Constant Field Values

Contents

• com.compomics.*

com.compomics.*

com.compomics.software.CommandLineUtils

Modifier and Type	Constant Field	Value
public static final String	SEPARATOR	","

com.compomics.software.ToolFactory

Modifier and Type	Constant Field	Value
public static final String	outputFolderOption	"-output_folder"
public static final String	peptideShakerFileOption	"-cps"
public static final String	peptideShakerPxAccessionOption	"-pxAccession"
public static final String	peptideShakerPxAccessionPrivateOption	"-pxAccessionPrivate"
public static final String	peptideShakerUrlDownloadFolderOption	"-zipUrlFolder"
public static final String	peptideShakerUrlOption	"-zipUrl"
public static final String	searchGuiParametersFileOption	"-identification_parameters"
public static final String	searchGuiRawFileOption	"-raw"
public static final String	searchGuiSpectrumFileOption	"-mgf"
public static final String	speciesOption	"-species"
public static final String	speciesTypeOption	"-species_type"

com.compomics.software.autoupdater.MavenJarFile

Modifier and Type	Constant Field	Value
public static final int	CENATT	36
public static final int	CENATX	38
public static final int	CENCOM	32
public static final int	CENCRC	16
public static final int	CENDSK	34
public static final int	CENEXT	30
public static final int	CENFLG	8
public static final int	CENHDR	46
public static final int	CENHOW	10
public static final int	CENLEN	24
public static final int	CENNAM	28
public static final int	CENOFF	42
public static final long	CENSIG	33639248L
public static final int	CENSIZ	20
public static final int	CENTIM	12
public static final int	CENVEM	4
public static final int	CENVER	6
public static final int	ENDCOM	20
public static final int	ENDHDR	22
public static final int	ENDOFF	16
public static final long	ENDSIG	101010256L
public static final int	ENDSIZ	12
public static final int	ENDSUB	8
public static final int	ENDTOT	10
public static final int	EXTCRC	4
public static final int	EXTHDR	16
public static final int	EXTLEN	12
public static final long	EXTSIG	134695760L
public static final int	EXTSIZ	8
public static final int	LOCCRC	14
public static final int	LOCEXT	28
public static final int	LOCFLG	6
public static final int	LOCHDR	30
public static final int	LOCHOW	8
public static final int	LOCLEN	22
public static final int	LOCNAM	26
public static final long	LOCSIG	67324752L
public static final int	LOCSIZ	18
public static final int	LOCTIM	10
public static final int	LOCVER	4

com.compomics.software.settings.UtilitiesPathPreferences

Modifier and Type	Constant Field	Value
public static final String	configurationFileName	"resources/conf/paths.txt"
public static final String	defaultPath	"default"
public static final String	separator	"="

com.compomics.util.BinaryArrayImpl

Modifier and Type	Constant Field	Value
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.Util

Modifier and Type	Constant Field	Value
public static final String	separator	"_cus_"

com.compomics.util.db.ObjectsDB

Modifier and Type	Constant Field	Value
public static final String	CONNECTION_LOG_TABLE	"connection_log_table"
public static final String	derbyConnectionID	"objectsDB"
public static final String	LONG_KEY_PREFIX	"long_key_"
public static final String	LONG_KEY_TABLE	"long_key_table"
public static final String	LONG_TABLE_NAMES	"long_tables"
public static final int	MAX_KEY_LENGTH	1000
public static final int	TABLE_NAME_MAX_LENGTH	128
public static final int	VARCHAR_MAX_LENGTH	32672

com.compomics.util.experiment.Constants

Modifier and Type	Constant Field	Value
public static final double	AMU_NO_EXP	1.660538921
public static final double	AVOGADRO_NO_EXP	6.02214129

com.compomics.util.experiment.MsExperiment

Modifier and Type	Constant Field	Value
public static final String	experimentObjectName	"experiment"

com.compomics.util.experiment.biology.Peptide

Modifier and Type	Constant Field	Value
public static final String	MODIFICATION_LOCALIZATION_SEPARATOR	"-ATAA-"
public static final String	MODIFICATION_SEPARATOR	"_"

com.compomics.util.experiment.biology.PTM

Modifier and Type	Constant Field	Value
public static final int	MODAA	0
public static final int	MODC	3
public static final int	MODCAA	4
public static final int	MODCP	7
public static final int	MODCPAA	8
public static final int	MODMAX	9
public static final int	MODN	1
public static final int	MODNAA	2
public static final int	MODNP	5
public static final int	MODNPAA	6

com.compomics.util.experiment.biology.PTMFactory

Modifier and Type	Constant Field	Value
public static final String	SINGLE_AA_SUFFIX	"|single_aa"

com.compomics.util.experiment.biology.genes.GeneFactory

Modifier and Type	Constant Field	Value
public static final String	GENE_MAPPING_FILE_SUFFIX	"_gene_mappings"
public static final String	GO_MAPPING_FILE_SUFFIX	"_go_mappings"
public static final String	SEPARATOR	"\t"

com.compomics.util.experiment.biology.genes.ensembl.GeneMapping

Modifier and Type	Constant Field	Value
public static final String	SEPARATOR	"\t"

com.compomics.util.experiment.biology.genes.go.GoDomains

Modifier and Type	Constant Field	Value
public static final String	SEPARATOR	"\t"

com.compomics.util.experiment.biology.genes.go.GoMapping

Modifier and Type	Constant Field	Value
public static final String	SEPARATOR	"\t"

com.compomics.util.experiment.biology.ions.ElementaryIon

Modifier and Type	Constant Field	Value
public static final int	PROTON	0

com.compomics.util.experiment.biology.ions.Glycan

Modifier and Type	Constant Field	Value
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

Modifier and Type	Constant Field	Value
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

Modifier and Type	Constant Field	Value
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

Modifier and Type	Constant Field	Value
public static final int	PRECURSOR	0

com.compomics.util.experiment.biology.ions.TagFragmentIon

Modifier and Type	Constant Field	Value
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.taxonomy.SpeciesFactory

Modifier and Type	Constant Field	Value
public static final String	BIOMART_ENSEMBL_FILENAME	"ensembl_biomart"
public static final String	BIOMART_ENSEMBL_GENOME_FILENAME	"ensembl-genome_biomart"
public static final String	ENSEMBL_GENOME_SPECIES	"ensembl-genome_species"
public static final String	ENSEMBL_SPECIES	"ensembl_species"
public static final String	UNIPROT_TAXONOMY_FILENAME	"uniprot_taxonomy"
public static final String	UNKNOWN	"Unknown"

com.compomics.util.experiment.biology.taxonomy.mappings.BiomartMapping

Modifier and Type	Constant Field	Value
public static final String	SEPARATOR	"\t"

com.compomics.util.experiment.biology.taxonomy.mappings.EnsemblGenomesSpecies

Modifier and Type	Constant Field	Value
public static final String	SEPARATOR	"\t"

com.compomics.util.experiment.biology.taxonomy.mappings.EnsemblSpecies

Modifier and Type	Constant Field	Value
public static final String	SEPARATOR	"\",\""

com.compomics.util.experiment.biology.taxonomy.mappings.UniprotTaxonomy

Modifier and Type	Constant Field	Value
public static final String	SEPARATOR	"\t"

com.compomics.util.experiment.identification.IdentificationMethod

Modifier and Type	Constant Field	Value
public static final int	MS2_IDENTIFICATION	1
public static final int	PEPTIDE_FINGERPRINTING	0

com.compomics.util.experiment.identification.identification_parameters.IdentificationParametersFactory

Modifier and Type	Constant Field	Value
public static final String	PARAMETERS_EXTENSION	".par"
public static final String	PARAMETERS_FOLDER	"identification_parameters"

com.compomics.util.experiment.identification.identification_parameters.tool_specific.MsAmandaParameters

Modifier and Type	Constant Field	Value
public static final int	MAX_MS_AMANDA_FASTA_FILE_NAME_LENGTH	80

com.compomics.util.experiment.identification.matches.ProteinMatch

Modifier and Type	Constant Field	Value
public static final String	PROTEIN_KEY_SPLITTER	"_cus_"

com.compomics.util.experiment.identification.matches_iterators.PeptideMatchesIterator

Modifier and Type	Constant Field	Value
public final int	defaultBatchSize	1000
public final double	defaultMargin	0.1

com.compomics.util.experiment.identification.matches_iterators.ProteinMatchesIterator

Modifier and Type	Constant Field	Value
public final int	defaultBatchSize	1000
public final double	defaultMargin	0.1

com.compomics.util.experiment.identification.matches_iterators.PsmIterator

Modifier and Type	Constant Field	Value
public final int	defaultBatchSize	1000
public final double	defaultMargin	0.1

com.compomics.util.experiment.identification.protein_inference.proteintree.Node

Modifier and Type	Constant Field	Value
public static final int	proteinBatchSize	100

com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTree

Modifier and Type	Constant Field	Value
public static final int	proteinBatchSize	100
public static final String	version	"1.1.2"

com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTreeComponentsFactory

Modifier and Type	Constant Field	Value
public static final String	dbName	"proteinTree"
public static final String	folderSeparator	"_cus_"

com.compomics.util.experiment.identification.protein_sequences.SequenceFactory

Modifier and Type	Constant Field	Value
public static final long	TIME_OUT	10000L

com.compomics.util.experiment.identification.psm_scoring.psm_scores.AAIntensityRankScore

Modifier and Type	Constant Field	Value
public static final int	nBins	10

com.compomics.util.experiment.identification.ptm.ptmscores.PhosphoRS

Modifier and Type	Constant Field	Value
public static final int	MAX_DEPTH	8
public static final int	MIN_DEPTH	2

com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator

Modifier and Type	Constant Field	Value
protected static final boolean	subtractIsotope	false

com.compomics.util.experiment.io.identifications.idfilereaders.DirecTagIdfileReader

Modifier and Type	Constant Field	Value
public final double	cTermCorrection	0.0
public final double	nTermCorrection	0.0

com.compomics.util.experiment.io.identifications.idfilereaders.PepNovoIdfileReader

Modifier and Type	Constant Field	Value
public final double	nTermCorrection	0.0
public static final String	tableHeader	"#Index\tRnkScr\tPnvScr\tN-Gap\tC-Gap\t[M+H]\tCharge\tSequence"

com.compomics.util.experiment.massspectrometry.Charge

Modifier and Type	Constant Field	Value
public static final int	MINUS	-1
public static final int	NEUTRAL	0
public static final int	PLUS	1

com.compomics.util.experiment.massspectrometry.Spectrum

Modifier and Type	Constant Field	Value
public static final String	SPECTRUM_KEY_SPLITTER	"_cus_"

com.compomics.util.experiment.massspectrometry.SpectrumFactory

Modifier and Type	Constant Field	Value
public static final long	timeOut	10000L

com.compomics.util.experiment.personalization.UrParameter

Modifier and Type	Constant Field	Value
public static final long	serialVersionUID	6808590175195298797L

com.compomics.util.general.MassCalc

Modifier and Type	Constant Field	Value
public static final int	MONOAA	1
public static final int	MONOELEMENTS	0
public static final int	MONONUCLEOTIDES	2
public static final int	SELFDEFINED	-1

com.compomics.util.gui.error_handlers.BugReport

Modifier and Type	Constant Field	Value
public static final String	lastSelectedFolderKey	"bug_report"

com.compomics.util.gui.genes.SpeciesDialog

Modifier and Type	Constant Field	Value
public static final String	NO_SPECIES_TAG	"-- (no selection) --"
public static final String	SELECT_SPECIES_TAG	"-- Select Species --"

com.compomics.util.gui.parameters.identification_parameters.SearchSettingsDialog

Modifier and Type	Constant Field	Value
public static final String	MODIFICATION_SEPARATOR	"//"

com.compomics.util.gui.protein.ModificationProfile

Modifier and Type	Constant Field	Value
public static final int	SCORE_1_ROW_INDEX	0
public static final int	SCORE_2_ROW_INDEX	1

com.compomics.util.gui.spectrum.GraphicsPanel

Modifier and Type	Constant Field	Value
public final int	ANNOTATED_STATUS	1
public final int	INTERACTIVE_STATUS	0

com.compomics.util.gui.spectrum.MassErrorBubblePlot

Modifier and Type	Constant Field	Value
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

Modifier and Type	Constant Field	Value
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

Modifier and Type	Constant Field	Value
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

Modifier and Type	Constant Field	Value
public static final int	FTP_PORT	21

com.compomics.util.io.export.ExportFeature

Modifier and Type	Constant Field	Value
public static final long	serialVersionUID	-4158077697265471589L

com.compomics.util.io.export.ExportWriter

Modifier and Type	Constant Field	Value
public static final String	lastFolderKey	"export"

com.compomics.util.io.filefilters.FileFilterUtils

Modifier and Type	Constant Field	Value
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.maps.KeyUtils

Modifier and Type	Constant Field	Value
public static final String	SEPARATOR	"_"

com.compomics.util.preferences.GenePreferences

Modifier and Type	Constant Field	Value
public static final String	GENE_MAPPING_FILE_SUFFIX	"_gene_mappings"
public static final String	GO_MAPPING_FILE_SUFFIX	"_go_mappings"

com.compomics.util.pride.PrideObjectsFactory

Modifier and Type	Constant Field	Value
public static final String	extension	".cus"

com.compomics.util.pride.PtmToPrideMap

Modifier and Type	Constant Field	Value
public static final String	fileName	"modMapUniMod.cus"

com.compomics.util.protein.DualEnzyme

Modifier and Type	Constant Field	Value
public static final int	CTERMINAL	1
public static final int	NTERMINAL	0

com.compomics.util.protein.Enzyme

Modifier and Type	Constant Field	Value
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

Modifier and Type	Constant Field	Value
public static final int	CTERMTRUNC	2
public static final int	NTERMTRUNC	1

com.compomics.util.protein_sequences_manager.ProteinSequencesManager

Modifier and Type	Constant Field	Value
public static final String	DNA_FOLDER	"dna"
public static final String	TEMP_FOLDER	".temp"
public static final String	UNIPROT_FOLDER	"uniprot"
public static final String	USER_FOLDER	"user"

com.compomics.util.protein_sequences_manager.gui.SequenceDbDetailsDialog

Modifier and Type	Constant Field	Value
public static final String	lastFolderKey	"fastaFile"

com.compomics.util.waiting.WaitingHandler

Modifier and Type	Constant Field	Value
public static final String	TAB_HTML	"        "
public static final String	TAB_NON_HTML	" "