Constant Field Values

Contents

• uk.ac.*

uk.ac.*

uk.ac.ebi.pride.jmztab2.model.MZTabConstants

Modifier and Type	Constant Field	Value
public static final String	ABUNDANCE_PREFIX	"abundance_"
public static final char	BAR	124
public static final String	BAR_S	"|"
public static final String	CALCULATE_ERROR	"NaN"
public static final char	COLON	58
public static final char	COMMA	44
public static final String	CV_PREFIX	"cv_"
public static final String	GLOBAL	"global"
public static final String	INFINITY	"INF"
public static final char	MINUS	45
public static final String	NEW_LINE	"\r\n"
public static final String	NULL	"null"
public static final String	OPT_PREFIX	"opt_"
public static final String	REGEX_ABUNDANCE_ASSAY_COLUMN_NAME	"assay\\[(\\d+)\\]"
public static final String	REGEX_ABUNDANCE_COLUMN_NAME	"abundance_(.+)"
public static final String	REGEX_ADDUCT	"^\\[\\d*M([+-][\\w\\d]+)*\\]\\d*[+-]$"
public static final String	REGEX_CV_PARAM_OPT_COLUMN_NAME	"cv(_([A-Za-z0-9\\-\\[\\]:\\.]+))?(_([A-Za-z0-9_\\-\\[\\]:\\.]+)*)"
public static final String	REGEX_DEFAULT_RELIABILITY	"[1234]{1}"
public static final String	REGEX_EMAIL	"[_A-Za-z0-9-]+(\\.[_A-Za-z0-9-\']+)*@[A-Za-z0-9]+(?:[-.][A-Za-z0-9]+)*(\\.[A-Za-z]{2,})"
public static final String	REGEX_INDEXED_VALUE	"\\[(\\d+)\\]"
public static final String	REGEX_MZTAB_M	"(?<major>[2]{1})\\.(?<minor>\\d{1})\\.(?<micro>\\d{1})-(?<profile>[M]{1})"
public static final String	REGEX_NORMAL_METADATA	"(\\w+)(\\[(\\w+)\\])?(-(\\w+)(\\[(\\w+)\\])?)?(-(\\w+))?"
public static final String	REGEX_OPT_COLUMN_NAME	"opt_((assay|study_variable|ms_run)\\[(\\w+)\\]|global)_([A-Za-z0-9_\\-\\[\\]:\\.]+)"
public static final String	REGEX_PARAM_SPLIT	",(?=([^\"]*\"[^\"]*\")*[^\"]*$)"
public static final String	REGEX_SPECTRA_REF_FILE	"file=[\\w]+"
public static final String	REGEX_SPECTRA_REF_INDEX	"index=[\\d]+"
public static final String	REGEX_SPECTRA_REF_MZML_UNIQUE	"[\\w]+"
public static final String	REGEX_SPECTRA_REF_SCAN	"scan=[\\d]+"
public static final String	REGEX_SPECTRA_REF_SPECTRUM	"spectrum=[\\d]+"
public static final String	REGEX_SPECTRA_REF_THERMO_NATIVE	"controllerType=[\\d]+ controllerNumber=[1-9]\\d* scan=[1-9]\\d*"
public static final String	REGEX_SPECTRA_REF_WATERS_NATIVE	"function=[1-9]\\d* process=[\\d]+ scan=[\\d]+"
public static final String	REGEX_SPECTRA_REF_WIFF_NATIVE	"sample=[\\d]+ period=[\\d]+ cycle=[\\d]+ experiment=[\\d]+"
public static final String	REGEX_STUDY_VARIABLE_COLUMN_NAME	"study_variable\\[(\\d+)\\]"
public static final char	TAB	9
public static final String	TAB_STRING	"\t"
public static final String	VERSION_MZTAB_M	"2.0.0-M"

uk.ac.ebi.pride.jmztab2.model.OptionColumn

Modifier and Type	Constant Field	Value
public static final String	GLOBAL	"global"
public static final String	OPT	"opt"

uk.ac.ebi.pride.jmztab2.model.ParameterOptionColumn

Modifier and Type	Constant Field	Value
public static final String	CV	"cv_"

uk.ac.ebi.pride.jmztab2.utils.MZTabProperties

Modifier and Type	Constant Field	Value
public static final String	MZTAB_ERROR_OVERFLOW_EXCEPTION_MESSAGE	"System error queue overflow!\r\n"
public static final String	MZTAB_EXCEPTION_MESSAGE	"There exist errors in the metadata section or protein/peptide/small_molecule/small_molecule_feature/small_molecule_evidence header section! Validation will stop, and ignore data table check!\r\n"

uk.ac.ebi.pride.jmztab2.utils.errors.MZTabConversionException

Modifier and Type	Constant Field	Value
public static final String	ERROR_AMBIGUITY	"mzTab do not support one protein in more than one ambiguity groups."