msparser/help/resfile_input_8cpp-example.html

/*

##############################################################################

# file: resfile_input.cpp                                                    #

# 'msparser' toolkit example code                                            #

##############################################################################

# COPYRIGHT NOTICE                                                           #

# Copyright 1998-2005 Matrix Science Limited  All Rights Reserved.           #

#                                                                            #

##############################################################################

#    $Source: parser/examples/test_cxx/resfile_input.cpp $ #

#     $Author: robertog@matrixscience.com $                                                      #

#       $Date: 2024-09-04 10:23:46 +0100 $                                         #

#   $Revision: 526921a73137894bb1eae0b0fc8ccb4bb52ea662 | MSPARSER_REL_3_0_0-2024-09-24-0-g93ebaeb4f4 $                                                         #

# $NoKeywords::                                                            $ #

##############################################################################

*/

#include "msparser.hpp"

#include <iostream>

#include <vector>


// All the classes are part of the matrix_science namespace

using namespace matrix_science;


/*****************************************************************************/

/* Local functions                                                           */

/* (This test harness is 'C' and not C++)                                    */

/*****************************************************************************/

static void inputData(ms_mascotresfilebase & file);


/*****************************************************************************/

/* main                                                                      */

/* Call this program with a single argument - the name of the .dat file      */

/*****************************************************************************/

int main(int argc, char * argv[])

{

    if (argc == 2)

    {

        ms_mascotresfilebase file = ms_mascotresfilebase::createResfileBase(argv[1]);


        if (file.isValid())

        {

            inputData(file);

        }

        else

            std::cout << "Error: " << file.getLastErrorString() << std::endl;

    }

    else

        std::cout << "Must supply the name of a .dat file as a command line argument" << std::endl;

    return 0;

}


/*****************************************************************************/

/* inputData                                                                 */

/* Display input data                                                        */

/*****************************************************************************/

static void inputData(ms_mascotresfilebase & file)

{

    //display input data via inputquery get functions

    for (int i = 1; i <= 1 /* file.getNumQueries()*/; i++)

    {

        std::cout << "Input data for query number " << i              << std::endl;

        std::cout << "========================================="      << std::endl;

        ms_inputquery q(file, i);


        std::cout << "    title       : " << q.getStringTitle(1).c_str()<< std::endl;

        std::cout << "    mass_min    : " << q.getMassMin()             << std::endl;

        std::cout << "    mass_max    : " << q.getMassMax()             << std::endl;

        std::cout << "    int_min     : " << q.getIntMin()              << std::endl;

        std::cout << "    int_max     : " << q.getIntMax()              << std::endl;

        std::cout << "    num_vals    : " << q.getNumVals()             << std::endl;

        std::cout << "    num_used1   : " << q.getNumUsed()             << std::endl;

        std::cout << "    ions1       : " << q.getStringIons1().c_str() << std::endl;

        std::cout << "    ions2       : " << q.getStringIons2().c_str() << std::endl;

        std::cout << "    ions3       : " << q.getStringIons3().c_str() << std::endl;

        std::cout << "    peptol      : " << q.getPepTol()              << std::endl;

        std::cout << "    peptol units: " << q.getPepTolUnits().c_str() << std::endl;

        std::cout << "    peptol str  : " << q.getPepTolString().c_str()<< std::endl;

        std::cout << "    INSTRUMENT  : " << q.getINSTRUMENT().c_str()  << std::endl;

        std::cout << "    RULES       : " << q.getRULES().c_str()       << std::endl;

        std::cout << "    IT_MODS     : " << q.getIT_MODS().c_str()     << std::endl;

        std::cout << "    repeat srch : " << file.getRepeatSearchString(i).c_str() << std::endl;


        std::vector< std::pair< double, double > > tmp = q.getPeakList(1);

        for (unsigned int j=0; j < tmp.size(); j++)

        {

            std::cout << tmp[j].first << ", " << tmp[j].second << std::endl;

        }

    }

    std::cout << std::endl;

}


/*

will give the output:


Input data for query number 1

=========================================

        title       : dp210198c                      21 Jan 98 DERIVED SPECTRUM    P9

        mass_min    : 214.8

        mass_max    : 1228.7

        int_min     : 7

        int_max     : 114465

        num_vals    : 443

        num_used1   : 0

        ions1       : 288.200000:2137,371.127841:1663,472.096295:2.939e+04,567.000000:5.469e+04,663.100000:1.145e+05,758

.200000:7.356e+04,871.200000:2.539e+04,956.100000:2241,1055.000000:1.227e+04,1167.994665:1.725e+04,1215.400000:257,314.2

00000:1308,377.992647:1088,501.400000:1.043e+04,584.997427:3.906e+04,654.180103:3.006e+04,759.300000:1.557e+04,841.90000

0:1.917e+04,972.292156:1874,1056.300000:3799,1169.100000:1.123e+04,1225.200000:58,242.800000:417,377.000000:828,454.1000

00:5162,586.200000:5258,662.700000:1.83e+04,728.800000:1397,842.900000:4893,956.800000:443,1029.300000:1846,1170.200000:

1280,1216.200000:51,313.900000:187,387.200000:656,473.200000:1342,568.100000:5122,663.600000:9782,729.200000:626,872.300

000:4300,973.515686:255,1100.300000:1290,1198.200000:117,1217.500000:45,243.200000:159,379.100000:231,502.400000:556,599

.100000:1504,655.000000:1672,814.100000:277,841.200000:215,958.138974:195,1056.000000:492,1196.900000:96,1226.400000:38,

286.100000:83,408.200000:187,428.200000:283,614.400000:1403,710.900000:1144,730.000000:214,843.600000:194,1011.400000:78

,1057.200000:416,1198.900000:80,1227.000000:20,289.000000:60,353.300000:136,500.700000:143,551.300000:800,665.994513:565

,757.300000:182,873.300000:166,955.000000:51,1101.262914:302,1197.600000:53,1228.700000:19,253.900000:44,394.000000:115,

426.400000:75,566.263208:424,665.300000:563,801.800000:171,827.400000:165,1002.100000:46,1030.500000:193,1168.500000:42,

290.200000:25,388.100000:63,444.100000:75,542.000000:399,664.600000:388,760.000000:160,825.200000:76,937.900000:38,1082.

400000:126,1170.500000:40,287.100000:23,342.800000:48,454.900000:64,614.100000:373,644.000000:290,769.300000:111,902.100

000:67,917.300000:37,1029.800000:125,1149.800000:38,214.800000:18,242.100000:19,252.100000:20,315.200000:44,325.800000:1

7,333.100000:21,347.500000:19,348.700000:13,349.500000:23,352.600000:47,359.100000:28,366.000000:36,367.900000:7,376.100

000:14,380.100000:46,407.300000:11,410.900000:22,412.400000:31,418.000000:17,429.900000:57,431.000000:15,436.400000:11,4

44.900000:27,447.200000:18,453.200000:11,455.500000:33,456.100000:14,459.900000:15,461.600000:19,463.300000:7,465.600000

:22,470.400000:12,470.900000:51,474.200000:44,477.100000:15,477.900000:32,483.900000:37,486.200000:20,496.900000:11,497.

600000:14,499.100000:41,503.800000:24,505.400000:22,508.300000:12,508.900000:17,511.800000:19,513.000000:20,515.000000:1

8,517.000000:16,522.100000:58,523.900000:15,524.600000:78,525.300000:19,525.900000:370,526.700000:36,532.900000:11,533.5

00000:14,536.900000:19,538.200000:44,539.261607:224,540.200000:39,541.100000:133,543.043902:41,545.100000:9,545.600000:3

0,547.300000:23,547.900000:13,548.700000:340,549.600000:81,550.200000:41,551.700000:16,552.300000:69,555.500000:29,557.0

68975:361,558.300000:54,560.100000:7,561.100000:24,563.400000:39,564.100000:101,567.600000:35,568.900000:37,569.500000:1

4,570.000000:49,571.100000:45,572.300000:76,574.000000:99,574.600000:22,576.300000:18,580.800000:34,582.300000:41,587.10

0000:131,587.900000:53,590.300000:12,591.800000:17,592.500000:18,594.800000:9,595.300000:56,596.100000:97,596.600000:62,

597.100000:27,597.700000:63,600.000000:57,602.100000:28,603.900000:16,605.200000:69,606.800000:24,607.500000:13,608.5000

00:57,608.800000:12,610.200000:50,610.500000:12,611.200000:96,612.200000:24,613.200000:13,615.000000:194,615.600000:19,6

16.200000:23,618.400000:15,619.100000:31,621.100000:120,621.700000:36,622.600000:11,623.200000:43,624.100000:147,624.800

000:32,626.000000:22,627.000000:53,627.900000:21,628.900000:16,629.500000:29,630.500000:14,631.400000:45,633.200000:61,6

35.000000:58,635.736413:184,636.600000:29,637.500000:78,638.600000:14,639.800000:72,640.500000:51,641.100000:33,641.7000

00:40,642.400000:121,642.800000:170,643.300000:57,644.600000:48,645.700000:36,646.500000:39,647.400000:28,648.500000:30,

649.500000:108,650.000000:13,650.600000:43,651.800000:107,652.300000:33,652.900000:33,656.300000:178,657.100000:78,658.2

00000:19,658.800000:76,660.590741:108,661.900000:216,667.000000:193,677.300000:8,680.500000:13,683.500000:38,684.500000:

28,685.500000:24,686.200000:13,687.275862:87,688.200000:28,688.900000:28,689.400000:50,691.500000:28,692.700000:25,693.2

00000:15,694.000000:31,697.100000:8,698.300000:42,700.300000:17,700.900000:21,703.500000:39,704.200000:20,704.900000:14,

708.300000:15,709.000000:42,711.500000:90,711.800000:119,713.100000:35,715.200000:29,718.500000:57,719.900000:52,721.500

000:78,722.400000:29,725.400000:30,731.100000:13,731.800000:13,734.500000:36,735.300000:46,735.700000:28,738.600000:23,7

39.900000:20,740.500000:81,741.800000:64,744.700000:23,745.500000:18,747.400000:23,751.100000:21,751.900000:34,755.20000

0:13,756.200000:28,760.900000:21,762.800000:19,764.100000:19,767.600000:41,768.200000:75,771.200000:9,771.800000:10,773.

800000:10,776.100000:21,777.500000:39,783.400000:39,785.100000:26,786.800000:15,788.200000:23,789.300000:14,791.700000:2

1,792.600000:29,795.700000:53,796.200000:25,798.900000:13,799.400000:14,800.200000:12,800.700000:32,802.300000:25,802.80

0000:103,804.000000:26,805.200000:83,807.900000:15,808.700000:25,809.800000:36,810.900000:50,811.500000:85,812.100000:36

,813.400000:22,814.600000:78,815.100000:52,815.900000:25,817.300000:21,821.300000:30,822.000000:9,827.800000:33,828.9000

00:20,832.100000:13,834.800000:18,835.700000:25,836.600000:20,846.700000:8,851.100000:25,852.054545:66,853.200000:20,854

.400000:28,857.000000:21,857.800000:21,859.500000:14,861.100000:17,864.500000:20,867.800000:49,868.800000:47,869.100000:

19,869.700000:22,872.900000:22,877.100000:16,880.800000:20,885.000000:21,885.800000:12,886.300000:16,888.800000:11,890.5

00000:10,899.339024:41,907.800000:39,909.400000:8,911.200000:27,911.900000:9,925.900000:10,928.800000:30,930.700000:26,9

33.700000:9,935.700000:13,945.100000:20,948.900000:10,953.600000:14,960.500000:14,974.100000:36,994.000000:37,1003.30000

0:18,1010.200000:18,1010.800000:27,1012.100000:21,1014.000000:14,1020.100000:20,1021.000000:31,1028.900000:118,1031.0000

00:18,1031.600000:40,1033.100000:14,1037.900000:55,1041.100000:17,1045.300000:13,1054.000000:92,1057.700000:19,1061.9000

00:20,1069.100000:16,1083.600000:41,1093.400000:49,1098.500000:32,1099.800000:46,1102.500000:52,1103.200000:18,1104.5000

00:9,1125.400000:16,1131.800000:24,1132.400000:21,1139.800000:12,1150.800000:22,1152.900000:15,1157.600000:8,1165.300000

:14,1166.700000:11,1178.700000:25,1179.500000:23,1180.400000:25,1185.800000:12,1192.800000:18,1194.800000:12,1214.700000

:35

    ions2       :

    ions3       :

    ions2       :

    ions3       :

    peptol      : 0

    peptol units:

    peptol str  :

    repeat srch : 1341.784350 from(671.900000,2+)  title(dp210198c%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20

%20%20%20%2021%2dJan%2d98%20DERIVED%20SPECTRUM%20%20%20%20%239)  query(1)

371.128, 1663

472.096, 29390

567, 54690

663.1, 114500

758.2, 73560

871.2, 25390

956.1, 2241

1055, 12270

1167.99, 17250

1215.4, 257

314.2, 1308

377.993, 1088

501.4, 10430

584.997, 39060

654.18, 30060

759.3, 15570

841.9, 19170

972.292, 1874

1056.3, 3799

1169.1, 11230

1225.2, 58

242.8, 417

377, 828

454.1, 5162

586.2, 5258

662.7, 18300

728.8, 1397

842.9, 4893

956.8, 443

1029.3, 1846

1170.2, 1280

1216.2, 51

313.9, 187

387.2, 656

473.2, 1342

568.1, 5122

663.6, 9782

729.2, 626

872.3, 4300

973.516, 255

1100.3, 1290

1198.2, 117

1217.5, 45

243.2, 159

379.1, 231

502.4, 556

599.1, 1504

655, 1672

814.1, 277

841.2, 215

958.139, 195

1056, 492

1196.9, 96

1226.4, 38

286.1, 83

408.2, 187

428.2, 283

614.4, 1403

710.9, 1144

730, 214

843.6, 194

1011.4, 78

1057.2, 416

1198.9, 80

1227, 20

289, 60

353.3, 136

500.7, 143

551.3, 800

665.995, 565

757.3, 182

873.3, 166

955, 51

1101.26, 302

1197.6, 53

1228.7, 19

253.9, 44

394, 115

426.4, 75

566.263, 424

665.3, 563

801.8, 171

827.4, 165

1002.1, 46

1030.5, 193

1168.5, 42

290.2, 25

388.1, 63

444.1, 75

542, 399

664.6, 388

760, 160

825.2, 76

937.9, 38

1082.4, 126

1170.5, 40

287.1, 23

342.8, 48

454.9, 64

614.1, 373

644, 290

769.3, 111

902.1, 67

917.3, 37

1029.8, 125

1149.8, 38

214.8, 18

242.1, 19

252.1, 20

315.2, 44

325.8, 17

333.1, 21

347.5, 19

348.7, 13

349.5, 23

352.6, 47

359.1, 28

366, 36

367.9, 7

376.1, 14

380.1, 46

407.3, 11

410.9, 22

412.4, 31

418, 17

429.9, 57

431, 15

436.4, 11

444.9, 27

447.2, 18

453.2, 11

455.5, 33

456.1, 14

459.9, 15

461.6, 19

463.3, 7

465.6, 22

470.4, 12

470.9, 51

474.2, 44

477.1, 15

477.9, 32

483.9, 37

486.2, 20

496.9, 11

497.6, 14

499.1, 41

503.8, 24

505.4, 22

508.3, 12

508.9, 17

511.8, 19

513, 20

515, 18

517, 16

522.1, 58

523.9, 15

524.6, 78

525.3, 19

525.9, 370

526.7, 36

532.9, 11

533.5, 14

536.9, 19

538.2, 44

539.262, 224

540.2, 39

541.1, 133

543.044, 41

545.1, 9

545.6, 30

547.3, 23

547.9, 13

548.7, 340

549.6, 81

550.2, 41

551.7, 16

552.3, 69

555.5, 29

557.069, 361

558.3, 54

560.1, 7

561.1, 24

563.4, 39

564.1, 101

567.6, 35

568.9, 37

569.5, 14

570, 49

571.1, 45

572.3, 76

574, 99

574.6, 22

576.3, 18

580.8, 34

582.3, 41

587.1, 131

587.9, 53

590.3, 12

591.8, 17

592.5, 18

594.8, 9

595.3, 56

596.1, 97

596.6, 62

597.1, 27

597.7, 63

600, 57

602.1, 28

603.9, 16

605.2, 69

606.8, 24

607.5, 13

608.5, 57

608.8, 12

610.2, 50

610.5, 12

611.2, 96

612.2, 24

613.2, 13

615, 194

615.6, 19

616.2, 23

618.4, 15

619.1, 31

621.1, 120

621.7, 36

622.6, 11

623.2, 43

624.1, 147

624.8, 32

626, 22

627, 53

627.9, 21

628.9, 16

629.5, 29

630.5, 14

631.4, 45

633.2, 61

635, 58

635.736, 184

636.6, 29

637.5, 78

638.6, 14

639.8, 72

640.5, 51

641.1, 33

641.7, 40

642.4, 121

642.8, 170

643.3, 57

644.6, 48

645.7, 36

646.5, 39

647.4, 28

648.5, 30

649.5, 108

650, 13

650.6, 43

651.8, 107

652.3, 33

652.9, 33

656.3, 178

657.1, 78

658.2, 19

658.8, 76

660.591, 108

661.9, 216

667, 193

677.3, 8

680.5, 13

683.5, 38

684.5, 28

685.5, 24

686.2, 13

687.276, 87

688.2, 28

688.9, 28

689.4, 50

691.5, 28

692.7, 25

693.2, 15

694, 31

697.1, 8

698.3, 42

700.3, 17

700.9, 21

703.5, 39

704.2, 20

704.9, 14

708.3, 15

709, 42

711.5, 90

711.8, 119

713.1, 35

715.2, 29

718.5, 57

719.9, 52

721.5, 78

722.4, 29

725.4, 30

731.1, 13

731.8, 13

734.5, 36

735.3, 46

735.7, 28

738.6, 23

739.9, 20

740.5, 81

741.8, 64

744.7, 23

745.5, 18

747.4, 23

751.1, 21

751.9, 34

755.2, 13

756.2, 28

760.9, 21

762.8, 19

764.1, 19

767.6, 41

768.2, 75

771.2, 9

771.8, 10

773.8, 10

776.1, 21

777.5, 39

783.4, 39

785.1, 26

786.8, 15

788.2, 23

789.3, 14

791.7, 21

792.6, 29

795.7, 53

796.2, 25

798.9, 13

799.4, 14

800.2, 12

800.7, 32

802.3, 25

802.8, 103

804, 26

805.2, 83

807.9, 15

808.7, 25

809.8, 36

810.9, 50

811.5, 85

812.1, 36

813.4, 22

814.6, 78

815.1, 52

815.9, 25

817.3, 21

821.3, 30

822, 9

827.8, 33

828.9, 20

832.1, 13

834.8, 18

835.7, 25

836.6, 20

846.7, 8

851.1, 25

852.055, 66

853.2, 20

854.4, 28

857, 21

857.8, 21

859.5, 14

861.1, 17

864.5, 20

867.8, 49

868.8, 47

869.1, 19

869.7, 22

872.9, 22

877.1, 16

880.8, 20

885, 21

885.8, 12

886.3, 16

888.8, 11

890.5, 10

899.339, 41

907.8, 39

909.4, 8

911.2, 27

911.9, 9

925.9, 10

928.8, 30

930.7, 26

933.7, 9

935.7, 13

945.1, 20

948.9, 10

953.6, 14

960.5, 14

974.1, 36

994, 37

1003.3, 18

1010.2, 18

1010.8, 27

1012.1, 21

1014, 14

1020.1, 20

1021, 31

1028.9, 118

1031, 18

1031.6, 40

v1033.1, 14

1037.9, 55

1041.1, 17

1045.3, 13

1054, 92

1057.7, 19

1061.9, 20

1069.1, 16

1083.6, 41

1093.4, 49

1098.5, 32

1099.8, 46

1102.5, 52

1103.2, 18

1104.5, 9

1125.4, 16

1131.8, 24

1132.4, 21

1139.8, 12

1150.8, 22

1152.9, 15

1157.6, 8

1165.3, 14

1166.7, 11

1178.7, 25

1179.5, 23

1180.4, 25

1185.8, 12

1192.8, 18

1194.8, 12

1214.7, 35


*/

matrix_science::ms_errors::isValid
bool isValid() const
Call this function to determine if there have been any errors.
Definition: ms_errors.cpp:1472

matrix_science::ms_inputquery
This class encapsulates the input queries (peak lists) in the Mascot results file.
Definition: ms_inputquery.hpp:43

matrix_science::ms_mascotresfilebase
Abstract base class of ms_mascotresfile_dat and ms_mascotresfile_msr.
Definition: ms_mascotresfilebase.hpp:72

matrix_science::ms_mascotresfilebase::getLastErrorString
std::string getLastErrorString() const
Return the last error number - or an empty string.
Definition: ms_mascotresfilebase.cpp:824

matrix_science::ms_mascotresfilebase::getRepeatSearchString
virtual std::string getRepeatSearchString(const int query, const bool fullQuery=false) const =0
To perform a repeat search need to build up appropriate string.