/// <summary>
/// Wrapper class for driving all facets of the analysis pipeline
/// </summary>
/// <param name="MS1MatchFilePath"></param>
/// <param name="glycosylationSiteFilePath"></param>
/// <param name="MS2DeconFilePath"></param>
/// <param name="modelFilePath"></param>
/// <param name="pythonInterpreterPath">
/// Passed along to the ScriptManager, used to locate the Python Interpreter executable
/// </param>
/// <param name="rscriptPath">
/// Passed along to the ScriptManager, used to locate the Rscript executable
/// </param>
/// <param name="scriptsRoot">
/// Passed along to the ScriptManager, used to locate the script pipeline files
/// </param>
public AnalysisPipeline(String MS1MatchFilePath, String glycosylationSiteFilePath,
String MS2DeconFilePath, String modelFilePath = null,
String outputFilePath = null, double ms1MatchingTolerance = 1e-5,
double ms2MatchingTolerance = 2e-5, String proteinProspectorXMLFilePath = null, String method = "full_random_forest",
String pythonInterpreterPath = null, String rscriptPath = null,
String scriptsRoot = null, int numProcesses = 2, bool onlyRandomDecoys = false,
int numDecoys = 20)
{
this.MS1MatchFilePath = MS1MatchFilePath;
this.GlycosylationSiteFilePath = glycosylationSiteFilePath;
this.MS2DeconFilePath = MS2DeconFilePath;
this.ModelFilePath = modelFilePath;
this.ResultFilePath = outputFilePath;
this.ResultsTable = null;
this.State = TandemGlycoPeptideTaskState.New;
this.MS1MatchingTolerance = ms1MatchingTolerance;
this.MS2MatchingTolerance = ms2MatchingTolerance;
this.Method = method;
this.ProteinProspectorXMLFilePath = proteinProspectorXMLFilePath;
this.NumDecoys = numDecoys;
this.NumProcesses = numProcesses;
this.OnlyRandomDecoys = onlyRandomDecoys;
//Make sure that all needed resources can be found
this.Scripter = new ScriptManager(pythonInterpreterPath, rscriptPath, scriptsRoot);
Scripter.VerifyFileSystemTargets();
}
public WebResultsViewer(ResultsRepresentation modelData)
{
InitializeComponent();
this.Model = modelData;
this.DataProvider = BootstrapModelString(Model);
this.FileName = Path.GetFileName(Model.SourceFile);
BrowserCtrl.IsWebBrowserContextMenuEnabled = true;
var indexURI = new Uri(Path.Combine(Application.StartupPath, "Web", "index.html")).AbsoluteUri;
BrowserCtrl.ObjectForScripting = this;
BrowserCtrl.Navigate(indexURI);
//Set up page, feeding in data and registering native-web interfaces
BrowserCtrl.DocumentCompleted += new WebBrowserDocumentCompletedEventHandler(delegate(Object o, WebBrowserDocumentCompletedEventArgs e)
{
JavaScriptAction(@"window.objects = window.external.DataProvider;
registerDataChange(PredictionResults.parse(window.external.DataProvider), window.external.FileName);
");
//Remove previously registered click handler and adds native save
//function call
JavaScriptAction("$('#save-results-btn .save-all-results-anchor').off('click').click(function(evt){window.external.SaveResultsToFile()})");
//JavaScriptAction("console.log = window.external.ExternLog");
});
BrowserCtrl.ScriptErrorsSuppressed = false;
}
public ModelLabelView(ResultsRepresentation model)
{
InitializeComponent();
Model = model;
Binder = new BindingSource();
MS2MatchDataGridView.AutoGenerateColumns = false;
MS2MatchDataGridView.AutoSize = false;
MS2MatchDataGridView.AutoSizeColumnsMode = DataGridViewAutoSizeColumnsMode.AllCells;
MS2MatchDataGridView.DataSource = Binder;
InitGridView();
}
/// <summary>
/// Load an already generated results CSV and view it using the WebResultsViewer
/// </summary>
/// <param name="sender"></param>
/// <param name="e"></param>
private void ViewResultsButton_Click(object sender, EventArgs e)
{
Console.WriteLine("Viewing Results");
DialogResult modelFileDialogResult = openFileDialog1.ShowDialog();
if (modelFileDialogResult == DialogResult.OK)
{
try
{
ResultsRepresentation resultFile = new ResultsRepresentation(openFileDialog1.FileName);
WebResultsViewer resultsView = new WebResultsViewer(resultFile);
resultsView.Show();
}
catch (IOException ex)
{
MessageBox.Show("Could not open " + openFileDialog1.FileName +
". Error: " + ex.Message);
}
}
}
/// <summary>
/// View a previously generated model file. If no model is loaded, show an open
/// file dialog and set the model path, and load the model into a ModelLabelView
/// </summary>
/// <param name="sender"></param>
/// <param name="e"></param>
private void ViewModelButton_Click(object sender, EventArgs e)
{
ResultsRepresentation model = null;
try
{
model = new ResultsRepresentation(Controller.ModelFilePath);
}
catch (Exception ex)
{
Console.WriteLine(ex);
bool didSelect = SetModelFilePath_Action(sender, e);
//If the user didn't actually select a model, cancelling the dialog, do nothing
if (!didSelect)
{
return;
}
model = new ResultsRepresentation(Controller.ModelFilePath);
}
var modelView = new ModelLabelView(model);
modelView.Show();
}
/// <summary>
/// Given a ResultsRepresentation, show them in a ModelLabelView
/// </summary>
/// <param name="preparedModelData"></param>
private void ShowModelLabelView(ResultsRepresentation preparedModelData)
{
Console.WriteLine("Showing Model Label View");
ModelLabelView labelView = new ModelLabelView(preparedModelData);
labelView.Show();
}
/// <summary>
/// Given a ResultsRepresentation, show them in a WebResultsView
/// </summary>
/// <param name="classifierData"></param>
private void ShowClassifierResultsView(ResultsRepresentation classifierData)
{
WebResultsViewer resultsView = new WebResultsViewer(classifierData);
resultsView.Show();
}
public ClassifierResultsView(ResultsRepresentation model)
: base(model)
{
InitializeComponent();
Console.WriteLine();
}
public ResultsRepresentation RunReclassification(String targetFilePath, String modelFilePath)
{
String outfile = Scripter.RunReclassifyWithModelTask(targetFilePath, modelFilePath, Method);
ResultsRepresentation resultsTable = new ResultsRepresentation(outfile);
this.ResultFilePath = outfile;
this.ResultsTable = resultsTable;
return resultsTable;
}
public ResultsRepresentation RunModelBuilder()
{
String outfile = Scripter.RunModelBuildingPythonPipeline(this.MS1MatchFilePath,
this.GlycosylationSiteFilePath,
this.MS2DeconFilePath,
ms1MatchingTolerance:this.MS1MatchingTolerance,
ms2MatchingTolerance:this.MS2MatchingTolerance,
proteinProspectorXMLFilePath: this.ProteinProspectorXMLFilePath,
method:Method);
ResultsRepresentation model = new ResultsRepresentation(outfile);
return model;
}
/// <summary>
///
/// </summary>
/// <returns></returns>
public ResultsRepresentation RunClassification()
{
String outfile = Scripter.RunClassificationPythonPipeline(this.MS1MatchFilePath,
this.GlycosylationSiteFilePath,
this.MS2DeconFilePath,
modelDataFilePath:this.ModelFilePath,
ms1MatchingTolerance:this.MS1MatchingTolerance,
ms2MatchingTolerance:this.MS2MatchingTolerance,
proteinProspectorXMLFilePath:this.ProteinProspectorXMLFilePath,
method:Method,
outputFilePath:this.ResultFilePath,
numProcesses: NumProcesses);
this.ResultFilePath = outfile;
ResultsRepresentation resultsTable = new ResultsRepresentation(outfile);
this.ResultsTable = resultsTable;
return resultsTable;
}
/// <summary>
/// Get the raw string contents of the ResultsRepresentation model as a CSV by writing
/// it to a temporary file and reading it back out and returns it.
/// </summary>
/// <param name="model"></param>
/// <returns></returns>
protected string BootstrapModelString(ResultsRepresentation model)
{
string tempFile = Path.GetTempFileName();
StreamWriter tempWriter = new StreamWriter(File.OpenWrite(tempFile));
model.WriteToJson(tempWriter);
string modelString = File.ReadAllText(tempFile);
File.Delete(tempFile);
return modelString;
}