to be overwritten if necessary.
- afterElementsAdded(ListAddEvent<E>) - Method in interface info.bioinfweb.commons.collections.observable.ListChangeListener
-
Called after one or more elements have been added to monitored list.
- afterElementsRemoved(ListRemoveEvent<E, E>) - Method in class info.bioinfweb.commons.collections.observable.ListChangeAdapter
-
Empty implementation to be overwritten if necessary.
- afterElementsRemoved(ListRemoveEvent<E, E>) - Method in interface info.bioinfweb.commons.collections.observable.ListChangeListener
-
Called after one or more elements have been removed from monitored list.
- afterRemove(int, Collection<? extends E>) - Method in class info.bioinfweb.commons.collections.ListDecorator
-
This method is called at the end of all methods of this list that remove elements from it, including
methods called on the results of
ListDecorator.subList(int, int) or iterators.
- afterRemove(int, E) - Method in class info.bioinfweb.commons.collections.ListIteratorDecorator
-
- afterRemove(int, Collection<? extends E>) - Method in class info.bioinfweb.commons.collections.observable.ObservableList
-
- afterReplace(int, E, E) - Method in class info.bioinfweb.commons.collections.ListDecorator
-
- afterReplace(int, E, E) - Method in class info.bioinfweb.commons.collections.ListIteratorDecorator
-
- afterReplace(int, E, E) - Method in class info.bioinfweb.commons.collections.observable.ObservableList
-
- align(CharSequence, CharSequence) - Method in class info.bioinfweb.commons.bio.alignment.pairwise.NeedlemanWunschAligner
-
- align(CharSequence, CharSequence) - Method in interface info.bioinfweb.commons.bio.alignment.pairwise.PairwiseAligner
-
- Alignment<S extends org.biojava3.core.sequence.template.Sequence<C>,C extends org.biojava3.core.sequence.template.Compound> - Interface in info.bioinfweb.commons.bio.biojava3.alignment.template
-
Classes implementing this interface represent an aligned set of sequences.
- AlignmentAmbiguityDNACompoundSet - Class in info.bioinfweb.commons.bio.biojava3.core.sequence.compound
-
- AlignmentAmbiguityDNACompoundSet() - Constructor for class info.bioinfweb.commons.bio.biojava3.core.sequence.compound.AlignmentAmbiguityDNACompoundSet
-
Returns a new instance of this class.
- AlignmentAmbiguityNucleotideCompoundSet - Class in info.bioinfweb.commons.bio.biojava3.core.sequence.compound
-
- AlignmentAmbiguityNucleotideCompoundSet() - Constructor for class info.bioinfweb.commons.bio.biojava3.core.sequence.compound.AlignmentAmbiguityNucleotideCompoundSet
-
Returns a new instance of this class.
- AlignmentAmbiguityRNACompoundSet - Class in info.bioinfweb.commons.bio.biojava3.core.sequence.compound
-
- AlignmentAmbiguityRNACompoundSet() - Constructor for class info.bioinfweb.commons.bio.biojava3.core.sequence.compound.AlignmentAmbiguityRNACompoundSet
-
Returns a new instance of this class.
- AlignmentReader<S extends org.biojava3.core.sequence.template.Sequence<C>,C extends org.biojava3.core.sequence.template.Compound> - Interface in info.bioinfweb.commons.bio.biojava3.alignment.io
-
- AlignmentWriter<S extends org.biojava3.core.sequence.template.Sequence<C>,C extends org.biojava3.core.sequence.template.Compound> - Interface in info.bioinfweb.commons.bio.biojava3.alignment.io
-
- ALL_DNA_CHARS - Static variable in class info.bioinfweb.commons.bio.SequenceUtils
-
- ALL_RNA_CHARS - Static variable in class info.bioinfweb.commons.bio.SequenceUtils
-
- ALPHA_STRING - Static variable in enum info.bioinfweb.commons.appversion.ApplicationType
-
- AlphaImageAssembler - Class in info.bioinfweb.commons.graphics
-
- AlphaImageAssembler() - Constructor for class info.bioinfweb.commons.graphics.AlphaImageAssembler
-
- AMBIGUITY_DNA_TO_N_RNA_MAP - Static variable in class info.bioinfweb.commons.bio.biojava3.core.sequence.views.ReplaceNucleotideSequenceView
-
Replaces all other ambiguity codes with N and T with U.
- AMBIGUITY_RNA_TO_N_DNA_MAP - Static variable in class info.bioinfweb.commons.bio.biojava3.core.sequence.views.ReplaceNucleotideSequenceView
-
Replaces all other ambiguity codes with N and U with T.
- AMBIGUITY_TO_N_MAP - Static variable in class info.bioinfweb.commons.bio.biojava3.core.sequence.views.ReplaceNucleotideSequenceView
-
Replaces all other ambiguity codes with N.
- AMBIGUITY_UNKNOWN_DNA_TO_N_RNA_MAP - Static variable in class info.bioinfweb.commons.bio.biojava3.core.sequence.views.ReplaceNucleotideSequenceView
-
Replaces all other ambiguity codes and ? with N and T with U.
- AMBIGUITY_UNKNOWN_RNA_TO_N_DNA_MAP - Static variable in class info.bioinfweb.commons.bio.biojava3.core.sequence.views.ReplaceNucleotideSequenceView
-
Replaces all other ambiguity codes and ? with N and U with T.
- AmbiguityBaseScore - Class in info.bioinfweb.commons.bio
-
- AmbiguityBaseScore(double[]) - Constructor for class info.bioinfweb.commons.bio.AmbiguityBaseScore
-
Note that no deep copy of the array will be made.
- AmbiguityBaseScore(double, double, double, double) - Constructor for class info.bioinfweb.commons.bio.AmbiguityBaseScore
-
Creates a new instance of this class.
- AmbiguityBaseScore(double, double, double, double, double) - Constructor for class info.bioinfweb.commons.bio.AmbiguityBaseScore
-
Creates a new instance of this class and directly scales is to the specified sum.
- AmbiguityNoGapDNACompoundSet - Class in info.bioinfweb.commons.bio.biojava3.core.sequence.compound
-
Nucleotide compound set that contains all DNA compounds and ambiguity codes but no gap - character.
- AmbiguityNoGapDNACompoundSet() - Constructor for class info.bioinfweb.commons.bio.biojava3.core.sequence.compound.AmbiguityNoGapDNACompoundSet
-
Returns a new instance of this class.
- AmbiguityNoGapNucleotideCompoundSet - Class in info.bioinfweb.commons.bio.biojava3.core.sequence.compound
-
Nucleotide compound set that contains all DNA and RNA compounds and ambiguity codes
but no gap - character.
- AmbiguityNoGapNucleotideCompoundSet() - Constructor for class info.bioinfweb.commons.bio.biojava3.core.sequence.compound.AmbiguityNoGapNucleotideCompoundSet
-
Returns a new instance of this class.
- AmbiguityNoGapRNACompoundSet - Class in info.bioinfweb.commons.bio.biojava3.core.sequence.compound
-
Nucleotide compound set that contains all RNA compounds and ambiguity codes but no gap - character.
- AmbiguityNoGapRNACompoundSet() - Constructor for class info.bioinfweb.commons.bio.biojava3.core.sequence.compound.AmbiguityNoGapRNACompoundSet
-
Returns a new instance of this class.
- aminoAcidConsensus(String[]) - Static method in class info.bioinfweb.commons.bio.SequenceUtils
-
- aminoAcidFrequencies(String[]) - Static method in class info.bioinfweb.commons.bio.SequenceUtils
-
- ApplicationLogger - Interface in info.bioinfweb.commons.log
-
Provides a simple logging API that can be used by applications to output log messages to the user.
- ApplicationLoggerDialog - Class in info.bioinfweb.commons.log
-
- ApplicationLoggerDialog(Frame) - Constructor for class info.bioinfweb.commons.log.ApplicationLoggerDialog
-
- ApplicationLoggerMessage - Class in info.bioinfweb.commons.log
-
- ApplicationLoggerMessage(ApplicationLoggerMessageType, String) - Constructor for class info.bioinfweb.commons.log.ApplicationLoggerMessage
-
- ApplicationLoggerMessage(ApplicationLoggerMessageType, String, int) - Constructor for class info.bioinfweb.commons.log.ApplicationLoggerMessage
-
- ApplicationLoggerMessageType - Enum in info.bioinfweb.commons.log
-
Enumerates the different types of messages which can be send to an
ApplicationLogger.
- ApplicationLoggerParameterMap - Class in info.bioinfweb.commons.log
-
- ApplicationLoggerParameterMap() - Constructor for class info.bioinfweb.commons.log.ApplicationLoggerParameterMap
-
- ApplicationType - Enum in info.bioinfweb.commons.appversion
-
Enumerates the possible types of releases of an application versioned with
ApplicationVersion.
- ApplicationVersion - Class in info.bioinfweb.commons.appversion
-
Stores the version of an application.
- ApplicationVersion() - Constructor for class info.bioinfweb.commons.appversion.ApplicationVersion
-
Creates a new instance of this class with the default values 0.0.0.0 (stable).
- ApplicationVersion(int, int, int, long, ApplicationType) - Constructor for class info.bioinfweb.commons.appversion.ApplicationVersion
-
Creates a new instance of this class using the specified values.
- apply() - Method in class info.bioinfweb.commons.swing.DecimalInputDialog
-
- apply() - Method in class info.bioinfweb.commons.swing.OkCancelApplyDialog
-
This method is called if the user clicks OK or Apply.
- AppVersionXMLConstants - Class in info.bioinfweb.commons.appversion
-
- AppVersionXMLConstants() - Constructor for class info.bioinfweb.commons.appversion.AppVersionXMLConstants
-
- AppVersionXMLReadWrite - Class in info.bioinfweb.commons.appversion
-
- AppVersionXMLReadWrite() - Constructor for class info.bioinfweb.commons.appversion.AppVersionXMLReadWrite
-
- argCount() - Method in class info.bioinfweb.commons.CommandLineReader
-
- array - Variable in class info.bioinfweb.commons.collections.PackedIntegerArrayList
-
The array containing the bits used to store values contained in this list.
- askToSave() - Method in class info.bioinfweb.commons.io.AbstractSaver
-
- askToSave() - Method in interface info.bioinfweb.commons.io.Savable
-
Promts the user wheather to save changed data and calls save() if necessary.
- askToSave(Component) - Method in interface info.bioinfweb.commons.swing.SwingSavable
-
- askToSave() - Method in class info.bioinfweb.commons.swing.SwingSaver
-
- askToSave(Component) - Method in class info.bioinfweb.commons.swing.SwingSaver
-
- asMap() - Method in class info.bioinfweb.commons.bio.biojava3.alignment.SimpleAlignment
-
Returns this alignment as a map with sequence names as keys and sequences as values.
- asMap() - Method in interface info.bioinfweb.commons.bio.biojava3.alignment.template.Alignment
-
- assemble(BufferedImage, BufferedImage) - Static method in class info.bioinfweb.commons.graphics.AlphaImageAssembler
-
- Assert2 - Class in info.bioinfweb.commons.testing
-
Provides assert methods of general use.
- Assert2() - Constructor for class info.bioinfweb.commons.testing.Assert2
-
- assertAttribute(QName, String, StartElement) - Static method in class info.bioinfweb.commons.testing.XMLAssert
-
- assertAttribute(QName, String, int, XMLStreamReader) - Static method in class info.bioinfweb.commons.testing.XMLAssert
-
- assertAttribute(QName, StartElement) - Static method in class info.bioinfweb.commons.testing.XMLAssert
-
- assertAttribute(QName, int, XMLStreamReader) - Static method in class info.bioinfweb.commons.testing.XMLAssert
-
- assertAttributeCount(int, StartElement) - Static method in class info.bioinfweb.commons.testing.XMLAssert
-
- assertAttributeCount(int, XMLStreamReader) - Static method in class info.bioinfweb.commons.testing.XMLAssert
-
- assertCharactersEvent(String, XMLEventReader) - Static method in class info.bioinfweb.commons.testing.XMLAssert
-
- assertCharactersEvent(String, XMLStreamReader) - Static method in class info.bioinfweb.commons.testing.XMLAssert
-
- assertCollectionElementTypes(Collection<?>, Collection<?>) - Static method in class info.bioinfweb.commons.testing.Assert2
-
- assertCommentEvent(String, XMLEventReader) - Static method in class info.bioinfweb.commons.testing.XMLAssert
-
- assertCommentEvent(String, XMLStreamReader) - Static method in class info.bioinfweb.commons.testing.XMLAssert
-
- assertDefaultNamespace(QName, StartElement) - Static method in class info.bioinfweb.commons.testing.XMLAssert
-
- assertDefaultNamespace(QName, int, XMLStreamReader) - Static method in class info.bioinfweb.commons.testing.XMLAssert
-
- assertEmptyElement(QName, XMLEventReader) - Static method in class info.bioinfweb.commons.testing.XMLAssert
-
- assertEmptyElement(QName, XMLStreamReader) - Static method in class info.bioinfweb.commons.testing.XMLAssert
-
- assertEndDocument(XMLEventReader) - Static method in class info.bioinfweb.commons.testing.XMLAssert
-
- assertEndDocument(XMLStreamReader) - Static method in class info.bioinfweb.commons.testing.XMLAssert
-
- assertEndElement(QName, XMLEventReader) - Static method in class info.bioinfweb.commons.testing.XMLAssert
-
- assertEndElement(QName, XMLStreamReader) - Static method in class info.bioinfweb.commons.testing.XMLAssert
-
- assertNamespace(QName, boolean, StartElement) - Static method in class info.bioinfweb.commons.testing.XMLAssert
-
- assertNamespace(QName, boolean, int, XMLStreamReader) - Static method in class info.bioinfweb.commons.testing.XMLAssert
-
- assertNamespaceCount(int, StartElement) - Static method in class info.bioinfweb.commons.testing.XMLAssert
-
- assertNamespaceCount(int, XMLStreamReader) - Static method in class info.bioinfweb.commons.testing.XMLAssert
-
- assertShortElement(QName, String, XMLEventReader) - Static method in class info.bioinfweb.commons.testing.XMLAssert
-
- assertShortElement(QName, String, XMLStreamReader) - Static method in class info.bioinfweb.commons.testing.XMLAssert
-
- assertShortElement(QName, XMLEventReader) - Static method in class info.bioinfweb.commons.testing.XMLAssert
-
This method can be used to assert the presence of an XML element that only contains character content,
if the exact content should not be asserted.
- assertShortElement(QName, XMLStreamReader) - Static method in class info.bioinfweb.commons.testing.XMLAssert
-
- assertStartDocument(XMLEventReader) - Static method in class info.bioinfweb.commons.testing.XMLAssert
-
- assertStartDocument(XMLStreamReader) - Static method in class info.bioinfweb.commons.testing.XMLAssert
-
- assertStartElement(QName, XMLEventReader) - Static method in class info.bioinfweb.commons.testing.XMLAssert
-
- assertStartElement(QName, XMLStreamReader) - Static method in class info.bioinfweb.commons.testing.XMLAssert
-
- ATTR_APP_TYPE - Static variable in class info.bioinfweb.commons.appversion.AppVersionXMLConstants
-
- ATTR_BUILD_NO - Static variable in class info.bioinfweb.commons.appversion.AppVersionXMLConstants
-
- ATTR_MAJOR_APP_VERSION - Static variable in class info.bioinfweb.commons.appversion.AppVersionXMLConstants
-
- ATTR_MINOR_APP_VERSION - Static variable in class info.bioinfweb.commons.appversion.AppVersionXMLConstants
-
- ATTR_PATCH_LEVEL - Static variable in class info.bioinfweb.commons.appversion.AppVersionXMLConstants
-
- ATTR_SCHEMA_LOCATION - Static variable in class info.bioinfweb.commons.io.XMLUtils
-
- ATTR_SCHEMA_LOCATION_LOCAL_PART - Static variable in class info.bioinfweb.commons.io.XMLUtils
-
- ATTR_XSI_NAMESPACE - Static variable in class info.bioinfweb.commons.io.XMLUtils
-
- available() - Method in class info.bioinfweb.commons.io.LimitedInputStream
-
- availableCharacters() - Method in class info.bioinfweb.commons.io.LimitedInputStream
-
The number of bytes available, before the specified maximum number will have been read from the decorated input stream.
- availableCharacters() - Method in class info.bioinfweb.commons.io.LimitedReader
-
The number of characters available, before the specified maximum number will have been read from the decorated reader.
