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N

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
Same as NucleotideCompoundSet but also includes the gap character("-").
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.
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