Constant Field Values
Contents
com.compomics.*
-
com.compomics.software.ToolFactory Modifier and Type Constant Field Value public static final String
OUTPUT_FOLDER_OPTION
"-output_folder"
public static final String
PEPTIDE_SHAKER_FILE_OPTION
"-psdb"
public static final String
PEPTIDE_SHAKER_PX_ACCESSION_OPTION
"-pxAccession"
public static final String
PEPTIDE_SHAKER_PX_ACCESSION_PRIVATE_OPTION
"-pxAccessionPrivate"
public static final String
PEPTIDE_SHAKER_URL_DOWNLOAD_FOLDER_OPTION
"-zipUrlFolder"
public static final String
PEPTIDE_SHAKER_URL_OPTION
"-zipUrl"
public static final String
PROJEC_NAME_OPTION
"-project_name"
public static final String
SEARCHGUI_FASTA_FILE_OPTION
"-fasta"
public static final String
SEARCHGUI_PARAMETERS_FILE_OPTION
"-identification_parameters"
public static final String
SEARCHGUI_RAW_FILE_OPTION
"-raw"
public static final String
SEARCHGUI_SPECTRUM_FILE_OPTION
"-mgf"
public static final String
SPECIES_OPTION
"-species"
public static final String
SPECIES_TYPE_OPTION
"-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.cli.CommandLineUtils Modifier and Type Constant Field Value public static final String
FORMATTER
"%-35s"
public static final String
SEPARATOR
","
-
com.compomics.software.settings.UtilitiesPathParameters 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
"="
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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"
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com.compomics.util.Util Modifier and Type Constant Field Value public static final String
DEFAULT_COLUMN_SEPARATOR
"\t"
public static final String
ENCODING
"UTF-8"
public static final double
MASS_PER_AA
100.0
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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
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com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider 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"
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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.ions.impl.ElementaryIon Modifier and Type Constant Field Value public static final int
PROTON
0
-
com.compomics.util.experiment.biology.ions.impl.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.impl.PrecursorIon Modifier and Type Constant Field Value public static final int
PRECURSOR
0
-
com.compomics.util.experiment.biology.modifications.ModificationFactory Modifier and Type Constant Field Value public static final String
SINGLE_AA_SUFFIX
"|single_aa"
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com.compomics.util.experiment.biology.proteins.Peptide Modifier and Type Constant Field Value public static final String
MODIFICATION_LOCALIZATION_SEPARATOR
"-ATAA-"
public static final String
MODIFICATION_SEPARATOR
"_"
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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"
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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"
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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
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com.compomics.util.experiment.identification.filtering.MatchFilter Modifier and Type Constant Field Value public static final String
MANUAL_SELECTION
"manual selection"
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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_4"
-
com.compomics.util.experiment.identification.modification.mapping.ModificationLocalizationMapper Modifier and Type Constant Field Value public static final double
MASS_PER_AA
100.0
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com.compomics.util.experiment.identification.modification.mapping.ModificationNameMapper Modifier and Type Constant Field Value public static final double
MOD_MASS_TOLERANCE
0.01
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com.compomics.util.experiment.identification.modification.scores.PhosphoRS Modifier and Type Constant Field Value public static final int
MAX_DEPTH
8
public static final int
MIN_DEPTH
2
public static final double
WINDOW_SIZE
100.0
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com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.FeaturesMap Modifier and Type Constant Field Value public static final int
currentVersion
0
-
com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.AAIdentityFeatureAbsolute Modifier and Type Constant Field Value public static final int
index
9
-
com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.AAIdentityFeatureRelative Modifier and Type Constant Field Value public static final int
index
10
-
com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.AAPropertyFeatureAbsolute Modifier and Type Constant Field Value public static final int
index
6
-
com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.AAPropertyFeatureRelative Modifier and Type Constant Field Value public static final int
index
7
-
com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.AAPropertyRelationshipFeature Modifier and Type Constant Field Value public static final int
index
8
-
com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.ComplementaryIonAminoAcidFeature Modifier and Type Constant Field Value public static final int
index
5
-
com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.ComplementaryIonFeature Modifier and Type Constant Field Value public static final int
index
3
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com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.ForwardIonAminoAcidFeature Modifier and Type Constant Field Value public static final int
index
4
-
com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.ForwardIonFeature Modifier and Type Constant Field Value public static final int
index
2
-
com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.ModificationFeature Modifier and Type Constant Field Value public static final int
index
11
-
com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.PeptideAminoAcidFeature Modifier and Type Constant Field Value public static final int
index
1
-
com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.PeptideFeature Modifier and Type Constant Field Value public static final int
index
0
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com.compomics.util.experiment.identification.peptide_shaker.ModificationScoring Modifier and Type Constant Field Value public static final int
CONFIDENT
2
public static final int
DOUBTFUL
1
public static final int
NOT_FOUND
-1
public static final int
RANDOM
0
public static final String
SEPARATOR
"|"
public static final int
VERY_CONFIDENT
3
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com.compomics.util.experiment.identification.peptide_shaker.PSParameter Modifier and Type Constant Field Value public static final int
NOT_GROUP
0
public static final int
RELATED
1
public static final int
RELATED_AND_UNRELATED
2
public static final int
UNRELATED
3
-
com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator Modifier and Type Constant Field Value protected static final boolean
SUBTRACT_ISOTOPE
false
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com.compomics.util.experiment.io.biology.protein.iterators.FastaIterator Modifier and Type Constant Field Value public static final char
forbiddenCharacter
42
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com.compomics.util.experiment.io.identification.idfilereaders.DirecTagIdfileReader Modifier and Type Constant Field Value public final double
cTermCorrection
0.0
public final double
nTermCorrection
0.0
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com.compomics.util.experiment.io.identification.idfilereaders.OnyaseIdfileReader Modifier and Type Constant Field Value public static final char
comment
35
public static final String
ENCODING
"UTF-8"
public static final String
fastaTag
"Fasta File:"
public static final String
paramsTag
"Parameters File:"
public static final char
separator
32
public static final String
spectraTag
"Spectrum File:"
public static final String
versionTag
"Version:"
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com.compomics.util.experiment.io.identification.idfilereaders.PepNovoIdfileReader Modifier and Type Constant Field Value public static final String
DEFAULT_HEADER
"#Index\tRnkScr\tPnvScr\tN-Gap\tC-Gap\t[M+H]\tCharge\tSequence"
public final double
nTermCorrection
0.0
-
com.compomics.util.experiment.io.identification.writers.SimpleMzIdentMLExporter Modifier and Type Constant Field Value public static final String
ANALYSIS_SECTION
"ANALYSIS_SECTION"
public static final String
DATA_SECTION
"DATA_SECTION"
public static final String
HEAD_SECTION
"HEAD_SECTION"
public static final int
MAX_NEUTRAL_LOSSES
2
public static final int
N_AA
1
public static final String
PEPTIDE_EVIDENCE_SECTION
"PEPTIDE_EVIDENCE_SECTION"
public static final String
PEPTIDE_SECTION
"PEPTIDE_SECTION"
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com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFileUtils Modifier and Type Constant Field Value public static final String
EXTENSION
".cms"
public static final String
TITLE_SEPARATOR
"\t"
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com.compomics.util.experiment.io.mass_spectrometry.mzml.MSNumpress Modifier and Type Constant Field Value public static final String
ACC_NUMPRESS_LINEAR
"MS:1002312"
public static final String
ACC_NUMPRESS_PIC
"MS:1002313"
public static final String
ACC_NUMPRESS_SLOF
"MS:1002314"
-
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
LAST_SELECTED_FOLDER_KEY
"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 --"
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com.compomics.util.gui.parameters.identification.search.SequenceDbDetailsDialog Modifier and Type Constant Field Value public static final String
lastFolderKey
"fastaFile"
public static final int
SAMPLE_BATCH_SIZE
50
-
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.IoUtil Modifier and Type Constant Field Value public static final String
DEFAULT_SEPARATOR
"\t"
public static final String
ENCODING
"UTF-8"
-
com.compomics.util.io.compression.GzUtils Modifier and Type Constant Field Value public static final int
BUFFER_LENGTH
1024
public static final String
GZ_EXTENSION
".gz"
-
com.compomics.util.io.compression.TarUtils Modifier and Type Constant Field Value public static final int
BUFFER_SIZE
1024
-
com.compomics.util.io.compression.ZipUtils Modifier and Type Constant Field Value public static final int
BUFFER_SIZE
1024
-
com.compomics.util.io.compression.SectionGzWriter.WriterBySection Modifier and Type Constant Field Value public static final int
CHAR_BUFFER_SIZE
512
-
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
LAST_FOLDER_KEY
"export"
-
com.compomics.util.io.file.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.file.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.parameters.identification.IdentificationParameters Modifier and Type Constant Field Value public static final String
CURRENT_VERSION
"5.0.1"
public final String
version
"5.0.1"
-
com.compomics.util.parameters.identification.search.SearchParameters Modifier and Type Constant Field Value public static final int
preferredMaxVariableModifications
6
public static final int
preferredMinSequences
1000
public final String
version
"5.0.1"
-
com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters Modifier and Type Constant Field Value public static final int
MAX_MS_AMANDA_FASTA_FILE_NAME_LENGTH
80
-
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.waiting.WaitingHandler Modifier and Type Constant Field Value public static final String
TAB_HTML
" "
public static final String
TAB_NON_HTML
" "