Constant Field Values


Contents
com.compomics.*

com.compomics.util.experiment.biology.Ion
public static final int ELEMENTARY_ION 3
public static final int GLYCON_FRAGMENT 1
public static final int PEPTIDE_FRAGMENT 0
public static final int REPORTER_ION 2

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.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.ReporterIon
public static final int ITRAQ_113 113
public static final int ITRAQ_114 114
public static final int ITRAQ_115 115
public static final int ITRAQ_116 116
public static final int ITRAQ_117 117
public static final int ITRAQ_118 118
public static final int ITRAQ_119 119
public static final int ITRAQ_121 121
public static final int TMT0 126
public static final int TMT1 127
public static final int TMT2 128
public static final int TMT3 129
public static final int TMT4 130
public static final int TMT5 131

com.compomics.util.experiment.identification.Advocate
public static final int MASCOT 0
public static final int OMSSA 1
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 java.lang.String EXTENTION ".cuh"

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

com.compomics.util.experiment.identification.SpectrumAnnotator
public static final java.lang.String SEPARATOR "|"

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

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

com.compomics.util.experiment.quantification.QuantificationMethod
public static final int ITRAQ_4PLEX 0
public static final int ITRAQ_8PLEX 1
public static final int TMT2 3
public static final int TMT6 2

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 java.lang.String CTERMINUS "1"
public static final int MONOISOTOPIC 0
public static final java.lang.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 java.lang.String HOST "HOST"
public static final java.lang.String LIMIT "LIMIT"
public static final java.lang.String PASSWORD "PASSWORD"
public static final java.lang.String PICKUP "PICKUP"
public static final java.lang.String TEXTMODE "TEXTMODE"
public static final java.lang.String USER "USER"

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

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

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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