Skip navigation links
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 

A

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
 
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
Basic implementation of the ProgressMonitor interface.
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
Creates a file from dir and name and delegates to ExtensionFileFilter.accept(File).
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(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.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
This method is called at the end of ListIteratorDecorator.add(Object) to indicate that an element has been inserted.
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 add 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
This method is called at the end of ListIteratorDecorator.remove() to indicate that an element has been removed from the associated list.
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
This method is called at the end of ListDecorator.set(int, Object) to indicate that an element has been replaced.
afterReplace(int, E, E) - Method in class info.bioinfweb.commons.collections.ListIteratorDecorator
This method is called at the end of ListIteratorDecorator.set(Object) to indicate that an element has been replaced.
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
Extension of AlignmentAmbiguityDNACompoundSet that also includes the ? character.
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
Extension of AlignmentAmbiguityRNACompoundSet that also includes the ? character.
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
Extension of AlignmentAmbiguityRNACompoundSet that also includes the ? character.
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
A dialog displaying the log send to an ApplicationLogger.
ApplicationLoggerDialog(Frame) - Constructor for class info.bioinfweb.commons.log.ApplicationLoggerDialog
 
ApplicationLoggerMessage - Class in info.bioinfweb.commons.log
Represents a message send to an ApplicationLogger.
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
Constants used for the XML representation of an instance of ApplicationVersion as they are used by AppVersionXMLReadWrite.
AppVersionXMLConstants() - Constructor for class info.bioinfweb.commons.appversion.AppVersionXMLConstants
 
AppVersionXMLReadWrite - Class in info.bioinfweb.commons.appversion
Reads or writes an XML tag describing an ApplicationVersion object.
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.
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 
Skip navigation links