bdb 0.0.1

Efficient APIs to parse from and export to file formats commonly used in biology, for both proteomics and genetics workflows.
Documentation 
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//! Shared helper utilities for mass spectra unit testing.

use super::peak::Peak;
use super::record::Record;

// RECORDS

/// Create a record from a sample MGF scan.
pub fn mgf_33450() -> Record {
    Record {
        num: 33450,
        ms_level: 0,
        rt: 8692.,
        parent_mz: 775.15625,
        parent_intensity: 170643.953125,
        parent_z: 4,
        file: String::from("QPvivo_2015_11_10_1targetmethod"),
        filter: String::from(""),
        peaks: vec![
            Peak { mz: 205.9304178, intensity: 0.0, z: 0 },
            Peak { mz: 205.9320046, intensity: 0.0, z: 0 },
            Peak { mz: 205.9335913, intensity: 0.0, z: 0 },
            Peak { mz: 205.9351781, intensity: 0.0, z: 0 },
            Peak { mz: 257.514984, intensity: 0.0, z: 0 },
            Peak { mz: 257.5172029, intensity: 0.0, z: 0 },
            Peak { mz: 257.5194218, intensity: 0.0, z: 0 },
            Peak { mz: 257.5216407, intensity: 0.0, z: 0 },
            Peak { mz: 257.5238596, intensity: 457.499206543, z: 0 },
            Peak { mz: 257.5260786, intensity: 742.1607666016, z: 0 },
            Peak { mz: 257.5282976, intensity: 832.3284301758, z: 0 },
            Peak { mz: 257.5305166, intensity: 666.099609375, z: 0 },
            Peak { mz: 257.5327357, intensity: 353.6197509766, z: 0 },
            Peak { mz: 257.5349181, intensity: 0.0, z: 0 },
            Peak { mz: 257.5371372, intensity: 0.0, z: 0 },
            Peak { mz: 257.5393564, intensity: 0.0, z: 0 },
            Peak { mz: 257.5415756, intensity: 0.0, z: 0 },
            Peak { mz: 266.3775252, intensity: 0.0, z: 0 },
            Peak { mz: 266.3798596, intensity: 0.0, z: 0 },
            Peak { mz: 266.382194, intensity: 0.0, z: 0 },
            Peak { mz: 266.3845284, intensity: 0.0, z: 0 },
            Peak { mz: 266.3868629, intensity: 395.335723877, z: 0 },
            Peak { mz: 266.3891974, intensity: 687.4059448242, z: 0 },
            Peak { mz: 266.3915319, intensity: 839.1334228516, z: 0 },
            Peak { mz: 266.3938665, intensity: 753.7129516602, z: 0 },
            Peak { mz: 266.3962011, intensity: 483.698425293, z: 0 },
            Peak { mz: 266.3985627, intensity: 0.0, z: 0 },
            Peak { mz: 266.4008973, intensity: 0.0, z: 0 },
            Peak { mz: 266.403232, intensity: 0.0, z: 0 },
            Peak { mz: 266.4055668, intensity: 0.0, z: 0 },
            Peak { mz: 274.490484, intensity: 0.0, z: 0 },
            Peak { mz: 274.4929259, intensity: 0.0, z: 0 },
            Peak { mz: 274.4953677, intensity: 0.0, z: 0 },
            Peak { mz: 274.4978097, intensity: 0.0, z: 0 },
            Peak { mz: 274.5002516, intensity: 359.3305664063, z: 0 },
            Peak { mz: 274.5026936, intensity: 691.2191162109, z: 0 },
            Peak { mz: 274.5051356, intensity: 1342.998046875, z: 0 },
            Peak { mz: 274.5075776, intensity: 1104.1827392578, z: 0 },
            Peak { mz: 274.5100197, intensity: 459.472442627, z: 0 },
            Peak { mz: 274.5124333, intensity: 0.0, z: 0 },
            Peak { mz: 274.5148754, intensity: 0.0, z: 0 },
            Peak { mz: 274.5173176, intensity: 0.0, z: 0 },
            Peak { mz: 274.5197598, intensity: 0.0, z: 0 },
            Peak { mz: 288.185445, intensity: 0.0, z: 0 },
            Peak { mz: 288.1880718, intensity: 0.0, z: 0 },
            Peak { mz: 288.1906987, intensity: 0.0, z: 0 },
            Peak { mz: 288.1933256, intensity: 0.0, z: 0 },
            Peak { mz: 288.1959526, intensity: 513.036315918, z: 0 },
            Peak { mz: 288.1985796, intensity: 1173.0286865234, z: 0 },
            Peak { mz: 288.2012066, intensity: 1705.58203125, z: 0 },
            Peak { mz: 288.2038337, intensity: 1740.2529296875, z: 0 },
            Peak { mz: 288.2064608, intensity: 1205.7132568359, z: 0 },
            Peak { mz: 288.2090879, intensity: 441.4267272949, z: 0 },
            Peak { mz: 288.2116643, intensity: 0.0, z: 0 },
            Peak { mz: 288.2142915, intensity: 0.0, z: 0 },
            Peak { mz: 288.2169188, intensity: 0.0, z: 0 },
            Peak { mz: 288.219546, intensity: 0.0, z: 0 },
            Peak { mz: 296.4551094, intensity: 0.0, z: 0 },
            Peak { mz: 296.4578501, intensity: 0.0, z: 0 },
            Peak { mz: 296.4605908, intensity: 0.0, z: 0 },
            Peak { mz: 296.4633316, intensity: 0.0, z: 0 },
            Peak { mz: 296.4660725, intensity: 195.8185119629, z: 0 },
            Peak { mz: 296.4688134, intensity: 706.2313232422, z: 0 },
            Peak { mz: 296.4715543, intensity: 1314.5838623047, z: 0 },
            Peak { mz: 296.4742952, intensity: 1367.2843017578, z: 0 },
            Peak { mz: 296.4770362, intensity: 595.6688842773, z: 0 },
            Peak { mz: 296.4797232, intensity: 0.0, z: 0 },
            Peak { mz: 296.4824643, intensity: 0.0, z: 0 },
            Peak { mz: 296.4852054, intensity: 0.0, z: 0 }],
        parent: vec![],
        children: vec![],
    }
}

/// Create a sample empty MGF scan.
pub fn mgf_empty() -> Record {
    Record {
        num: 33450,
        ms_level: 0,
        rt: 8692.,
        parent_mz: 775.15625,
        parent_intensity: 170643.953125,
        parent_z: 4,
        file: String::from("QPvivo_2015_11_10_1targetmethod"),
        filter: String::from(""),
        peaks: vec![],
        parent: vec![],
        children: vec![]
    }
}

// FULLMS MGF
// TODO(ahuszagh)   Implement...

// MSCONVERT MGF

/// Constant string for the MSConvert sample scan export.
#[cfg(feature = "mgf")]
pub const MSCONVERT_33450_MGF: &'static str = "BEGIN IONS\nTITLE=QPvivo_2015_11_10_1targetmethod.33450.33450.0 File:\"QPvivo_2015_11_10_1targetmethod\", NativeID:\"controllerType=0 controllerNumber=1 scan=33450\"\nRTINSECONDS=8692.0\nPEPMASS=775.15625 170643.953125\nCHARGE=4+\n205.9304178 0.0\n205.9320046 0.0\n205.9335913 0.0\n205.9351781 0.0\n257.514984 0.0\n257.5172029 0.0\n257.5194218 0.0\n257.5216407 0.0\n257.5238596 457.499206543\n257.5260786 742.1607666016\n257.5282976 832.3284301758\n257.5305166 666.099609375\n257.5327357 353.6197509766\n257.5349181 0.0\n257.5371372 0.0\n257.5393564 0.0\n257.5415756 0.0\n266.3775252 0.0\n266.3798596 0.0\n266.382194 0.0\n266.3845284 0.0\n266.3868629 395.335723877\n266.3891974 687.4059448242\n266.3915319 839.1334228516\n266.3938665 753.7129516602\n266.3962011 483.698425293\n266.3985627 0.0\n266.4008973 0.0\n266.403232 0.0\n266.4055668 0.0\n274.490484 0.0\n274.4929259 0.0\n274.4953677 0.0\n274.4978097 0.0\n274.5002516 359.3305664063\n274.5026936 691.2191162109\n274.5051356 1342.998046875\n274.5075776 1104.1827392578\n274.5100197 459.472442627\n274.5124333 0.0\n274.5148754 0.0\n274.5173176 0.0\n274.5197598 0.0\n288.185445 0.0\n288.1880718 0.0\n288.1906987 0.0\n288.1933256 0.0\n288.1959526 513.036315918\n288.1985796 1173.0286865234\n288.2012066 1705.58203125\n288.2038337 1740.2529296875\n288.2064608 1205.7132568359\n288.2090879 441.4267272949\n288.2116643 0.0\n288.2142915 0.0\n288.2169188 0.0\n288.219546 0.0\n296.4551094 0.0\n296.4578501 0.0\n296.4605908 0.0\n296.4633316 0.0\n296.4660725 195.8185119629\n296.4688134 706.2313232422\n296.4715543 1314.5838623047\n296.4742952 1367.2843017578\n296.4770362 595.6688842773\n296.4797232 0.0\n296.4824643 0.0\n296.4852054 0.0\nEND IONS\n";

/// Constant string for the MSConvert empty scan export.
#[cfg(feature = "mgf")]
pub const MSCONVERT_EMPTY_MGF: &'static str = "BEGIN IONS\nTITLE=QPvivo_2015_11_10_1targetmethod.33450.33450.0 File:\"QPvivo_2015_11_10_1targetmethod\", NativeID:\"controllerType=0 controllerNumber=1 scan=33450\"\nRTINSECONDS=8692.0\nPEPMASS=775.15625 170643.953125\nCHARGE=4+\nEND IONS\n";

// PAVA MGF

/// Constant string for the Pava sample scan export.
#[cfg(feature = "mgf")]
pub const PAVA_33450_MGF: &'static str = "BEGIN IONS\nTITLE=Scan 33450 (rt=8692.0) [QPvivo_2015_11_10_1targetmethod]\nPEPMASS=775.15625\t170643.953125\nCHARGE=4+\n205.9304178\t0.0\n205.9320046\t0.0\n205.9335913\t0.0\n205.9351781\t0.0\n257.514984\t0.0\n257.5172029\t0.0\n257.5194218\t0.0\n257.5216407\t0.0\n257.5238596\t457.499206543\n257.5260786\t742.1607666016\n257.5282976\t832.3284301758\n257.5305166\t666.099609375\n257.5327357\t353.6197509766\n257.5349181\t0.0\n257.5371372\t0.0\n257.5393564\t0.0\n257.5415756\t0.0\n266.3775252\t0.0\n266.3798596\t0.0\n266.382194\t0.0\n266.3845284\t0.0\n266.3868629\t395.335723877\n266.3891974\t687.4059448242\n266.3915319\t839.1334228516\n266.3938665\t753.7129516602\n266.3962011\t483.698425293\n266.3985627\t0.0\n266.4008973\t0.0\n266.403232\t0.0\n266.4055668\t0.0\n274.490484\t0.0\n274.4929259\t0.0\n274.4953677\t0.0\n274.4978097\t0.0\n274.5002516\t359.3305664063\n274.5026936\t691.2191162109\n274.5051356\t1342.998046875\n274.5075776\t1104.1827392578\n274.5100197\t459.472442627\n274.5124333\t0.0\n274.5148754\t0.0\n274.5173176\t0.0\n274.5197598\t0.0\n288.185445\t0.0\n288.1880718\t0.0\n288.1906987\t0.0\n288.1933256\t0.0\n288.1959526\t513.036315918\n288.1985796\t1173.0286865234\n288.2012066\t1705.58203125\n288.2038337\t1740.2529296875\n288.2064608\t1205.7132568359\n288.2090879\t441.4267272949\n288.2116643\t0.0\n288.2142915\t0.0\n288.2169188\t0.0\n288.219546\t0.0\n296.4551094\t0.0\n296.4578501\t0.0\n296.4605908\t0.0\n296.4633316\t0.0\n296.4660725\t195.8185119629\n296.4688134\t706.2313232422\n296.4715543\t1314.5838623047\n296.4742952\t1367.2843017578\n296.4770362\t595.6688842773\n296.4797232\t0.0\n296.4824643\t0.0\n296.4852054\t0.0\nEND IONS\n\n";

/// Constant string for the Pava empty scan export.
#[cfg(feature = "mgf")]
pub const PAVA_EMPTY_MGF: &'static str = "BEGIN IONS\nTITLE=Scan 33450 (rt=8692.0) [QPvivo_2015_11_10_1targetmethod]\nPEPMASS=775.15625\t170643.953125\nCHARGE=4+\nEND IONS\n\n";

// PWIZ MGF

/// Constant string for the Pwiz sample scan export.
#[cfg(feature = "mgf")]
pub const PWIZ_33450_MGF: &'static str = "BEGIN IONS\nTITLE=QPvivo_2015_11_10_1targetmethod Spectrum0 scans: 33450\nPEPMASS=775.15625 170643.953125\nCHARGE=4+\nRTINSECONDS=8692\nSCANS=33450\n205.9304178 0.0\n205.9320046 0.0\n205.9335913 0.0\n205.9351781 0.0\n257.514984 0.0\n257.5172029 0.0\n257.5194218 0.0\n257.5216407 0.0\n257.5238596 457.499206543\n257.5260786 742.1607666016\n257.5282976 832.3284301758\n257.5305166 666.099609375\n257.5327357 353.6197509766\n257.5349181 0.0\n257.5371372 0.0\n257.5393564 0.0\n257.5415756 0.0\n266.3775252 0.0\n266.3798596 0.0\n266.382194 0.0\n266.3845284 0.0\n266.3868629 395.335723877\n266.3891974 687.4059448242\n266.3915319 839.1334228516\n266.3938665 753.7129516602\n266.3962011 483.698425293\n266.3985627 0.0\n266.4008973 0.0\n266.403232 0.0\n266.4055668 0.0\n274.490484 0.0\n274.4929259 0.0\n274.4953677 0.0\n274.4978097 0.0\n274.5002516 359.3305664063\n274.5026936 691.2191162109\n274.5051356 1342.998046875\n274.5075776 1104.1827392578\n274.5100197 459.472442627\n274.5124333 0.0\n274.5148754 0.0\n274.5173176 0.0\n274.5197598 0.0\n288.185445 0.0\n288.1880718 0.0\n288.1906987 0.0\n288.1933256 0.0\n288.1959526 513.036315918\n288.1985796 1173.0286865234\n288.2012066 1705.58203125\n288.2038337 1740.2529296875\n288.2064608 1205.7132568359\n288.2090879 441.4267272949\n288.2116643 0.0\n288.2142915 0.0\n288.2169188 0.0\n288.219546 0.0\n296.4551094 0.0\n296.4578501 0.0\n296.4605908 0.0\n296.4633316 0.0\n296.4660725 195.8185119629\n296.4688134 706.2313232422\n296.4715543 1314.5838623047\n296.4742952 1367.2843017578\n296.4770362 595.6688842773\n296.4797232 0.0\n296.4824643 0.0\n296.4852054 0.0\nEND IONS\n\n";

/// Constant string for the Pwiz empty scan export.
#[cfg(feature = "mgf")]
pub const PWIZ_EMPTY_MGF: &'static str = "BEGIN IONS\nTITLE=QPvivo_2015_11_10_1targetmethod Spectrum0 scans: 33450\nPEPMASS=775.15625 170643.953125\nCHARGE=4+\nRTINSECONDS=8692\nSCANS=33450\nEND IONS\n\n";