annotate resources/XSeeker/config/models.R @ 0:15c9fbefeaf1 draft

" master branch Updating"

tryCatch({
    DBModelR::ModelDefinition(table="yui", fields=list(yui="INTEGER"))
}, error=function(e) {
    stop("Please, install DBModelR before you source this file.")
})

list(
    adduct=DBModelR::ModelDefinition(
        table="adduct",
        fields=list(
            name="TEXT",
            mass="FLOAT",
            charge="INTEGER",
            multi="INTEGER",
            formula_add="TEXT",
            formula_ded="TEXT",
            sign="TEXT",
            oidscore="INTEGER",
            quasi="INTEGER",
            ips="FLOAT"
        )
    ),
    cluster=DBModelR::ModelDefinition(
        table="cluster",
        fields=list(
            clusterID="INTEGER",
            formula="TEXT",
            annotation="TEXT",
            coeff="FLOAT",
            r_squared="FLOAT",
            charge="INTEGER",
            mean_rt="FLOAT",
            score="FLOAT",
            deviation="FLOAT",
            status="TEXT",
            # adduct="TEXT",
            curent_group="INTEGER",
            pc_group="INTEGER",
            align_group="INTEGER",
            xcms_group="INTEGER"
        ),
        one=list("compound", "adduct"),
        many=list("sample")
    ),
    compound=DBModelR::ModelDefinition(
        table="compound",
        fields=list(
            name="TEXT",
            common_name="TEXT",
            formula="TEXT",
            charge="INTEGER",
            date="TEXT",
            mz="FLOAT"
        )
    ),
    feature=DBModelR::ModelDefinition(
        table="feature",
        fields=list(
            featureID="INTEGER",
            mz="FLOAT",
            mz_min="FLOAT",
            mz_max="FLOAT",
            rt="FLOAT",
            rt_min="FLOAT",
            rt_max="FLOAT",
            int_o="FLOAT",
            int_b="FLOAT",
            max_o="FLOAT",
            iso="TEXT",
            abundance="FLOAT"
        ),
        one=list("cluster"),
        many=list("sample")
    ),
    instrument=DBModelR::ModelDefinition(
        table="instrument",
        fields=list(
            model="TEXT",
            manufacturer="TEXT",
            analyzer="TEXT",
            detector_type="TEXT",
            ion_source="TEXT"
        )
    ),
    instrument_config=DBModelR::ModelDefinition(
        table="instrument_config",
        fields=list(
            resolution="TEXT",
            agc_target="TEXT",
            maximum_IT="TEXT",
            number_of_scan_range="TEXT",
            scan_range="TEXT",
            version="TEXT"
        )
    ),
    project=DBModelR::ModelDefinition(
        table="project",
        fields=list(
            name="TEXT",
            comment="TEXT"
        ),
        one=list("sample")
    ),
    sample=DBModelR::ModelDefinition(
        table="sample",
        fields=list(
            name="TEXT",
            path="TEXT",
            polarity="TEXT",
            kind="TEXT", ## rdata or mxml or enriched_rdata
            raw="BLOB"
        ),
        one=list(
            "peak_picking_parameters",
            "pairing_parameters",
            "alignmenmt_parameters",
            "camera_parameters",
            "instrument",
            "instrument_config",
            "software",
            "smol_xcms_set"
        )
    ),
    smol_xcms_set=DBModelR::ModelDefinition(
        table="smol_xcms_set",
        fields=list(
            raw="BLOB"
        )
    ),
    software=DBModelR::ModelDefinition(
        table="software",
        fields=list(
            name="TEXT",
            version="TEXT"
        )
    ),
    # camera_parameters=DBModelR::ModelDefinition(
    #     table="camera_parameters",
    #     fields=list()
    # ),
    # pairing_parameters=DBModelR::ModelDefinition(
    #     table="pairing_parameters",
    #     fields=list()
    # ),
    peak_picking_parameters=DBModelR::ModelDefinition(
        table="peak_picking_parameters",
        fields=list(
            ppm="FLOAT",
            peakwidth="TEXT",
            snthresh="TEXT",
            prefilterStep="TEXT",
            prefilterLevel="TEXT",
            mzdiff="TEXT",
            fitgauss="TEXT",
            noise="TEXT",
            mzCenterFun="TEXT",
            integrate="INTEGER",
            firstBaselineCheck="TEXT",
            snthreshIsoROIs="TEXT",
            maxCharge="INTEGER",
            maxIso="INTEGER",
            mzIntervalExtension="TEXT"
        )
    ),
    alignmenmt_parameters=DBModelR::ModelDefinition(
        table="alignmenmt_parameters",
        fields=list(
            binSize="TEXT",
            centerSample="TEXT",
            response="TEXT",
            distFun="TEXT",
            gapInit="TEXT",
            gapExtend="TEXT",
            factorDiag="TEXT",
            factorGap="TEXT",
            localAlignment="INTEGER",
            initPenalty="TEXT",
            bw="TEXT",
            minFraction="TEXT",
            minSamples="TEXT",
            maxFeatures="TEXT"
        )
    )
)