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" |
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 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
FORMATTER |
"%-35s" |
public static final String |
SEPARATOR |
"," |
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 |
"=" |
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" |
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 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final double |
AMU_NO_EXP |
1.660538921 |
public static final double |
AVOGADRO_NO_EXP |
6.02214129 |
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" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
SEPARATOR |
"\t" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
SEPARATOR |
"\t" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
SEPARATOR |
"\t" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
PROTON |
0 |
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 |
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 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
PRECURSOR |
0 |
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 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
SINGLE_AA_SUFFIX |
"|single_aa" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
MODIFICATION_LOCALIZATION_SEPARATOR |
"-ATAA-" |
public static final String |
MODIFICATION_SEPARATOR |
"_" |
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" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
SEPARATOR |
"\t" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
SEPARATOR |
"\t" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
SEPARATOR |
"\",\"" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
SEPARATOR |
"\t" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
MS2_IDENTIFICATION |
1 |
public static final int |
PEPTIDE_FINGERPRINTING |
0 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
MANUAL_SELECTION |
"manual selection" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
PARAMETERS_EXTENSION |
".par" |
public static final String |
PARAMETERS_FOLDER |
"identification_parameters_4" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final double |
MASS_PER_AA |
100.0 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final double |
MOD_MASS_TOLERANCE |
0.01 |
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 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
currentVersion |
0 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
index |
9 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
index |
10 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
index |
6 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
index |
7 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
index |
8 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
index |
5 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
index |
3 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
index |
4 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
index |
2 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
index |
11 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
index |
1 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
index |
0 |
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 |
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 |
Modifier and Type | Constant Field | Value |
---|---|---|
protected static final boolean |
SUBTRACT_ISOTOPE |
false |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final char |
FORBIDDEN_CHARACTER |
42 |
Modifier and Type | Constant Field | Value |
---|---|---|
public final double |
cTermCorrection |
0.0 |
public final double |
nTermCorrection |
0.0 |
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:" |
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 |
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" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
EXTENSION |
".cms" |
public static final String |
TITLE_SEPARATOR |
"\t" |
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" |
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 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
LAST_SELECTED_FOLDER_KEY |
"bug_report" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
NO_SPECIES_TAG |
"-- (no selection) --" |
public static final String |
SELECT_SPECIES_TAG |
"-- Select Species --" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
lastFolderKey |
"fastaFile" |
public static final int |
SAMPLE_BATCH_SIZE |
50 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
SCORE_1_ROW_INDEX |
0 |
public static final int |
SCORE_2_ROW_INDEX |
1 |
Modifier and Type | Constant Field | Value |
---|---|---|
public final int |
ANNOTATED_STATUS |
1 |
public final int |
INTERACTIVE_STATUS |
0 |
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 |
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" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
DEFAULT_SEPARATOR |
"\t" |
public static final String |
ENCODING |
"UTF-8" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
BUFFER_LENGTH |
1024 |
public static final String |
GZ_EXTENSION |
".gz" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
BUFFER_SIZE |
1024 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
BUFFER_SIZE |
1024 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
CHAR_BUFFER_SIZE |
512 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final long |
serialVersionUID |
-4158077697265471589L |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
LAST_FOLDER_KEY |
"export" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
type |
"Annotation Settings" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
type |
"Fragment Ions Summary" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
type |
"Identification Algorithm Results" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
type |
"Input Filters" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
type |
"Peptide Identification Summary" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
type |
"Project Details" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
type |
"Protein Identification Summary" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
type |
"Peptide Spectrum Matching Summary" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
type |
"PTM Scoring Settings" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
type |
"Database Search Parameters" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
type |
"Spectrum Counting Parameters" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
type |
"Validation Summary" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
type |
"Peptide Reporter Quantification Summary" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
type |
"Protein Reporter Quantification Summary" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
type |
"PSM Reporter Quantification Summary" |
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" |
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" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
FTP_PORT |
21 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
CURRENT_VERSION |
"5.0.1" |
public final String |
version |
"5.0.1" |
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" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
MAX_MS_AMANDA_FASTA_FILE_NAME_LENGTH |
80 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
extension |
".cus" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
fileName |
"modMapUniMod.cus" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
CTERMINAL |
1 |
public static final int |
NTERMINAL |
0 |
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 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
CTERMTRUNC |
2 |
public static final int |
NTERMTRUNC |
1 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
TAB_HTML |
" " |
public static final String |
TAB_NON_HTML |
" " |
Copyright © 2021. All rights reserved.