Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
SEPARATOR |
"," |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
outputFolderOption |
"-output_folder" |
public static final String |
peptideShakerFileOption |
"-cps" |
public static final String |
searchGuiParametersFileOption |
"-search_parameters" |
public static final String |
searchGuiSpectrumFileOption |
"-mgf" |
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 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 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
SEARCH_SUFFIX |
"|search-only" |
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 |
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 |
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 |
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 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
EXTENTION |
".cuh" |
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 |
PROTEIN_KEY_SPLITTER |
"_cus_" |
Modifier and Type | Constant Field | Value |
---|---|---|
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" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
MINUS |
-1 |
public static final int |
NEUTRAL |
0 |
public static final int |
PLUS |
1 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
SPECTRUM_KEY_SPLITTER |
"_cus_" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final long |
serialVersionUID |
6808590175195298797L |
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 int |
A_SCORE_ROW_INDEX |
1 |
public static final int |
DELTA_SCORE_ROW_INDEX |
0 |
Modifier and Type | Constant Field | Value |
---|---|---|
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 |
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 String |
tab |
" " |
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 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 int |
FTP_PORT |
21 |
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 String |
extension |
".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 |
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