001package uk.ac.ebi.pride.jmztab2.model;
002
003/**
004 * Define a couple of constants used in the jmzTab API.
005 *
006 * @author qingwei
007 * @author nilshoffmann
008 * @since 08/03/13
009 * 
010 */
011public final class MZTabConstants {
012    /** Constant <code>NEW_LINE="System.getProperty(line.separator)"</code> */
013    public static final String NEW_LINE = "\r\n";//System.getProperty("line.separator");
014    /** Constant <code>NULL="null"</code> */
015    public static final String NULL = "null";
016    /** Constant <code>INFINITY="INF"</code> */
017    public static final String INFINITY = "INF";
018    /** Constant <code>CALCULATE_ERROR="NaN"</code> */
019    public static final String CALCULATE_ERROR = "NaN";
020
021    /** Constant <code>TAB='\u0009'</code> */
022    public static final char TAB = '\u0009';
023    /** Constant <code>TABs=""+'\u0009'</code> */
024    public static final String TAB_STRING = ""+TAB;
025    /** Constant <code>MINUS='-'</code> */
026    public static final char MINUS = '-';
027    /** Constant <code>BAR='\u007c'</code> */
028    public static final char BAR = '\u007c';
029    /** Constant <code>BAR='\u007c'</code> */
030    public static final String BAR_S = ""+BAR;
031    /** Constant <code>COLON=':'</code> */
032    public static final char COLON = ':';
033    /** Constant <code>COMMA=','</code> */
034    public static final char COMMA = ',';
035    /** Constant <code>VERSION="2.0.0-M"</code> */
036    public static final String VERSION_MZTAB_M = "2.0.0-M";
037    /** Constant <code>OPT_PREFIX="opt_"</code> */
038    public static final String OPT_PREFIX = "opt_";
039    /** Constant <code>ABUNDANCE_PREFIX="abundance_"</code> */
040    public static final String ABUNDANCE_PREFIX = "abundance_";
041    /** Constant <code>GLOBAL="global"</code> */
042    public static final String GLOBAL = "global";
043    /** Constant <code>CV_PREFIX="cv_"</code> */
044    public static final String CV_PREFIX = "cv_";
045    
046    /*
047     Regular expressions that are not directly applicable to domain objects.
048    */
049    /** Constant <code>REGEX_INDEXED_VALUE="\\[(\\d+)\\]"</code> */
050    public static final String REGEX_INDEXED_VALUE = "\\[(\\d+)\\]";
051    /** Constant <code>REGEX_CV_PARAM_OPT_COLUMN_NAME="cv(_([A-Za-z0-9\\-\\[\\]:\\.]+))?(_([A-Za-z0-9_\\-\\[\\]:\\.]+)*)"</code> */
052    public static final String REGEX_CV_PARAM_OPT_COLUMN_NAME = "cv(_([A-Za-z0-9\\-\\[\\]:\\.]+))?(_([A-Za-z0-9_\\-\\[\\]:\\.]+)*)";
053    /** Constant <code>REGEX_OPT_COLUMN_NAME="opt_((assay|study_variable|ms_run)\\[(\\w+)\\]|global)_([A-Za-z0-9_\\-\\[\\]:\\.]+)"</code> */
054    public static final String REGEX_OPT_COLUMN_NAME = "opt_((assay|study_variable|ms_run)\\[(\\w+)\\]|global)_([A-Za-z0-9_\\-\\[\\]:\\.]+)";
055    /** Constant <code>REGEX_ABUNDANCE_COLUMN_NAME="abundance_(.+)"</code> */
056    public static final String REGEX_ABUNDANCE_COLUMN_NAME = "abundance_(.+)";
057    /** Constant <code>REGEX_ABUNDANCE_ASSAY_COLUMN_NAME="assay\\[(\\d+)\\]"</code> */
058    public static final String REGEX_ABUNDANCE_ASSAY_COLUMN_NAME = "assay"+REGEX_INDEXED_VALUE;
059    /** Constant <code>REGEX_STUDY_VARIABLE_COLUMN_NAME="study_variable\\[(\\d+)\\]"</code> */
060    public static final String REGEX_STUDY_VARIABLE_COLUMN_NAME = "study_variable"+REGEX_INDEXED_VALUE;
061    /** Constant <code>REGEX_NORMAL_METADATA="(\\w+)(\\[(\\w+)\\])?(-(\\w+)(\\[(\\w+)\\])?)?(-(\\w+))?"</code> */
062    public static final String REGEX_NORMAL_METADATA = "(\\w+)(\\[(\\w+)\\])?(-(\\w+)(\\[(\\w+)\\])?)?(-(\\w+))?";
063    /** Constant <code>REGEX_EMAIL="[_A-Za-z0-9-]+(\\.[_A-Za-z0-9-']+)*@[A-Za-z0-9]+(?:[-.][A-Za-z0-9]+)*(\\.[A-Za-z]{2,})"</code> */
064    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,})";
065    /** Constant {@code REGEX_MZTAB_M="(?<major>[2]{1})\\.(?<minor>\\d{1})\\.(?<micro>\\d{1})-(?<profile>[M]{1})"} */
066    public static final String REGEX_MZTAB_M = "(?<major>[2]{1})\\.(?<minor>\\d{1})\\.(?<micro>\\d{1})-(?<profile>[M]{1})";
067    /** Constant <code>REGEX_PARAM_SPLIT=",(?=([^\"]*\"[^\"]*\")*[^\"]*$)"</code> */
068    public static final String REGEX_PARAM_SPLIT = ",(?=([^\"]*\"[^\"]*\")*[^\"]*$)";
069    /** Constant <code>REGEX_DEFAULT_RELIABILITY="[1234]{1}"</code> */
070    public static final String REGEX_DEFAULT_RELIABILITY = "[1234]{1}";
071    /** More complex for isotopes: \[\d*M([\w\d]+)*([+-][\w\d]+)*\]\d*[+-] **/
072    /** Constant <code>REGEX_ADDUCT="^\[\d*M([+-][\w\d]+)*\]\d*[+-]$"</code> */
073    public static final String REGEX_ADDUCT = "^\\[\\d*M([+-][\\w\\d]+)*\\]\\d*[+-]$";
074    
075    /** Constant <code>REGEX_SPECTRA_REF_THERMO_NATIVE = "controllerType=[\\d]+ controllerNumber=[1-9]\\d* scan=[1-9]\\d*"</code> */
076    public static final String REGEX_SPECTRA_REF_THERMO_NATIVE = "controllerType=[\\d]+ controllerNumber=[1-9]\\d* scan=[1-9]\\d*";
077    /** Constant <code>REGEX_SPECTRA_REF_WATERS_NATIVE = "function=[1-9]\\d* process=[\\d]+ scan=[\\d]+"</code> */
078    public static final String REGEX_SPECTRA_REF_WATERS_NATIVE = "function=[1-9]\\d* process=[\\d]+ scan=[\\d]+";
079    /** Constant <code>REGEX_SPECTRA_REF_WIFF_NATIVE = "sample=[\\d]+ period=[\\d]+ cycle=[\\d]+ experiment=[\\d]+"</code> */
080    public static final String REGEX_SPECTRA_REF_WIFF_NATIVE = "sample=[\\d]+ period=[\\d]+ cycle=[\\d]+ experiment=[\\d]+";
081//    /** Constant <code>REGEX_SPECTRA_REF_SCIEX_TOF_TOF_NATIVE = "jobRun=[\\d]+ spotLabel=[\\d]+ spectrum=[\\d]+"</code> */
082//    public static final String REGEX_SPECTRA_REF_SCIEX_TOF_TOF_NATIVE = "jobRun=[\\d]+ spotLabel=[\\w]+ spectrum=[\\d]+";
083    /** Constant <code>REGEX_SPECTRA_REF_INDEX = "index=[\\d]+"</code> */
084    public static final String REGEX_SPECTRA_REF_INDEX = "index=[\\d]+";
085    /** Constant <code>REGEX_SPECTRA_REF_FILE = "file=[\\w]+"</code> */
086    public static final String REGEX_SPECTRA_REF_FILE = "file=[\\w]+";
087    /** Constant <code>REGEX_SPECTRA_REF_SPECTRUM = "spectrum=[\\d]+"</code> */
088    public static final String REGEX_SPECTRA_REF_SPECTRUM = "spectrum=[\\d]+";
089    /** Constant <code>REGEX_SPECTRA_REF_MZML_UNIQUE = "[\\w]+"</code> */
090    public static final String REGEX_SPECTRA_REF_MZML_UNIQUE = "[\\w]+";
091    /** Constant <code>REGEX_SPECTRA_REF_SCAN = "scan=[\\d]+"</code> */
092    public static final String REGEX_SPECTRA_REF_SCAN = "scan=[\\d]+";
093}