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GAP_CHAR - Static variable in class info.bioinfweb.commons.bio.SequenceUtils
 
GAP_CHARACTER - Static variable in class info.bioinfweb.commons.bio.biojava3.core.sequence.compound.AlignmentAmbiguityNucleotideCompoundSet
 
GAP_SCORE - Static variable in class info.bioinfweb.commons.bio.alignment.pairwise.NeedlemanWunschAligner
 
generateBeans(HttpServletRequest, HttpServletResponse) - Method in class info.bioinfweb.commons.servlet.Model2Servlet
Implementations of this method are called before this servlet delegates to the output JSP.
generateNext() - Method in class info.bioinfweb.commons.graphics.UniqueColorLister
Returns a new color which differs from all colors previously returned by this method.
GenericChangeEvent<S> - Class in info.bioinfweb.commons.events
A change event that returns its source as a generic type.
GenericChangeEvent(S) - Constructor for class info.bioinfweb.commons.events.GenericChangeEvent
 
GenericEventObject<S> - Class in info.bioinfweb.commons.events
An event state object that returns its source as a generic type.
GenericEventObject(S) - Constructor for class info.bioinfweb.commons.events.GenericEventObject
 
geraterThan(FormatVersion) - Method in class info.bioinfweb.commons.io.FormatVersion
Returns whether this version is newer than the specified argument.
get(int) - Method in class info.bioinfweb.commons.collections.ListDecorator
 
get(long) - Method in class info.bioinfweb.commons.collections.PackedIntegerArrayList
Returns the element stored at the specified index.
get(int) - Method in class info.bioinfweb.commons.collections.PackedObjectArrayList
 
get(int) - Method in class info.bioinfweb.commons.io.IOProgressListenerVector
 
get(Object) - Method in class info.bioinfweb.commons.swing.ActionMap
 
getAccession() - Method in class info.bioinfweb.commons.bio.biojava3.core.sequence.views.ConcatenatedSequenceView
Returns the accession ID of the first viewed sequence.
getAdenineScore() - Method in class info.bioinfweb.commons.bio.AmbiguityBaseScore
 
getAffectedElement() - Method in class info.bioinfweb.commons.collections.observable.ListMultipleChangesEvent
Returns the first affected element.
getAffectedElement() - Method in class info.bioinfweb.commons.collections.observable.ListRemoveEvent
Returns the first affected element.
getAffectedElements() - Method in class info.bioinfweb.commons.collections.observable.ListMultipleChangesEvent
Returns a collection of all elements that will be or have been affected by the list modification (e.g.
getAffectedElements() - Method in class info.bioinfweb.commons.collections.observable.ListRemoveEvent
Returns a collection of all elements that will be or have been removed from the list.
getAlignmentAmbiguityDNACompoundSet() - Static method in class info.bioinfweb.commons.bio.biojava3.core.sequence.compound.AlignmentAmbiguityDNACompoundSet
Returns a shared instance of this class.
getAlignmentAmbiguityNucleotideCompoundSet() - Static method in class info.bioinfweb.commons.bio.biojava3.core.sequence.compound.AlignmentAmbiguityNucleotideCompoundSet
Returns a shared instance of this class.
getAlignmentAmbiguityRNACompoundSet() - Static method in class info.bioinfweb.commons.bio.biojava3.core.sequence.compound.AlignmentAmbiguityRNACompoundSet
Returns a shared instance of this class.
getAmbiguityNoGapDNACompoundSet() - Static method in class info.bioinfweb.commons.bio.biojava3.core.sequence.compound.AmbiguityNoGapDNACompoundSet
Returns a shared instance of this class.
getAmbiguityNoGapNucleotideCompoundSet() - Static method in class info.bioinfweb.commons.bio.biojava3.core.sequence.compound.AmbiguityNoGapNucleotideCompoundSet
Returns a shared instance of this class.
getAmbiguityNoGapRNACompoundSet() - Static method in class info.bioinfweb.commons.bio.biojava3.core.sequence.compound.AmbiguityNoGapRNACompoundSet
Returns a shared instance of this class.
getAminoAcidOneLetterCodes(boolean) - Static method in class info.bioinfweb.commons.bio.SequenceUtils
Returns a set of all amino acid one letter codes in upper case.
getAminoAcidThreeLetterCodes(boolean) - Static method in class info.bioinfweb.commons.bio.SequenceUtils
Returns a set of all amino acid three letter codes in upper case.
getApplicationLogger(String, ApplicationLogger) - Method in class info.bioinfweb.commons.collections.ParameterMap
Checks if a ApplicationLogger object is stored under the specified key.
getApplicationLogger(String) - Method in class info.bioinfweb.commons.collections.ParameterMap
Returns the application logger registered for the specified key.
getApplicationLogger() - Method in class info.bioinfweb.commons.log.ApplicationLoggerParameterMap
Returns a stored ApplicationLogger object or a new instance of VoidApplicationLogger if no appropriate object is stored.
getApplyButton() - Method in class info.bioinfweb.commons.swing.OkCancelApplyDialog
This method initializes applyButton
getArg(int) - Method in class info.bioinfweb.commons.CommandLineReader
 
getAscent(Font) - Method in class info.bioinfweb.commons.graphics.FontCalculator
 
getAscentToHeight(String, int, float) - Method in class info.bioinfweb.commons.graphics.FontCalculator
 
getAskToSaveMessageBeginnung() - Method in class info.bioinfweb.commons.swing.SwingSaverMessages
 
getAskToSaveMessageEnd() - Method in class info.bioinfweb.commons.swing.SwingSaverMessages
 
getAskToSaveTitle() - Method in class info.bioinfweb.commons.swing.SwingSaverMessages
 
getAsList() - Method in class info.bioinfweb.commons.bio.biojava3.core.sequence.views.ConcatenatedSequenceView
 
getAspectRatio(Font, String) - Method in class info.bioinfweb.commons.graphics.FontCalculator
Returns the width of the given text divided by the height.
getAvailablePeek() - Method in class info.bioinfweb.commons.io.PeekReader
Returns the number of characters that can be previewed in front of the current position in the stream.
getBioEnd() - Method in class info.bioinfweb.commons.bio.biojava3.core.sequence.views.ConcatenatedSequenceView
 
getBioStart() - Method in class info.bioinfweb.commons.bio.biojava3.core.sequence.views.ConcatenatedSequenceView
 
getBioStart() - Method in class info.bioinfweb.commons.bio.biojava3.core.sequence.views.ConcatenatedSequenceView.ViewedSequence
 
getBitsPerValue() - Method in class info.bioinfweb.commons.collections.PackedIntegerArrayList
Returns the length in bits of an entry in this list.
getBlockListener() - Method in class info.bioinfweb.commons.bio.biojavax.bio.phylo.io.nexus.SetsBlockParser
 
getBoolean(String, boolean) - Method in class info.bioinfweb.commons.collections.ParameterMap
Checks if a Boolean object is stored under the specified key.
getBooleanParameter(HttpServletRequest, String, boolean) - Static method in class info.bioinfweb.commons.servlet.ServletUtils
 
getBuildNumber() - Method in class info.bioinfweb.commons.appversion.ApplicationVersion
 
getButtonCancel() - Method in class info.bioinfweb.commons.swing.SwingSaverMessages
 
getButtonNo() - Method in class info.bioinfweb.commons.swing.SwingSaverMessages
 
getButtonsPanel() - Method in class info.bioinfweb.commons.swing.OkCancelApplyDialog
This method initializes buttonPanel
getButtonYes() - Method in class info.bioinfweb.commons.swing.SwingSaverMessages
 
getCancelButton() - Method in class info.bioinfweb.commons.swing.OkCancelApplyDialog
This method initializes cancelButton
getCancelButton() - Method in class info.bioinfweb.commons.swing.ProgressDialog
 
getChangeMonitor() - Method in class info.bioinfweb.commons.swing.DecimalInput
 
getCharacterOffset() - Method in class info.bioinfweb.commons.io.PeekReader
Returns the number of characters that have been read from this reader since the beginning of the underlying stream.
getCharacterOffset() - Method in class info.bioinfweb.commons.io.StreamLocation
 
getCharacterOffset() - Method in interface info.bioinfweb.commons.io.StreamLocationProvider
Returns the number of characters that have been read from this instance since the beginning of the underlying stream.
getCharSet(String) - Method in class info.bioinfweb.commons.bio.biojavax.bio.phylo.io.nexus.SetsBlock
 
getCharSets() - Method in class info.bioinfweb.commons.bio.biojava3.alignment.SimpleAlignment
 
getCharSets() - Method in interface info.bioinfweb.commons.bio.biojava3.alignment.template.Alignment
 
getClassDir(Class<?>) - Static method in class info.bioinfweb.commons.io.IOUtils
 
getClassLocation(Class<?>) - Static method in class info.bioinfweb.commons.io.IOUtils
Returns either the path to the class file of the specified class without the package path or the path top the archive file that contains it (e.g.
getColumnNumber() - Method in class info.bioinfweb.commons.io.PeekReader
Returns the column of the current line, where the cursor of this reader is currently located.
getColumnNumber() - Method in class info.bioinfweb.commons.io.StreamLocation
 
getColumnNumber() - Method in interface info.bioinfweb.commons.io.StreamLocationProvider
Returns the column of the current line, where the cursor of this instance is currently located.
getComboBox() - Method in class info.bioinfweb.commons.swing.JDropDownSpinner
The combo box used inside this component.
getCompoundAt(int) - Method in class info.bioinfweb.commons.bio.biojava3.core.sequence.views.ConcatenatedSequenceView
 
getCompoundAt(int) - Method in class info.bioinfweb.commons.bio.biojava3.core.sequence.views.RemoveSequenceView
 
getCompoundAt(int) - Method in class info.bioinfweb.commons.bio.biojava3.core.sequence.views.ReplaceNucleotideSequenceView
 
getCompoundAt(int) - Method in class info.bioinfweb.commons.bio.biojava3.core.sequence.views.UpperCaseSequenceView
 
getCompoundSet() - Method in class info.bioinfweb.commons.bio.biojava3.core.sequence.views.ConcatenatedSequenceView
 
getConnection() - Method in class info.bioinfweb.commons.servlet.SQLManipulator
 
getConnection(String, String, String, String, String) - Static method in class info.bioinfweb.commons.sql.SQLConnector
 
getConsensusBase() - Method in class info.bioinfweb.commons.bio.AmbiguityBaseScore
 
getContent() - Method in class info.bioinfweb.commons.tokenizer.StrToken
 
getContrastColor(Color, Color, int) - Static method in class info.bioinfweb.commons.graphics.GraphicsUtils
Returns the specified color if it differs enough from the given background color.
getCount() - Method in class info.bioinfweb.commons.io.DefaultNameManager
 
getCountry() - Method in class info.bioinfweb.commons.servlet.acceptlanguage.AcceptLanguageEntry
 
getCurrentDirectory() - Method in class info.bioinfweb.commons.swing.FileChooserDirModel
 
getCytosineScore() - Method in class info.bioinfweb.commons.bio.AmbiguityBaseScore
 
getDBDriver() - Method in class info.bioinfweb.commons.sql.sqlproperties.ConcreteSQLProperties
 
getDBDriver() - Method in interface info.bioinfweb.commons.sql.sqlproperties.SQLProperties
 
getDBHost() - Method in class info.bioinfweb.commons.sql.sqlproperties.ConcreteSQLProperties
 
getDBHost() - Method in interface info.bioinfweb.commons.sql.sqlproperties.SQLProperties
 
getDBName() - Method in class info.bioinfweb.commons.sql.sqlproperties.ConcreteSQLProperties
 
getDBName() - Method in interface info.bioinfweb.commons.sql.sqlproperties.SQLProperties
 
getDBPassword() - Method in class info.bioinfweb.commons.sql.sqlproperties.ConcreteSQLProperties
 
getDBPassword() - Method in interface info.bioinfweb.commons.sql.sqlproperties.SQLProperties
 
getDBUser() - Method in class info.bioinfweb.commons.sql.sqlproperties.ConcreteSQLProperties
 
getDBUser() - Method in interface info.bioinfweb.commons.sql.sqlproperties.SQLProperties
 
getDecimalFormat() - Method in class info.bioinfweb.commons.swing.DecimalInput
 
getDecimalInput() - Method in class info.bioinfweb.commons.swing.DecimalInputDialog
 
getDefaultExtension() - Method in class info.bioinfweb.commons.io.AbstractSaver
 
getDefaultExtension() - Method in class info.bioinfweb.commons.io.ExtensionFileFilter
Returns the default file extension of this filter.
getDefaultExtension() - Method in interface info.bioinfweb.commons.io.Savable
The file extension which should be add to file name chosen in the save as dialog, if not one of the allowed ones is already present.
getDefaultLanguage() - Method in class info.bioinfweb.commons.servlet.acceptlanguage.AcceptLanguageRedirectServlet
 
getDefaultName() - Method in class info.bioinfweb.commons.io.AbstractSaver
 
getDefaultName() - Method in interface info.bioinfweb.commons.io.Savable
The path that should be proposed by the saveAs()-method if no path has been assigned.
getDefaultNameOrPath() - Method in class info.bioinfweb.commons.io.AbstractSaver
 
getDefaultNameOrPath() - Method in interface info.bioinfweb.commons.io.Savable
The path of the assigned file or the default name if no file has been specified.
getDefaultSymbol() - Method in enum info.bioinfweb.commons.bio.CharacterSymbolMeaning
Returns the symbol usually used to represent this meaning.
getDescent(Font) - Method in class info.bioinfweb.commons.graphics.FontCalculator
 
getDescentToHeight(String, int, float) - Method in class info.bioinfweb.commons.graphics.FontCalculator
 
getDescription() - Method in class info.bioinfweb.commons.io.ExtensionFileFilter
 
getDescription() - Method in class info.bioinfweb.commons.io.InternationalFileFilter
 
getDocument() - Method in class info.bioinfweb.commons.log.SwingDocumentApplicationLogger
 
getDouble(String, double) - Method in class info.bioinfweb.commons.collections.ParameterMap
Checks if a Double object is stored under the specified key.If the stored object has another numeric type, it is converted to double.
getDoubleValue() - Method in class info.bioinfweb.commons.swing.DecimalInputDialog
 
getEdit(int) - Method in class info.bioinfweb.commons.swing.AccessibleUndoManager
 
getElementAt(int) - Method in class info.bioinfweb.commons.swing.ListBackedListModel
 
getElementAt(int) - Method in class info.bioinfweb.commons.swing.LocaleComboBoxModel
 
getExtensions() - Method in class info.bioinfweb.commons.io.ExtensionFileFilter
Returns a list of all extensions accepted by this filter.
getExtensionsAsString() - Method in class info.bioinfweb.commons.io.ExtensionFileFilter
Returns all extensions stored in this filter as a single string.
getFile(String, File) - Method in class info.bioinfweb.commons.collections.ParameterMap
Checks if a File object is stored under the specified key.
getFile(String) - Method in class info.bioinfweb.commons.collections.ParameterMap
Checks if a File object is stored under the specified key.
getFile() - Method in class info.bioinfweb.commons.io.AbstractSaver
 
getFile() - Method in interface info.bioinfweb.commons.io.Savable
Returns the assigned file.
getFileChooser() - Method in interface info.bioinfweb.commons.swing.SwingSavable
 
getFileChooser() - Method in class info.bioinfweb.commons.swing.SwingSaver
Returns the file dialog used by this instance in SwingSaver.saveAs() and SwingSaver.saveAs(Component).
getFileExtensions() - Method in class info.bioinfweb.commons.io.AbstractSaver
 
getFileExtensions() - Method in interface info.bioinfweb.commons.io.Savable
 
getFillUpChar() - Method in class info.bioinfweb.commons.text.UniqueNameMapParameters
 
getFirst(Cookie[], String) - Static method in class info.bioinfweb.commons.servlet.CookieManager
 
getFirstPos(T) - Method in interface info.bioinfweb.commons.collections.SequenceIntervalPositionAdapter
 
getFirstPos() - Method in class info.bioinfweb.commons.collections.SimpleSequenceInterval
 
getFirstPos(SimpleSequenceInterval) - Method in class info.bioinfweb.commons.collections.SimpleSequenceIntervalPositionAdapter
 
getFloat(String, float) - Method in class info.bioinfweb.commons.collections.ParameterMap
Checks if a Float object is stored under the specified key.
getFloatValue() - Method in class info.bioinfweb.commons.swing.DecimalInputDialog
 
getFontSizeByTextHeight(float, String, int) - Method in class info.bioinfweb.commons.graphics.FontCalculator
 
getGapChar() - Method in class info.bioinfweb.commons.bio.alignment.pairwise.NeedlemanWunschAligner
 
getGuanineScore() - Method in class info.bioinfweb.commons.bio.AmbiguityBaseScore
 
getHeight() - Method in class info.bioinfweb.commons.graphics.DoubleDimension
 
getHeight(Font) - Method in class info.bioinfweb.commons.graphics.FontCalculator
Deprecated.
As of release 2.2.0, replaced by FontCalculator.getTextHeightByFontSize(Font).
getHeightSizeRatio(String, int) - Method in class info.bioinfweb.commons.graphics.FontCalculator
 
getHelpCode() - Method in class info.bioinfweb.commons.log.ApplicationLoggerMessage
 
getID() - Method in class info.bioinfweb.commons.tokenizer.StrToken
 
getIndex() - Method in exception info.bioinfweb.commons.collections.bitstorage.exception.BitIndexOutOfBoundException
Returns the invalid bit index.
getIndex() - Method in class info.bioinfweb.commons.collections.observable.ListChangeEvent
Returns the index the first inserted element has in the list.
getIndexOf(C) - Method in class info.bioinfweb.commons.bio.biojava3.core.sequence.views.ConcatenatedSequenceView
 
getInstance() - Static method in class info.bioinfweb.commons.bio.ConsensusSequenceCreator
 
getInstance() - Static method in class info.bioinfweb.commons.graphics.FontCalculator
 
getInstance() - Static method in class info.bioinfweb.commons.servlet.acceptlanguage.QualityComparator
 
getInstance() - Static method in class info.bioinfweb.commons.testing.TestLogger
 
getInt(int) - Method in class info.bioinfweb.commons.collections.bitstorage.AbstractIntegerBitList
 
getInteger(String, int) - Method in class info.bioinfweb.commons.collections.ParameterMap
Checks if a Integer object is stored under the specified key.
getIntervalLength() - Method in class info.bioinfweb.commons.collections.SequenceIntervalList
 
getIntervalStart() - Method in class info.bioinfweb.commons.collections.SequenceIntervalList.IntervalInformation
 
getIntParameter(HttpServletRequest, String, int) - Static method in class info.bioinfweb.commons.servlet.ServletUtils
 
getIntValue() - Method in class info.bioinfweb.commons.swing.DecimalInputDialog
 
getInverse() - Method in class info.bioinfweb.commons.bio.biojava3.core.sequence.views.ConcatenatedSequenceView
 
getIsSubedit() - Method in class info.bioinfweb.commons.swing.AbstractDocumentEdit
 
getLabel() - Method in class info.bioinfweb.commons.swing.DecimalInput
 
getLabel() - Method in class info.bioinfweb.commons.swing.ProgressDialog
 
getLanguage() - Method in class info.bioinfweb.commons.servlet.acceptlanguage.AcceptLanguageEntry
 
getLastElement(List<E>) - Static method in class info.bioinfweb.commons.collections.CollectionUtils
 
getLastIndexOf(C) - Method in class info.bioinfweb.commons.bio.biojava3.core.sequence.views.ConcatenatedSequenceView
 
getLastPos(T) - Method in interface info.bioinfweb.commons.collections.SequenceIntervalPositionAdapter
 
getLastPos() - Method in class info.bioinfweb.commons.collections.SimpleSequenceInterval
 
getLastPos(SimpleSequenceInterval) - Method in class info.bioinfweb.commons.collections.SimpleSequenceIntervalPositionAdapter
 
getLength() - Method in class info.bioinfweb.commons.bio.biojava3.core.sequence.views.ConcatenatedSequenceView
 
getLength() - Method in class info.bioinfweb.commons.bio.biojava3.core.sequence.views.RemoveSequenceView
 
getLimit() - Method in class info.bioinfweb.commons.io.LimitedInputStream
Returns the maximum number of bytes that will be read from the decorated stream.
getLimit() - Method in class info.bioinfweb.commons.io.LimitedReader
Returns the maximum number of characters that will be read from the decorated reader.
getLineLength() - Method in class info.bioinfweb.commons.bio.biojava3.core.sequence.io.MapFastaWriter
 
getLineNumber() - Method in class info.bioinfweb.commons.io.PeekReader
Returns the number of the line in the stream, where the cursor of this reader is currently located.
getLineNumber() - Method in class info.bioinfweb.commons.io.StreamLocation
 
getLineNumber() - Method in interface info.bioinfweb.commons.io.StreamLocationProvider
Returns the number of the line in the stream, where the cursor of this instance is currently located.
getLineSeparator() - Method in class info.bioinfweb.commons.bio.biojava3.core.sequence.io.MapFastaWriter
 
getList() - Method in class info.bioinfweb.commons.log.MessageListApplicationLogger
 
getList() - Method in class info.bioinfweb.commons.swing.ListBackedListModel
 
getLocaleAt(int) - Method in class info.bioinfweb.commons.swing.LocaleComboBoxModel
 
getLog(String) - Method in class info.bioinfweb.commons.testing.TestLogger
Returns the log with the specified name.
getLogger() - Method in class info.bioinfweb.commons.log.ApplicationLoggerDialog
 
getLoggers() - Method in class info.bioinfweb.commons.log.MultipleApplicationLoggersAdapter
 
getLong(String, long) - Method in class info.bioinfweb.commons.collections.ParameterMap
Checks if a Long object is stored under the specified key.
getLongParameter(HttpServletRequest, String, long) - Static method in class info.bioinfweb.commons.servlet.ServletUtils
 
getLongValue() - Method in class info.bioinfweb.commons.swing.DecimalInputDialog
 
getMajor() - Method in class info.bioinfweb.commons.io.FormatVersion
 
getMajorRelease() - Method in class info.bioinfweb.commons.appversion.ApplicationVersion
 
getMap() - Method in class info.bioinfweb.commons.swing.ActionMap
 
getMap() - Method in class info.bioinfweb.commons.text.UniqueNameMap
 
getMaximumFactor() - Method in class info.bioinfweb.commons.swing.RelativeRangeModel
 
getMaxNameLength() - Method in class info.bioinfweb.commons.text.UniqueNameMapParameters
 
getMaxObjectTypeCount() - Method in class info.bioinfweb.commons.collections.PackedObjectArrayList
Returns the number of different objects this list can manage.
getMaxScore() - Method in class info.bioinfweb.commons.bio.AmbiguityBaseScore
 
getMaxTaxonNameLength() - Method in class info.bioinfweb.commons.bio.biojava3.alignment.io.hennig86.Hennig86Writer
 
getMaxValue() - Method in class info.bioinfweb.commons.collections.PackedIntegerArrayList
Returns the maximum value that can be represented by an element of this list.
getMessage() - Method in class info.bioinfweb.commons.log.ApplicationLoggerMessage
 
getMessageList() - Method in class info.bioinfweb.commons.log.MessageListApplicationLogger
 
getMessages() - Method in class info.bioinfweb.commons.io.streammessage.MessageReader
 
getMinor() - Method in class info.bioinfweb.commons.io.FormatVersion
 
getMinorRelease() - Method in class info.bioinfweb.commons.appversion.ApplicationVersion
 
getMinValue() - Method in class info.bioinfweb.commons.collections.PackedIntegerArrayList
Returns the minimum value that can be represented by an element of this list.
getName() - Method in class info.bioinfweb.commons.bio.biojavax.bio.phylo.io.nexus.CharSet
 
getName() - Method in class info.bioinfweb.commons.graphics.ZoomableFont
Returns the font name.
getNameMap() - Method in class info.bioinfweb.commons.bio.biojava3.alignment.io.AbstractAlignmentWriter
 
getNameMap() - Method in interface info.bioinfweb.commons.bio.biojava3.alignment.io.AlignmentWriter
 
getNewElement() - Method in class info.bioinfweb.commons.collections.observable.ListReplaceEvent
Returns the element that is now contained in the list.
getNoGapDNACompoundSet() - Static method in class info.bioinfweb.commons.bio.biojava3.core.sequence.compound.NoGapDNACompoundSet
Returns a shared instance of this class.
getNoGapNucleotideCompoundSet() - Static method in class info.bioinfweb.commons.bio.biojava3.core.sequence.compound.NoGapNucleotideCompoundSet
Returns a shared instance of this class.
getNoGapRNACompoundSet() - Static method in class info.bioinfweb.commons.bio.biojava3.core.sequence.compound.NoGapRNACompoundSet
Returns a shared instance of this class.
getNonGapCompoundSet() - Method in class info.bioinfweb.commons.bio.biojava3.core.sequence.views.UnalignedSequenceView
Returns the set of compounds representing non-gap positions in the underlying sequence.
getNoOfStates() - Method in class info.bioinfweb.commons.bio.biojava3.alignment.io.hennig86.Hennig86Writer
 
getNucleotideCharacters() - Static method in class info.bioinfweb.commons.bio.SequenceUtils
Returns a set of all nucleotide characters, including 'T' and 'U' as well as all IUPAC ambiguity codes in upper case.
getNucleotideCompoundSet() - Static method in class info.bioinfweb.commons.bio.biojava3.core.sequence.compound.NucleotideCompoundSet
Returns a shared instance of this class.
getNumberOfBits() - Method in exception info.bioinfweb.commons.collections.bitstorage.exception.InvalidBitNumberForPrimitiveException
Returns the invalid bit index.
getNumericValue(String) - Method in class info.bioinfweb.commons.testing.TestLogger
 
getObject(String, Object) - Method in class info.bioinfweb.commons.collections.ParameterMap
Returns the stored object for the key or defaultValue if no object is found.
getObject(String, O, Class<O>) - Method in class info.bioinfweb.commons.collections.ParameterMap
Returns the stored object for the key if it is an instance of the specified class.
getOkButton() - Method in class info.bioinfweb.commons.swing.OkCancelApplyDialog
This method initializes okButton
getOldElement() - Method in class info.bioinfweb.commons.collections.observable.ListReplaceEvent
Returns the element that has been replaced or will be replaced.
getOriginalHeader() - Method in class info.bioinfweb.commons.bio.biojava3.core.sequence.views.ReplaceAbstractSequenceView
 
getOriginalHeight() - Method in class info.bioinfweb.commons.graphics.ZoomableFont
Returns the font size for a zoom factor of 100 %.
getOutputJSP() - Method in class info.bioinfweb.commons.servlet.Model2Servlet
 
getOverlapList() - Method in class info.bioinfweb.commons.collections.SequenceIntervalList.IntervalInformation
 
getOverlappingElements(int, int) - Method in class info.bioinfweb.commons.collections.NonOverlappingIntervalList
 
getOverlappingElements(int, int) - Method in class info.bioinfweb.commons.collections.SequenceIntervalList
 
getParameters() - Method in class info.bioinfweb.commons.text.UniqueNameMap
 
getPatchLevel() - Method in class info.bioinfweb.commons.appversion.ApplicationVersion
 
getPathPrefix() - Method in class info.bioinfweb.commons.swing.ExtendedAbstractAction
 
getPos() - Method in class info.bioinfweb.commons.tokenizer.StrToken
 
getPositionAdapter() - Method in class info.bioinfweb.commons.collections.SequenceIntervalList
 
GetPostServlet - Class in info.bioinfweb.commons.servlet
 
GetPostServlet() - Constructor for class info.bioinfweb.commons.servlet.GetPostServlet
 
GetPostServlet(String) - Constructor for class info.bioinfweb.commons.servlet.GetPostServlet
 
getPreferences() - Method in class info.bioinfweb.commons.ProgramMainClass
Returns the associated preferences object.
getPreferredSize() - Method in class info.bioinfweb.commons.swing.scrollpaneselector.ExtendedScrollPaneSelector
 
getPreferredSize() - Method in class org.jdesktop.swingx.scrollpaneselector.ScrollPaneBidule
 
getPreferredSize() - Method in class org.jdesktop.swingx.scrollpaneselector.ScrollPaneSelector
 
getPrefix() - Method in class info.bioinfweb.commons.beans.PropertyChangeEventForwarder
 
getPrefix() - Method in class info.bioinfweb.commons.io.DefaultNameManager
 
getPrimitiveSize() - Method in exception info.bioinfweb.commons.collections.bitstorage.exception.InvalidBitNumberForPrimitiveException
Returns the number of bits the primitive where the bit should have been stored can contain.
getPrivateField(Class<? extends Object>, String) - Static method in class info.bioinfweb.commons.testing.TestTools
 
getPrivateFieldValue(Object, String) - Static method in class info.bioinfweb.commons.testing.TestTools
 
getPrivateMethod(Class<? extends Object>, String, Class...) - Static method in class info.bioinfweb.commons.testing.TestTools
Returns an accessible private method.
getProcessedName(String) - Method in class info.bioinfweb.commons.text.UniqueNameMap
 
getProgressBar() - Method in class info.bioinfweb.commons.swing.ProgressDialog
 
getProgressText() - Method in class info.bioinfweb.commons.progress.AbstractProgressMonitor
 
getProgressText() - Method in interface info.bioinfweb.commons.progress.ProgressMonitor
 
getProgressText() - Method in class info.bioinfweb.commons.swing.ProgressDialog
 
getProgressValue() - Method in class info.bioinfweb.commons.progress.AbstractProgressMonitor
 
getProgressValue() - Method in interface info.bioinfweb.commons.progress.ProgressMonitor
 
getProgressValue() - Method in class info.bioinfweb.commons.swing.ProgressDialog
 
getPropertyName() - Method in class info.bioinfweb.commons.changemonitor.PropertyChangeMonitor
Returns the name of the property this monitor listens to.
getQuality() - Method in class info.bioinfweb.commons.servlet.acceptlanguage.AcceptLanguageEntry
 
getRedoEdit(int) - Method in class info.bioinfweb.commons.swing.AccessibleUndoManager
Returns the specified redo edit where the first to be redone has the index 0.
getRedoMenu() - Method in class info.bioinfweb.commons.swing.AbstractUndoActionManagement
 
getRedoPresentationName() - Method in class info.bioinfweb.commons.swing.AbstractDocumentEdit
 
getRemainingPositions() - Method in class info.bioinfweb.commons.bio.biojava3.core.sequence.views.RemoveSequenceView
 
getReplacements() - Method in class info.bioinfweb.commons.text.UniqueNameMapParameters
 
getScore() - Method in class info.bioinfweb.commons.bio.alignment.pairwise.NeedlemanWunschAligner
 
getScoreByIndex(int) - Method in class info.bioinfweb.commons.bio.AmbiguityBaseScore
 
getSelectedItem() - Method in class info.bioinfweb.commons.swing.JDropDownSpinner
Delegates to JComboBox.getSelectedItem() of JDropDownSpinner.getComboBox().
getSelectedItem() - Method in class info.bioinfweb.commons.swing.ListBackedComboBoxModel
 
getSelectedItem() - Method in class info.bioinfweb.commons.swing.LocaleComboBoxModel
 
getSelectedLocale() - Method in class info.bioinfweb.commons.swing.LocaleComboBoxModel
 
getSequence(int) - Method in class info.bioinfweb.commons.bio.biojava3.alignment.SimpleAlignment
 
getSequence(String) - Method in class info.bioinfweb.commons.bio.biojava3.alignment.SimpleAlignment
 
getSequence(int) - Method in interface info.bioinfweb.commons.bio.biojava3.alignment.template.Alignment
 
getSequence(String) - Method in interface info.bioinfweb.commons.bio.biojava3.alignment.template.Alignment
 
getSequence() - Method in class info.bioinfweb.commons.bio.biojava3.core.sequence.views.ConcatenatedSequenceView.ViewedSequence
 
getSequence() - Method in class info.bioinfweb.commons.io.PeekReader.ReadResult
The character sequence that was read from the underlying data source.
getSequenceAsString() - Method in class info.bioinfweb.commons.bio.biojava3.core.sequence.views.ConcatenatedSequenceView
 
getSequenceCreator() - Method in class info.bioinfweb.commons.bio.biojava3.alignment.io.AbstractAlignmentReader
 
getSize() - Method in class info.bioinfweb.commons.swing.ListBackedListModel
 
getSize() - Method in class info.bioinfweb.commons.swing.LocaleComboBoxModel
 
getSource() - Method in exception info.bioinfweb.commons.collections.bitstorage.exception.BitIndexOutOfBoundException
 
getSource() - Method in interface info.bioinfweb.commons.collections.bitstorage.exception.BitStorageException
Returns the bit field where the exception occurred.
getSource() - Method in exception info.bioinfweb.commons.collections.bitstorage.exception.InvalidBitNumberForPrimitiveException
 
getSource() - Method in class info.bioinfweb.commons.collections.observable.ListChangeEvent
Returns the list instance where the change occurred.
getSource() - Method in class info.bioinfweb.commons.events.GenericChangeEvent
 
getSource() - Method in class info.bioinfweb.commons.events.GenericEventObject
 
getStartList() - Method in class info.bioinfweb.commons.collections.SequenceIntervalList.IntervalInformation
 
getStatement() - Method in class info.bioinfweb.commons.servlet.SQLManipulator
 
getString(String, String) - Method in class info.bioinfweb.commons.collections.ParameterMap
Checks if an object is stored under the specified key.
getString(String) - Method in class info.bioinfweb.commons.collections.ParameterMap
Checks if an object is stored under the specified key.
getStyle() - Method in class info.bioinfweb.commons.graphics.ZoomableFont
Returns the font style.
getSubSequence(Integer, Integer) - Method in class info.bioinfweb.commons.bio.biojava3.core.sequence.views.ConcatenatedSequenceView
 
getSum() - Method in class info.bioinfweb.commons.bio.AmbiguityBaseScore
Returns the sum of all scores.
getTabbedPane() - Method in class info.bioinfweb.commons.swing.AboutDialog
 
getTablePrefix() - Method in class info.bioinfweb.commons.sql.sqlproperties.ConcreteSQLProperties
 
getTablePrefix() - Method in interface info.bioinfweb.commons.sql.sqlproperties.SQLProperties
 
getTargets() - Method in class info.bioinfweb.commons.beans.PropertyChangeEventForwarder
 
getTestStrategy() - Method in class info.bioinfweb.commons.io.ContentExtensionFileFilter
The strategy that is currently used to determine whether a file shall be accepted by this filter or not.
getTextArea() - Method in class info.bioinfweb.commons.log.JTextAreaApplicationLogger
 
getTextField() - Method in class info.bioinfweb.commons.swing.DecimalInput
 
getTextHeightByFontSize(float, String, int) - Method in class info.bioinfweb.commons.graphics.FontCalculator
 
getTextHeightByFontSize(Font) - Method in class info.bioinfweb.commons.graphics.FontCalculator
 
getTextWidthToFontSize(String, int, String, float) - Method in class info.bioinfweb.commons.graphics.FontCalculator
 
getTextWidthToTextHeigth(String, int, String, float) - Method in class info.bioinfweb.commons.graphics.FontCalculator
 
getThymineScore() - Method in class info.bioinfweb.commons.bio.AmbiguityBaseScore
 
getTime() - Method in class info.bioinfweb.commons.log.ApplicationLoggerMessage
 
getType() - Method in class info.bioinfweb.commons.appversion.ApplicationVersion
 
getType() - Method in class info.bioinfweb.commons.collections.observable.ListChangeEvent
Returns the type of change that happened.
getType() - Method in class info.bioinfweb.commons.io.streammessage.Message
 
getType() - Method in class info.bioinfweb.commons.log.ApplicationLoggerMessage
 
getUnderlyingIterator() - Method in class info.bioinfweb.commons.collections.ListIteratorDecorator
Returns the list iterator that has been decorated by this instance.
getUnderlyingList() - Method in class info.bioinfweb.commons.collections.ListDecorator
Returns the list that is decorated by this instance.
getUndoEdit(int) - Method in class info.bioinfweb.commons.swing.AccessibleUndoManager
Returns the specified undo edit where the first to be undone has the index 0.
getUndoManager() - Method in class info.bioinfweb.commons.swing.AbstractUndoActionManagement
 
getUndoMenu() - Method in class info.bioinfweb.commons.swing.AbstractUndoActionManagement
 
getUndoPresentationName() - Method in class info.bioinfweb.commons.swing.AbstractDocumentEdit
 
getURL(String) - Method in class info.bioinfweb.commons.servlet.acceptlanguage.AcceptLanguageRedirectServlet
 
getURL() - Method in class info.bioinfweb.commons.swing.actions.OpenWebsiteAction
 
getVersion() - Method in class info.bioinfweb.commons.io.streammessage.Message
 
getVersion() - Method in class info.bioinfweb.commons.ProgramMainClass
 
getViewedSequence() - Method in class info.bioinfweb.commons.bio.biojava3.core.sequence.views.ConcatenatedSequenceView
Returns the first viewed sequence.
getViewedSequenceByPosition(int) - Method in class info.bioinfweb.commons.bio.biojava3.core.sequence.views.ConcatenatedSequenceView
 
getViewedSequenceCount() - Method in class info.bioinfweb.commons.bio.biojava3.core.sequence.views.ConcatenatedSequenceView
 
getWidth() - Method in class info.bioinfweb.commons.graphics.DoubleDimension
 
getWidth(Font, String) - Method in class info.bioinfweb.commons.graphics.FontCalculator
 
getWidthToHeigth(String, int, String, float) - Method in class info.bioinfweb.commons.graphics.FontCalculator
Deprecated.
GraphicsUtils - Class in info.bioinfweb.commons.graphics
Contains method that implement general graphic tasks.
GraphicsUtils() - Constructor for class info.bioinfweb.commons.graphics.GraphicsUtils
 
GUANINE_INDEX - Static variable in class info.bioinfweb.commons.bio.AmbiguityBaseScore
 
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