private void dataSourceFilesRadioButton_CheckedChanged(object sender, EventArgs e)
{
panelFilesProps.Visible = dataSourceFilesRadioButton.Checked;
var useFiles = dataSourceFilesRadioButton.Checked;
ceCombo.Visible = !useFiles;
ceLabel.Visible = !useFiles;
if (useFiles)
{
iRTPeptidesLabel.Location = _iRTLabelPos;
comboStandards.Location = _iRTComboPos;
}
else
{
iRTPeptidesLabel.Location = _actionLabelPos;
comboStandards.Location = _actionComboPos;
PrositUIHelpers.CheckPrositSettings(this, _skylineWindow);
}
btnNext.Text = dataSourceFilesRadioButton.Checked ? Resources.BuildLibraryDlg_btnPrevious_Click__Next__ : Resources.BuildLibraryDlg_OkWizardPage_Finish;
}
private void dataSourceFilesRadioButton_CheckedChanged(object sender, EventArgs e)
{
panelFilesProps.Visible = dataSourceFilesRadioButton.Checked;
var useFiles = dataSourceFilesRadioButton.Checked;
ceCombo.Visible = !useFiles;
ceLabel.Visible = !useFiles;
if (useFiles)
{
iRTPeptidesLabel.Location = _iRTLabelPos;
comboStandards.Location = _iRTComboPos;
if (!Settings.Default.IrtStandardList.Contains(IrtStandard.AUTO))
{
Settings.Default.IrtStandardList.Insert(1, IrtStandard.AUTO);
}
}
else
{
iRTPeptidesLabel.Location = _actionLabelPos;
comboStandards.Location = _actionComboPos;
Settings.Default.IrtStandardList.Remove(IrtStandard.AUTO);
PrositUIHelpers.CheckPrositSettings(this, _skylineWindow);
}
_driverStandards.LoadList(IrtStandard.EMPTY.GetKey());
btnNext.Text = dataSourceFilesRadioButton.Checked ? Resources.BuildLibraryDlg_btnPrevious_Click__Next__ : Resources.BuildLibraryDlg_OkWizardPage_Finish;
}
private bool ValidateBuilder(bool validateInputFiles)
{
string name;
if (!_helper.ValidateNameTextBox(textName, out name))
{
return(false);
}
string outputPath = textPath.Text;
if (string.IsNullOrEmpty(outputPath))
{
_helper.ShowTextBoxError(textPath, Resources.BuildLibraryDlg_ValidateBuilder_You_must_specify_an_output_file_path, outputPath);
return(false);
}
if (Directory.Exists(outputPath))
{
_helper.ShowTextBoxError(textPath, Resources.BuildLibraryDlg_ValidateBuilder_The_output_path__0__is_a_directory_You_must_specify_a_file_path, outputPath);
return(false);
}
string outputDir = Path.GetDirectoryName(outputPath);
if (string.IsNullOrEmpty(outputDir) || !Directory.Exists(outputDir))
{
_helper.ShowTextBoxError(textPath, Resources.BuildLibraryDlg_ValidateBuilder_The_directory__0__does_not_exist, outputDir);
return(false);
}
if (!outputPath.EndsWith(BiblioSpecLiteSpec.EXT))
{
outputPath += BiblioSpecLiteSpec.EXT;
}
try
{
using (var sfLib = new FileSaver(outputPath))
{
if (!sfLib.CanSave(this))
{
textPath.Focus();
textPath.SelectAll();
return(false);
}
}
}
catch (UnauthorizedAccessException)
{
_helper.ShowTextBoxError(textPath, TextUtil.LineSeparate(Resources.BuildLibraryDlg_ValidateBuilder_Access_violation_attempting_to_write_to__0__,
Resources.BuildLibraryDlg_ValidateBuilder_Please_check_that_you_have_write_access_to_this_folder_), outputDir);
return(false);
}
catch (IOException)
{
_helper.ShowTextBoxError(textPath, TextUtil.LineSeparate(Resources.BuildLibraryDlg_ValidateBuilder_Failure_attempting_to_create_a_file_in__0__,
Resources.BuildLibraryDlg_ValidateBuilder_Please_check_that_you_have_write_access_to_this_folder_), outputDir);
return(false);
}
double cutOffScore;
if (!_helper.ValidateDecimalTextBox(textCutoff, 0, 1.0, out cutOffScore))
{
return(false);
}
Settings.Default.LibraryResultCutOff = cutOffScore;
var libraryBuildAction = LibraryBuildAction;
if (validateInputFiles)
{
var inputFilesChosen = new List <string>();
foreach (int i in listInputFiles.CheckedIndices)
{
inputFilesChosen.Add(_inputFileNames[i]);
}
List <Target> targetPeptidesChosen = null;
if (cbFilter.Checked)
{
targetPeptidesChosen = new List <Target>();
var doc = _documentUiContainer.Document;
foreach (PeptideDocNode nodePep in doc.Peptides)
{
// Add light modified sequences
targetPeptidesChosen.Add(nodePep.ModifiedTarget);
// Add heavy modified sequences
foreach (var nodeGroup in nodePep.TransitionGroups)
{
if (nodeGroup.TransitionGroup.LabelType.IsLight)
{
continue;
}
targetPeptidesChosen.Add(doc.Settings.GetModifiedSequence(nodePep.Peptide.Target,
nodeGroup.TransitionGroup.LabelType,
nodePep.ExplicitMods));
}
}
}
if (prositDataSourceRadioButton.Checked)
{
// TODO: Need to figure out a better way to do this, use PrositPeptidePrecursorPair?
var doc = _documentUiContainer.DocumentUI;
var peptides = doc.Peptides.ToArray();
var precursorCount = doc.PeptideTransitionGroupCount;
var peptidesPerPrecursor = new PeptideDocNode[precursorCount];
var precursors = new TransitionGroupDocNode[precursorCount];
int index = 0;
for (var i = 0; i < peptides.Length; ++i)
{
var groups = peptides[i].TransitionGroups.ToArray();
Array.Copy(Enumerable.Repeat(peptides[i], groups.Length).ToArray(), 0, peptidesPerPrecursor, index,
groups.Length);
Array.Copy(groups, 0, precursors, index, groups.Length);
index += groups.Length;
}
try
{
PrositUIHelpers.CheckPrositSettings(this, _skylineWindow);
// Still construct the library builder, otherwise a user might configure Prosit
// incorrectly, causing the build to silently fail
Builder = new PrositLibraryBuilder(doc, name, outputPath, () => true, IrtStandard,
peptidesPerPrecursor, precursors, NCE);
}
catch (Exception ex)
{
_helper.ShowTextBoxError(this, ex.Message);
return(false);
}
}
else
{
Builder = new BiblioSpecLiteBuilder(name, outputPath, inputFilesChosen, targetPeptidesChosen)
{
Action = libraryBuildAction,
IncludeAmbiguousMatches = cbIncludeAmbiguousMatches.Checked,
KeepRedundant = LibraryKeepRedundant,
CutOffScore = cutOffScore,
Id = Helpers.MakeId(textName.Text),
IrtStandard = _driverStandards.SelectedItem,
PreferEmbeddedSpectra = PreferEmbeddedSpectra
};
}
}
return(true);
}
