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S

Savable - Interface in info.bioinfweb.commons.io
 
save() - Method in class info.bioinfweb.commons.io.AbstractSaver
 
save() - Method in interface info.bioinfweb.commons.io.Savable
This method should save the data to a file defined by the path and should call saveAs() if no path was assigned.
saveAs() - Method in class info.bioinfweb.commons.io.AbstractSaver
 
saveAs() - Method in interface info.bioinfweb.commons.io.Savable
Promts the user der select a path to save the data.
saveAs(Component) - Method in interface info.bioinfweb.commons.swing.SwingSavable
 
saveAs() - Method in class info.bioinfweb.commons.swing.SwingSaver
Opens a save dialog and asks the user where to save the file.
saveAs(Component) - Method in class info.bioinfweb.commons.swing.SwingSaver
Opens a save dialog and asks the user where to save the file.
saveCurrentTime(String) - Method in class info.bioinfweb.commons.testing.TestLogger
 
saveDataToFile(File) - Method in class info.bioinfweb.commons.io.AbstractSaver
 
ScrolledCompositeSyncListener - Class in info.bioinfweb.commons.swt
Selection listener that synchronizes ScrolledComposite components in horizontal or vertical direction.
ScrolledCompositeSyncListener(Collection<ScrolledComposite>, boolean) - Constructor for class info.bioinfweb.commons.swt.ScrolledCompositeSyncListener
Creates a new instance of this class which uses a deep copy of scrolledComposites.
ScrolledCompositeSyncListener(ScrolledComposite[], boolean) - Constructor for class info.bioinfweb.commons.swt.ScrolledCompositeSyncListener
Creates a new instance of this class which uses a deep copy of scrolledComposites.
ScrollPaneBidule - Class in org.jdesktop.swingx.scrollpaneselector
 
ScrollPaneBidule(JScrollPane) - Constructor for class org.jdesktop.swingx.scrollpaneselector.ScrollPaneBidule
 
ScrollPaneSelectable - Interface in info.bioinfweb.commons.swing.scrollpaneselector
Classes implementing this interface are able to paint their own preview thumbnail if they are positioned inside a JScrollPane which uses ExetededScrollPaneSelector.
Although componenets which do not implement this interface can be previewed too, the advantige of is that the component is able to paint a more sharp preview or to highlight special elements.
ScrollPaneSelector - Class in org.jdesktop.swingx.scrollpaneselector
ScrollPaneSelector is a little utility class that provides a means to quickly scroll both vertically and horizontally on a single mouse click, by dragging a selection rectangle over a "thumbnail" of the scrollPane's viewport view.
SequenceCompareUtils - Class in info.bioinfweb.commons.bio.biojava3.core.sequence
Helper class that allows to compare sequences by taking ambiguity codes into account or not.
SequenceCompareUtils() - Constructor for class info.bioinfweb.commons.bio.biojava3.core.sequence.SequenceCompareUtils
 
SequenceIntervalList<E> - Class in info.bioinfweb.commons.collections
Instances of this class are able to manage a set of sequence intervals.
SequenceIntervalList(SequenceIntervalPositionAdapter<? super E>) - Constructor for class info.bioinfweb.commons.collections.SequenceIntervalList
Equivalent to calling SequenceIntervalList(positionAdapter, SequenceIntervalList.DEFAULT_INITIAL_SEQUENCE_LENGTH, DEFAULT_INTERVAL_LENGTH).
SequenceIntervalList(SequenceIntervalPositionAdapter<? super E>, int, int) - Constructor for class info.bioinfweb.commons.collections.SequenceIntervalList
Creates a new instance of this class.
SequenceIntervalList.IntervalInformation - Class in info.bioinfweb.commons.collections
 
SequenceIntervalPositionAdapter<T> - Interface in info.bioinfweb.commons.collections
 
SequenceIntervalPositionAdapterForComparable<T extends java.lang.Comparable<? super T>> - Class in info.bioinfweb.commons.collections
Abstract implementation of SequenceIntervalPositionAdapter to be used with elements that already implement the Comparable interface.
SequenceIntervalPositionAdapterForComparable() - Constructor for class info.bioinfweb.commons.collections.SequenceIntervalPositionAdapterForComparable
 
sequencesAsList() - Method in class info.bioinfweb.commons.bio.biojava3.core.sequence.views.ConcatenatedSequenceView
Returns a list implementation that allows to edit the underlying list of viewed sequences.
sequencesEqual(Sequence<? extends Compound>, Sequence<? extends Compound>) - Static method in class info.bioinfweb.commons.bio.biojava3.core.sequence.SequenceCompareUtils
Tests if the two symbols at each according position of the two sequences are exactly equal.
sequencesEquivalent(CompoundSet<? super C>, S, S) - Static method in class info.bioinfweb.commons.bio.biojava3.core.sequence.SequenceCompareUtils
Uses the AbstractCompoundSet.compoundsEquivalent(Compound, Compound) method of the specified compound set to check if the values at each position of the two sequences are equal.
SequenceUtils - Class in info.bioinfweb.commons.bio
Useful tools to manipulate nucleotide and amino acid sequences stored as character sequences.
SequenceUtils() - Constructor for class info.bioinfweb.commons.bio.SequenceUtils
 
sequncesEqual(Alignment<?, ?>) - Method in class info.bioinfweb.commons.bio.biojava3.alignment.SimpleAlignment
Checks if this alignment contains the same sequences (name and sequence) as the specified one.
sequncesEqual(Alignment<?, ?>) - Method in interface info.bioinfweb.commons.bio.biojava3.alignment.template.Alignment
 
ServletUtils - Class in info.bioinfweb.commons.servlet
Utility class for common tasks related to servlets.
ServletUtils() - Constructor for class info.bioinfweb.commons.servlet.ServletUtils
 
set(int, E) - Method in class info.bioinfweb.commons.collections.ListDecorator
 
set(E) - Method in class info.bioinfweb.commons.collections.ListIteratorDecorator
 
set(long, long) - Method in class info.bioinfweb.commons.collections.PackedIntegerArrayList
Replaces the value at the specified position with the new value.
set(int, E) - Method in class info.bioinfweb.commons.collections.PackedObjectArrayList
 
set(int, E) - Method in class info.bioinfweb.commons.collections.PackedPrimitiveWrapperArrayList
 
set(int, E) - Method in class info.bioinfweb.commons.swing.ListBackedListModel
 
setAcceptFilesWithExceptions(boolean) - Method in class info.bioinfweb.commons.io.ContentExtensionFileFilter
Specifies whether this filter accepts files where IOExceptions were thrown while they were tested with ContentExtensionFileFilter.acceptContent(File).
setAdeninScore(double) - Method in class info.bioinfweb.commons.bio.AmbiguityBaseScore
 
setAllowClose(boolean) - Method in class info.bioinfweb.commons.io.LimitedInputStream
Allows to specify whether closing this input stream shall currently be prevented.
setAllowClose(boolean) - Method in class info.bioinfweb.commons.io.LimitedReader
Allows to specify whether closing this reader shall currently be prevented.
setAskToSaveMessageBeginnung(String) - Method in class info.bioinfweb.commons.swing.SwingSaverMessages
 
setAskToSaveMessageEnd(String) - Method in class info.bioinfweb.commons.swing.SwingSaverMessages
 
setAskToSaveTitle(String) - Method in class info.bioinfweb.commons.swing.SwingSaverMessages
 
setBuildNumber(long) - Method in class info.bioinfweb.commons.appversion.ApplicationVersion
 
setButtonCancel(String) - Method in class info.bioinfweb.commons.swing.SwingSaverMessages
 
setButtonNo(String) - Method in class info.bioinfweb.commons.swing.SwingSaverMessages
 
setButtonYes(String) - Method in class info.bioinfweb.commons.swing.SwingSaverMessages
 
setContent(String) - Method in class info.bioinfweb.commons.tokenizer.StrToken
 
setCountry(String) - Method in class info.bioinfweb.commons.servlet.acceptlanguage.AcceptLanguageEntry
 
setCurrentDirectory(File) - Method in class info.bioinfweb.commons.swing.FileChooserDirModel
 
setCytosinScore(double) - Method in class info.bioinfweb.commons.bio.AmbiguityBaseScore
 
setDBDriver(String) - Method in class info.bioinfweb.commons.sql.sqlproperties.ConcreteSQLProperties
 
setDBDriver(String) - Method in interface info.bioinfweb.commons.sql.sqlproperties.SQLProperties
 
setDBHost(String) - Method in class info.bioinfweb.commons.sql.sqlproperties.ConcreteSQLProperties
 
setDBHost(String) - Method in interface info.bioinfweb.commons.sql.sqlproperties.SQLProperties
 
setDBName(String) - Method in class info.bioinfweb.commons.sql.sqlproperties.ConcreteSQLProperties
 
setDBName(String) - Method in interface info.bioinfweb.commons.sql.sqlproperties.SQLProperties
 
setDBPassword(String) - Method in class info.bioinfweb.commons.sql.sqlproperties.ConcreteSQLProperties
 
setDBPassword(String) - Method in interface info.bioinfweb.commons.sql.sqlproperties.SQLProperties
 
setDBUser(String) - Method in class info.bioinfweb.commons.sql.sqlproperties.ConcreteSQLProperties
 
setDBUser(String) - Method in interface info.bioinfweb.commons.sql.sqlproperties.SQLProperties
 
setDecimalFormatStr(String) - Method in class info.bioinfweb.commons.swing.DecimalInput
 
setDefaultExtension(String) - Method in class info.bioinfweb.commons.io.AbstractSaver
 
setDefaultExtension(String) - Method in interface info.bioinfweb.commons.io.Savable
 
setDefaultLocale() - Method in class info.bioinfweb.commons.io.InternationalFileFilter
 
setDefaultLocale() - Method in class info.bioinfweb.commons.swing.SwingSaverMessages
 
setDefaultName(String) - Method in class info.bioinfweb.commons.io.AbstractSaver
 
setDefaultName(String) - Method in interface info.bioinfweb.commons.io.Savable
Sets the path that should be proposed by the saveAs()-method if no path has been assigned.
setEnabled(boolean) - Method in class info.bioinfweb.commons.swing.DecimalInput
 
setFile(File) - Method in class info.bioinfweb.commons.io.AbstractSaver
 
setFile(File) - Method in interface info.bioinfweb.commons.io.Savable
Manually assignes a path.
setFillUp(boolean) - Method in class info.bioinfweb.commons.text.UniqueNameMapParameters
 
setFillUpChar(char) - Method in class info.bioinfweb.commons.text.UniqueNameMapParameters
 
setFirstPos(T, int) - Method in interface info.bioinfweb.commons.collections.SequenceIntervalPositionAdapter
 
setFirstPos(int) - Method in class info.bioinfweb.commons.collections.SimpleSequenceInterval
 
setFirstPos(SimpleSequenceInterval, int) - Method in class info.bioinfweb.commons.collections.SimpleSequenceIntervalPositionAdapter
 
setGapChar(char) - Method in class info.bioinfweb.commons.bio.alignment.pairwise.NeedlemanWunschAligner
 
setGuaninScore(double) - Method in class info.bioinfweb.commons.bio.AmbiguityBaseScore
 
setHelpCode(int) - Method in class info.bioinfweb.commons.log.ApplicationLoggerMessage
 
setID(int) - Method in class info.bioinfweb.commons.tokenizer.StrToken
 
setIsSubedit(boolean) - Method in class info.bioinfweb.commons.swing.AbstractDocumentEdit
Indicates whether this edit is independent or part of another edit.
setLanguage(String) - Method in class info.bioinfweb.commons.servlet.acceptlanguage.AcceptLanguageEntry
 
setLastPos(T, int) - Method in interface info.bioinfweb.commons.collections.SequenceIntervalPositionAdapter
 
setLastPos(int) - Method in class info.bioinfweb.commons.collections.SimpleSequenceInterval
 
setLastPos(SimpleSequenceInterval, int) - Method in class info.bioinfweb.commons.collections.SimpleSequenceIntervalPositionAdapter
 
setLineLength(int) - Method in class info.bioinfweb.commons.bio.biojava3.core.sequence.io.MapFastaWriter
 
setLineSeparator(String) - Method in class info.bioinfweb.commons.bio.biojava3.core.sequence.io.MapFastaWriter
 
setList(List<E>) - Method in class info.bioinfweb.commons.swing.ListBackedListModel
 
setLocale(Locale) - Method in class info.bioinfweb.commons.io.InternationalFileFilter
 
setLocale(Locale) - Method in class info.bioinfweb.commons.swing.SwingSaverMessages
 
setMajor(int) - Method in class info.bioinfweb.commons.io.FormatVersion
 
setMajorRelease(int) - Method in class info.bioinfweb.commons.appversion.ApplicationVersion
 
setMaximumFactor(double) - Method in class info.bioinfweb.commons.swing.RelativeRangeModel
Sets the current maximum factor and recalculates the maximum.
setMaxNameLength(int) - Method in class info.bioinfweb.commons.text.UniqueNameMapParameters
 
setMaxTaxonNameLength(int) - Method in class info.bioinfweb.commons.bio.biojava3.alignment.io.hennig86.Hennig86Writer
 
setMessage(String) - Method in class info.bioinfweb.commons.log.ApplicationLoggerMessage
 
setMinor(int) - Method in class info.bioinfweb.commons.io.FormatVersion
 
setMinorRelease(int) - Method in class info.bioinfweb.commons.appversion.ApplicationVersion
 
setName(String) - Method in class info.bioinfweb.commons.bio.biojavax.bio.phylo.io.nexus.CharSet
 
setName(String) - Method in class info.bioinfweb.commons.graphics.ZoomableFont
Sets a new font name.
setNativeLF() - Static method in class info.bioinfweb.commons.swing.SwingUtils
Sets the native look and feel of the current operating system by invoking UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName()).
setNoOfStates(String) - Method in class info.bioinfweb.commons.bio.biojava3.alignment.io.hennig86.Hennig86Writer
 
setNumericValue(String, long) - Method in class info.bioinfweb.commons.testing.TestLogger
 
setOriginalHeight(double) - Method in class info.bioinfweb.commons.graphics.ZoomableFont
Sets a new font size for a zoom factor of 100 %.
setPatchLevel(int) - Method in class info.bioinfweb.commons.appversion.ApplicationVersion
 
setPos(int) - Method in class info.bioinfweb.commons.tokenizer.StrToken
 
setPositionAdapter(SequenceIntervalPositionAdapter<? super E>) - Method in class info.bioinfweb.commons.collections.SequenceIntervalList
Calling this methods leads to resorting of all elements in the list.
setPrefix(String) - Method in class info.bioinfweb.commons.io.DefaultNameManager
 
setPrintDirectly(boolean) - Method in class info.bioinfweb.commons.testing.TestLogger
 
setProgressValue(double, String) - Method in class info.bioinfweb.commons.progress.AbstractProgressMonitor
 
setProgressValue(double) - Method in class info.bioinfweb.commons.progress.AbstractProgressMonitor
 
setProgressValue(double) - Method in interface info.bioinfweb.commons.progress.ProgressMonitor
 
setProgressValue(double, String) - Method in interface info.bioinfweb.commons.progress.ProgressMonitor
 
setProgressValue(double) - Method in class info.bioinfweb.commons.swing.ProgressDialog
 
setProgressValue(double, String) - Method in class info.bioinfweb.commons.swing.ProgressDialog
 
setQuality(double) - Method in class info.bioinfweb.commons.servlet.acceptlanguage.AcceptLanguageEntry
 
SETS_BLOCK - Static variable in class info.bioinfweb.commons.bio.biojavax.bio.phylo.io.nexus.SetsBlock
 
SETS_LIST_START - Static variable in class info.bioinfweb.commons.bio.biojavax.bio.phylo.io.nexus.SetsBlockParser
 
setSaveCanceled(boolean) - Method in class info.bioinfweb.commons.swing.FileChooserDirModel
If setSaveCanceled(true) is called the current directory is also updated if the user cancels the file chooser dialog.
Default value is true.
SetsBlock - Class in info.bioinfweb.commons.bio.biojavax.bio.phylo.io.nexus
Represents a part of the contents of a SETS block of a Nexus file.
SetsBlock() - Constructor for class info.bioinfweb.commons.bio.biojavax.bio.phylo.io.nexus.SetsBlock
 
SetsBlockBuilder - Class in info.bioinfweb.commons.bio.biojavax.bio.phylo.io.nexus
Builds a SETS Nexus block by listening to events.
SetsBlockBuilder() - Constructor for class info.bioinfweb.commons.bio.biojavax.bio.phylo.io.nexus.SetsBlockBuilder
 
SetsBlockListener - Interface in info.bioinfweb.commons.bio.biojavax.bio.phylo.io.nexus
 
SetsBlockParser - Class in info.bioinfweb.commons.bio.biojavax.bio.phylo.io.nexus
Parses a Nexus SETS block and fires events to a SetsBlockListener.
SetsBlockParser(SetsBlockListener) - Constructor for class info.bioinfweb.commons.bio.biojavax.bio.phylo.io.nexus.SetsBlockParser
 
setScoreByIndex(int, double) - Method in class info.bioinfweb.commons.bio.AmbiguityBaseScore
 
setSelectedItem(Object) - Method in class info.bioinfweb.commons.swing.ListBackedComboBoxModel
Sets the selected item of this model.
setSelectedItem(Object) - Method in class info.bioinfweb.commons.swing.LocaleComboBoxModel
Sets the selected item.
setSelectedLocale(Locale) - Method in class info.bioinfweb.commons.swing.LocaleComboBoxModel
 
setSize(double, double) - Method in class info.bioinfweb.commons.graphics.DoubleDimension
 
setStyle(int) - Method in class info.bioinfweb.commons.graphics.ZoomableFont
Sets a new font style.
setTablePrefix(String) - Method in class info.bioinfweb.commons.sql.sqlproperties.ConcreteSQLProperties
 
setTablePrefix(String) - Method in interface info.bioinfweb.commons.sql.sqlproperties.SQLProperties
 
setTestStrategy(ContentExtensionFileFilter.TestStrategy) - Method in class info.bioinfweb.commons.io.ContentExtensionFileFilter
Specifies a new test strategy to determine whether a file shall be accepted by this filter or not.
setThyminScore(double) - Method in class info.bioinfweb.commons.bio.AmbiguityBaseScore
 
setTime(Date) - Method in class info.bioinfweb.commons.log.ApplicationLoggerMessage
 
setTime(long) - Method in class info.bioinfweb.commons.log.ApplicationLoggerMessage
 
setTimeToNow() - Method in class info.bioinfweb.commons.log.ApplicationLoggerMessage
 
setType(ApplicationType) - Method in class info.bioinfweb.commons.appversion.ApplicationVersion
 
setType(ApplicationLoggerMessageType) - Method in class info.bioinfweb.commons.log.ApplicationLoggerMessage
 
setUseErrorStream(boolean) - 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.
setValue(float) - Method in class info.bioinfweb.commons.swing.DecimalInput
 
setValue(double) - Method in class info.bioinfweb.commons.swing.DecimalInput
 
setValue(int) - Method in class info.bioinfweb.commons.swing.DecimalInput
 
setValue(long) - Method in class info.bioinfweb.commons.swing.DecimalInput
 
setValue(int) - Method in class info.bioinfweb.commons.swing.RelativeRangeModel
Sets the value of this model.
setVisible(boolean) - Method in class info.bioinfweb.commons.swing.ToolBarPopup
 
show(int) - Method in class info.bioinfweb.commons.swing.AboutDialog
 
show() - Method in class info.bioinfweb.commons.swing.ToolBarPopup
Deprecated.
show(boolean) - Method in class info.bioinfweb.commons.swing.ToolBarPopup
Deprecated.
SimpleAlignment<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
Default implementation of Alignment.
SimpleAlignment() - Constructor for class info.bioinfweb.commons.bio.biojava3.alignment.SimpleAlignment
 
SimpleSequenceInterval - Class in info.bioinfweb.commons.collections
Basic implementation representing an interval in a SequenceIntervalList.
SimpleSequenceInterval(int, int) - Constructor for class info.bioinfweb.commons.collections.SimpleSequenceInterval
 
SimpleSequenceIntervalFirstPosComparator - Class in info.bioinfweb.commons.collections
Comparator that compare two SimpleSequenceInterval objects simply by their first (start) position.
SimpleSequenceIntervalFirstPosComparator() - Constructor for class info.bioinfweb.commons.collections.SimpleSequenceIntervalFirstPosComparator
 
SimpleSequenceIntervalLastPosComparator - Class in info.bioinfweb.commons.collections
Comparator that compare two SimpleSequenceInterval objects simply by their last (end) position.
SimpleSequenceIntervalLastPosComparator() - Constructor for class info.bioinfweb.commons.collections.SimpleSequenceIntervalLastPosComparator
 
SimpleSequenceIntervalPositionAdapter - Class in info.bioinfweb.commons.collections
SimpleSequenceIntervalPositionAdapter() - Constructor for class info.bioinfweb.commons.collections.SimpleSequenceIntervalPositionAdapter
 
size() - Method in class info.bioinfweb.commons.bio.biojava3.alignment.SimpleAlignment
 
size() - Method in interface info.bioinfweb.commons.bio.biojava3.alignment.template.Alignment
 
size() - Method in class info.bioinfweb.commons.collections.ListDecorator
 
size() - Method in class info.bioinfweb.commons.collections.NonStoringCollection
Since no objects are stored in this collection its size will always be 0.
size() - Method in class info.bioinfweb.commons.collections.PackedIntegerArrayList
Returns the number of elements currently contained in this list.
size() - Method in class info.bioinfweb.commons.collections.PackedObjectArrayList
 
size() - Method in class info.bioinfweb.commons.collections.PackedPrimitiveWrapperArrayList
 
size() - Method in class info.bioinfweb.commons.collections.SequenceIntervalList
 
size() - Method in class info.bioinfweb.commons.io.IOProgressListenerVector
 
size() - Method in class info.bioinfweb.commons.swing.ActionMap
 
size() - Method in class info.bioinfweb.commons.text.UniqueNameMap
 
skip(long) - Method in class info.bioinfweb.commons.io.LimitedInputStream
 
skip(long) - Method in class info.bioinfweb.commons.io.LimitedReader
 
SQL_SET_SEPARATOR - Static variable in class info.bioinfweb.commons.sql.SQLUtils
 
SQLConnector - Class in info.bioinfweb.commons.sql
 
SQLConnector() - Constructor for class info.bioinfweb.commons.sql.SQLConnector
 
SQLManipulator - Class in info.bioinfweb.commons.servlet
 
SQLManipulator(String, String, String, String) - Constructor for class info.bioinfweb.commons.servlet.SQLManipulator
 
SQLProperties - Interface in info.bioinfweb.commons.sql.sqlproperties
Classes implementing this interface provide a bean to store information to connect to a SQL database.
SQLUtils - Class in info.bioinfweb.commons.sql
Utility class for common tasks related to SQL operations.
SQLUtils() - Constructor for class info.bioinfweb.commons.sql.SQLUtils
 
SQLXMLConstants - Interface in info.bioinfweb.commons.sql.sqlproperties
XML constants for the namespace http://bioinfweb.info/xmlns/SQLConnection.
SQLXMLReader - Class in info.bioinfweb.commons.sql.sqlproperties
Reads data necessary to connect to a SQL database.
SQLXMLReader(QName) - Constructor for class info.bioinfweb.commons.sql.sqlproperties.SQLXMLReader
Creates a new instance.
STABLE_STRING - Static variable in enum info.bioinfweb.commons.appversion.ApplicationType
 
START_END_SEPARATER - Static variable in class info.bioinfweb.commons.bio.biojavax.bio.phylo.io.nexus.SetsBlockParser
 
startBlockObject() - Method in class info.bioinfweb.commons.bio.biojavax.bio.phylo.io.nexus.SetsBlockBuilder
 
stateChanged(ChangeEvent) - Method in class info.bioinfweb.commons.swing.SwingChangeMonitor
 
STOP_CODON_CHAR - Static variable in class info.bioinfweb.commons.bio.SequenceUtils
 
StreamLocation - Class in info.bioinfweb.commons.io
A read only implementation of StreamLocationProvider, which can be used to store a static location.
StreamLocation(long, long, long) - Constructor for class info.bioinfweb.commons.io.StreamLocation
 
StreamLocation(StreamLocationProvider) - Constructor for class info.bioinfweb.commons.io.StreamLocation
 
StreamLocation(Location) - Constructor for class info.bioinfweb.commons.io.StreamLocation
 
StreamLocationProvider - Interface in info.bioinfweb.commons.io
Interface to be implemented by classes (e.g.
StreamLocationProviderOffsetComparator - Class in info.bioinfweb.commons.io
Comparator for instances of StreamLocationProvider, which uses StreamLocationProvider.getCharacterOffset() as the only comparison criterion.
StreamLocationProviderOffsetComparator() - Constructor for class info.bioinfweb.commons.io.StreamLocationProviderOffsetComparator
 
StringUtils - Class in info.bioinfweb.commons.text
Provides general methods to use with character sequences.
StringUtils() - Constructor for class info.bioinfweb.commons.text.StringUtils
 
StrToken - Class in info.bioinfweb.commons.tokenizer
 
StrToken() - Constructor for class info.bioinfweb.commons.tokenizer.StrToken
 
StrToken(int, String, int) - Constructor for class info.bioinfweb.commons.tokenizer.StrToken
 
StrTokenizer - Class in info.bioinfweb.commons.tokenizer
 
StrTokenizer() - Constructor for class info.bioinfweb.commons.tokenizer.StrTokenizer
 
subList(int, int) - Method in class info.bioinfweb.commons.collections.ListDecorator
 
sum1ToN(int) - Static method in class info.bioinfweb.commons.Math2
Returns the sum of all integers from 1 to the specified value.
SwingChangeMonitor - Class in info.bioinfweb.commons.swing
 
SwingChangeMonitor() - Constructor for class info.bioinfweb.commons.swing.SwingChangeMonitor
 
SwingDocumentApplicationLogger - Class in info.bioinfweb.commons.log
This implementation of ApplicationLogger appends all messages to a Document.
SwingDocumentApplicationLogger(Document) - Constructor for class info.bioinfweb.commons.log.SwingDocumentApplicationLogger
 
SwingSavable - Interface in info.bioinfweb.commons.swing
Interface for a SwingSaver.
SwingSaver - Class in info.bioinfweb.commons.swing
Implements the interface Savable with Swing-Dialogs.
SwingSaver() - Constructor for class info.bioinfweb.commons.swing.SwingSaver
 
SwingSaver(String) - Constructor for class info.bioinfweb.commons.swing.SwingSaver
 
SwingSaverMessages - Class in info.bioinfweb.commons.swing
 
SwingSaverMessages() - Constructor for class info.bioinfweb.commons.swing.SwingSaverMessages
 
SwingUtils - Class in info.bioinfweb.commons.swing
 
SwingUtils() - Constructor for class info.bioinfweb.commons.swing.SwingUtils
 
SWTUtils - Class in info.bioinfweb.commons.swt
Provides methods of general use in SWT.
SWTUtils() - Constructor for class info.bioinfweb.commons.swt.SWTUtils
 
symbolToNucleotideCompound(Symbol) - Static method in class info.bioinfweb.commons.bio.biojava3.core.sequence.BioJava1SymbolTranslator
 
SystemBrowserHyperlinkListener - Class in info.bioinfweb.commons.swing
An implementation of HyperlinkListener that opens URLs in the system browser.
SystemBrowserHyperlinkListener(Component) - Constructor for class info.bioinfweb.commons.swing.SystemBrowserHyperlinkListener
 
SystemBrowserHyperlinkListener() - Constructor for class info.bioinfweb.commons.swing.SystemBrowserHyperlinkListener
 
SystemUtils - Class in info.bioinfweb.commons
An extension of the apache commons class SystemUtils.
SystemUtils() - Constructor for class info.bioinfweb.commons.SystemUtils
It is unnecessary to create instances of this class.
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