Example program for retrieving input spectrum data.
/* ############################################################################## # file: resfile_input.java # # 'msparser' toolkit # # Test harness / example code # ############################################################################## # COPYRIGHT NOTICE # # Copyright 1998-2003 Matrix Science Limited All Rights Reserved. # # # ############################################################################## # $Archive:: /MowseBranches/ms_mascotresfile_1.2/test_java/test_inputda $ # # $Author: villek@matrixscience.com $ # # $Date: 2018-07-30 16:23:53 +0100 $ # # $Revision: 1b450440f9c97e1e41d0fc6016a27d68951d4532 | MSPARSER_REL_2_8_1-0-gea32989045 $ # # $NoKeywords:: $ # ############################################################################## */ import java.util.Date; import matrix_science.msparser.*; public class resfile_input { static { try { System.loadLibrary("msparserj"); } catch (UnsatisfiedLinkError e) { System.err.println("Native code library failed to load. " + "Is msparserj.dll on the path?\n" + e); System.exit(0); } } public static void main(String argv[]) { // ----- Object creation ----- if(argv.length < 1) { System.out.println("Must specify results filename as parameter"); System.exit(0); } ms_mascotresfile file = new ms_mascotresfile(argv[0], 0, ""); if (file.isValid()) { inputData(file); } else { System.out.println("Error number: "+file.getLastError()); System.out.println("Error string: "+file.getLastErrorString()); System.exit(0); } } private static void inputData(ms_mascotresfile file) { int i; int j; int num_peaks; // display input data via inputquery get functions for(i=1; i <=1; i++) { // replace i<=1 with i<=file.getNumQueries() for complete dataset System.out.println("Input data for query number "+i); System.out.println("========================================="); ms_inputquery q=new ms_inputquery(file,i); System.out.println(" title : "+q.getStringTitle(true)); System.out.println(" mass_min : "+q.getMassMin()); System.out.println(" mass_max : "+q.getMassMax()); System.out.println(" int_min : "+q.getIntMin()); System.out.println(" int_max : "+q.getIntMax()); System.out.println(" num_vals : "+q.getNumVals()); System.out.println(" num_used1 : "+q.getNumUsed()); System.out.println(" ions1 : "+q.getStringIons1()); System.out.println(" ions2 : "+q.getStringIons2()); System.out.println(" ions3 : "+q.getStringIons3()); System.out.println(" peptol : "+q.getPepTol()); System.out.println(" peptol units: "+q.getPepTolUnits()); System.out.println(" peptol str : "+q.getPepTolString()); System.out.println(" INSTRUMENT : "+q.getINSTRUMENT()); System.out.println(" RULES : "+q.getRULES()); System.out.println(" IT_MODS : "+q.getIT_MODS()); System.out.println(" repeat srch : "+file.getRepeatSearchString(i)); num_peaks = q.getNumberOfPeaks(1); for(j=1; j <= num_peaks; j++) { System.out.println(roundWholeNumber(q.getPeakMass(1,j))+", "+roundWholeNumber(q.getPeakIntensity(1,j))); } } System.out.println("\n"); } private static int toBinary(boolean bool) { if(bool) return 1; return 0; } private static String roundWholeNumber (double toRound) { String myInt = ""+toRound; myInt += "\n"; if(myInt.indexOf(".0\n")>-1) { return myInt.substring(0,myInt.indexOf(".0\n")); } return ""+toRound; } } /* will give the output: C>java -classpath .;../java/msparser.jar resfile_input F981123.dat Input data for query number 1 ========================================= title : dp210198c 21-Jan-98 DERIVED SPECTRUM #9 mass_min : 214.8 mass_max : 1228.7 int_min : 7.0 int_max : 114465.0 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+05,758.2 00000:7.356e+04,871.200000:2.539e+04,956.100000:2241,1055.000000:1.227e+04,1167.994665:1.725e+04,1215.400000:257,314.200 000:1308,377.992647:1088,501.400000:1.043e+04,584.997427:3.906e+04,654.180103:3.006e+04,759.300000:1.557e+04,841.900000: 1.917e+04,972.292156:1874,1056.300000:3799,1169.100000:1.123e+04,1225.200000:58,242.800000:417,377.000000:828,454.100000 :5162,586.200000:5258,662.700000:1.83e+04,728.800000:1397,842.900000:4893,956.800000:443,1029.300000:1846,1170.200000:12 80,1216.200000:51,313.900000:187,387.200000:656,473.200000:1342,568.100000:5122,663.600000:9782,729.200000:626,872.30000 0:4300,973.515686:255,1100.300000:1290,1198.200000:117,1217.500000:45,243.200000:159,379.100000:231,502.400000:556,599.1 00000:1504,655.000000:1672,814.100000:277,841.200000:215,958.138974:195,1056.000000:492,1196.900000:96,1226.400000:38,28 6.100000:83,408.200000:187,428.200000:283,614.400000:1403,710.900000:1144,730.000000:214,843.600000:194,1011.400000:78,1 057.200000:416,1198.900000:80,1227.000000:20,289.000000:60,353.300000:136,500.700000:143,551.300000:800,665.994513:565,7 57.300000:182,873.300000:166,955.000000:51,1101.262914:302,1197.600000:53,1228.700000:19,253.900000:44,394.000000:115,42 6.400000:75,566.263208:424,665.300000:563,801.800000:171,827.400000:165,1002.100000:46,1030.500000:193,1168.500000:42,29 0.200000:25,388.100000:63,444.100000:75,542.000000:399,664.600000:388,760.000000:160,825.200000:76,937.900000:38,1082.40 0000:126,1170.500000:40,287.100000:23,342.800000:48,454.900000:64,614.100000:373,644.000000:290,769.300000:111,902.10000 0:67,917.300000:37,1029.800000:125,1149.800000:38,214.800000:18,242.100000:19,252.100000:20,315.200000:44,325.800000:17, 333.100000:21,347.500000:19,348.700000:13,349.500000:23,352.600000:47,359.100000:28,366.000000:36,367.900000:7,376.10000 0:14,380.100000:46,407.300000:11,410.900000:22,412.400000:31,418.000000:17,429.900000:57,431.000000:15,436.400000:11,444 .900000:27,447.200000:18,453.200000:11,455.500000:33,456.100000:14,459.900000:15,461.600000:19,463.300000:7,465.600000:2 2,470.400000:12,470.900000:51,474.200000:44,477.100000:15,477.900000:32,483.900000:37,486.200000:20,496.900000:11,497.60 0000:14,499.100000:41,503.800000:24,505.400000:22,508.300000:12,508.900000:17,511.800000:19,513.000000:20,515.000000:18, 517.000000:16,522.100000:58,523.900000:15,524.600000:78,525.300000:19,525.900000:370,526.700000:36,532.900000:11,533.500 000:14,536.900000:19,538.200000:44,539.261607:224,540.200000:39,541.100000:133,543.043902:41,545.100000:9,545.600000:30, 547.300000:23,547.900000:13,548.700000:340,549.600000:81,550.200000:41,551.700000:16,552.300000:69,555.500000:29,557.068 975:361,558.300000:54,560.100000:7,561.100000:24,563.400000:39,564.100000:101,567.600000:35,568.900000:37,569.500000:14, 570.000000:49,571.100000:45,572.300000:76,574.000000:99,574.600000:22,576.300000:18,580.800000:34,582.300000:41,587.1000 00:131,587.900000:53,590.300000:12,591.800000:17,592.500000:18,594.800000:9,595.300000:56,596.100000:97,596.600000:62,59 7.100000:27,597.700000:63,600.000000:57,602.100000:28,603.900000:16,605.200000:69,606.800000:24,607.500000:13,608.500000 :57,608.800000:12,610.200000:50,610.500000:12,611.200000:96,612.200000:24,613.200000:13,615.000000:194,615.600000:19,616 .200000:23,618.400000:15,619.100000:31,621.100000:120,621.700000:36,622.600000:11,623.200000:43,624.100000:147,624.80000 0:32,626.000000:22,627.000000:53,627.900000:21,628.900000:16,629.500000:29,630.500000:14,631.400000:45,633.200000:61,635 .000000:58,635.736413:184,636.600000:29,637.500000:78,638.600000:14,639.800000:72,640.500000:51,641.100000:33,641.700000 :40,642.400000:121,642.800000:170,643.300000:57,644.600000:48,645.700000:36,646.500000:39,647.400000:28,648.500000:30,64 9.500000:108,650.000000:13,650.600000:43,651.800000:107,652.300000:33,652.900000:33,656.300000:178,657.100000:78,658.200 000:19,658.800000:76,660.590741:108,661.900000:216,667.000000:193,677.300000:8,680.500000:13,683.500000:38,684.500000:28 ,685.500000:24,686.200000:13,687.275862:87,688.200000:28,688.900000:28,689.400000:50,691.500000:28,692.700000:25,693.200 000:15,694.000000:31,697.100000:8,698.300000:42,700.300000:17,700.900000:21,703.500000:39,704.200000:20,704.900000:14,70 8.300000:15,709.000000:42,711.500000:90,711.800000:119,713.100000:35,715.200000:29,718.500000:57,719.900000:52,721.50000 0:78,722.400000:29,725.400000:30,731.100000:13,731.800000:13,734.500000:36,735.300000:46,735.700000:28,738.600000:23,739 .900000:20,740.500000:81,741.800000:64,744.700000:23,745.500000:18,747.400000:23,751.100000:21,751.900000:34,755.200000: 13,756.200000:28,760.900000:21,762.800000:19,764.100000:19,767.600000:41,768.200000:75,771.200000:9,771.800000:10,773.80 0000:10,776.100000:21,777.500000:39,783.400000:39,785.100000:26,786.800000:15,788.200000:23,789.300000:14,791.700000:21, 792.600000:29,795.700000:53,796.200000:25,798.900000:13,799.400000:14,800.200000:12,800.700000:32,802.300000:25,802.8000 00:103,804.000000:26,805.200000:83,807.900000:15,808.700000:25,809.800000:36,810.900000:50,811.500000:85,812.100000:36,8 13.400000:22,814.600000:78,815.100000:52,815.900000:25,817.300000:21,821.300000:30,822.000000:9,827.800000:33,828.900000 :20,832.100000:13,834.800000:18,835.700000:25,836.600000:20,846.700000:8,851.100000:25,852.054545:66,853.200000:20,854.4 00000:28,857.000000:21,857.800000:21,859.500000:14,861.100000:17,864.500000:20,867.800000:49,868.800000:47,869.100000:19 ,869.700000:22,872.900000:22,877.100000:16,880.800000:20,885.000000:21,885.800000:12,886.300000:16,888.800000:11,890.500 000:10,899.339024:41,907.800000:39,909.400000:8,911.200000:27,911.900000:9,925.900000:10,928.800000:30,930.700000:26,933 .700000:9,935.700000:13,945.100000:20,948.900000:10,953.600000:14,960.500000:14,974.100000:36,994.000000:37,1003.300000: 18,1010.200000:18,1010.800000:27,1012.100000:21,1014.000000:14,1020.100000:20,1021.000000:31,1028.900000:118,1031.000000 :18,1031.600000:40,1033.100000:14,1037.900000:55,1041.100000:17,1045.300000:13,1054.000000:92,1057.700000:19,1061.900000 :20,1069.100000:16,1083.600000:41,1093.400000:49,1098.500000:32,1099.800000:46,1102.500000:52,1103.200000:18,1104.500000 :9,1125.400000:16,1131.800000:24,1132.400000:21,1139.800000:12,1150.800000:22,1152.900000:15,1157.600000:8,1165.300000:1 4,1166.700000:11,1178.700000:25,1179.500000:23,1180.400000:25,1185.800000:12,1192.800000:18,1194.800000:12,1214.700000:3 5 ions2 : ions3 : peptol : 0.0 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) 288.2, 2137 371.127841, 1663 472.096295, 29390 567, 54690 663.1, 114500 758.2, 73560 871.2, 25390 956.1, 2241 1055, 12270 1167.994665, 17250 1215.4, 257 314.2, 1308 377.992647, 1088 501.4, 10430 584.997427, 39060 654.180103, 30060 759.3, 15570 841.9, 19170 972.292156, 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 973.515686, 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, 215 958.138974, 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, 800 665.994513, 565 757.3, 182 873.3, 166 955, 51 1101.262914, 302 1197.6, 53 1228.7, 19 253.9, 44 394, 115 426.4, 75 566.263208, 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, 44 539.261607, 224 540.2, 39 541.1, 133 543.043902, 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, 29 557.068975, 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, 58 635.736413, 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, 76 660.590741, 108 661.9, 216 667, 193 677.3, 8 680.5, 13 683.5, 38 684.5, 28 685.5, 24 686.2, 13 687.275862, 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, 25 852.054545, 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, 10 899.339024, 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 1033.1, 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 */
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