Constant Field Values

Contents

• uk.ac.*

uk.ac.*

uk.ac.ebi.pride.utilities.data.controller.access.MzGraphDataAccess

Modifier and Type	Constant Field	Value
public static final String	CHROMATOGRAM_TYPE	"Chromatogram"
public static final String	MZGRAPH_TYPE	"MzGraph"
public static final String	SPECTRUM_TYPE	"Spectrum"

uk.ac.ebi.pride.utilities.data.controller.cache.CachedMap<K,V>

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

uk.ac.ebi.pride.utilities.data.core.QuantitativeSample

Modifier and Type	Constant Field	Value
public static final int	MAX_SUB_SAMPLE_SIZE	8

uk.ac.ebi.pride.utilities.data.exporters.HQMzIdentMLMzTabConverter

Modifier and Type	Constant Field	Value
public static final String	NO_THRESHOLD	"no threshold"
public static final String	NO_THRESHOLD_MS_AC	"MS:1001494"

uk.ac.ebi.pride.utilities.data.exporters.MzIdentMLMzTabConverter

Modifier and Type	Constant Field	Value
public static final String	CHEMMOD	"CHEMMOD"
public static final String	PEPTIDE_C_TERM	"MS:1001190"
public static final String	PEPTIDE_N_TERM	"MS:1001189"
public static final String	PROTEIN_C_TERM	"MS:1002058"
public static final String	PROTEIN_N_TERM	"MS:1002057"
public static final String	UNKNOWN_MODIFICATION	"unknown modification"

uk.ac.ebi.pride.utilities.data.exporters.PRIDEMzTabConverter

Modifier and Type	Constant Field	Value
public static final String	EMPAI	"empai"
public static final String	GEL_COORDINATES	"gel_coordinates"
public static final String	GEL_IDENTIFIER	"gel_identifier"
public static final String	GEL_SPOTIDENTIFIER	"gel_spotidentifier"

uk.ac.ebi.pride.utilities.data.utils.Constants

Modifier and Type	Constant Field	Value
public static final String	APL_EXT	".apl"
public static final String	DTA_EXT	".dta"
public static final String	INTEGER	"[+-]?\\d+"
public static final String	MGF_EXT	".mgf"
public static final String	MS2_EXT	".ms2"
public static final String	MZML_EXT	".mzML"
public static final String	MZTAB_EXT	".mztab"
public static final String	MZXML_EXT	".mzxml"
public static final String	NOT_AVAILABLE	"N/A"
public static final String	PKL_EXT	".pkl"
public static final String	WIFF_EXT	".wiff"
public static final String	XML_EXT	".xml"

uk.ac.ebi.pride.utilities.data.utils.MzTabUtils

Modifier and Type	Constant Field	Value
public static final String	CUSTOM_CHROM_INF_PARAM	"Chromosome information present"
public static final String	OPTIONAL_CHROM_COLUMN	"chom"
public static final String	OPTIONAL_CHROMEND_COLUMN	"chomend"
public static final String	OPTIONAL_CHROMSTART_COLUMN	"chomstart"
public static final String	OPTIONAL_DECOY_COLUMN	"cv_MS:1002217_decoy_peptide"
public static final String	OPTIONAL_ID_COLUMN	"mzidentml_original_ID"
public static final String	OPTIONAL_PREDICTION_COLUMN	"prediction"
public static final String	OPTIONAL_PROTEIN_NAME_COLUMN	"protein_name"
public static final String	OPTIONAL_PSM_FDRSCORE_COLUMN	"cv_MS:1002356_PSM-level_combined_FDRScore"
public static final String	OPTIONAL_RANK_COLUMN	"cv_PRIDE:0000091_rank"
public static final String	OPTIONAL_SEQUENCE_COLUMN	"protein_sequence"
public static final String	OPTIONAL_STRAND_COLUMN	"strand"

uk.ac.ebi.pride.utilities.data.utils.PRIDEUtils

Modifier and Type	Constant Field	Value
public static final String	DUP_PROTEINS_BEST_SEARCH_ENGINES_SCORE	"duplicated_proteins_best_search_engines_score"
public static final String	DUP_PROTEINS_HAD_QUANT	"duplicated_proteins_had_quantification"
public static final String	DUP_PROTEINS_SEARCH_ENGINES	"duplicated_proteins_search_engines"
public static final String	DUP_PROTEINS_SEARCH_ENGINES_SCORES	"duplicated_proteins_search_engines_scores"
public static final String	NUM_MERGE_PROTEINS	"num_merge_proteins"