- DATA_TYPE_ANY_URI - Static variable in interface info.bioinfweb.commons.io.W3CXSConstants
-
- DATA_TYPE_BASE_64_BINARY - Static variable in interface info.bioinfweb.commons.io.W3CXSConstants
-
- DATA_TYPE_BOOLEAN - Static variable in interface info.bioinfweb.commons.io.W3CXSConstants
-
- DATA_TYPE_BYTE - Static variable in interface info.bioinfweb.commons.io.W3CXSConstants
-
- DATA_TYPE_DATE - Static variable in interface info.bioinfweb.commons.io.W3CXSConstants
-
- DATA_TYPE_DATE_TIME - Static variable in interface info.bioinfweb.commons.io.W3CXSConstants
-
- DATA_TYPE_DECIMAL - Static variable in interface info.bioinfweb.commons.io.W3CXSConstants
-
- DATA_TYPE_DOUBLE - Static variable in interface info.bioinfweb.commons.io.W3CXSConstants
-
- DATA_TYPE_DURATION - Static variable in interface info.bioinfweb.commons.io.W3CXSConstants
-
- DATA_TYPE_FLOAT - Static variable in interface info.bioinfweb.commons.io.W3CXSConstants
-
- DATA_TYPE_G_DAY - Static variable in interface info.bioinfweb.commons.io.W3CXSConstants
-
- DATA_TYPE_G_MONTH - Static variable in interface info.bioinfweb.commons.io.W3CXSConstants
-
- DATA_TYPE_G_MONTH_DAY - Static variable in interface info.bioinfweb.commons.io.W3CXSConstants
-
- DATA_TYPE_G_YEAR - Static variable in interface info.bioinfweb.commons.io.W3CXSConstants
-
- DATA_TYPE_G_YEAR_MONTH - Static variable in interface info.bioinfweb.commons.io.W3CXSConstants
-
- DATA_TYPE_HEX_BINARY - Static variable in interface info.bioinfweb.commons.io.W3CXSConstants
-
- DATA_TYPE_INT - Static variable in interface info.bioinfweb.commons.io.W3CXSConstants
-
- DATA_TYPE_INTEGER - Static variable in interface info.bioinfweb.commons.io.W3CXSConstants
-
- DATA_TYPE_LONG - Static variable in interface info.bioinfweb.commons.io.W3CXSConstants
-
- DATA_TYPE_NAME - Static variable in interface info.bioinfweb.commons.io.W3CXSConstants
-
- DATA_TYPE_NC_NAME - Static variable in interface info.bioinfweb.commons.io.W3CXSConstants
-
- DATA_TYPE_NEGATIVE_INTEGER - Static variable in interface info.bioinfweb.commons.io.W3CXSConstants
-
- DATA_TYPE_NON_NEGATIVE_INTEGER - Static variable in interface info.bioinfweb.commons.io.W3CXSConstants
-
- DATA_TYPE_NON_POSITIVE_INTEGER - Static variable in interface info.bioinfweb.commons.io.W3CXSConstants
-
- DATA_TYPE_NORMALIZED_STRING - Static variable in interface info.bioinfweb.commons.io.W3CXSConstants
-
- DATA_TYPE_POSITIVE_INTEGER - Static variable in interface info.bioinfweb.commons.io.W3CXSConstants
-
- DATA_TYPE_QNAME - Static variable in interface info.bioinfweb.commons.io.W3CXSConstants
-
- DATA_TYPE_SHORT - Static variable in interface info.bioinfweb.commons.io.W3CXSConstants
-
- DATA_TYPE_STRING - Static variable in interface info.bioinfweb.commons.io.W3CXSConstants
-
- DATA_TYPE_TIME - Static variable in interface info.bioinfweb.commons.io.W3CXSConstants
-
- DATA_TYPE_TOKEN - Static variable in interface info.bioinfweb.commons.io.W3CXSConstants
-
- DATA_TYPE_UNSIGNED_BYTE - Static variable in interface info.bioinfweb.commons.io.W3CXSConstants
-
- DATA_TYPE_UNSIGNED_INT - Static variable in interface info.bioinfweb.commons.io.W3CXSConstants
-
- DATA_TYPE_UNSIGNED_LONG - Static variable in interface info.bioinfweb.commons.io.W3CXSConstants
-
- DATA_TYPE_UNSIGNED_SHORT - Static variable in interface info.bioinfweb.commons.io.W3CXSConstants
-
- DatabaseException - Exception in info.bioinfweb.commons.servlet
-
- DatabaseException() - Constructor for exception info.bioinfweb.commons.servlet.DatabaseException
-
- DatabaseException(String) - Constructor for exception info.bioinfweb.commons.servlet.DatabaseException
-
- DATATYPE_CONTINUOUS - Static variable in class info.bioinfweb.commons.bio.biojava3.alignment.io.nexus.NexusWriter
-
- DATATYPE_DNA - Static variable in class info.bioinfweb.commons.bio.biojava3.alignment.io.hennig86.Hennig86Writer
-
- DATATYPE_DNA - Static variable in class info.bioinfweb.commons.bio.biojava3.alignment.io.mega.MEGAWriter
-
- DATATYPE_DNA - Static variable in class info.bioinfweb.commons.bio.biojava3.alignment.io.nexus.NexusWriter
-
- DATATYPE_NUCLEOTIDE - Static variable in class info.bioinfweb.commons.bio.biojava3.alignment.io.nexus.NexusWriter
-
- DATATYPE_PROTEIN - Static variable in class info.bioinfweb.commons.bio.biojava3.alignment.io.hennig86.Hennig86Writer
-
- DATATYPE_PROTEIN - Static variable in class info.bioinfweb.commons.bio.biojava3.alignment.io.mega.MEGAWriter
-
- DATATYPE_PROTEIN - Static variable in class info.bioinfweb.commons.bio.biojava3.alignment.io.nexus.NexusWriter
-
- DATATYPE_RNA - Static variable in class info.bioinfweb.commons.bio.biojava3.alignment.io.nexus.NexusWriter
-
- DATATYPE_STANDARD - Static variable in class info.bioinfweb.commons.bio.biojava3.alignment.io.nexus.NexusWriter
-
- DE_ASK_TO_SAVE_MESSAGE_BEGINNING - Static variable in class info.bioinfweb.commons.swing.SwingSaverMessages
-
- DE_ASK_TO_SAVE_MESSAGE_END - Static variable in class info.bioinfweb.commons.swing.SwingSaverMessages
-
- DE_ASK_TO_SAVE_TITLE - Static variable in class info.bioinfweb.commons.swing.SwingSaverMessages
-
- DE_BUTTON_CANCEL - Static variable in class info.bioinfweb.commons.swing.SwingSaverMessages
-
- DE_BUTTON_NO - Static variable in class info.bioinfweb.commons.swing.SwingSaverMessages
-
- DE_BUTTON_YES - Static variable in class info.bioinfweb.commons.swing.SwingSaverMessages
-
- DecimalInput - Class in info.bioinfweb.commons.swing
-
Swing input for decimal values using a text field and a slider.
- DecimalInput(String, JPanel, int, String) - Constructor for class info.bioinfweb.commons.swing.DecimalInput
-
- DecimalInput(String, JPanel, int, int, String) - Constructor for class info.bioinfweb.commons.swing.DecimalInput
-
- DecimalInput(String, JPanel, int, int, String, boolean) - Constructor for class info.bioinfweb.commons.swing.DecimalInput
-
- DecimalInputDialog - Class in info.bioinfweb.commons.swing
-
- DecimalInputDialog(Frame) - Constructor for class info.bioinfweb.commons.swing.DecimalInputDialog
-
- DecimalInputDialog(Dialog) - Constructor for class info.bioinfweb.commons.swing.DecimalInputDialog
-
- decimalToString(double, int) - Static method in class info.bioinfweb.commons.Math2
-
- DEFAULT_CONTENT_TYPE - Static variable in class info.bioinfweb.commons.servlet.GetPostServlet
-
- DEFAULT_COUNTRY - Static variable in class info.bioinfweb.commons.servlet.acceptlanguage.AcceptLanguageEntry
-
- DEFAULT_FILL_UP_CHAR - Static variable in class info.bioinfweb.commons.text.UniqueNameMapParameters
-
- DEFAULT_GAP_CHAR - Static variable in class info.bioinfweb.commons.bio.biojava3.alignment.io.mega.MEGAWriter
-
- DEFAULT_INITIAL_SEQUENCE_LENGTH - Static variable in class info.bioinfweb.commons.collections.SequenceIntervalList
-
- DEFAULT_INTERVAL_LENGTH - Static variable in class info.bioinfweb.commons.collections.SequenceIntervalList
-
- DEFAULT_MAX_NAME_LENGTH - Static variable in class info.bioinfweb.commons.bio.biojava3.alignment.io.phylip.PhylipWriter
-
- DEFAULT_PEEK_BUFFER_SIZE - Static variable in class info.bioinfweb.commons.io.PeekReader
-
- DEFAULT_PROGRESS_FORMAT - Static variable in class info.bioinfweb.commons.swing.ProgressDialog
-
- DEFAULT_QUALITY - Static variable in class info.bioinfweb.commons.servlet.acceptlanguage.AcceptLanguageEntry
-
- DEFAULT_TITLE - Static variable in class info.bioinfweb.commons.bio.biojava3.alignment.io.mega.MEGAWriter
-
- DefaultNameManager - Class in info.bioinfweb.commons.io
-
- DefaultNameManager(String) - Constructor for class info.bioinfweb.commons.io.DefaultNameManager
-
- DefaultNameManager() - Constructor for class info.bioinfweb.commons.io.DefaultNameManager
-
- deleteAllGaps(CharSequence) - Static method in class info.bioinfweb.commons.bio.SequenceUtils
-
Returns the specified sequence without any gaps.
- deleteEntry(String) - Method in class info.bioinfweb.commons.servlet.CaptchaDBManagement
-
- deleteFromDB(String, String, String) - Method in class info.bioinfweb.commons.servlet.SQLManipulator
-
- deleteFromLeft(String, int) - Static method in class info.bioinfweb.commons.bio.SequenceUtils
-
Deletes count characters from the left side of the sequence which are not gaps
("-").
- deleteFromRight(String, int) - Static method in class info.bioinfweb.commons.bio.SequenceUtils
-
Deletes count characters from the left side of the sequence which are not gaps
("-").
- deleteGapsFromLeft(String, int) - Static method in class info.bioinfweb.commons.bio.SequenceUtils
-
Deletes the specified number of gaps from the sequence starting on the left side.
- deleteGapsFromRight(String, int) - Static method in class info.bioinfweb.commons.bio.SequenceUtils
-
Deletes the specified number of gaps from the sequence starting on the right side.
- deleteLeadingGaps(String) - Static method in class info.bioinfweb.commons.bio.SequenceUtils
-
Deletes all leading gaps from a sequence.
- deleteLeadingTrailingGaps(String) - Static method in class info.bioinfweb.commons.bio.SequenceUtils
-
Deletes all leading and trailing gaps of the specified sequence.
- deleteTrailingGaps(String) - Static method in class info.bioinfweb.commons.bio.SequenceUtils
-
Deletes all trailing gaps from a sequence.
- description - Variable in class info.bioinfweb.commons.io.InternationalFileFilter
-
- die() - Method in class info.bioinfweb.commons.swing.AbstractDocumentEdit
-
- dirSize(ZipFile, String) - Static method in class info.bioinfweb.commons.io.IOUtils
-
Calculates the overall uncompressed size of all files included in the specified directory of
an archive.
- disconnect() - Method in class info.bioinfweb.commons.servlet.SQLManipulator
-
- display() - Method in class info.bioinfweb.commons.log.ApplicationLoggerDialog
-
Positions and shows this modal dialog if the message list is not empty.
- divAbove(int, int) - Static method in class info.bioinfweb.commons.Math2
-
- DNA_CHARS - Static variable in class info.bioinfweb.commons.bio.SequenceUtils
-
- DNA_TO_RNA_MAP - Static variable in class info.bioinfweb.commons.bio.biojava3.core.sequence.views.ReplaceNucleotideSequenceView
-
Replaces T/i> with U.
- dnaToRNA(String) - Static method in class info.bioinfweb.commons.bio.SequenceUtils
-
- doGet(HttpServletRequest, HttpServletResponse) - Method in class info.bioinfweb.commons.servlet.GetPostServlet
-
- doGetPost(HttpServletRequest, HttpServletResponse) - Method in class info.bioinfweb.commons.servlet.acceptlanguage.AcceptLanguageRedirectServlet
-
- doGetPost(HttpServletRequest, HttpServletResponse) - Method in class info.bioinfweb.commons.servlet.GetPostServlet
-
- doGetPost(HttpServletRequest, HttpServletResponse) - Method in class info.bioinfweb.commons.servlet.HTTPIncludeServlet
-
- doGetPost(HttpServletRequest, HttpServletResponse) - Method in class info.bioinfweb.commons.servlet.Model2Servlet
-
- doPost(HttpServletRequest, HttpServletResponse) - Method in class info.bioinfweb.commons.servlet.GetPostServlet
-
- doRead(DataInputStream, int) - Method in class info.bioinfweb.commons.io.streammessage.Message
-
Subclasses should implement this method to read the data this message
object contains.
- DOUBLE_FORMAT - Static variable in class info.bioinfweb.commons.swing.DecimalInput
-
- DOUBLE_FORMAT - Static variable in class info.bioinfweb.commons.text.StringUtils
-
- DoubleBufferedApplet - Class in info.bioinfweb.commons.applet
-
- DoubleBufferedApplet() - Constructor for class info.bioinfweb.commons.applet.DoubleBufferedApplet
-
- DoubleDimension - Class in info.bioinfweb.commons.graphics
-
- DoubleDimension(double, double) - Constructor for class info.bioinfweb.commons.graphics.DoubleDimension
-
- drawStringInRectangle(Graphics2D, Rectangle2D, String) - Static method in class info.bioinfweb.commons.graphics.GraphicsUtils
-
Draws the specified string into the center of the specified rectangle.
