- 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
-
- 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
-
- 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
-
- 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
-
- 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
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- GetPostServlet() - Constructor for class info.bioinfweb.commons.servlet.GetPostServlet
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- GetPostServlet(String) - Constructor for class info.bioinfweb.commons.servlet.GetPostServlet
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- getPreferences() - Method in class info.bioinfweb.commons.ProgramMainClass
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Returns the associated preferences object.
- getPreferredSize() - Method in class info.bioinfweb.commons.swing.scrollpaneselector.ExtendedScrollPaneSelector
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- getPreferredSize() - Method in class org.jdesktop.swingx.scrollpaneselector.ScrollPaneBidule
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- getPreferredSize() - Method in class org.jdesktop.swingx.scrollpaneselector.ScrollPaneSelector
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- getPrefix() - Method in class info.bioinfweb.commons.beans.PropertyChangeEventForwarder
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- getPrefix() - Method in class info.bioinfweb.commons.io.DefaultNameManager
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- getPrimitiveSize() - Method in exception info.bioinfweb.commons.collections.bitstorage.exception.InvalidBitNumberForPrimitiveException
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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
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- getPrivateFieldValue(Object, String) - Static method in class info.bioinfweb.commons.testing.TestTools
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- getPrivateMethod(Class<? extends Object>, String, Class...) - Static method in class info.bioinfweb.commons.testing.TestTools
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Returns an accessible private method.
- getProcessedName(String) - Method in class info.bioinfweb.commons.text.UniqueNameMap
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- getProgressBar() - Method in class info.bioinfweb.commons.swing.ProgressDialog
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- getProgressText() - Method in class info.bioinfweb.commons.progress.AbstractProgressMonitor
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- getProgressText() - Method in interface info.bioinfweb.commons.progress.ProgressMonitor
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- getProgressText() - Method in class info.bioinfweb.commons.swing.ProgressDialog
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- getProgressValue() - Method in class info.bioinfweb.commons.progress.AbstractProgressMonitor
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- getProgressValue() - Method in interface info.bioinfweb.commons.progress.ProgressMonitor
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- getProgressValue() - Method in class info.bioinfweb.commons.swing.ProgressDialog
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- getPropertyName() - Method in class info.bioinfweb.commons.changemonitor.PropertyChangeMonitor
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Returns the name of the property this monitor listens to.
- getQuality() - Method in class info.bioinfweb.commons.servlet.acceptlanguage.AcceptLanguageEntry
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- getRedoEdit(int) - Method in class info.bioinfweb.commons.swing.AccessibleUndoManager
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Returns the specified redo edit where the first to be redone has the index 0.
- getRedoMenu() - Method in class info.bioinfweb.commons.swing.AbstractUndoActionManagement
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- getRedoPresentationName() - Method in class info.bioinfweb.commons.swing.AbstractDocumentEdit
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- getRemainingPositions() - Method in class info.bioinfweb.commons.bio.biojava3.core.sequence.views.RemoveSequenceView
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- getReplacements() - Method in class info.bioinfweb.commons.text.UniqueNameMapParameters
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- getScore() - Method in class info.bioinfweb.commons.bio.alignment.pairwise.NeedlemanWunschAligner
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- getScoreByIndex(int) - Method in class info.bioinfweb.commons.bio.AmbiguityBaseScore
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- getSelectedItem() - Method in class info.bioinfweb.commons.swing.JDropDownSpinner
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- getSelectedItem() - Method in class info.bioinfweb.commons.swing.ListBackedComboBoxModel
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- getSelectedItem() - Method in class info.bioinfweb.commons.swing.LocaleComboBoxModel
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- getSelectedLocale() - Method in class info.bioinfweb.commons.swing.LocaleComboBoxModel
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- getSequence(int) - Method in class info.bioinfweb.commons.bio.biojava3.alignment.SimpleAlignment
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- getSequence(String) - Method in class info.bioinfweb.commons.bio.biojava3.alignment.SimpleAlignment
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- getSequence(int) - Method in interface info.bioinfweb.commons.bio.biojava3.alignment.template.Alignment
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- getSequence(String) - Method in interface info.bioinfweb.commons.bio.biojava3.alignment.template.Alignment
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- getSequence() - Method in class info.bioinfweb.commons.bio.biojava3.core.sequence.views.ConcatenatedSequenceView.ViewedSequence
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- getSequence() - Method in class info.bioinfweb.commons.io.PeekReader.ReadResult
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The character sequence that was read from the underlying data source.
- getSequenceAsString() - Method in class info.bioinfweb.commons.bio.biojava3.core.sequence.views.ConcatenatedSequenceView
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- getSequenceCreator() - Method in class info.bioinfweb.commons.bio.biojava3.alignment.io.AbstractAlignmentReader
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- getSize() - Method in class info.bioinfweb.commons.swing.ListBackedListModel
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- getSize() - Method in class info.bioinfweb.commons.swing.LocaleComboBoxModel
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- getSource() - Method in exception info.bioinfweb.commons.collections.bitstorage.exception.BitIndexOutOfBoundException
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- getSource() - Method in interface info.bioinfweb.commons.collections.bitstorage.exception.BitStorageException
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Returns the bit field where the exception occurred.
- getSource() - Method in exception info.bioinfweb.commons.collections.bitstorage.exception.InvalidBitNumberForPrimitiveException
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- getSource() - Method in class info.bioinfweb.commons.collections.observable.ListChangeEvent
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Returns the list instance where the change occurred.
- getSource() - Method in class info.bioinfweb.commons.events.GenericChangeEvent
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- getSource() - Method in class info.bioinfweb.commons.events.GenericEventObject
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- getStartList() - Method in class info.bioinfweb.commons.collections.SequenceIntervalList.IntervalInformation
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- getStatement() - Method in class info.bioinfweb.commons.servlet.SQLManipulator
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- getString(String, String) - Method in class info.bioinfweb.commons.collections.ParameterMap
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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
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- getSum() - Method in class info.bioinfweb.commons.bio.AmbiguityBaseScore
-
Returns the sum of all scores.
- getTabbedPane() - Method in class info.bioinfweb.commons.swing.AboutDialog
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- getTablePrefix() - Method in class info.bioinfweb.commons.sql.sqlproperties.ConcreteSQLProperties
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- getTablePrefix() - Method in interface info.bioinfweb.commons.sql.sqlproperties.SQLProperties
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- 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
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- 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
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- 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
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- 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
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- getUndoMenu() - Method in class info.bioinfweb.commons.swing.AbstractUndoActionManagement
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- getUndoPresentationName() - Method in class info.bioinfweb.commons.swing.AbstractDocumentEdit
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- getURL(String) - Method in class info.bioinfweb.commons.servlet.acceptlanguage.AcceptLanguageRedirectServlet
-
- getURL() - Method in class info.bioinfweb.commons.swing.actions.OpenWebsiteAction
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- getVersion() - Method in class info.bioinfweb.commons.io.streammessage.Message
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- getVersion() - Method in class info.bioinfweb.commons.ProgramMainClass
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- 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
-
- GraphicsUtils - Class in info.bioinfweb.commons.graphics
-
Contains method that implement general graphic tasks.
- GraphicsUtils() - Constructor for class info.bioinfweb.commons.graphics.GraphicsUtils
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- GUANINE_INDEX - Static variable in class info.bioinfweb.commons.bio.AmbiguityBaseScore
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