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@LucasSchmidt97
LucasSchmidt97 committed Nov 20, 2017
1 parent 83eba57 commit 6df85b4
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138 changes: 137 additions & 1 deletion java/deisotoper/src/main/java/ch/fgcz/proteomics/R/FeaturesBasedDeisotoping.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -119,7 +119,9 @@ public String getSummary() {
List<Peak> peakic = new ArrayList<>();

for (IsotopicCluster ic : is.getIsotopicSet()) {
peakic.addAll(ic.getIsotopicCluster());
if (ic.getIsotopicCluster() != null) {
peakic.addAll(ic.getIsotopicCluster());
}
}

Set<Double> titles = new HashSet<Double>();
Expand All @@ -143,4 +145,138 @@ public String getSummary() {

return sb.toString();
}

// public static void main(String[] args) {
// double[] mz = { 110.0715485, 110.1648788, 112.0395432, 113.0712204,
// 114.0746384, 115.05056, 115.9784622,
// 120.080986, 120.0833893, 121.0843735, 125.7498245, 129.0659332, 129.1023102,
// 130.0863342, 130.1057281,
// 131.0815735, 132.0849609, 132.5098419, 137.0346222, 141.0658417, 143.0816193,
// 145.0608368, 147.1128235,
// 149.0233917, 150.0266876, 153.0657654, 157.0970917, 159.076416, 160.0798035,
// 162.0875397, 162.0912323,
// 167.0816345, 170.092392, 171.0762177, 172.8989868, 175.118927, 180.0767212,
// 185.0920105, 189.1023407,
// 198.0873413, 199.0907135, 204.0980682, 205.0570374, 207.1127777, 208.0717316,
// 210.0866547, 210.7322388,
// 211.5193329, 212.10289, 214.0822296, 216.0977783, 223.0636444, 224.1031799,
// 225.0603638, 226.0820923,
// 227.0399933, 227.1023407, 228.098175, 230.1135101, 231.1125488, 231.1492462,
// 232.0926361, 232.2126312,
// 233.1646729, 235.1072845, 240.09758, 241.129364, 242.1128387, 246.1234741,
// 249.098175, 253.0928345,
// 254.1314087, 254.6329193, 255.1085358, 258.1084595, 259.1398315, 263.1368713,
// 267.1086426, 268.1119995,
// 269.1243591, 271.1038513, 273.1199646, 274.1184998, 276.1701965, 277.0926819,
// 277.1541138, 278.4438171,
// 279.108429, 285.1191101, 287.1348877, 289.650177, 292.1772461, 294.1808777,
// 295.1038513, 295.184082,
// 296.1346436, 297.1190491, 299.0617065, 300.133606, 301.0583801, 303.1295166,
// 310.4591064, 314.1459961,
// 315.129303, 318.1446228, 318.1605225, 324.1297607, 328.1278992, 331.8494568,
// 332.1560364, 333.1555786,
// 334.114502, 338.1456299, 342.1403198, 343.1411133, 346.176239, 351.1661377,
// 356.1558228, 357.1579285,
// 357.6632385, 358.1647949, 360.1513672, 360.6679077, 361.1502075, 363.2023926,
// 366.6683655, 368.6846924,
// 375.1660156, 375.2023926, 379.1607361, 381.2128296, 382.2158813, 387.1657104,
// 388.1895447, 390.9455261,
// 395.1658325, 397.1503906, 397.1950684, 397.6967163, 400.1613159, 403.135437,
// 403.1973877, 411.1614075,
// 418.1715698, 420.2235107, 421.1462402, 421.2265015, 426.1759949, 438.2343445,
// 439.2384644, 443.2040405,
// 444.1874084, 454.1725464, 461.2140198, 462.1977844, 471.1980896, 472.2180786,
// 479.2248535, 482.1990967,
// 489.2085571, 490.2118835, 490.2296448, 495.2563477, 507.2199402, 507.2555847,
// 508.2598572, 525.2663574,
// 526.2697754, 577.2515259, 578.2937012, 584.8656006, 596.3037109, 597.3069458,
// 617.3034668, 618.2872925,
// 635.3146362, 636.3175049, 653.3252563, 654.3284302 };
// double[] intensity = { 6250.6640625, 563.5891113281, 787.7743530273,
// 42913.109375, 927.4467773438,
// 2023.1707763672, 529.0408325195, 25228.6796875, 1165.1545410156,
// 603.5643310547, 528.4467773438,
// 7070.5766601563, 31543.533203125, 19388.078125, 833.7221679688, 81864.546875,
// 3091.2973632813,
// 582.6003417969, 6660.9750976563, 34947.4921875, 684.2407836914,
// 3036.4206542969, 36999.45703125,
// 2973.7102050781, 829.9125366211, 6804.5180664063, 1259.5620117188,
// 46302.8125, 2067.9748535156,
// 1154.1105957031, 765.7245483398, 794.5812988281, 4291.3037109375,
// 888.9245605469, 606.1282958984,
// 766.3591918945, 14302.1279296875, 3288.0661621094, 688.5368652344,
// 35533.54296875, 2225.658203125,
// 670.2319335938, 677.4953613281, 6984.8188476563, 2347.3420410156,
// 594.0815429688, 2258.9313964844,
// 568.3290405273, 802.1146850586, 3599.0229492188, 7246.6596679688,
// 2139.9233398438, 828.2638549805,
// 884.8049316406, 1193.3479003906, 566.4050292969, 786.0283813477,
// 615.2380981445, 1079.8623046875,
// 1339.6888427734, 806.2881469727, 9631.443359375, 569.907409668,
// 1065.3564453125, 991.0939331055,
// 690.4099731445, 3580.0187988281, 672.0654296875, 845.2703857422,
// 1281.3441162109, 559.6304931641,
// 4143.1162109375, 1155.7521972656, 2598.6123046875, 953.2352905273,
// 3944.8764648438, 7301.6743164063,
// 4961.2807617188, 569.8205566406, 2566.8024902344, 795.173828125,
// 757.6403808594, 3254.8908691406,
// 7315.53515625, 1220.8388671875, 1115.0716552734, 524.3715820313,
// 676.455871582, 2324.4851074219,
// 808.6432495117, 1269.125, 581.4161376953, 31443.404296875, 2546.380859375,
// 2911.2058105469,
// 780.770324707, 738.4011230469, 1135.4598388672, 1176.7568359375,
// 3533.0815429688, 2457.2565917969,
// 562.0629882813, 928.1300048828, 1034.6174316406, 1035.1872558594,
// 2155.4260253906, 3214.2192382813,
// 586.0258178711, 545.24609375, 2240.283203125, 3230.6267089844,
// 1323.4107666016, 924.3392944336,
// 8073.1616210938, 767.8354492188, 789.9375610352, 2135.9985351563,
// 999.5626831055, 642.1485595703,
// 7692.0913085938, 1246.6643066406, 4829.984375, 799.643371582,
// 3193.9008789063, 1350.830078125,
// 901.1105957031, 687.5123901367, 996.9341430664, 1064.1864013672,
// 911.1711425781, 16409.24609375,
// 1171.5484619141, 960.3439331055, 935.4268188477, 677.4844970703,
// 657.7783813477, 2241.4836425781,
// 8700.474609375, 782.1491699219, 686.3291015625, 785.7287597656,
// 753.0210571289, 714.055847168,
// 2145.2751464844, 5911.2006835938, 1220.7615966797, 623.0693969727,
// 634.6696777344, 33137.39453125,
// 5135.7211914063, 813.663269043, 1231.4427490234, 933.5162963867,
// 3532.599609375, 1009.3364868164,
// 3219.3342285156, 800.7995605469, 3228.8891601563, 1368.7080078125,
// 6327.9125976563, 810.8509521484,
// 1239.9750976563, 791.6758422852, 1281.634765625, 6519.0903320313,
// 575.096496582, 65968.4140625,
// 11777.5908203125, 2284.7736816406, 2809.2331542969, 622.4571533203,
// 22998.53515625, 3657.8000488281,
// 1279.3221435547, 1236.6485595703, 9816.9814453125, 1331.3529052734,
// 87058.9140625, 21567.640625 };
//
// FeaturesBasedDeisotoping dtoper = new FeaturesBasedDeisotoping();
//
// double[] aa = { 99.06841 };
//
// dtoper.setConfiguration(aa, 0.8, 0.5, 0.1, 0.1, 0.1, 0.03, 0.3, 1.0, 0,
// true);
//
// dtoper.setMz(mz);
// dtoper.setIntensity(intensity);
// dtoper.setPepMass(1.2345);
// dtoper.setCharge(2);
//
// dtoper.deisotope("none");
//
// double[] mzout = dtoper.getMz();
// double[] intensityout = dtoper.getIntensity();
//
// System.out.println("Output Peaklist:");
// for (int i = 0; i < mzout.length || i < intensityout.length; i++) {
// System.out.print(mzout[i] + " ");
// System.out.println(intensityout[i]);
// }
// System.out.println();
//
// System.out.println(dtoper.getSummary());
// }
}
4 changes: 2 additions & 2 deletions java/deisotoper/src/main/java/ch/fgcz/proteomics/Version.java
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Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ private static String versionOfDTO() {
}

private static String versionOfFBDM() {
return "Java Package: FBDM, Date: 2017-11-16, Author: Lucas Schmidt";
return "Java Package: FBDM, Date: 2017-11-20, Author: Lucas Schmidt";
}

private static String versionOfMSPY() {
Expand All @@ -23,7 +23,7 @@ private static String versionOfMGF() {
}

private static String versionOfRAdapter() {
return "Java Package: RAdapter, Date: 2017-11-16, Author: Lucas Schmidt";
return "Java Package: RAdapter, Date: 2017-11-20, Author: Lucas Schmidt";
}

private static String versionOfUtilities() {
Expand Down
37 changes: 8 additions & 29 deletions java/deisotoper/src/main/java/ch/fgcz/proteomics/fbdm/Deisotoper.java
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Original file line number Diff line number Diff line change
Expand Up @@ -103,14 +103,9 @@ private ListMassSpectrum makeGraph(MassSpectrum input, IsotopicMassSpectrum ims,
List<Double> mz = new ArrayList<>();

for (IsotopicSet is : ims.getIsotopicMassSpectrum()) {
IsotopicClusterGraph icg = new IsotopicClusterGraph(is);
GraphPath<IsotopicCluster, Connection> bp = is.getBestpath();

icg.scoreIsotopicClusterGraph(input.getPeptideMass(), input.getChargeState(), config.getErrortolerance(),
new Peaklist(input.getMz(), input.getIntensity()), config);

this.icglist.add(icg);

GraphPath<IsotopicCluster, Connection> bp = icg.bestPath(getStart(icg), getEnd(icg));
this.icglist.add(is.getIcg());

ListMassSpectrum list2 = new ListMassSpectrum();

Expand Down Expand Up @@ -165,10 +160,12 @@ private void saveAnnotatedSpectrum(IsotopicMassSpectrum ims) {

for (IsotopicSet is : ims.getIsotopicMassSpectrum()) {
for (IsotopicCluster ic : is.getIsotopicSet()) {
for (Peak p : ic.getIsotopicCluster()) {
sb.append(is.getSetID()).append(",").append(ic.getClusterID()).append(",").append(p.getPeakID())
.append(",").append(ic.getCharge()).append(",").append(p.getMz()).append(",")
.append(p.getIntensity()).append(linesep);
if (ic.getIsotopicCluster() != null) {
for (Peak p : ic.getIsotopicCluster()) {
sb.append(is.getSetID()).append(",").append(ic.getClusterID()).append(",").append(p.getPeakID())
.append(",").append(ic.getCharge()).append(",").append(p.getMz()).append(",")
.append(p.getIntensity()).append(linesep);
}
}
}
}
Expand Down Expand Up @@ -203,22 +200,4 @@ private ListMassSpectrum decharge(ListMassSpectrum list, Configuration config) {

return list2;
}

private IsotopicCluster getStart(IsotopicClusterGraph icg) {
for (IsotopicCluster e : icg.getIsotopicclustergraph().vertexSet()) {
if (e.getIsotopicCluster() == null && e.getStatus() == "start") {
return e;
}
}
return null;
}

private IsotopicCluster getEnd(IsotopicClusterGraph icg) {
for (IsotopicCluster e : icg.getIsotopicclustergraph().vertexSet()) {
if (e.getIsotopicCluster() == null && e.getStatus() == "end") {
return e;
}
}
return null;
}
}
8 changes: 4 additions & 4 deletions java/deisotoper/src/main/java/ch/fgcz/proteomics/fbdm/IsotopicClusterGraph.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -99,12 +99,12 @@ public String toDOTGraph() {
return sb.toString();
}

public IsotopicClusterGraph(IsotopicSet is) {
public IsotopicClusterGraph(List<IsotopicCluster> is) {
this.min = Double.MAX_VALUE;
is.getIsotopicSet().add(new IsotopicCluster("start"));
is.add(new IsotopicCluster("start"));

for (IsotopicCluster ic1 : is.getIsotopicSet()) {
for (IsotopicCluster ic2 : is.getIsotopicSet()) {
for (IsotopicCluster ic1 : is) {
for (IsotopicCluster ic2 : is) {
String color = calculateConnection(ic1, ic2);

// Start
Expand Down
6 changes: 3 additions & 3 deletions java/deisotoper/src/main/java/ch/fgcz/proteomics/fbdm/IsotopicMassSpectrum.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -18,10 +18,10 @@ public List<IsotopicSet> getIsotopicMassSpectrum() {
}

public IsotopicMassSpectrum(MassSpectrum massspectrum, double delta, Configuration config) {
this(new Peaklist(massspectrum), delta, config);
this(massspectrum, new Peaklist(massspectrum), delta, config);
}

public IsotopicMassSpectrum(Peaklist peaklist, double delta, Configuration config) {
public IsotopicMassSpectrum(MassSpectrum massspectrum, Peaklist peaklist, double delta, Configuration config) {
int id = 0;
for (int i = 0; i < peaklist.getPeaklist().size(); i++) {
List<Peak> isotopicset = new ArrayList<>();
Expand Down Expand Up @@ -49,7 +49,7 @@ public IsotopicMassSpectrum(Peaklist peaklist, double delta, Configuration confi
}

if (1 < isotopicset.size()) {
IsotopicSet is = new IsotopicSet(isotopicset, delta, id, config);
IsotopicSet is = new IsotopicSet(massspectrum, isotopicset, delta, id, config);
id++;

this.isotopicmassspectrum.add(is);
Expand Down
49 changes: 48 additions & 1 deletion java/deisotoper/src/main/java/ch/fgcz/proteomics/fbdm/IsotopicSet.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -12,8 +12,14 @@
import java.util.List;
import java.util.Set;

import org.jgrapht.GraphPath;

import ch.fgcz.proteomics.dto.MassSpectrum;

public class IsotopicSet {
private List<IsotopicCluster> isotopicset = new ArrayList<>();
private IsotopicClusterGraph icg;
private GraphPath<IsotopicCluster, Connection> bestpath;
private int setID;

public int getSetID() {
Expand All @@ -24,7 +30,28 @@ public List<IsotopicCluster> getIsotopicSet() {
return isotopicset;
}

public IsotopicSet(List<Peak> isotopicset, double delta, int setid, Configuration config) {
public IsotopicClusterGraph getIcg() {
return icg;
}

public GraphPath<IsotopicCluster, Connection> getBestpath() {
return bestpath;
}

private void setBestPath(MassSpectrum ms, List<IsotopicCluster> is, Configuration config) {
IsotopicClusterGraph icg = new IsotopicClusterGraph(is);

icg.scoreIsotopicClusterGraph(ms.getPeptideMass(), ms.getChargeState(), config.getErrortolerance(),
new Peaklist(ms.getMz(), ms.getIntensity()), config);

GraphPath<IsotopicCluster, Connection> bp = icg.bestPath(getStart(icg), getEnd(icg));

this.icg = icg;
this.bestpath = bp;
}

public IsotopicSet(MassSpectrum massspectrum, List<Peak> isotopicset, double delta, int setid,
Configuration config) {
try {
rangeCheck(isotopicset, config);
} catch (Exception e) {
Expand All @@ -48,6 +75,8 @@ public IsotopicSet(List<Peak> isotopicset, double delta, int setid, Configuratio
cluster.setClusterID(clusterid);
clusterid++;
}

setBestPath(massspectrum, is, config);

this.isotopicset = is;
this.setID = setid;
Expand Down Expand Up @@ -143,4 +172,22 @@ private static void rangeCheck(List<Peak> peaks, Configuration config) throws Ex
}
}
}

private IsotopicCluster getStart(IsotopicClusterGraph icg) {
for (IsotopicCluster e : icg.getIsotopicclustergraph().vertexSet()) {
if (e.getIsotopicCluster() == null && e.getStatus() == "start") {
return e;
}
}
return null;
}

private IsotopicCluster getEnd(IsotopicClusterGraph icg) {
for (IsotopicCluster e : icg.getIsotopicclustergraph().vertexSet()) {
if (e.getIsotopicCluster() == null && e.getStatus() == "end") {
return e;
}
}
return null;
}
}
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