//Other Functions#######################################################
//This function loads the current feature and output it.
public Feature readFeature()
{
Feature Ans = new Feature();
try
{
String path = Application.StartupPath + "\\FeatureCurrent.fea";
FileStream FS = new FileStream(path, FileMode.Open, FileAccess.Read);
StreamReader read1 = new StreamReader(FS);
String line = read1.ReadLine();
String[] Lines = line.Split(',');
Ans.Initial = Convert.ToDouble(Lines[0]);
Ans.numChargeStates = Convert.ToDouble(Lines[1]);
Ans.ScanDensity = Convert.ToDouble(Lines[2]);
Ans.numModiStates = Convert.ToDouble(Lines[3]);
Ans.totalVolume = Convert.ToDouble(Lines[4]);
Ans.ExpectedA = Convert.ToDouble(Lines[5]);
Ans.CentroidScan = Convert.ToDouble(Lines[6]);
Ans.numOfScan = Convert.ToDouble(Lines[7]);
Ans.avgSigNoise = Convert.ToDouble(Lines[8]);
read1.Close();
FS.Close();
}
catch
{
try
{
String path = Application.StartupPath + "\\FeatureDefault.fea";
FileStream FS2 = new FileStream(path, FileMode.Open, FileAccess.Read);
StreamReader read2 = new StreamReader(FS2);
String line = read2.ReadLine();
String[] Lines = line.Split(',');
Ans.Initial = Convert.ToDouble(Lines[0]);
Ans.numChargeStates = Convert.ToDouble(Lines[1]);
Ans.ScanDensity = Convert.ToDouble(Lines[2]);
Ans.numModiStates = Convert.ToDouble(Lines[3]);
Ans.totalVolume = Convert.ToDouble(Lines[4]);
Ans.ExpectedA = Convert.ToDouble(Lines[5]);
Ans.CentroidScan = Convert.ToDouble(Lines[6]);
Ans.numOfScan = Convert.ToDouble(Lines[7]);
Ans.avgSigNoise = Convert.ToDouble(Lines[8]);
read2.Close();
FS2.Close();
}
catch (Exception ex)
{
//MessageBox.Show("Unable to load feature files. Error code:" + ex);
}
}
return Ans;
}
public List<ResultsGroup>[] run(OpenFileDialog FileLinks)
{
List<ResultsGroup>[] AllFinalResults = new List<ResultsGroup>[Convert.ToInt32(FileLinks.FileNames.Count())];
Int32 Count = 0;
//Each data file is treated separately, hence the for loop.
foreach (String filename in FileLinks.FileNames)
{
//Get the Parameters.
ParametersForm parameter = new ParametersForm();
ParametersForm.ParameterSettings paradata = parameter.GetParameters();
//Perform the First and second grouping and getting data for the features by the Grouping function.
List<ResultsGroup> LRLR = new List<ResultsGroup>();
LRLR = Groupings(filename, paradata);
//##############Logistic Regression####################
Features fe = new Features();
//current features
Feature featureData = fe.readFeature();
//default features
String defaultpath = Application.StartupPath + "\\FeatureDefault.fea";
Feature defaultData = fe.readFeature(defaultpath);
//Features that will be used
Feature finalfeatureData = new Feature();
//Here are the beta values in logistic regression.
finalfeatureData.Initial = featureData.Initial * 0.5 + defaultData.Initial * 0.5;
finalfeatureData.numChargeStates = featureData.numChargeStates * 0.5 + defaultData.numChargeStates * 0.5;
finalfeatureData.ScanDensity = featureData.ScanDensity * 0.5 + defaultData.ScanDensity * 0.5;
finalfeatureData.numModiStates = featureData.numModiStates * 0.5 + defaultData.numModiStates * 0.5;
finalfeatureData.totalVolume = featureData.totalVolume * 0.5 + defaultData.totalVolume * 0.5;
finalfeatureData.ExpectedA = featureData.ExpectedA * 0.5 + defaultData.ExpectedA * 0.5;
finalfeatureData.CentroidScan = featureData.CentroidScan * 0.5 + defaultData.CentroidScan * 0.5;
finalfeatureData.numOfScan = featureData.numOfScan * 0.5 + defaultData.numOfScan * 0.5;
finalfeatureData.avgSigNoise = featureData.avgSigNoise * 0.5 + defaultData.avgSigNoise * 0.5;
//Generate scores.
SupervisedLearner sl = new SupervisedLearner();
AllFinalResults[Count] = sl.Scorings(LRLR, finalfeatureData, paradata);
Count++;
}
return AllFinalResults;
}
public List<ResultsGroup>[] evaluate(OpenFileDialog FileLinks, Feature featureData)
{
List<ResultsGroup>[] AllFinalResults = new List<ResultsGroup>[Convert.ToInt32(FileLinks.FileNames.Count())];
Int32 Count = 0;
//Each data file is treated separately, hence the for loop.
foreach (String filename in FileLinks.FileNames)
{
//Get the Parameters.
ParametersForm parameterForm = new ParametersForm();
ParametersForm.ParameterSettings parameters = parameterForm.GetParameters();
//Perform the First and second grouping and getting data for the features by the Grouping function.
List<ResultsGroup> LRLR = new List<ResultsGroup>();
LRLR = Groupings(filename, parameters);
//Generate scores.
SupervisedLearner sl = new SupervisedLearner();
AllFinalResults[Count] = sl.Scorings(LRLR, featureData, parameters);
Count++;
}
return AllFinalResults;
}
//This is used by the Features class to evaluate the features
public List<ResultsGroup>[] EvaluateFeature(OpenFileDialog FileLinks, List<CompositionHypothesisEntry> comhyp, Feature dfeatureData)
{
//Initialize storage variables.
List<ResultsGroup>[] AllFinalResults = new List<ResultsGroup>[Convert.ToInt32(FileLinks.FileNames.Count())];
Int32 Count = 0;
//Each data file is treated separately, hence the for loop.
foreach (String filename in FileLinks.FileNames)
{
//Get the Parameters.
ParametersForm parameter = new ParametersForm();
ParametersForm.ParameterSettings paradata = parameter.GetParameters();
//Perform the First and second grouping, matching and getting data for the features by the Grouping function.
Double Mas = new Double();
Mas = adductMass(comhyp);
List<ResultsGroup> LRLR = new List<ResultsGroup>();
LRLR = Groupings(filename, paradata, Mas, comhyp);
//Error prevention
if (LRLR.Count == 1)
{
MessageBox.Show("There is no match between the hypothesis and the data. Unable to generate results from the file:" + filename);
List<ResultsGroup> FinalResult = LRLR;
AllFinalResults[Count] = FinalResult;
Count++;
continue;
}
//##############Logistic Regression####################
Feature featureData = FitLogisticRegression(LRLR);
//Generate scores.
AllFinalResults[Count] = Scorings(LRLR, featureData, paradata);
Count++;
}
return AllFinalResults;
}
private void oFDLoadFeature_FileOk(object sender, CancelEventArgs e)
{
//Read Feature from file
Feature Ans = new Feature();
String path = oFDLoadFeature.FileName;
FileStream FS = new FileStream(path, FileMode.Open, FileAccess.Read);
StreamReader read1 = new StreamReader(FS);
String line = read1.ReadLine();
String[] Lines = line.Split(',');
Ans.Initial = Convert.ToDouble(Lines[0]);
Ans.numChargeStates = Convert.ToDouble(Lines[1]);
Ans.ScanDensity = Convert.ToDouble(Lines[2]);
Ans.numModiStates = Convert.ToDouble(Lines[3]);
Ans.totalVolume = Convert.ToDouble(Lines[4]);
Ans.ExpectedA = Convert.ToDouble(Lines[5]);
Ans.CentroidScan = Convert.ToDouble(Lines[6]);
Ans.numOfScan = Convert.ToDouble(Lines[7]);
Ans.avgSigNoise = Convert.ToDouble(Lines[8]);
read1.Close();
FS.Close();
//Write feature to storage.
String currentpath = Application.StartupPath + "\\FeatureCurrent.fea";
FileStream FS2 = new FileStream(currentpath, FileMode.Create, FileAccess.Write);
StreamWriter Write1 = new StreamWriter(FS2);
Write1.Write(Ans.Initial + "," + Ans.numChargeStates + "," + Ans.ScanDensity + "," + Ans.numModiStates + "," + Ans.totalVolume + "," + Ans.ExpectedA + "," + Ans.CentroidScan + "," + Ans.numOfScan + "," + Ans.avgSigNoise);
Write1.Flush();
Write1.Close();
FS.Close();
}
void bw_DoWork(object sender, DoWorkEventArgs e)
{
//Obtain Feature
Feature Ans = new Feature();
SupervisedLearner SL = new SupervisedLearner();
CompositionHypothesisTabbedForm comp = new CompositionHypothesisTabbedForm();
List<CompositionHypothesisEntry> comhy = comp.getCompHypo(oFDComposition.FileName);
Ans = SL.obtainFeatures(oFDTrain, comhy);
//Write Features to File
String path = Application.StartupPath + "\\FeatureCurrent.fea";
FileStream FS = new FileStream(path, FileMode.Create, FileAccess.Write);
StreamWriter Write1 = new StreamWriter(FS);
Write1.Write(Ans.Initial + "," + Ans.numChargeStates + "," + Ans.ScanDensity + "," + Ans.numModiStates + "," + Ans.totalVolume + "," + Ans.ExpectedA + "," + Ans.CentroidScan + "," + Ans.numOfScan + "," + Ans.avgSigNoise);
Write1.Flush();
Write1.Close();
FS.Close();
}
//This is used by the Feature Class to generate Features
public Feature obtainFeatures(OpenFileDialog FileLinks, List<CompositionHypothesisEntry> comhyp)
{
List<Double> Ini = new List<Double>();
List<Double> nCS = new List<Double>();
List<Double> SD = new List<Double>();
List<Double> nMS = new List<Double>();
List<Double> tV = new List<Double>();
List<Double> EA = new List<Double>();
List<Double> CS = new List<Double>();
List<Double> NS = new List<Double>();
List<Double> SN = new List<Double>();
//Each data file is treated separately, hence the for loop.
foreach (String filename in FileLinks.FileNames)
{
//Get the Parameters.
ParametersForm parameter = new ParametersForm();
ParametersForm.ParameterSettings paradata = parameter.GetParameters();
//Perform the First and second grouping, matching and getting data for the features by the Grouping function.
Double Mas = new Double();
Mas = adductMass(comhyp);
List<ResultsGroup> LRLR = new List<ResultsGroup>();
LRLR = Groupings(filename, paradata, Mas, comhyp);
//Error prevention
if (LRLR.Count == 1)
{
MessageBox.Show("There is no match between the hypothesis and the data. Unable to generate results from the file:" + filename);
continue;
}
//##############Logistic Regression####################
//Perform logistic regression to get the Parameters
Feature featureData = new Feature();
featureData = FitLogisticRegression(LRLR);
Ini.Add(featureData.Initial);
nCS.Add(featureData.numChargeStates);
SD.Add(featureData.ScanDensity);
nMS.Add(featureData.numModiStates);
tV.Add(featureData.totalVolume);
EA.Add(featureData.ExpectedA);
CS.Add(featureData.CentroidScan);
NS.Add(featureData.numOfScan);
SN.Add(featureData.avgSigNoise);
}
// Get the average of all features.
Feature finalans = new Feature();
finalans.Initial = Ini.Average();
finalans.numChargeStates = nCS.Average();
finalans.ScanDensity = SD.Average();
finalans.numModiStates = nMS.Average();
finalans.totalVolume = tV.Average();
finalans.ExpectedA = EA.Average();
finalans.CentroidScan = CS.Average();
finalans.numOfScan = NS.Average();
finalans.avgSigNoise = SN.Average();
return finalans;
}
//This class performs logistic regression from data obtained from the Groupings Function
private Feature FitLogisticRegression(List<ResultsGroup> LRLR)
{
int numofMatches = 0;
//now, put LRLR into a table of arrays so that the regression function can read it.
Double[][] inputs = new Double[LRLR.Count][];
Double[] output = new Double[LRLR.Count];
for (int i = 0; i < LRLR.Count; i++)
{
inputs[i] = new Double[] { Convert.ToDouble(LRLR[i].NumChargeStates), Convert.ToDouble(LRLR[i].ScanDensity), Convert.ToDouble(LRLR[i].NumModiStates), Convert.ToDouble(LRLR[i].TotalVolume), Convert.ToDouble(LRLR[i].ExpectedA), Convert.ToDouble(LRLR[i].CentroidScan), Convert.ToDouble(LRLR[i].NumOfScan), Convert.ToDouble(LRLR[i].AvgSigNoise) };
output[i] = Convert.ToDouble(LRLR[i].Match);
if (LRLR[i].Match == true)
numofMatches++;
}
if (numofMatches < 10)
{
Features FeaturesMenu = new Features();
Feature defaultFeatures = FeaturesMenu.readFeature();
MessageBox.Show("Warning: there are less than 10 matches. Currently Loaded Features will be used instead.");
return defaultFeatures;
}
//Perform logistic regression to get the Parameters
LogisticRegression regression = new LogisticRegression(inputs: 8);
var results = new IterativeReweightedLeastSquares(regression);
double delta = 0;
do
{
// Perform an iteration
delta = results.Run(inputs, output);
} while (delta > 0.001);
Feature answer = new Feature();
//Here are the beta values in logistic regression.
answer.Initial = regression.Coefficients[0];
answer.numChargeStates = regression.Coefficients[1];
answer.ScanDensity = regression.Coefficients[2];
answer.numModiStates = regression.Coefficients[3];
answer.totalVolume = regression.Coefficients[4];
answer.ExpectedA = regression.Coefficients[5];
answer.CentroidScan = regression.Coefficients[6];
answer.numOfScan = regression.Coefficients[7];
answer.avgSigNoise = regression.Coefficients[8];
return answer;
}
//This runs the linear regression and generate score for the grouping results
public List<ResultsGroup> Scorings(List<ResultsGroup> LRLR, Feature featureData, ParametersForm.ParameterSettings paradata)
{
//Now, load current features from the software, if it doesn't exist, use default features.
Features fea = new Features();
Feature dfeatureData = fea.readFeature();
String defaultpath = Application.StartupPath + "\\FeatureDefault.fea";
Feature defaultData = fea.readFeature(defaultpath);
Double initial = featureData.Initial * 0.9 + dfeatureData.Initial * 0.05 + defaultData.Initial * 0.05;
Double bnumChargeStates = featureData.numChargeStates * 0.9 + dfeatureData.numChargeStates * 0.05 + defaultData.numChargeStates * 0.05;
Double bScanDensity = featureData.ScanDensity * 0.9 + dfeatureData.ScanDensity * 0.05 + defaultData.ScanDensity * 0.05;
Double bnumModiStates = featureData.numModiStates * 0.9 + dfeatureData.numModiStates * 0.05 + defaultData.numModiStates * 0.05;
Double btotalVolume = featureData.totalVolume * 0.9 + dfeatureData.totalVolume * 0.05 + defaultData.totalVolume * 0.05;
Double bExpectedA = featureData.ExpectedA * 0.9 + dfeatureData.totalVolume * 0.05 + defaultData.totalVolume * 0.05;
Double bCentroid = featureData.CentroidScan * 0.9 + dfeatureData.CentroidScan * 0.05 + defaultData.CentroidScan * 0.05;
Double bnumOfScan = featureData.numOfScan * 0.9 + dfeatureData.numOfScan * 0.05 + defaultData.numOfScan * 0.05;
Double bavgSigNoise = featureData.avgSigNoise * 0.9 + dfeatureData.avgSigNoise * 0.05 + defaultData.avgSigNoise * 0.05;
if (dfeatureData.Initial != defaultData.Initial)
{
//Here are the beta values in logistic regression. 0.75 is from default, 0.25 is from calculation.
initial = featureData.Initial * 0.7 + dfeatureData.Initial * 0.2 + defaultData.Initial * 0.1;
bnumChargeStates = featureData.numChargeStates * 0.7 + dfeatureData.numChargeStates * 0.2 + defaultData.numChargeStates * 0.1;
bScanDensity = featureData.ScanDensity * 0.7 + dfeatureData.ScanDensity * 0.2 + defaultData.ScanDensity * 0.1;
bnumModiStates = featureData.numModiStates * 0.7 + dfeatureData.numModiStates * 0.2 + defaultData.numModiStates * 0.1;
btotalVolume = featureData.totalVolume * 0.7 + dfeatureData.totalVolume * 0.2 + defaultData.totalVolume * 0.1;
bExpectedA = featureData.ExpectedA * 0.7 + dfeatureData.totalVolume * 0.2 + defaultData.totalVolume * 0.1;
bCentroid = featureData.CentroidScan * 0.7 + dfeatureData.CentroidScan * 0.2 + defaultData.CentroidScan * 0.1;
bnumOfScan = featureData.numOfScan * 0.7 + dfeatureData.numOfScan * 0.2 + defaultData.numOfScan * 0.1;
bavgSigNoise = featureData.avgSigNoise * 0.7 + dfeatureData.avgSigNoise * 0.2 + defaultData.avgSigNoise * 0.1;
}
Double e = Math.E;
try
{
//Now calculate the scores for each of them.
Double scoreInput = new Double();
Double Score = new Double();
for (int o = 0; o < LRLR.Count; o++)
{
scoreInput = (initial + bnumChargeStates * Convert.ToDouble(LRLR[o].NumChargeStates) + bScanDensity * Convert.ToDouble(LRLR[o].ScanDensity) + bnumModiStates * Convert.ToDouble(LRLR[o].NumModiStates) + btotalVolume * Convert.ToDouble(LRLR[o].TotalVolume) + bExpectedA * Convert.ToDouble(LRLR[o].ExpectedA) + bCentroid * Convert.ToDouble(LRLR[o].CentroidScan) + bnumOfScan * Convert.ToDouble(LRLR[o].NumOfScan) + bavgSigNoise * Convert.ToDouble(LRLR[o].AvgSigNoise));
Double store = Math.Pow(e, (-1 * scoreInput));
Score = 1 / (1 + store);
if (Score >= 0.5)
{
store = Math.Pow(e, (-0.6 * scoreInput));
Score = (0.8512 / (1 + store)) + 0.1488;
}
else
{
store = Math.Pow(e, (-0.6 * scoreInput -0.3));
Score = 1 / (1 + store);
}
LRLR[o].Score = Score;
}
//Implement score threshold
LRLR = LRLR.OrderByDescending(a => a.Score).ToList();
if (LRLR[0].Score + LRLR[1].Score + LRLR[2].Score > 2.94)
{
scoreInput = (initial + bnumChargeStates * Convert.ToDouble(LRLR[0].NumChargeStates) + bScanDensity * Convert.ToDouble(LRLR[0].ScanDensity) + bnumModiStates * Convert.ToDouble(LRLR[0].NumModiStates) + btotalVolume * Convert.ToDouble(LRLR[0].TotalVolume) + bExpectedA * Convert.ToDouble(LRLR[0].ExpectedA) + bCentroid * Convert.ToDouble(LRLR[0].CentroidScan) + bnumOfScan * Convert.ToDouble(LRLR[0].NumOfScan) + bavgSigNoise * Convert.ToDouble(LRLR[0].AvgSigNoise));
scoreInput = scoreInput + (initial + bnumChargeStates * Convert.ToDouble(LRLR[1].NumChargeStates) + bScanDensity * Convert.ToDouble(LRLR[1].ScanDensity) + bnumModiStates * Convert.ToDouble(LRLR[1].NumModiStates) + btotalVolume * Convert.ToDouble(LRLR[1].TotalVolume) + bExpectedA * Convert.ToDouble(LRLR[1].ExpectedA) + bCentroid * Convert.ToDouble(LRLR[1].CentroidScan) + bnumOfScan * Convert.ToDouble(LRLR[1].NumOfScan) + bavgSigNoise * Convert.ToDouble(LRLR[1].AvgSigNoise));
scoreInput = scoreInput + (initial + bnumChargeStates * Convert.ToDouble(LRLR[2].NumChargeStates) + bScanDensity * Convert.ToDouble(LRLR[2].ScanDensity) + bnumModiStates * Convert.ToDouble(LRLR[2].NumModiStates) + btotalVolume * Convert.ToDouble(LRLR[2].TotalVolume) + bExpectedA * Convert.ToDouble(LRLR[2].ExpectedA) + bCentroid * Convert.ToDouble(LRLR[2].CentroidScan) + bnumOfScan * Convert.ToDouble(LRLR[2].NumOfScan) + bavgSigNoise * Convert.ToDouble(LRLR[2].AvgSigNoise));
scoreInput = scoreInput / 3;
Double n = -2.9444389791664404600090274318879 / scoreInput;
for (int o = 0; o < LRLR.Count; o++)
{
if (LRLR[o].Score >= 0.57444251681)
{
scoreInput = (initial + bnumChargeStates * Convert.ToDouble(LRLR[o].NumChargeStates) + bScanDensity * Convert.ToDouble(LRLR[o].ScanDensity) + bnumModiStates * Convert.ToDouble(LRLR[o].NumModiStates) + btotalVolume * Convert.ToDouble(LRLR[o].TotalVolume) + bExpectedA * Convert.ToDouble(LRLR[o].ExpectedA) + bCentroid * Convert.ToDouble(LRLR[o].CentroidScan) + bnumOfScan * Convert.ToDouble(LRLR[o].NumOfScan) + bavgSigNoise * Convert.ToDouble(LRLR[o].AvgSigNoise));
Double store = Math.Pow(e, (n* scoreInput));
Score = (0.8512 / (1 + store)) + 0.1488;
LRLR[o].Score = Score;
}
}
}
Int32 scoreCutOff = LRLR.Count() + 1;
for (int t = 0; t < LRLR.Count(); t++)
{
if (LRLR[t].Score < paradata.MinScoreThreshold)
{
scoreCutOff = t;
break;
}
}
if (scoreCutOff != LRLR.Count() + 1)
{
LRLR.RemoveRange(scoreCutOff, LRLR.Count() - scoreCutOff);
}
}
catch
{
for (int o = 0; o < LRLR.Count; o++)
{
LRLR[o].Score = 0;
}
}
return LRLR;
}
