M-Index

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M

M(double, double) - Static method in class bacnet.scripts.core.stat.AMtools: Calculate M = x1-x2
Represents the variability within expression value x1 and x2
Macroarray - Class in bacnet.scripts.listeriomics.technology
Macroarray() - Constructor for class bacnet.scripts.listeriomics.technology.Macroarray
main(String[]) - Static method in class org.biojava3.core.sequence.DNASequence
main(String[]) - Static method in class org.biojava3.core.sequence.io.CasePreservingProteinSequenceCreator
main(String[]) - Static method in class org.biojava3.core.sequence.io.FastaGeneWriter
main(String[]) - Static method in class org.biojava3.core.sequence.io.FastaReader
main(String[]) - Static method in class org.biojava3.core.sequence.io.FastaReaderHelper
main(String[]) - Static method in class org.biojava3.core.sequence.io.FastaWriter
main(String[]) - Static method in class org.biojava3.core.sequence.io.GenericFastaHeaderParser
main(String[]) - Static method in class org.biojava3.core.sequence.loader.UniprotProxySequenceReader
main(String[]) - Static method in class org.biojava3.core.sequence.ProteinSequence
main(String[]) - Static method in class org.biojava3.core.util.UncompressInputStream
main(String[]) - Static method in class org.biojava3.genome.App
main(String[]) - Static method in class org.biojava3.genome.GeneFeatureHelper
main(String[]) - Static method in class org.biojava3.genome.parsers.geneid.GeneIDXMLReader
main(String[]) - Static method in class org.biojava3.genome.parsers.gff.Feature: Deprecated.
main(String[]) - Static method in class org.biojava3.genome.parsers.gff.FeatureList: Deprecated.
main(String[]) - Static method in class org.biojava3.genome.parsers.gff.GeneIDGFF2Reader
main(String[]) - Static method in class org.biojava3.genome.parsers.gff.GeneMarkGTFReader
main(String[]) - Static method in class org.biojava3.genome.parsers.gff.GFF3Reader
main(String[]) - Static method in class org.biojava3.genome.parsers.gff.GFF3Writer
main(String[]) - Static method in class org.biojava3.genome.parsers.gff.Location: Deprecated.
main(String[]) - Static method in class org.biojava3.genome.parsers.gff.LocIterator: Deprecated.
main(String[]) - Static method in class org.biojava3.genome.query.BlastXMLQuery
main(String[]) - Static method in class org.biojava3.genome.query.OutputHitsGFF
main(String[]) - Static method in class org.biojava3.genome.uniprot.UniprotToFasta
main(String[]) - Static method in class org.biojava3.genome.util.SplitFasta
MAIN_ENTRYPOINT - Static variable in class bacnet.e4.rap.BasicApplication
MAIN_ENTRYPOINT - Static variable in class bacnet.e4.rap.setup.BasicApplication
MainListeriomics - Class in bacnet.scripts.listeriomics
MainListeriomics() - Constructor for class bacnet.scripts.listeriomics.MainListeriomics
makeblastdb - Static variable in class bacnet.scripts.blast.Blast
makeblastdb - Static variable in class bacnet.scripts.database.HomologCreation: Shortcut for running makeblastdb
MANDINFC_MAP - Static variable in class bacnet.datamodel.annotation.GlaserFCannotation
MANNWHIT - Enum constant in enum bacnet.scripts.core.stat.StatTest.TypeStat
mark(int) - Method in class org.biojava3.core.sequence.io.BufferedReaderBytesRead: Marks the present position in the stream.
markSupported() - Method in class org.biojava3.core.sequence.io.BufferedReaderBytesRead: Tells whether this stream supports the mark() operation, which it does.
markSupported() - Method in class org.biojava3.core.util.UncompressInputStream: This stream does not support mark/reset on the stream.
MARKUP_ENABLED - Static variable in class bacnet.utils.RWTUtils
MathUtils - Class in bacnet.utils
MathUtils() - Constructor for class bacnet.utils.MathUtils
MatrixSize - Class in bacnet.table.core
MatrixSize() - Constructor for class bacnet.table.core.MatrixSize
max(double[]) - Static method in class bacnet.utils.VectorUtils: Find maximum value of a vector
max(double[][]) - Static method in class bacnet.utils.ArrayUtils
max(ExpressionMatrix) - Static method in class bacnet.utils.ExpressionMatrixStat: Search for the maximum of all the values
max(ExpressionMatrix, int) - Static method in class bacnet.utils.ExpressionMatrixStat: Search for the maximum on one column
MAX_RESOLVER - Static variable in class org.biojava3.core.sequence.location.FuzzyPoint: Always uses the max point to resolve a location
mean(double[]) - Static method in class bacnet.utils.VectorUtils: Calculate mean of a vector
mean(double[][]) - Static method in class bacnet.utils.ArrayUtils: Return the mean of the whole array
mean(double, double) - Static method in class bacnet.utils.MathUtils: Calculate the mean between two numbers
mean(ExpressionMatrix) - Static method in class bacnet.utils.ExpressionMatrixStat: Calculate the mean of the ExpressionMatrix
mean(ExpressionMatrix, int) - Static method in class bacnet.utils.ExpressionMatrixStat: Calculate the mean of the ExpressionMatrix
mean(Double[]) - Static method in class bacnet.utils.VectorUtils
MEAN_RESOLVER - Static variable in class org.biojava3.core.sequence.location.FuzzyPoint: Combines min and max and then gets the mean of it
median(double[]) - Static method in class bacnet.utils.VectorUtils: Calculate median of a vector
median(ExpressionMatrix, int) - Static method in class bacnet.utils.ExpressionMatrixStat: Calculate the median of the ExpressionMatrix
median(Double[]) - Static method in class bacnet.utils.VectorUtils: Calculate median of a vector
MedianNormalization - Class in bacnet.scripts.core.normalization
MedianNormalization() - Constructor for class bacnet.scripts.core.normalization.MedianNormalization
merge(ArrayList<ExpressionMatrix>, boolean) - Static method in class bacnet.datamodel.dataset.ExpressionMatrix: Create a fusion of a list of ExpressionMatrix
midline - Variable in class bacnet.scripts.blast.BlastResult
min(double[]) - Static method in class bacnet.utils.VectorUtils: Find minimum value of a vector
min(double[][]) - Static method in class bacnet.utils.ArrayUtils
min(ExpressionMatrix) - Static method in class bacnet.utils.ExpressionMatrixStat: Search for the minimum on all the values
min(ExpressionMatrix, int) - Static method in class bacnet.utils.ExpressionMatrixStat: Search for the minimum on one column
MIN_RESOLVER - Static variable in class org.biojava3.core.sequence.location.FuzzyPoint: Always uses the min point to resolve a location
MINIMAL_BP_NB - Static variable in class bacnet.genomeBrowser.core.Zoom
MINIMAL_SEQUENCE_DATA - Enum constant in enum org.biojava3.core.sequence.SequenceOptimizationHints.SequenceUsage
MINIMINAL_SEQUENCES - Enum constant in enum org.biojava3.core.sequence.SequenceOptimizationHints.SequenceCollection
MINIMUM_DATA_SIZE - Variable in class bacnet.genomeBrowser.tracksGUI.TrackCanvasData: Minimal height of a data track
minus - Enum constant in enum bacnet.datamodel.proteomics.NTerm.MappingFrame
minus() - Method in class org.biojava3.genome.parsers.gff.Location: Return location that is in same position on negative strand.
minus(double[], double[]) - Static method in class bacnet.utils.VectorUtils
minus(ExpressionMatrix, ExpressionMatrix) - Static method in class bacnet.utils.ExpressionMatrixStat: Perform a soustraction between two ExpressionMatrix
First the intersection in term of RowNames and headers is found, then addition is done for each row
minusM - Enum constant in enum bacnet.datamodel.proteomics.NTerm.MappingFrame
minusP - Enum constant in enum bacnet.datamodel.proteomics.NTerm.MappingFrame
MISSING_VALUE - Static variable in class bacnet.datamodel.dataset.OmicsData: Every Found missing values are replaced by this number
MITOCHONDRIAL - Enum constant in enum org.biojava3.core.sequence.DNASequence.DNAType
MODEL_CAS9 - Variable in class bacnet.views.CRISPRPredictView
modifHeader(String, String) - Method in class bacnet.datamodel.dataset.ExpressionMatrix
modifyApp(String, EPartService) - Static method in class bacnet.e4.rap.AppSpecificMethods
modifyHTMLwithFile(String, String) - Static method in class bacnet.raprcp.SaveFileUtils: Replace "_FileName" by fileName in the htmlFile found in bacnet/html/ folder
modifyID(String, String) - Static method in class bacnet.datamodel.sequence.Genome: Modify id of gene, to be sure that the suffix number is always of 4 numbers
ex: replace lmpc1 by lmpc0001, lmpc12 by lmpc0012
modifyPathArray() - Method in class bacnet.datamodel.proteomics.NTermCreateData: Check PATHARRAY and had columns if needed

Two types of array are possible: one with only one experiment (contains only one column with "# spectra") one with only multiple experiments (contains many columns containing "# spectra")

For The first type:
Check if PATHARRAY table is complete = has 8 columns, first column is the list of peptide, soluble and insoluble contains "TRUE" and "FALSE" and no "yes"
Change "TRUE" and "FALSE" to "yes" and "no" Remove line with NH2-free peptide

For the second type:
modulateCircularIndex(int, int) - Static method in class org.biojava3.core.sequence.location.LocationHelper: Takes a point on a circular location and moves it left until it falls at the earliest possible point that represents the same base.
modulateCircularIndex(int, int) - Static method in class org.biojava3.core.sequence.location.template.Location.Tools: Takes a point on a circular location and moves it left until it falls at the earliest possible point that represents the same base.
MOUSE_ANNOTTABLE - Static variable in class bacnet.datamodel.annotation.Annotation
mouseDoubleClick(MouseEvent) - Method in class bacnet.genomeBrowser.tracksGUI.TracksComposite
mouseDoubleClick(MouseEvent) - Method in class bacnet.sequenceTools.GeneView
mouseDoubleClick(MouseEvent) - Method in class bacnet.sequenceTools.SrnaView
mouseDown(MouseEvent) - Method in class bacnet.genomeBrowser.tracksGUI.TracksComposite
mouseDown(MouseEvent) - Method in class bacnet.sequenceTools.GeneView
mouseDown(MouseEvent) - Method in class bacnet.sequenceTools.SrnaView
mouseMove(MouseEvent) - Method in class bacnet.genomeBrowser.tracksGUI.TrackCanvasData: If the mouse is over the genome viewer, detect it is on the annotation, and display the corresponding gene, sRNA, asRNA
mouseMove(MouseEvent) - Method in class bacnet.genomeBrowser.tracksGUI.TrackCanvasGenome: If the mouse is over the genome viewer, detect it is on the annotation, and display the corresponding gene, sRNA, asRNA
mouseUp(MouseEvent) - Method in class bacnet.genomeBrowser.tracksGUI.TracksComposite
mouseUp(MouseEvent) - Method in class bacnet.sequenceTools.GeneView
mouseUp(MouseEvent) - Method in class bacnet.sequenceTools.SrnaView
moveHorizontally(int) - Method in class bacnet.genomeBrowser.core.Region
moveHorizontally(int) - Method in class bacnet.genomeBrowser.core.Track
moveHorizontally(int) - Method in class bacnet.genomeBrowser.tracksGUI.TracksComposite: Move horizontally the tracks
moveVertically(int) - Method in class bacnet.genomeBrowser.tracksGUI.TrackCanvasData: From the position of the vertical bar draw the corresponding part of the data
MSF - Enum constant in enum org.biojava3.core.sequence.template.LightweightProfile.StringFormat
multiAlign(ArrayList<Sequence>, String, String) - Static method in class bacnet.scripts.listeriomics.nterm.NTermConservationWithRiboProfiling: Run a Blast for each sRNA on a list of Genomes given in tempDatabase
multipleFrameTranslation(Sequence<NucleotideCompound>, Frame...) - Method in class org.biojava3.core.sequence.transcription.TranscriptionEngine: A way of translating DNA in a number of frames
MultipleSequenceAlignment<S extends Sequence<C>,C extends Compound> - Class in org.biojava3.core.sequence: Implements a minimal data structure for reading and writing a sequence alignment.
MultipleSequenceAlignment() - Constructor for class org.biojava3.core.sequence.MultipleSequenceAlignment
MultiSequenceBlastProtein - Class in bacnet.scripts.blast
MultiSequenceBlastProtein() - Constructor for class bacnet.scripts.blast.MultiSequenceBlastProtein
MultiSequenceTBlastNProtein - Class in bacnet.scripts.blast
MultiSequenceTBlastNProtein() - Constructor for class bacnet.scripts.blast.MultiSequenceTBlastNProtein
multiSpeciesAlign() - Static method in class bacnet.scripts.listeriomics.srna.SrnaAlignmentBlastN: Run a Blast for each sRNA on a list of Genomes given in tempDatabase
multiSpeciesAlign(ArrayList<Srna>) - Static method in class bacnet.scripts.listeriomics.srna.SrnaAlignmentBlastN: Run a Blast for each sRNA on a list of Genomes given in tempDatabase
multiSpeciesAlign10403S() - Static method in class bacnet.scripts.listeriomics.srna.SrnaAlignmentBlastN: Run a Blast for each sRNA (found in Oliver et al. in 10403S genome) on a list of Genomes given in tempDatabase
multiSpeciesAlignBlastN(ArrayList<Gene>) - Static method in class bacnet.scripts.listeriomics.srna.SmallPeptidesSearch: Deprecated.
multiSpeciesAlignNucleotide(ArrayList<Sequence>, boolean) - Static method in class bacnet.scripts.blast.Blast: Run a Blast for each sRNA on a list of Genomes given in tempDatabase
multiSpeciesAlignProtein(ArrayList<String>, ArrayList<String>, String, double) - Static method in class bacnet.scripts.blast.Blast: Run a BlastP given a a list of sequence name, amino acid sequences, and a database name
multiSpeciesAlignTblastN(ArrayList<String>, ArrayList<String>, String, double) - Static method in class bacnet.scripts.blast.Blast: Run TblastN on multy amino acid sequence against nucleotide database that will be translated in the 6 frame

A B C D E F G H I J L M N O P Q R S T U V W X Y Z
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form