- main(String[]) - Static method in class info.bioinfweb.commons.HTMLTruncater
-
- majorityRuleConsensus(Sequence<NucleotideCompound>[]) - Method in class info.bioinfweb.commons.bio.ConsensusSequenceCreator
-
Constructs a majority rule consensus sequence.
- majorityRuleConsensus(List<? extends Sequence<NucleotideCompound>>) - Method in class info.bioinfweb.commons.bio.ConsensusSequenceCreator
-
- majorityRuleConsensusAsString(List<? extends Sequence<NucleotideCompound>>) - Method in class info.bioinfweb.commons.bio.ConsensusSequenceCreator
-
- majorityRuleConsensusAsString(Sequence<NucleotideCompound>[]) - Method in class info.bioinfweb.commons.bio.ConsensusSequenceCreator
-
Constructs a majority rule consensus sequence.
- MapFastaWriter<S extends org.biojava3.core.sequence.template.Sequence<?>> - Class in info.bioinfweb.commons.bio.biojava3.core.sequence.io
-
Writes a map which contains sequence names as keys and sequences as values to a FASTA file.
- MapFastaWriter() - Constructor for class info.bioinfweb.commons.bio.biojava3.core.sequence.io.MapFastaWriter
-
- mark(int) - Method in class info.bioinfweb.commons.io.LimitedInputStream
-
- mark(int) - Method in class info.bioinfweb.commons.io.LimitedReader
-
- markSupported() - Method in class info.bioinfweb.commons.io.LimitedInputStream
-
- markSupported() - Method in class info.bioinfweb.commons.io.LimitedReader
-
- markSupported() - Method in class info.bioinfweb.commons.io.PeekReader
-
- MATCH_CHAR - Static variable in class info.bioinfweb.commons.bio.SequenceUtils
-
- MATCH_SCORE - Static variable in class info.bioinfweb.commons.bio.alignment.pairwise.NeedlemanWunschAligner
-
- Math2 - Class in info.bioinfweb.commons
-
Provides static methods implementing mathematical functions not present in java.lang.Math.
- Math2() - Constructor for class info.bioinfweb.commons.Math2
-
- MATRIX_COMMAND - Static variable in class info.bioinfweb.commons.bio.biojava3.alignment.io.hennig86.Hennig86Writer
-
- MAX_ARRAY_LENGTH - Static variable in class info.bioinfweb.commons.collections.PackedIntegerArrayList
-
- maxDouble(double...) - Static method in class info.bioinfweb.commons.Math2
-
Returns the maximum of the specified values.
- maxFloat(float...) - Static method in class info.bioinfweb.commons.Math2
-
Returns the maximum of the specified values.
- maxInt(int...) - Static method in class info.bioinfweb.commons.Math2
-
Returns the maximum of the specified values.
- maxLong(long...) - Static method in class info.bioinfweb.commons.Math2
-
Returns the maximum of the specified values.
- maxSequenceLength() - Method in class info.bioinfweb.commons.bio.biojava3.alignment.SimpleAlignment
-
- maxSequenceLength() - Method in interface info.bioinfweb.commons.bio.biojava3.alignment.template.Alignment
-
- meaningByDefaultSymbol(char) - Static method in enum info.bioinfweb.commons.bio.CharacterSymbolMeaning
-
Returns the according meaning, if the specified character is one of ,
or .
- MEGAWriter<S extends org.biojava3.core.sequence.template.Sequence<C>,C extends org.biojava3.core.sequence.template.Compound> - Class in info.bioinfweb.commons.bio.biojava3.alignment.io.mega
-
Writes an alignment to a MEGA file.
- MEGAWriter(String, char) - Constructor for class info.bioinfweb.commons.bio.biojava3.alignment.io.mega.MEGAWriter
-
- MEGAWriter(String) - Constructor for class info.bioinfweb.commons.bio.biojava3.alignment.io.mega.MEGAWriter
-
- Message<T extends java.lang.Enum<T>> - Class in info.bioinfweb.commons.io.streammessage
-
Abstract base class for all messages send between the main and the VLCFrameGrab application.
- Message(T, int) - Constructor for class info.bioinfweb.commons.io.streammessage.Message
-
- MessageListApplicationLogger - Class in info.bioinfweb.commons.log
-
- MessageListApplicationLogger() - Constructor for class info.bioinfweb.commons.log.MessageListApplicationLogger
-
- MessageListApplicationLogger(List<ApplicationLoggerMessage>) - Constructor for class info.bioinfweb.commons.log.MessageListApplicationLogger
-
- MessageReader<T extends java.lang.Enum<T>> - Class in info.bioinfweb.commons.io.streammessage
-
Abstract factory class that provides an
EnumMap to generate and read the according
Message object when a message is send over the stream.
- MessageReader(Class<T>) - Constructor for class info.bioinfweb.commons.io.streammessage.MessageReader
-
- minDouble(double...) - Static method in class info.bioinfweb.commons.Math2
-
Returns the minimum of the specified values.
- minFloat(float...) - Static method in class info.bioinfweb.commons.Math2
-
Returns the minimum of the specified values.
- minimumLayoutSize(Container) - Method in class info.bioinfweb.commons.swing.WrapLayout
-
Returns the minimum dimensions needed to layout the visible
components contained in the specified target container.
- minInt(int...) - Static method in class info.bioinfweb.commons.Math2
-
Returns the minimum of the specified values.
- minLong(long...) - Static method in class info.bioinfweb.commons.Math2
-
Returns the minimum of the specified values.
- MISMATCH_SCORE - Static variable in class info.bioinfweb.commons.bio.alignment.pairwise.NeedlemanWunschAligner
-
- MISSING_DATA_CHAR - Static variable in class info.bioinfweb.commons.bio.SequenceUtils
-
- MOD_MASK - Static variable in class info.bioinfweb.commons.collections.PackedIntegerArrayList
-
- Model2Servlet - Class in info.bioinfweb.commons.servlet
-
Provides general functionality for servlets that are part of a model 2 architecture.
- Model2Servlet() - Constructor for class info.bioinfweb.commons.servlet.Model2Servlet
-
- Model2Servlet(String) - Constructor for class info.bioinfweb.commons.servlet.Model2Servlet
-
- Model2Servlet(String, String) - Constructor for class info.bioinfweb.commons.servlet.Model2Servlet
-
- move(E, int, int) - Method in class info.bioinfweb.commons.collections.SequenceIntervalList
-
Moves an element of the list to a different position.
- moveAllCharSetPositions(int, int) - Method in class info.bioinfweb.commons.bio.biojava3.alignment.SimpleAlignment
-
Moves all contained character sets by the specified offset.
- moveAllCharSetPositions(int, int) - Method in interface info.bioinfweb.commons.bio.biojava3.alignment.template.Alignment
-
- moveBetween(byte, byte, byte) - Static method in class info.bioinfweb.commons.Math2
-
Returns the specified value if it is between the specified minimum and maximum.
- moveBetween(int, int, int) - Static method in class info.bioinfweb.commons.Math2
-
Returns the specified value if it is between the specified minimum and maximum.
- moveBetween(long, long, long) - Static method in class info.bioinfweb.commons.Math2
-
Returns the specified value if it is between the specified minimum and maximum.
- moveBetween(float, float, float) - Static method in class info.bioinfweb.commons.Math2
-
Returns the specified value if it is between the specified minimum and maximum.
- moveBetween(double, double, double) - Static method in class info.bioinfweb.commons.Math2
-
Returns the specified value if it is between the specified minimum and maximum.
- moveBits(long, long, long) - Method in interface info.bioinfweb.commons.collections.bitstorage.BitField
-
Moves the specified number of bits from one position in the bit field to another.
- moveColorToCenter(Color, float) - Static method in class info.bioinfweb.commons.graphics.GraphicsUtils
-
The result of the method depends on the specified color.
- movePositions(int, int) - Method in class info.bioinfweb.commons.collections.NonOverlappingIntervalList
-
- MultipleApplicationLoggersAdapter - Class in info.bioinfweb.commons.log
-
This implementation of
ApplicationLogger delegates to a set of other classes implementing
this interface.
- MultipleApplicationLoggersAdapter() - Constructor for class info.bioinfweb.commons.log.MultipleApplicationLoggersAdapter
-
- multiplyColorChannels(Color, float) - Static method in class info.bioinfweb.commons.graphics.GraphicsUtils
-
Multiplies all color channels of the specified color with the specified value.
- MYSQL_DRIVER - Static variable in class info.bioinfweb.commons.servlet.SQLManipulator
-
- MYSQL_DRIVER - Static variable in class info.bioinfweb.commons.sql.SQLConnector
-
