Package uk.ac.ebi.pride.jmztab2.model
Class MZTabConstants
- java.lang.Object
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- uk.ac.ebi.pride.jmztab2.model.MZTabConstants
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public final class MZTabConstants extends Object
Define a couple of constants used in the jmzTab API.- Since:
- 08/03/13
- Author:
- qingwei, nilshoffmann
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Field Summary
Fields Modifier and Type Field Description static String
ABUNDANCE_PREFIX
ConstantABUNDANCE_PREFIX="abundance_"
static char
BAR
ConstantBAR='|'
static String
BAR_S
ConstantBAR='|'
static String
CALCULATE_ERROR
ConstantCALCULATE_ERROR="NaN"
static char
COLON
ConstantCOLON=':'
static char
COMMA
ConstantCOMMA=','
static String
CV_PREFIX
ConstantCV_PREFIX="cv_"
static String
GLOBAL
ConstantGLOBAL="global"
static String
INFINITY
ConstantINFINITY="INF"
static char
MINUS
ConstantMINUS='-'
static String
NEW_LINE
ConstantNEW_LINE="System.getProperty(line.separator)"
static String
NULL
ConstantNULL="null"
static String
OPT_PREFIX
ConstantOPT_PREFIX="opt_"
static String
REGEX_ABUNDANCE_ASSAY_COLUMN_NAME
ConstantREGEX_ABUNDANCE_ASSAY_COLUMN_NAME="assay\\[(\\d+)\\]"
static String
REGEX_ABUNDANCE_COLUMN_NAME
ConstantREGEX_ABUNDANCE_COLUMN_NAME="abundance_(.+)"
static String
REGEX_ADDUCT
ConstantREGEX_ADDUCT="^\[\d*M([+-][\w\d]+)*\]\d*[+-]$"
static String
REGEX_CV_PARAM_OPT_COLUMN_NAME
ConstantREGEX_CV_PARAM_OPT_COLUMN_NAME="cv(_([A-Za-z0-9\\-\\[\\]:\\.]+))?
static String
REGEX_DEFAULT_RELIABILITY
ConstantREGEX_DEFAULT_RELIABILITY="[1234]{1}"
static String
REGEX_EMAIL
ConstantREGEX_EMAIL="[_A-Za-z0-9-]+(\\.
static String
REGEX_INDEXED_VALUE
ConstantREGEX_INDEXED_VALUE="\\[(\\d+)\\]"
static String
REGEX_MZTAB_M
ConstantREGEX_MZTAB_M="(?<major>[2]{1})\\.(?<minor>\\d{1})\\.(?<micro>\\d{1})-(?<profile>[M]{1})"
static String
REGEX_NORMAL_METADATA
ConstantREGEX_NORMAL_METADATA="(\\w+)(\\[(\\w+)\\])?
static String
REGEX_OPT_COLUMN_NAME
ConstantREGEX_OPT_COLUMN_NAME="opt_((assay|study_variable|ms_run)\\[(\\w+)\\]|global)_([A-Za-z0-9_\\-\\[\\]:\\.]+)"
static String
REGEX_PARAM_SPLIT
ConstantREGEX_PARAM_SPLIT=",(?
static String
REGEX_SPECTRA_REF_FILE
ConstantREGEX_SPECTRA_REF_FILE = "file=[\\w]+"
static String
REGEX_SPECTRA_REF_INDEX
ConstantREGEX_SPECTRA_REF_INDEX = "index=[\\d]+"
static String
REGEX_SPECTRA_REF_MZML_UNIQUE
ConstantREGEX_SPECTRA_REF_MZML_UNIQUE = "[\\w]+"
static String
REGEX_SPECTRA_REF_SCAN
ConstantREGEX_SPECTRA_REF_SCAN = "scan=[\\d]+"
static String
REGEX_SPECTRA_REF_SPECTRUM
ConstantREGEX_SPECTRA_REF_SPECTRUM = "spectrum=[\\d]+"
static String
REGEX_SPECTRA_REF_THERMO_NATIVE
ConstantREGEX_SPECTRA_REF_THERMO_NATIVE = "controllerType=[\\d]+ controllerNumber=[1-9]\\d* scan=[1-9]\\d*"
static String
REGEX_SPECTRA_REF_WATERS_NATIVE
ConstantREGEX_SPECTRA_REF_WATERS_NATIVE = "function=[1-9]\\d* process=[\\d]+ scan=[\\d]+"
static String
REGEX_SPECTRA_REF_WIFF_NATIVE
ConstantREGEX_SPECTRA_REF_WIFF_NATIVE = "sample=[\\d]+ period=[\\d]+ cycle=[\\d]+ experiment=[\\d]+"
static String
REGEX_STUDY_VARIABLE_COLUMN_NAME
ConstantREGEX_STUDY_VARIABLE_COLUMN_NAME="study_variable\\[(\\d+)\\]"
static char
TAB
ConstantTAB=' '
static String
TAB_STRING
ConstantTABs=""+' '
static String
VERSION_MZTAB_M
ConstantVERSION="2.0.0-M"
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Constructor Summary
Constructors Constructor Description MZTabConstants()
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Field Detail
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NEW_LINE
public static final String NEW_LINE
ConstantNEW_LINE="System.getProperty(line.separator)"
- See Also:
- Constant Field Values
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NULL
public static final String NULL
ConstantNULL="null"
- See Also:
- Constant Field Values
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INFINITY
public static final String INFINITY
ConstantINFINITY="INF"
- See Also:
- Constant Field Values
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CALCULATE_ERROR
public static final String CALCULATE_ERROR
ConstantCALCULATE_ERROR="NaN"
- See Also:
- Constant Field Values
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TAB
public static final char TAB
ConstantTAB=' '
- See Also:
- Constant Field Values
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TAB_STRING
public static final String TAB_STRING
ConstantTABs=""+' '
- See Also:
- Constant Field Values
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MINUS
public static final char MINUS
ConstantMINUS='-'
- See Also:
- Constant Field Values
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BAR
public static final char BAR
ConstantBAR='|'
- See Also:
- Constant Field Values
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BAR_S
public static final String BAR_S
ConstantBAR='|'
- See Also:
- Constant Field Values
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COLON
public static final char COLON
ConstantCOLON=':'
- See Also:
- Constant Field Values
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COMMA
public static final char COMMA
ConstantCOMMA=','
- See Also:
- Constant Field Values
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VERSION_MZTAB_M
public static final String VERSION_MZTAB_M
ConstantVERSION="2.0.0-M"
- See Also:
- Constant Field Values
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OPT_PREFIX
public static final String OPT_PREFIX
ConstantOPT_PREFIX="opt_"
- See Also:
- Constant Field Values
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ABUNDANCE_PREFIX
public static final String ABUNDANCE_PREFIX
ConstantABUNDANCE_PREFIX="abundance_"
- See Also:
- Constant Field Values
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GLOBAL
public static final String GLOBAL
ConstantGLOBAL="global"
- See Also:
- Constant Field Values
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CV_PREFIX
public static final String CV_PREFIX
ConstantCV_PREFIX="cv_"
- See Also:
- Constant Field Values
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REGEX_INDEXED_VALUE
public static final String REGEX_INDEXED_VALUE
ConstantREGEX_INDEXED_VALUE="\\[(\\d+)\\]"
- See Also:
- Constant Field Values
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REGEX_CV_PARAM_OPT_COLUMN_NAME
public static final String REGEX_CV_PARAM_OPT_COLUMN_NAME
ConstantREGEX_CV_PARAM_OPT_COLUMN_NAME="cv(_([A-Za-z0-9\\-\\[\\]:\\.]+))?(_([A-Za-z0-9_\\-\\[\\]:\\.]+)*)"
- See Also:
- Constant Field Values
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REGEX_OPT_COLUMN_NAME
public static final String REGEX_OPT_COLUMN_NAME
ConstantREGEX_OPT_COLUMN_NAME="opt_((assay|study_variable|ms_run)\\[(\\w+)\\]|global)_([A-Za-z0-9_\\-\\[\\]:\\.]+)"
- See Also:
- Constant Field Values
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REGEX_ABUNDANCE_COLUMN_NAME
public static final String REGEX_ABUNDANCE_COLUMN_NAME
ConstantREGEX_ABUNDANCE_COLUMN_NAME="abundance_(.+)"
- See Also:
- Constant Field Values
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REGEX_ABUNDANCE_ASSAY_COLUMN_NAME
public static final String REGEX_ABUNDANCE_ASSAY_COLUMN_NAME
ConstantREGEX_ABUNDANCE_ASSAY_COLUMN_NAME="assay\\[(\\d+)\\]"
- See Also:
- Constant Field Values
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REGEX_STUDY_VARIABLE_COLUMN_NAME
public static final String REGEX_STUDY_VARIABLE_COLUMN_NAME
ConstantREGEX_STUDY_VARIABLE_COLUMN_NAME="study_variable\\[(\\d+)\\]"
- See Also:
- Constant Field Values
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REGEX_NORMAL_METADATA
public static final String REGEX_NORMAL_METADATA
ConstantREGEX_NORMAL_METADATA="(\\w+)(\\[(\\w+)\\])?(-(\\w+)(\\[(\\w+)\\])?)?(-(\\w+))?"
- See Also:
- Constant Field Values
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REGEX_EMAIL
public static final String REGEX_EMAIL
ConstantREGEX_EMAIL="[_A-Za-z0-9-]+(\\.[_A-Za-z0-9-']+)*@[A-Za-z0-9]+(?:[-.][A-Za-z0-9]+)*(\\.[A-Za-z]{2,})"
- See Also:
- Constant Field Values
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REGEX_MZTAB_M
public static final String REGEX_MZTAB_M
ConstantREGEX_MZTAB_M="(?<major>[2]{1})\\.(?<minor>\\d{1})\\.(?<micro>\\d{1})-(?<profile>[M]{1})"
- See Also:
- Constant Field Values
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REGEX_PARAM_SPLIT
public static final String REGEX_PARAM_SPLIT
ConstantREGEX_PARAM_SPLIT=",(?=([^\"]*\"[^\"]*\")*[^\"]*$)"
- See Also:
- Constant Field Values
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REGEX_DEFAULT_RELIABILITY
public static final String REGEX_DEFAULT_RELIABILITY
ConstantREGEX_DEFAULT_RELIABILITY="[1234]{1}"
- See Also:
- Constant Field Values
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REGEX_ADDUCT
public static final String REGEX_ADDUCT
ConstantREGEX_ADDUCT="^\[\d*M([+-][\w\d]+)*\]\d*[+-]$"
- See Also:
- Constant Field Values
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REGEX_SPECTRA_REF_THERMO_NATIVE
public static final String REGEX_SPECTRA_REF_THERMO_NATIVE
ConstantREGEX_SPECTRA_REF_THERMO_NATIVE = "controllerType=[\\d]+ controllerNumber=[1-9]\\d* scan=[1-9]\\d*"
- See Also:
- Constant Field Values
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REGEX_SPECTRA_REF_WATERS_NATIVE
public static final String REGEX_SPECTRA_REF_WATERS_NATIVE
ConstantREGEX_SPECTRA_REF_WATERS_NATIVE = "function=[1-9]\\d* process=[\\d]+ scan=[\\d]+"
- See Also:
- Constant Field Values
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REGEX_SPECTRA_REF_WIFF_NATIVE
public static final String REGEX_SPECTRA_REF_WIFF_NATIVE
ConstantREGEX_SPECTRA_REF_WIFF_NATIVE = "sample=[\\d]+ period=[\\d]+ cycle=[\\d]+ experiment=[\\d]+"
- See Also:
- Constant Field Values
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REGEX_SPECTRA_REF_INDEX
public static final String REGEX_SPECTRA_REF_INDEX
ConstantREGEX_SPECTRA_REF_INDEX = "index=[\\d]+"
- See Also:
- Constant Field Values
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REGEX_SPECTRA_REF_FILE
public static final String REGEX_SPECTRA_REF_FILE
ConstantREGEX_SPECTRA_REF_FILE = "file=[\\w]+"
- See Also:
- Constant Field Values
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REGEX_SPECTRA_REF_SPECTRUM
public static final String REGEX_SPECTRA_REF_SPECTRUM
ConstantREGEX_SPECTRA_REF_SPECTRUM = "spectrum=[\\d]+"
- See Also:
- Constant Field Values
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REGEX_SPECTRA_REF_MZML_UNIQUE
public static final String REGEX_SPECTRA_REF_MZML_UNIQUE
ConstantREGEX_SPECTRA_REF_MZML_UNIQUE = "[\\w]+"
- See Also:
- Constant Field Values
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REGEX_SPECTRA_REF_SCAN
public static final String REGEX_SPECTRA_REF_SCAN
ConstantREGEX_SPECTRA_REF_SCAN = "scan=[\\d]+"
- See Also:
- Constant Field Values
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Constructor Detail
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MZTabConstants
public MZTabConstants()
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