- NAME_CODE_COLUMN - Static variable in class info.bioinfweb.commons.servlet.CaptchaDBManagement
-
- NAME_FONT_NAME - Static variable in class info.bioinfweb.commons.servlet.CaptchaDBManagement
-
- NAME_ID_COLUMN - Static variable in class info.bioinfweb.commons.servlet.CaptchaDBManagement
-
- nameByIndex(int) - Method in class info.bioinfweb.commons.bio.biojava3.alignment.SimpleAlignment
-
- nameByIndex(int) - Method in interface info.bioinfweb.commons.bio.biojava3.alignment.template.Alignment
-
- nameIterator() - Method in class info.bioinfweb.commons.bio.biojava3.alignment.SimpleAlignment
-
- nameIterator() - Method in interface info.bioinfweb.commons.bio.biojava3.alignment.template.Alignment
-
- NAMESPACE_URI - Static variable in interface info.bioinfweb.commons.sql.sqlproperties.SQLXMLConstants
-
- NeedlemanWunschAligner - Class in info.bioinfweb.commons.bio.alignment.pairwise
-
Performs a global Needleman Wunsch pairwise alignment.
- NeedlemanWunschAligner() - Constructor for class info.bioinfweb.commons.bio.alignment.pairwise.NeedlemanWunschAligner
-
- newByteInstance(int, long, int) - Static method in class info.bioinfweb.commons.collections.PackedPrimitiveWrapperArrayList
-
Creates a new instance of this class using Byte elements.
- newDefaultName() - Method in class info.bioinfweb.commons.io.DefaultNameManager
-
- NewerMessageVersionException - Exception in info.bioinfweb.commons.io.streammessage
-
- NewerMessageVersionException() - Constructor for exception info.bioinfweb.commons.io.streammessage.NewerMessageVersionException
-
- NewerMessageVersionException(String, Throwable) - Constructor for exception info.bioinfweb.commons.io.streammessage.NewerMessageVersionException
-
- NewerMessageVersionException(String) - Constructor for exception info.bioinfweb.commons.io.streammessage.NewerMessageVersionException
-
- NewerMessageVersionException(Throwable) - Constructor for exception info.bioinfweb.commons.io.streammessage.NewerMessageVersionException
-
- newFile(String, String, long) - Method in interface info.bioinfweb.commons.io.IOProgressListener
-
This method is called only if the progress listeners is passed to a method that processes
several files.
- newFile(String) - Method in class info.bioinfweb.commons.io.IOProgressListenerAdapter
-
- newFile(String, String, long) - Method in class info.bioinfweb.commons.io.IOProgressListenerVector
-
- newIntegerInstance(int, long, int) - Static method in class info.bioinfweb.commons.collections.PackedPrimitiveWrapperArrayList
-
Creates a new instance of this class using Integer elements.
- newLinkedInstance(Iterable<ScrolledComposite>, boolean) - Static method in class info.bioinfweb.commons.swt.ScrolledCompositeSyncListener
-
Creates a new instance of this class that uses the specified collection as the source.
- newLongInstance(int, long, int) - Static method in class info.bioinfweb.commons.collections.PackedPrimitiveWrapperArrayList
-
Creates a new instance of this class using Long elements.
- newNucleotideCompound(String, String, String...) - Method in class info.bioinfweb.commons.bio.biojava3.core.sequence.template.AbstractNucleotideCompoundSet2
-
Creates a new nucleotide compound.
- newShortInstance(int, long, int) - Static method in class info.bioinfweb.commons.collections.PackedPrimitiveWrapperArrayList
-
Creates a new instance of this class using Short elements.
- newStandardErrorInstance() - Static method in class info.bioinfweb.commons.log.TextFileApplicationLogger
-
Creates a new instance of this class that writes to the standard error.
- newStandardOutInstance() - Static method in class info.bioinfweb.commons.log.TextFileApplicationLogger
-
Creates a new instance of this class that writes to the standard out.
- next() - Method in class info.bioinfweb.commons.collections.ListIteratorDecorator
-
- next() - Method in class info.bioinfweb.commons.collections.NumberedStringsIterator
-
- nextIndex() - Method in class info.bioinfweb.commons.collections.ListIteratorDecorator
-
- NexusReader<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.nexus
-
- NexusReader(SequenceCreatorInterface<C>) - Constructor for class info.bioinfweb.commons.bio.biojava3.alignment.io.nexus.NexusReader
-
- NexusWriter<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.nexus
-
Writes an
Alignment to a stream in Nexus format.
- NexusWriter(String, char, char, UniqueNameMap) - Constructor for class info.bioinfweb.commons.bio.biojava3.alignment.io.nexus.NexusWriter
-
Creates a new instance of this class.
- NexusWriter(String, UniqueNameMap) - Constructor for class info.bioinfweb.commons.bio.biojava3.alignment.io.nexus.NexusWriter
-
Creates a new instance of this class with "-" as gap data and "? as missing data character.
- NexusWriter(String, char, char) - Constructor for class info.bioinfweb.commons.bio.biojava3.alignment.io.nexus.NexusWriter
-
Creates a new instance of this class.
- NexusWriter(String) - Constructor for class info.bioinfweb.commons.bio.biojava3.alignment.io.nexus.NexusWriter
-
Creates a new instance of this class with "-" as gap data and "? as missing data character.
- NO_HELP_CODE - Static variable in class info.bioinfweb.commons.log.ApplicationLoggerMessage
-
- NO_OF_STATES_COMMAND - Static variable in class info.bioinfweb.commons.bio.biojava3.alignment.io.hennig86.Hennig86Writer
-
- NoGapDNACompoundSet - Class in info.bioinfweb.commons.bio.biojava3.core.sequence.compound
-
Nucleotide compound set that contains all DNA compounds but no gap - character (and without N).
- NoGapDNACompoundSet() - Constructor for class info.bioinfweb.commons.bio.biojava3.core.sequence.compound.NoGapDNACompoundSet
-
Returns a new instance of this class.
- NoGapNucleotideCompoundSet - Class in info.bioinfweb.commons.bio.biojava3.core.sequence.compound
-
Nucleotide compound set that contains all DNA and RNA compounds but no gap - or ambiguity character.
- NoGapNucleotideCompoundSet() - Constructor for class info.bioinfweb.commons.bio.biojava3.core.sequence.compound.NoGapNucleotideCompoundSet
-
Returns a new instance of this class.
- NoGapRNACompoundSet - Class in info.bioinfweb.commons.bio.biojava3.core.sequence.compound
-
Nucleotide compound set that contains all RNA compounds but no gap - character (and without N).
- NoGapRNACompoundSet() - Constructor for class info.bioinfweb.commons.bio.biojava3.core.sequence.compound.NoGapRNACompoundSet
-
Returns a new instance of this class.
- NonOverlappingIntervalList - Class in info.bioinfweb.commons.collections
-
Stores a set of non overlapping intervals of a sequence.
- NonOverlappingIntervalList() - Constructor for class info.bioinfweb.commons.collections.NonOverlappingIntervalList
-
- NonStoringCollection<E> - Class in info.bioinfweb.commons.collections
-
Instances of this class do not store objects add to them.
- NonStoringCollection() - Constructor for class info.bioinfweb.commons.collections.NonStoringCollection
-
- NucleotideCompoundSet - Class in info.bioinfweb.commons.bio.biojava3.core.sequence.compound
-
- NucleotideCompoundSet() - Constructor for class info.bioinfweb.commons.bio.biojava3.core.sequence.compound.NucleotideCompoundSet
-
Returns a new instance of this class.
- nucleotideCompoundToSymbol(NucleotideCompound) - Static method in class info.bioinfweb.commons.bio.biojava3.core.sequence.BioJava1SymbolTranslator
-
- nucleotideConsensus(char[]) - Static method in class info.bioinfweb.commons.bio.SequenceUtils
-
Returns the nucleotide that occurs most often in the specified alignment row.
- nucleotideConstituents(char) - Static method in class info.bioinfweb.commons.bio.SequenceUtils
-
If the specified nucleotide is an IUPAC ambiguity code this method returns an array
containing all nucleotides that could be represented by the code.
- nucleotideFrequencies(char[]) - Static method in class info.bioinfweb.commons.bio.SequenceUtils
-
Counts the nucleotide frequencies in the specified alignment column.
- nucleotideSequencesEquivalent(S, S) - Static method in class info.bioinfweb.commons.bio.biojava3.core.sequence.SequenceCompareUtils
-
The two sequences are considered equivalent of the symbols on each position match.
- NumberedStringsIterator - Class in info.bioinfweb.commons.collections
-
Implementation of Iterator that returns strings with defined prefix followed by an integer from a specified range.
- NumberedStringsIterator(String, long, long) - Constructor for class info.bioinfweb.commons.collections.NumberedStringsIterator
-
Creates a new instance of this class.
- NumberedStringsIterator(String, long) - Constructor for class info.bioinfweb.commons.collections.NumberedStringsIterator
-
Creates a new instance of this class starting with the index 0.
