Package uk.ac.ebi.pride.jmztab2.model

Class MZTabConstants

  • public final class MZTabConstants
extends java.lang.Object
    Define a couple of constants used in the jmzTab API.
    Since:
    08/03/13
    Author:
    qingwei, nilshoffmann

    • Field Summary

      Fields 
      Modifier and Type Field Description
      static java.lang.String ABUNDANCE_PREFIX
      Constant ABUNDANCE_PREFIX="abundance_"
      static char BAR
      Constant BAR='|'
      static java.lang.String BAR_S
      Constant BAR='|'
      static java.lang.String CALCULATE_ERROR
      Constant CALCULATE_ERROR="NaN"
      static char COLON
      Constant COLON=':'
      static char COMMA
      Constant COMMA=','
      static java.lang.String CV_PREFIX
      Constant CV_PREFIX="cv_"
      static java.lang.String GLOBAL
      Constant GLOBAL="global"
      static java.lang.String INFINITY
      Constant INFINITY="INF"
      static char MINUS
      Constant MINUS='-'
      static java.lang.String NEW_LINE
      Constant NEW_LINE="System.getProperty(line.separator)"
      static java.lang.String NULL
      Constant NULL="null"
      static java.lang.String OPT_PREFIX
      Constant OPT_PREFIX="opt_"
      static java.lang.String REGEX_ABUNDANCE_ASSAY_COLUMN_NAME
      Constant REGEX_ABUNDANCE_ASSAY_COLUMN_NAME="assay\\[(\\d+)\\]"
      static java.lang.String REGEX_ABUNDANCE_COLUMN_NAME
      Constant REGEX_ABUNDANCE_COLUMN_NAME="abundance_(.+)"
      static java.lang.String REGEX_ADDUCT
      Constant REGEX_ADDUCT="^\[\d*M([+-][\w\d]+)*\]\d*[+-]$"
      static java.lang.String REGEX_CV_PARAM_OPT_COLUMN_NAME
      Constant REGEX_CV_PARAM_OPT_COLUMN_NAME="cv(_([A-Za-z0-9\\-\\[\\]:\\.]+))?
      static java.lang.String REGEX_DEFAULT_RELIABILITY
      Constant REGEX_DEFAULT_RELIABILITY="[1234]{1}"
      static java.lang.String REGEX_EMAIL
      Constant REGEX_EMAIL="[_A-Za-z0-9-]+(\\.
      static java.lang.String REGEX_INDEXED_VALUE
      Constant REGEX_INDEXED_VALUE="\\[(\\d+)\\]"
      static java.lang.String REGEX_MZTAB_M
      Constant REGEX_MZTAB_M="(?<major>[2]{1})\\.(?<minor>\\d{1})\\.(?<micro>\\d{1})-(?<profile>[M]{1})"
      static java.lang.String REGEX_NORMAL_METADATA
      Constant REGEX_NORMAL_METADATA="(\\w+)(\\[(\\w+)\\])?
      static java.lang.String REGEX_OPT_COLUMN_NAME
      Constant REGEX_OPT_COLUMN_NAME="opt_((assay|study_variable|ms_run)\\[(\\w+)\\]|global)_([A-Za-z0-9_\\-\\[\\]:\\.]+)"
      static java.lang.String REGEX_PARAM_SPLIT
      Constant REGEX_PARAM_SPLIT=",(?
      static java.lang.String REGEX_STUDY_VARIABLE_COLUMN_NAME
      Constant REGEX_STUDY_VARIABLE_COLUMN_NAME="study_variable\\[(\\d+)\\]"
      static char TAB
      Constant TAB=' '
      static java.lang.String TAB_STRING
      Constant TABs=""+' '
      static java.lang.String VERSION_MZTAB_M
      Constant VERSION="2.0.0-M"

    • Constructor Summary

      Constructors 
      Constructor Description
      MZTabConstants()  

    • Method Summary

      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

    • Field Detail

      • NEW_LINE

        public static final java.lang.String NEW_LINE
        Constant NEW_LINE="System.getProperty(line.separator)"
        See Also:
        Constant Field Values

      • INFINITY

        public static final java.lang.String INFINITY
        Constant INFINITY="INF"
        See Also:
        Constant Field Values

      • CALCULATE_ERROR

        public static final java.lang.String CALCULATE_ERROR
        Constant CALCULATE_ERROR="NaN"
        See Also:
        Constant Field Values

      • TAB_STRING

        public static final java.lang.String TAB_STRING
        Constant TABs=""+' '
        See Also:
        Constant Field Values

      • VERSION_MZTAB_M

        public static final java.lang.String VERSION_MZTAB_M
        Constant VERSION="2.0.0-M"
        See Also:
        Constant Field Values

      • OPT_PREFIX

        public static final java.lang.String OPT_PREFIX
        Constant OPT_PREFIX="opt_"
        See Also:
        Constant Field Values

      • ABUNDANCE_PREFIX

        public static final java.lang.String ABUNDANCE_PREFIX
        Constant ABUNDANCE_PREFIX="abundance_"
        See Also:
        Constant Field Values

      • GLOBAL

        public static final java.lang.String GLOBAL
        Constant GLOBAL="global"
        See Also:
        Constant Field Values

      • CV_PREFIX

        public static final java.lang.String CV_PREFIX
        Constant CV_PREFIX="cv_"
        See Also:
        Constant Field Values

      • REGEX_INDEXED_VALUE

        public static final java.lang.String REGEX_INDEXED_VALUE
        Constant REGEX_INDEXED_VALUE="\\[(\\d+)\\]"
        See Also:
        Constant Field Values

      • REGEX_CV_PARAM_OPT_COLUMN_NAME

        public static final java.lang.String REGEX_CV_PARAM_OPT_COLUMN_NAME
        Constant REGEX_CV_PARAM_OPT_COLUMN_NAME="cv(_([A-Za-z0-9\\-\\[\\]:\\.]+))?(_([A-Za-z0-9_\\-\\[\\]:\\.]+)*)"
        See Also:
        Constant Field Values

      • REGEX_OPT_COLUMN_NAME

        public static final java.lang.String REGEX_OPT_COLUMN_NAME
        Constant REGEX_OPT_COLUMN_NAME="opt_((assay|study_variable|ms_run)\\[(\\w+)\\]|global)_([A-Za-z0-9_\\-\\[\\]:\\.]+)"
        See Also:
        Constant Field Values

      • REGEX_ABUNDANCE_COLUMN_NAME

        public static final java.lang.String REGEX_ABUNDANCE_COLUMN_NAME
        Constant REGEX_ABUNDANCE_COLUMN_NAME="abundance_(.+)"
        See Also:
        Constant Field Values

      • REGEX_ABUNDANCE_ASSAY_COLUMN_NAME

        public static final java.lang.String REGEX_ABUNDANCE_ASSAY_COLUMN_NAME
        Constant REGEX_ABUNDANCE_ASSAY_COLUMN_NAME="assay\\[(\\d+)\\]"
        See Also:
        Constant Field Values

      • REGEX_STUDY_VARIABLE_COLUMN_NAME

        public static final java.lang.String REGEX_STUDY_VARIABLE_COLUMN_NAME
        Constant REGEX_STUDY_VARIABLE_COLUMN_NAME="study_variable\\[(\\d+)\\]"
        See Also:
        Constant Field Values

      • REGEX_NORMAL_METADATA

        public static final java.lang.String REGEX_NORMAL_METADATA
        Constant REGEX_NORMAL_METADATA="(\\w+)(\\[(\\w+)\\])?(-(\\w+)(\\[(\\w+)\\])?)?(-(\\w+))?"
        See Also:
        Constant Field Values

      • REGEX_EMAIL

        public static final java.lang.String REGEX_EMAIL
        Constant REGEX_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

      • REGEX_MZTAB_M

        public static final java.lang.String REGEX_MZTAB_M
        Constant REGEX_MZTAB_M="(?<major>[2]{1})\\.(?<minor>\\d{1})\\.(?<micro>\\d{1})-(?<profile>[M]{1})"
        See Also:
        Constant Field Values

      • REGEX_PARAM_SPLIT

        public static final java.lang.String REGEX_PARAM_SPLIT
        Constant REGEX_PARAM_SPLIT=",(?=([^\"]*\"[^\"]*\")*[^\"]*$)"
        See Also:
        Constant Field Values

      • REGEX_DEFAULT_RELIABILITY

        public static final java.lang.String REGEX_DEFAULT_RELIABILITY
        Constant REGEX_DEFAULT_RELIABILITY="[1234]{1}"
        See Also:
        Constant Field Values

      • REGEX_ADDUCT

        public static final java.lang.String REGEX_ADDUCT
        Constant REGEX_ADDUCT="^\[\d*M([+-][\w\d]+)*\]\d*[+-]$"
        See Also:
        Constant Field Values

    • Constructor Detail

      • MZTabConstants

        public MZTabConstants()