Constant Field Values


Contents
com.compomics.*

com.compomics.util.BinaryArrayImpl
public static final String BIG_ENDIAN_LABEL "big"
public static final int BYTES_TO_HOLD_DOUBLE 8
public static final int BYTES_TO_HOLD_FLOAT 4
public static final String DOUBLE_PRECISION "64"
public static final String FLOAT_PRECISION "32"
public static final String LITTLE_ENDIAN_LABEL "little"

com.compomics.util.experiment.biology.PTM
public static final int MODC 3
public static final int MODCP 7
public static final int MODCPAA 8
public static final int MODCAA 4
public static final int MODMAX 9
public static final int MODN 1
public static final int MODNP 5
public static final int MODNPAA 6
public static final int MODNAA 2
public static final int MODAA 0

com.compomics.util.experiment.biology.ions.ElementaryIon
public static final int PROTON 0

com.compomics.util.experiment.biology.ions.Glycon
public static final int DEUTEROACETYLATED_MASS 4
public static final int DEUTEROMETHYLATED_MASS 2
public static final int PERACETYLATED_MASS 3
public static final int PERMETHYLATED_MASS 1
public static final int UNDERIVATED_MASS 0

com.compomics.util.experiment.biology.ions.ImmoniumIon
public static final int ALANINE 0
public static final int ARGININE 1
public static final int ASPARAGINE 2
public static final int ASPARTIC_ACID 3
public static final int CYSTEINE 4
public static final int GLUTAMIC_ACID 5
public static final int GLUTAMINE 6
public static final int GLYCINE 7
public static final int HISTIDINE 8
public static final int ISOLEUCINE 9
public static final int LEUCINE 10
public static final int LYSINE 11
public static final int METHIONINE 12
public static final int PHENYLALANINE 13
public static final int PROLINE 14
public static final int SELENOCYSTEINE 15
public static final int SERINE 16
public static final int THREONINE 17
public static final int TRYPTOPHAN 18
public static final int TYROSINE 19
public static final int VALINE 20

com.compomics.util.experiment.biology.ions.PeptideFragmentIon
public static final int A_ION 0
public static final int B_ION 1
public static final int C_ION 2
public static final int X_ION 3
public static final int Y_ION 4
public static final int Z_ION 5

com.compomics.util.experiment.biology.ions.PrecursorIon
public static final int PRECURSOR 0

com.compomics.util.experiment.identification.Advocate
public static final int ANDROMEDA 4
public static final int MASCOT 0
public static final int OMSSA 1
public static final int PEPTIDE_SHAKER 5
public static final int PEPTIZER 3
public static final long serialVersionUID -9081265337103997591L
public static final int XTANDEM 2

com.compomics.util.experiment.identification.Identification
public static final String EXTENTION ".cuh"

com.compomics.util.experiment.identification.IdentificationDB
public static final String matchSize "128k"
public static final String parametersSize "128k"

com.compomics.util.experiment.identification.IdentificationMethod
public static final int MS2_IDENTIFICATION 1
public static final int PEPTIDE_FINGERPRINTING 0

com.compomics.util.experiment.io.identifications.IdentificationParametersReader
public static final String CHARGE_ESTIMATION "OMSSA_CHARGE_ESTIMATION"
public static final String DATABASE_FILE "DATABASE_FILE"
public static final String ENZYME "ENZYME"
public static final String EVALUE_CUTOFF "EVALUE_CUTOFF"
public static final String FIXED_MODIFICATIONS "FIXED_MODIFICATIONS"
public static final String FRAGMENT_ION_MASS_ACCURACY "FRAGMENT_MASS_TOLERANCE"
public static final String FRAGMENT_ION_TYPE_1 "FRAGMENT_ION_TYPE_1"
public static final String FRAGMENT_ION_TYPE_2 "FRAGMENT_ION_TYPE_2"
public static final String MAX_PEPTIDE_SIZE "OMSSA_MAXIMAL_PEPTIDE_SIZE"
public static final String MAXIMUM_HITLIST_LENGTH "MAXIMUM_HITLIST_LENGTH"
public static final String MIN_PEPTIDE_SIZE "OMSSA_MINIMAL_PEPTIDE_SIZE"
public static final String MISSED_CLEAVAGES "MISSED_CLEAVAGES"
public static final String MODIFICATION_SEPARATOR "//"
public static final String MODIFICATION_USE_SEPARATOR "_"
public static final String PRECURSOR_CHARGE_LOWER_BOUND "PRECURSOR_CHARGE_LOWER_BOUND"
public static final String PRECURSOR_CHARGE_TO_CONSIDER_MULTIPLY_CHARGED_FRAGMENTS "OMSSA_PRECURSOR_CHARGE_TO_CONSIDER_MULTIPLY_CHARGED_FRAGMENTS"
public static final String PRECURSOR_CHARGE_UPPER_BOUND "PRECURSOR_CHARGE_UPPER_BOUND"
public static final String PRECURSOR_ELIMINATION "OMSSA_PRECURSOR_ELIMINATION"
public static final String PRECURSOR_MASS_ACCURACY_UNIT "PRECURSOR_MASS_TOLERANCE_UNIT"
public static final String PRECURSOR_MASS_TOLERANCE "PRECURSOR_MASS_TOLERANCE"
public static final String PRECURSOR_SCALING "OMSSA_PRECURSOR_SCALING"
public static final String VARIABLE_MODIFICATIONS "VARIABLE_MODIFICATIONS"

com.compomics.util.experiment.massspectrometry.Charge
public static final int MINUS -1
public static final int NEUTRAL 0
public static final int PLUS 1

com.compomics.util.experiment.massspectrometry.Spectrum
public static final String SPECTRUM_KEY_SPLITTER "_cus_"

com.compomics.util.experiment.personalization.UrParameter
public static final long serialVersionUID 6808590175195298797L

com.compomics.util.experiment.quantification.QuantificationDB
public static final String matchSize "128k"
public static final String parametersSize "8k"

com.compomics.util.general.MassCalc
public static final int MONOELEMENTS 0
public static final int MONONUCLEOTIDES 2
public static final int MONOAA 1
public static final int SELFDEFINED -1

com.compomics.util.gui.protein.ModificationProfile
public static final int A_SCORE_ROW_INDEX 1
public static final int DELTA_SCORE_ROW_INDEX 0

com.compomics.util.gui.spectrum.GraphicsPanel
public static final int ANNOTATED_STATUS 1
protected static final int DOTS 1
public static final int INTERACTIVE_STATUS 0
protected static final int LINES 0

com.compomics.util.gui.spectrum.MassErrorBubblePlot
public static final float DEFAULT_NON_VISIBLE_MARKER_ALPHA 0.0f
public static final float DEFAULT_VISIBLE_MARKER_ALPHA 1.0f

com.compomics.util.interfaces.Modification
public static final int AVERAGE 1
public static final String CTERMINUS "1"
public static final int MONOISOTOPIC 0
public static final String NTERMINUS "0"

com.compomics.util.io.FolderMonitor
public static final int FTP_TO_SPECIFIED_DESTINATION 0
public static final int GATHER_FILES_FOR_PICKUP 1
public static final String HOST "HOST"
public static final String LIMIT "LIMIT"
public static final String PASSWORD "PASSWORD"
public static final String PICKUP "PICKUP"
public static final String TEXTMODE "TEXTMODE"
public static final String USER "USER"

com.compomics.util.io.FTP
public static final int FTP_PORT 21

com.compomics.util.io.filefilters.FileFilterUtils
public static final String dat "dat"
public static final String DAT "DAT"
public static final String dta "dta"
public static final String DTA "DTA"
public static final String fas "fas"
public static final String FAS "FAS"
public static final String fasta "fasta"
public static final String FASTA "FASTA"
public static final String gif "gif"
public static final String GIF "GIF"
public static final String jpeg "jpeg"
public static final String JPEG "JPEG"
public static final String jpg "jpg"
public static final String JPG "JPG"
public static final String mgf "mgf"
public static final String MGF "MGF"
public static final String ms2 "ms2"
public static final String MS2 "MS2"
public static final String mzdata "mzdata"
public static final String mzData "mzData"
public static final String mzDATA "mzDATA"
public static final String MZDATA "MZDATA"
public static final String mzml "mzml"
public static final String mzML "mzML"
public static final String MZML "MZML"
public static final String mzxml "mzxml"
public static final String mzXML "mzXML"
public static final String MZXML "MZXML"
public static final String omx "omx"
public static final String OMX "OMX"
public static final String out "out"
public static final String OUT "OUT"
public static final String pdf "pdf"
public static final String PDF "PDF"
public static final String peff "peff"
public static final String PEFF "PEFF"
public static final String pep_xml "pep.xml"
public static final String PEP_XML "PEP.XML"
public static final String pepxml "pepxml"
public static final String PEPXML "PEPXML"
public static final String pkl "pkl"
public static final String PKL "PKL"
public static final String pkx "pkx"
public static final String PKX "PKX"
public static final String png "png"
public static final String PNG "PNG"
public static final String properties "properties"
public static final String PROPERTIES "PROPERTIES"
public static final String prot_xml "prot.xml"
public static final String PROT_XML "PROT.XML"
public static final String protxml "protxml"
public static final String PROTXML "PROTXML"
public static final String spo "spo"
public static final String SPO "SPO"
public static final String svg "svg"
public static final String SVG "SVG"
public static final String tiff "tiff"
public static final String TIFF "TIFF"
public static final String txt "txt"
public static final String TXT "TXT"
public static final String xml "xml"
public static final String XML "XML"

com.compomics.util.pride.PrideObjectsFactory
public static final String extension ".cus"

com.compomics.util.protein.DualEnzyme
public static final int CTERMINAL 1
public static final int NTERMINAL 0

com.compomics.util.protein.Enzyme
public static final int C_TERM_ENZYMATIC 3
public static final int CTERM 0
public static final int ENTIRELY_NOT_ENZYMATIC 4
public static final int FULLY_ENZYMATIC 1
public static final int N_TERM_ENZYMATIC 2
public static final int NTERM 1

com.compomics.util.protein.Protein
public static final int CTERMTRUNC 2
public static final int NTERMTRUNC 1



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