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frmMain.cs
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frmMain.cs
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using System;
using System.Collections.Generic;
// -------------------------------------------------------------------------------
// Written by Matthew Monroe for the Department of Energy (PNNL, Richland, WA)
// Program started October 11, 2003
// Copyright 2005, Battelle Memorial Institute. All Rights Reserved.
// E-mail: [email protected] or [email protected]
// Website: https://github.com/PNNL-Comp-Mass-Spec/ or https://panomics.pnnl.gov/ or https://www.pnnl.gov/integrative-omics
// -------------------------------------------------------------------------------
//
// Licensed under the 2-Clause BSD License; you may not use this file except
// in compliance with the License. You may obtain a copy of the License at
// https://opensource.org/licenses/BSD-2-Clause
using System.ComponentModel;
using System.Data;
using System.Diagnostics;
using System.Globalization;
using System.IO;
using System.Text;
using System.Threading;
using System.Windows.Forms;
using MASIC.DataInput;
using MASIC.Options;
using PRISM;
using PRISM.FileProcessor;
using PRISMDatabaseUtils;
using PRISMWin;
using ProgressFormNET;
using ShFolderBrowser.FolderBrowser;
namespace MASIC
{
/// <summary>
/// Main GUI window
/// </summary>
public partial class frmMain : Form
{
// ReSharper disable CommentTypo
// Ignore Spelling: Acet, Acq, Acetylated, amine, Checkbox, Combobox, CrLf, csv, Da, dpi, fracking frmMain
// Ignore Spelling: Golay, immonium, iTraq, Lys, mzml, Orbitrap Savitzky, Textbox
// ReSharper restore CommentTypo
/// <summary>
/// Constructor
/// </summary>
public frmMain() : base()
{
// This call is required by the Windows Form Designer.
InitializeComponent();
// Add any initialization after the InitializeComponent() call
mCacheOptions = new SpectrumCacheOptions();
mDefaultCustomSICList = new List<CustomSICEntryType>();
mLogMessages = new List<string>();
mReporterIonIndexToModeMap = new Dictionary<int, clsReporterIons.ReporterIonMassModeConstants>();
InitializeControls();
mMasic = new clsMASIC();
RegisterEvents(mMasic);
}
private const string XML_SETTINGS_FILE_NAME = "MASICParameters.xml";
private const string CUSTOM_SIC_VALUES_DATA_TABLE = "PeakMatchingThresholds";
private const string COL_NAME_MZ = "MZ";
private const string COL_NAME_MZ_TOLERANCE = "MZToleranceDa";
private const string COL_NAME_SCAN_CENTER = "Scan_Center";
private const string COL_NAME_SCAN_TOLERANCE = "Scan_Tolerance";
private const string COL_NAME_SCAN_COMMENT = "Scan_Comment";
private const string COL_NAME_CUSTOM_SIC_VALUE_ROW_ID = "UniqueRowID";
private struct CustomSICEntryType
{
public double MZ;
public float ScanCenter;
public string Comment;
}
private DataSet mCustomSICValuesDataset;
private readonly List<CustomSICEntryType> mDefaultCustomSICList;
private bool mWorking;
private string mXmlSettingsFilePath;
private string mPreferredInputFileExtension;
private readonly SpectrumCacheOptions mCacheOptions;
private bool mSuppressNoParentIonsError;
private bool mCompressMSSpectraData;
private bool mCompressMSMSSpectraData;
private double mCompressToleranceDivisorForDa;
private double mCompressToleranceDivisorForPPM;
private int mHeightAdjustForce;
private DateTime mHeightAdjustTime;
private readonly clsMASIC mMasic;
private frmProgress mProgressForm;
/// <summary>
/// Log messages, including warnings and errors, with the newest message at the top
/// </summary>
// ReSharper disable once CollectionNeverQueried.Local
private readonly List<string> mLogMessages;
private readonly Dictionary<int, clsReporterIons.ReporterIonMassModeConstants> mReporterIonIndexToModeMap;
private clsReporterIons.ReporterIonMassModeConstants SelectedReporterIonMode
{
get
{
return GetSelectedReporterIonMode();
}
set
{
try
{
cboReporterIonMassMode.SelectedIndex = GetReporterIonIndexFromMode(value);
}
catch (Exception)
{
// Ignore errors here
}
}
}
private void AddCustomSICRow(
double mz,
double mzToleranceDa,
float scanOrAcqTimeCenter,
float scanOrAcqTimeTolerance,
string comment,
out bool existingRowFound)
{
existingRowFound = false;
foreach (DataRow myDataRow in mCustomSICValuesDataset.Tables[CUSTOM_SIC_VALUES_DATA_TABLE].Rows)
{
if (Math.Abs(double.Parse(myDataRow[0].ToString()) - mz) < float.Epsilon &&
Math.Abs(float.Parse(myDataRow[1].ToString()) - scanOrAcqTimeCenter) < float.Epsilon)
{
existingRowFound = true;
break;
}
}
comment ??= string.Empty;
if (!existingRowFound)
{
var newDataRow = mCustomSICValuesDataset.Tables[CUSTOM_SIC_VALUES_DATA_TABLE].NewRow();
newDataRow[0] = Math.Round(mz, 4);
newDataRow[1] = Math.Round(mzToleranceDa, 4);
newDataRow[2] = Math.Round(scanOrAcqTimeCenter, 6);
newDataRow[3] = Math.Round(scanOrAcqTimeTolerance, 6);
newDataRow[4] = comment;
mCustomSICValuesDataset.Tables[CUSTOM_SIC_VALUES_DATA_TABLE].Rows.Add(newDataRow);
}
}
private void AppendCustomSICListItem(double mz, float scanCenter, string comment)
{
var customSicEntryItem = new CustomSICEntryType
{
MZ = mz,
ScanCenter = scanCenter,
Comment = comment
};
mDefaultCustomSICList.Add(customSicEntryItem);
}
private void AppendReporterIonMassMode(clsReporterIons.ReporterIonMassModeConstants reporterIonMassMode, string description)
{
cboReporterIonMassMode.Items.Add(description);
var currentIndex = cboReporterIonMassMode.Items.Count - 1;
// Add or update the value for key currentIndex
mReporterIonIndexToModeMap[currentIndex] = reporterIonMassMode;
}
private void AppendToLog(EventLogEntryType messageType, string message)
{
if (message.StartsWith("ProcessingStats") || message.StartsWith("Parameter file not specified"))
{
return;
}
string textToAppend;
var doEvents = false;
switch (messageType)
{
case EventLogEntryType.Error:
textToAppend = "Error: " + message;
tbsOptions.SelectTab(tbsOptions.TabCount - 1);
doEvents = true;
break;
case EventLogEntryType.Warning:
textToAppend = "Warning: " + message;
tbsOptions.SelectTab(tbsOptions.TabCount - 1);
doEvents = true;
break;
default:
// Includes Case EventLogEntryType.Information
textToAppend = message;
break;
}
mLogMessages.Insert(0, textToAppend);
txtLogMessages.AppendText(textToAppend + Environment.NewLine);
txtLogMessages.ScrollToCaret();
if (doEvents)
{
Application.DoEvents();
}
}
private void AutoPopulateCustomSICValues(bool confirmReplaceExistingResults)
{
GetCurrentCustomSICTolerances(out var defaultMZTolerance, out var defaultScanOrAcqTimeTolerance);
if (defaultScanOrAcqTimeTolerance > 1)
{
defaultScanOrAcqTimeTolerance = 0.6F;
}
if (ClearCustomSICList(confirmReplaceExistingResults))
{
// The default values use relative times, so make sure that mode is enabled
SetCustomSICToleranceType(clsCustomSICList.CustomSICScanTypeConstants.Relative);
txtCustomSICScanOrAcqTimeTolerance.Text = defaultScanOrAcqTimeTolerance.ToString(CultureInfo.InvariantCulture);
foreach (var item in mDefaultCustomSICList)
{
AddCustomSICRow(item.MZ, defaultMZTolerance, item.ScanCenter, defaultScanOrAcqTimeTolerance, item.Comment, out _);
}
}
}
private bool mUpdating;
private void CatchUnrequestedHeightChange()
{
if (mUpdating)
return;
if (mHeightAdjustForce == 0 || DateTime.UtcNow.Subtract(mHeightAdjustTime).TotalSeconds > 5.0)
return;
try
{
mUpdating = true;
Height = mHeightAdjustForce;
mHeightAdjustForce = 0;
mHeightAdjustTime = DateTime.Parse("1900-01-01");
}
catch (Exception)
{
// Ignore errors here
}
finally
{
mUpdating = false;
}
}
private void AutoToggleReporterIonStatsEnabled()
{
if (SelectedReporterIonMode == clsReporterIons.ReporterIonMassModeConstants.CustomOrNone)
{
if (chkReporterIonStatsEnabled.Checked)
{
chkReporterIonStatsEnabled.Checked = false;
}
}
else if (!chkReporterIonStatsEnabled.Checked)
{
chkReporterIonStatsEnabled.Checked = true;
}
}
private void AutoToggleReporterIonStatsMode()
{
if (chkReporterIonStatsEnabled.Checked)
{
if (SelectedReporterIonMode == clsReporterIons.ReporterIonMassModeConstants.CustomOrNone)
{
SelectedReporterIonMode = clsReporterIons.ReporterIonMassModeConstants.ITraqFourMZ;
}
}
else if (SelectedReporterIonMode != clsReporterIons.ReporterIonMassModeConstants.CustomOrNone)
{
SelectedReporterIonMode = clsReporterIons.ReporterIonMassModeConstants.CustomOrNone;
}
}
private void ClearAllRangeFilters()
{
txtScanStart.Text = "0";
txtScanEnd.Text = "0";
txtTimeStart.Text = "0";
txtTimeEnd.Text = "0";
}
/// <summary>
/// Clear the custom SIC list
/// </summary>
/// <param name="confirmReplaceExistingResults"></param>
/// <returns>
/// True if the CUSTOM_SIC_VALUES_DATA_TABLE is empty or if it was cleared
/// False if the user is queried about clearing and they do not click Yes
/// </returns>
private bool ClearCustomSICList(bool confirmReplaceExistingResults)
{
if (mCustomSICValuesDataset.Tables[CUSTOM_SIC_VALUES_DATA_TABLE].Rows.Count == 0)
return true;
DialogResult result;
if (confirmReplaceExistingResults)
{
result = MessageBox.Show("Are you sure you want to clear the Custom SIC list?", "Clear Custom SICs", MessageBoxButtons.YesNoCancel, MessageBoxIcon.Question, MessageBoxDefaultButton.Button2);
}
else
{
result = DialogResult.Yes;
}
if (result == DialogResult.Yes)
{
mCustomSICValuesDataset.Tables[CUSTOM_SIC_VALUES_DATA_TABLE].Rows.Clear();
return true;
}
return false;
}
private bool ConfirmPaths()
{
if (txtInputFilePath.TextLength == 0)
{
MessageBox.Show("Please define an input file path", "Missing Value", MessageBoxButtons.OK, MessageBoxIcon.Exclamation);
txtInputFilePath.Focus();
return false;
}
if (txtOutputDirectoryPath.TextLength == 0)
{
MessageBox.Show("Please define an output directory path", "Missing Value", MessageBoxButtons.OK, MessageBoxIcon.Exclamation);
txtOutputDirectoryPath.Focus();
return false;
}
return true;
}
private string CStrSafe(object item)
{
try
{
if (item == null)
{
return string.Empty;
}
if (Convert.IsDBNull(item))
{
return string.Empty;
}
return Convert.ToString(item);
}
catch (Exception)
{
return string.Empty;
}
}
private void DefineDefaultCustomSICList()
{
mDefaultCustomSICList.Clear();
this.AppendCustomSICListItem(824.47422, 0.176F, "Pep-09");
this.AppendCustomSICListItem(412.74102, 0.176F, "Pep-09");
this.AppendCustomSICListItem(484.28137, 0.092F, "Pep-11");
this.AppendCustomSICListItem(459.27687, 0.368F, "Pep-14");
this.AppendCustomSICListItem(740.01082, 0.574F, "Pep-16");
this.AppendCustomSICListItem(762.51852, 0.642F, "Pep-26");
this.AppendCustomSICListItem(657.42992, 0.192F, "Pep-16_Partial");
this.AppendCustomSICListItem(900.59222, 0.4F, "Pep-26_PartialA");
this.AppendCustomSICListItem(640.43972, 0.4F, "Pep-26_PartialB");
}
private void DefineOverviewText()
{
var msg = new StringBuilder();
msg.Append("When Export All Spectra Data Points is enabled, a separate file is created containing the raw data points (scan number, m/z, and intensity), using the specified file format. ");
msg.Append("If Export MS/MS Spectra is enabled, the fragmentation spectra are included, in addition to the survey scan spectra (MS1 scans). ");
msg.Append("If MS/MS spectra are not included, one can optionally renumber the survey scan spectra so that they increase in steps of 1, regardless of the number of MS/MS scans between each survey scan. ");
msg.Append("The Minimum Intensity and Maximum Ion Count options allow you to limit the number of data points exported for each spectrum.");
lblRawDataExportOverview.Text = msg.ToString();
msg.Clear();
msg.Append("These options control how the selected ion chromatogram (SIC) is created for each parent ion mass or custom SIC search mass. ");
msg.Append("The data in the survey scan spectra (MS1 scans) are searched +/- the SIC Tolerance, looking forward and backward in time until ");
msg.Append("the intensity of the matching data 1) falls below the Intensity Threshold Fraction Max Peak value, 2) falls below the Intensity ");
msg.Append("Threshold Absolute Minimum, or 3) spans more than the Maximum Peak Width forward or backward limits defined.");
lblSICOptionsOverview.Text = msg.ToString();
msg.Clear();
msg.Append("When processing Thermo MRM data files, a file named _MRMSettings.txt will be created listing the ");
msg.Append("parent and daughter m/z values monitored via SRM. ");
msg.Append("You can optionally export detailed MRM intensity data using these options:");
lblMRMInfo.Text = msg.ToString();
msg.Clear();
msg.Append("Select a comma or tab delimited file to read custom SIC search values from, ");
msg.Append("or define them in the Custom SIC Values table below. If using the file, ");
msg.Append("allowed column names are: ").Append(clsCustomSICListReader.GetCustomMZFileColumnHeaders()).Append(". ");
msg.Append("Note: use " +
clsCustomSICListReader.CUSTOM_SIC_COLUMN_SCAN_TIME + " and " +
clsCustomSICListReader.CUSTOM_SIC_COLUMN_TIME_TOLERANCE + " only when specifying ");
msg.Append("acquisition time-based values. When doing so, do not include " +
clsCustomSICListReader.CUSTOM_SIC_COLUMN_SCAN_CENTER + " and " +
clsCustomSICListReader.CUSTOM_SIC_COLUMN_SCAN_TOLERANCE + ".");
txtCustomSICFileDescription.Text = msg.ToString();
}
private void EnableDisableControls()
{
var createSICsAndRawData = !chkSkipSICAndRawDataProcessing.Checked;
var msmsProcessingEnabled = !chkSkipMSMSProcessing.Checked;
var exportRawDataOnly = chkExportRawDataOnly.Checked && chkExportRawSpectraData.Checked;
chkSkipMSMSProcessing.Enabled = createSICsAndRawData;
chkExportRawDataOnly.Enabled = createSICsAndRawData && chkExportRawSpectraData.Checked;
fraExportAllSpectraDataPoints.Enabled = createSICsAndRawData;
fraSICNoiseThresholds.Enabled = createSICsAndRawData && !exportRawDataOnly;
fraPeakFindingOptions.Enabled = fraSICNoiseThresholds.Enabled;
fraSmoothingOptions.Enabled = fraSICNoiseThresholds.Enabled;
fraSICSearchThresholds.Enabled = fraSICNoiseThresholds.Enabled;
fraMassSpectraNoiseThresholds.Enabled = createSICsAndRawData;
fraBinningIntensityOptions.Enabled = createSICsAndRawData && msmsProcessingEnabled && !exportRawDataOnly;
fraBinningMZOptions.Enabled = fraBinningIntensityOptions.Enabled;
fraSpectrumSimilarityOptions.Enabled = fraBinningIntensityOptions.Enabled;
fraCustomSICControls.Enabled = createSICsAndRawData && !exportRawDataOnly;
dgCustomSICValues.Enabled = createSICsAndRawData && !exportRawDataOnly;
var rawExportEnabled = chkExportRawSpectraData.Checked;
cboExportRawDataFileFormat.Enabled = rawExportEnabled;
chkExportRawDataIncludeMSMS.Enabled = rawExportEnabled;
if (chkExportRawDataIncludeMSMS.Checked)
{
chkExportRawDataRenumberScans.Enabled = false;
}
else
{
chkExportRawDataRenumberScans.Enabled = rawExportEnabled;
}
txtExportRawDataSignalToNoiseRatioMinimum.Enabled = rawExportEnabled;
txtExportRawDataMaxIonCountPerScan.Enabled = rawExportEnabled;
txtExportRawDataIntensityMinimum.Enabled = rawExportEnabled;
if (cboSICNoiseThresholdMode.SelectedIndex == (int)MASICPeakFinder.clsMASICPeakFinder.NoiseThresholdModes.AbsoluteThreshold)
{
txtSICNoiseThresholdIntensity.Enabled = true;
txtSICNoiseFractionLowIntensityDataToAverage.Enabled = false;
}
else if (cboSICNoiseThresholdMode.SelectedIndex is
(int)MASICPeakFinder.clsMASICPeakFinder.NoiseThresholdModes.TrimmedMeanByAbundance or
(int)MASICPeakFinder.clsMASICPeakFinder.NoiseThresholdModes.TrimmedMeanByCount or
(int)MASICPeakFinder.clsMASICPeakFinder.NoiseThresholdModes.TrimmedMedianByAbundance)
{
txtSICNoiseThresholdIntensity.Enabled = false;
txtSICNoiseFractionLowIntensityDataToAverage.Enabled = true;
}
else
{
// Unknown mode; disable both
txtSICNoiseThresholdIntensity.Enabled = false;
txtSICNoiseFractionLowIntensityDataToAverage.Enabled = false;
}
txtButterworthSamplingFrequency.Enabled = optUseButterworthSmooth.Checked;
txtSavitzkyGolayFilterOrder.Enabled = optUseSavitzkyGolaySmooth.Checked;
if (cboMassSpectraNoiseThresholdMode.SelectedIndex == (int)MASICPeakFinder.clsMASICPeakFinder.NoiseThresholdModes.AbsoluteThreshold)
{
txtMassSpectraNoiseThresholdIntensity.Enabled = true;
txtMassSpectraNoiseFractionLowIntensityDataToAverage.Enabled = false;
txtMassSpectraNoiseMinimumSignalToNoiseRatio.Enabled = false;
}
else if (cboMassSpectraNoiseThresholdMode.SelectedIndex is
(int)MASICPeakFinder.clsMASICPeakFinder.NoiseThresholdModes.TrimmedMeanByAbundance or
(int)MASICPeakFinder.clsMASICPeakFinder.NoiseThresholdModes.TrimmedMeanByCount or
(int)MASICPeakFinder.clsMASICPeakFinder.NoiseThresholdModes.TrimmedMedianByAbundance)
{
txtMassSpectraNoiseThresholdIntensity.Enabled = false;
txtMassSpectraNoiseFractionLowIntensityDataToAverage.Enabled = true;
txtMassSpectraNoiseMinimumSignalToNoiseRatio.Enabled = true;
}
else
{
// Unknown mode; disable both
txtMassSpectraNoiseThresholdIntensity.Enabled = false;
txtMassSpectraNoiseFractionLowIntensityDataToAverage.Enabled = false;
txtMassSpectraNoiseMinimumSignalToNoiseRatio.Enabled = false;
}
chkSaveExtendedStatsFileIncludeFilterText.Enabled = chkSaveExtendedStatsFile.Checked;
chkSaveExtendedStatsFileIncludeStatusLog.Enabled = chkSaveExtendedStatsFile.Checked;
txtStatusLogKeyNameFilterList.Enabled = chkSaveExtendedStatsFile.Checked && chkSaveExtendedStatsFileIncludeStatusLog.Checked;
chkConsolidateConstantExtendedHeaderValues.Enabled = chkSaveExtendedStatsFile.Checked;
EnableDisableCustomSICValueGrid();
}
private void EnableDisableCustomSICValueGrid()
{
bool enableGrid;
if (txtCustomSICFileName.TextLength > 0)
{
enableGrid = false;
dgCustomSICValues.CaptionText = "Custom SIC Values will be read from the file defined above";
}
else
{
enableGrid = true;
dgCustomSICValues.CaptionText = "Custom SIC Values";
}
cmdPasteCustomSICList.Enabled = enableGrid;
cmdCustomSICValuesPopulate.Enabled = enableGrid;
cmdClearCustomSICList.Enabled = enableGrid;
dgCustomSICValues.Enabled = enableGrid;
}
private void frmMain_Resize(object sender, EventArgs e)
{
CatchUnrequestedHeightChange();
}
private void GetCurrentCustomSICTolerances(out double defaultMZTolerance, out float defaultScanOrAcqTimeTolerance)
{
try
{
defaultMZTolerance = double.Parse(txtSICTolerance.Text);
if (optSICTolerancePPM.Checked)
{
defaultMZTolerance = clsUtilities.PPMToMass(defaultMZTolerance, 1000);
}
}
catch (Exception)
{
defaultMZTolerance = 0.6;
}
try
{
defaultScanOrAcqTimeTolerance = float.Parse(txtCustomSICScanOrAcqTimeTolerance.Text);
}
catch (Exception)
{
defaultScanOrAcqTimeTolerance = 0;
}
}
private clsCustomSICList.CustomSICScanTypeConstants GetCustomSICScanToleranceType()
{
if (optCustomSICScanToleranceAbsolute.Checked)
{
return clsCustomSICList.CustomSICScanTypeConstants.Absolute;
}
if (optCustomSICScanToleranceRelative.Checked)
{
return clsCustomSICList.CustomSICScanTypeConstants.Relative;
}
if (optCustomSICScanToleranceAcqTime.Checked)
{
return clsCustomSICList.CustomSICScanTypeConstants.AcquisitionTime;
}
// Assume absolute
return clsCustomSICList.CustomSICScanTypeConstants.Absolute;
}
private int GetReporterIonIndexFromMode(clsReporterIons.ReporterIonMassModeConstants reporterIonMassMode)
{
foreach (var item in mReporterIonIndexToModeMap)
{
if (item.Value == reporterIonMassMode)
{
return item.Key;
}
}
throw new InvalidEnumArgumentException("Dictionary mReporterIonIndexToModeMap is missing enum " + reporterIonMassMode);
}
private clsReporterIons.ReporterIonMassModeConstants GetReporterIonModeFromIndex(int comboboxIndex)
{
if (mReporterIonIndexToModeMap.TryGetValue(comboboxIndex, out var reporterIonMassMode))
{
return reporterIonMassMode;
}
throw new Exception("Dictionary mReporterIonIndexToModeMap is missing index " + comboboxIndex);
}
private clsReporterIons.ReporterIonMassModeConstants GetSelectedReporterIonMode()
{
return GetReporterIonModeFromIndex(cboReporterIonMassMode.SelectedIndex);
}
private string GetSettingsFilePath()
{
return ProcessFilesOrDirectoriesBase.GetSettingsFilePathLocal("MASIC", XML_SETTINGS_FILE_NAME);
}
private void IniFileLoadOptions(bool updateIOPaths)
{
// Prompts the user to select a file to load the options from
using var fileSelector = new OpenFileDialog
{
AddExtension = true,
CheckFileExists = true,
CheckPathExists = true,
DefaultExt = ".xml",
DereferenceLinks = true,
Multiselect = false,
ValidateNames = true,
Filter = "Settings files (*.xml)|*.xml|All files (*.*)|*.*",
FilterIndex = 1
};
var filePath = mXmlSettingsFilePath;
if (filePath.Length > 0)
{
try
{
fileSelector.InitialDirectory = Directory.GetParent(filePath)?.ToString();
}
catch
{
fileSelector.InitialDirectory = ProcessFilesOrDirectoriesBase.GetAppDirectoryPath();
}
}
else
{
fileSelector.InitialDirectory = ProcessFilesOrDirectoriesBase.GetAppDirectoryPath();
}
if (File.Exists(filePath))
{
fileSelector.FileName = Path.GetFileName(filePath);
}
fileSelector.Title = "Specify file to load options from";
var result = fileSelector.ShowDialog();
if (result == DialogResult.Cancel)
return;
if (fileSelector.FileName.Length > 0)
{
mXmlSettingsFilePath = fileSelector.FileName;
IniFileLoadOptions(mXmlSettingsFilePath, updateIOPaths);
}
}
private void IniFileLoadOptions(string filePath, bool updateIOPaths)
{
// Loads options from the given file
try
{
// Utilize MASIC's built-in LoadParameters function, then call ResetToDefaults
var masicInstance = new clsMASIC();
var success = masicInstance.LoadParameterFileSettings(filePath);
if (!success)
{
MessageBox.Show("LoadParameterFileSettings returned false for: " + Path.GetFileName(filePath), "Error", MessageBoxButtons.OK, MessageBoxIcon.Exclamation);
}
ResetToDefaults(false, masicInstance);
// Sleep for 100 msec, just to be safe
Thread.Sleep(100);
// Now load some custom options that aren't loaded by clsMASIC
var xmlFileReader = new XmlSettingsFileAccessor();
// Pass True to .LoadSettings() to turn off case sensitive matching
xmlFileReader.LoadSettings(filePath, false);
try
{
txtDatasetLookupFilePath.Text = xmlFileReader.GetParam(MASICOptions.XML_SECTION_DATABASE_SETTINGS, "DatasetLookupFilePath", txtDatasetLookupFilePath.Text);
try
{
if (!File.Exists(txtDatasetLookupFilePath.Text))
{
txtDatasetLookupFilePath.Text = string.Empty;
}
}
catch (Exception)
{
// Ignore any errors here
}
if (updateIOPaths)
{
txtInputFilePath.Text = xmlFileReader.GetParam(MASICOptions.XML_SECTION_IMPORT_OPTIONS, "InputFilePath", txtInputFilePath.Text);
}
Width = xmlFileReader.GetParam(MASICOptions.XML_SECTION_IMPORT_OPTIONS, "WindowWidth", Width);
Height = xmlFileReader.GetParam(MASICOptions.XML_SECTION_IMPORT_OPTIONS, "WindowHeight", Height);
// Uncomment to test DPI scaling
//var graphics = this.CreateGraphics();
//var dpiX = graphics.DpiX;
//var dpiY = graphics.DpiY;
//var savedWidth = xmlFileReader.GetParam(MASICOptions.XML_SECTION_IMPORT_OPTIONS, "WindowWidth", 0);
//var savedHeight = xmlFileReader.GetParam(MASICOptions.XML_SECTION_IMPORT_OPTIONS, "WindowHeight", 0);
//if (savedWidth > 0)
// Width = (int)Math.Floor(savedWidth * 96 / dpiX);
//if (savedHeight > 0)
// Height = (int)Math.Floor(savedHeight * 96 / dpiY);
if (updateIOPaths)
{
txtOutputDirectoryPath.Text = xmlFileReader.GetParam(MASICOptions.XML_SECTION_IMPORT_OPTIONS, "LastDirectory", txtOutputDirectoryPath.Text);
}
if (txtOutputDirectoryPath.TextLength == 0)
{
txtOutputDirectoryPath.Text = ProcessFilesOrDirectoriesBase.GetAppDirectoryPath();
}
mPreferredInputFileExtension = xmlFileReader.GetParam(MASICOptions.XML_SECTION_IMPORT_OPTIONS, "PreferredInputFileExtension", mPreferredInputFileExtension);
}
catch (Exception)
{
MessageBox.Show("Invalid parameter in settings file: " + Path.GetFileName(filePath), "Error", MessageBoxButtons.OK, MessageBoxIcon.Exclamation);
}
}
catch (Exception ex)
{
MessageBox.Show("Error loading settings from file: " + filePath + "; " + Environment.NewLine +
ex.Message + ";" + Environment.NewLine, "Error", MessageBoxButtons.OK, MessageBoxIcon.Exclamation);
}
}
private void IniFileSaveDefaultOptions()
{
var response = MessageBox.Show("Save the current options as defaults?", "Save Defaults", MessageBoxButtons.YesNoCancel, MessageBoxIcon.Question, MessageBoxDefaultButton.Button1);
if (response == DialogResult.Yes)
{
IniFileSaveOptions(GetSettingsFilePath(), false);
}
}
private void IniFileSaveOptions()
{
// Prompts the user to select a file to load the options from
using var fileSelector = new SaveFileDialog
{
AddExtension = true,
CheckFileExists = false,
CheckPathExists = true,
DefaultExt = ".xml",
DereferenceLinks = true,
OverwritePrompt = true,
ValidateNames = true,
Filter = "Settings files (*.xml)|*.xml|All files (*.*)|*.*",
FilterIndex = 1
};
var filePath = mXmlSettingsFilePath;
if (filePath.Length > 0)
{
try
{
fileSelector.InitialDirectory = Directory.GetParent(filePath)?.ToString();
}
catch
{
fileSelector.InitialDirectory = ProcessFilesOrDirectoriesBase.GetAppDirectoryPath();
}
}
else
{
fileSelector.InitialDirectory = ProcessFilesOrDirectoriesBase.GetAppDirectoryPath();
}
if (File.Exists(filePath))
{
fileSelector.FileName = Path.GetFileName(filePath);
}
fileSelector.Title = "Specify file to save options to";
var result = fileSelector.ShowDialog();
if (result == DialogResult.Cancel)
return;
if (fileSelector.FileName.Length > 0)
{
mXmlSettingsFilePath = fileSelector.FileName;
IniFileSaveOptions(mXmlSettingsFilePath, false);
}
}
private void IniFileSaveOptions(string filePath, bool saveWindowDimensionsOnly = false)
{
try
{
if (!saveWindowDimensionsOnly)
{
var masicInstance = new clsMASIC();
UpdateMasicSettings(masicInstance);
masicInstance.Options.SaveParameterFileSettings(filePath);
// Sleep for 100 msec, just to be safe
Thread.Sleep(100);
}
// Pass True to .LoadSettings() here so that newly made Xml files will have the correct capitalization
var xmlFileReader = new XmlSettingsFileAccessor();
xmlFileReader.LoadSettings(filePath, true);
try
{
if (!saveWindowDimensionsOnly)
{
try
{
if (File.Exists(txtDatasetLookupFilePath.Text))
{
xmlFileReader.SetParam(MASICOptions.XML_SECTION_DATABASE_SETTINGS, "DatasetLookupFilePath", txtDatasetLookupFilePath.Text);
}
}
catch (Exception)
{
// Ignore any errors here
}
xmlFileReader.SetParam(MASICOptions.XML_SECTION_IMPORT_OPTIONS, "InputFilePath", txtInputFilePath.Text);
}
xmlFileReader.SetParam(MASICOptions.XML_SECTION_IMPORT_OPTIONS, "LastDirectory", txtOutputDirectoryPath.Text);
xmlFileReader.SetParam(MASICOptions.XML_SECTION_IMPORT_OPTIONS, "PreferredInputFileExtension", mPreferredInputFileExtension);
xmlFileReader.SetParam(MASICOptions.XML_SECTION_IMPORT_OPTIONS, "WindowWidth", Width);
xmlFileReader.SetParam(MASICOptions.XML_SECTION_IMPORT_OPTIONS, "WindowHeight", Height);
}
catch (Exception)
{
MessageBox.Show("Error storing parameter in settings file: " + Path.GetFileName(filePath), "Error", MessageBoxButtons.OK, MessageBoxIcon.Exclamation);
}
xmlFileReader.SaveSettings();
}
catch (Exception ex)
{
ConsoleMsgUtils.ShowWarning("Error saving settings to file: " + filePath);
ConsoleMsgUtils.ShowWarning(ex.Message);
MessageBox.Show("Error saving settings to file: " + filePath, "Error", MessageBoxButtons.OK, MessageBoxIcon.Exclamation);
}
}
private void InitializeControls()
{
DefineDefaultCustomSICList();
PopulateComboBoxes();
InitializeCustomSICDataGrid();
DefineOverviewText();
mXmlSettingsFilePath = GetSettingsFilePath();
ProcessFilesOrDirectoriesBase.CreateSettingsFileIfMissing(mXmlSettingsFilePath);
mPreferredInputFileExtension = ".Raw";
mHeightAdjustForce = 0;
mHeightAdjustTime = DateTime.Parse("1900-01-01");
IniFileLoadOptions(mXmlSettingsFilePath, true);
SetToolTips();
}
private void InitializeCustomSICDataGrid()
{
// Make the Peak Matching Thresholds data table
var customSICValues = new DataTable(CUSTOM_SIC_VALUES_DATA_TABLE);
// Add the columns to the data table
DataTableUtils.AppendColumnDoubleToTable(customSICValues, COL_NAME_MZ);
DataTableUtils.AppendColumnDoubleToTable(customSICValues, COL_NAME_MZ_TOLERANCE);
DataTableUtils.AppendColumnDoubleToTable(customSICValues, COL_NAME_SCAN_CENTER);
DataTableUtils.AppendColumnDoubleToTable(customSICValues, COL_NAME_SCAN_TOLERANCE);
DataTableUtils.AppendColumnStringToTable(customSICValues, COL_NAME_SCAN_COMMENT, string.Empty);
DataTableUtils.AppendColumnIntegerToTable(customSICValues, COL_NAME_CUSTOM_SIC_VALUE_ROW_ID, 0, true, true);
var primaryKeyColumn = new[] { customSICValues.Columns[COL_NAME_CUSTOM_SIC_VALUE_ROW_ID] };
customSICValues.PrimaryKey = primaryKeyColumn;
// Instantiate the dataset
mCustomSICValuesDataset = new DataSet(CUSTOM_SIC_VALUES_DATA_TABLE);
// Add the new DataTable to the DataSet.
mCustomSICValuesDataset.Tables.Add(customSICValues);
// Bind the DataSet to the DataGrid
dgCustomSICValues.DataSource = mCustomSICValuesDataset;
dgCustomSICValues.DataMember = CUSTOM_SIC_VALUES_DATA_TABLE;
// Update the grid's table style
UpdateCustomSICDataGridTableStyle();
// Populate the table
AutoPopulateCustomSICValues(false);
}
private void PasteCustomSICValues(bool clearList)
{
var lineDelimiters = new[] { '\r', '\n' };
var columnDelimiters = new[] { '\t', ',' };
// Examine the clipboard contents
var clipboardData = Clipboard.GetDataObject();
if (clipboardData == null)
{
return;
}
if (!clipboardData.GetDataPresent(DataFormats.StringFormat, true))
{
return;
}
var data = Convert.ToString(clipboardData.GetData(DataFormats.StringFormat, true));
// Split data on carriage return or line feed characters
// Lines that end in CrLf will give two separate lines; one with the text, and one blank; that's OK
var dataLines = data.Split(lineDelimiters, 50000);
if (dataLines.Length == 0)
{
return;
}
GetCurrentCustomSICTolerances(out var defaultMZTolerance, out var defaultScanOrAcqTimeTolerance);
if (clearList)
{
if (!ClearCustomSICList(true))
return;
}
var rowsAlreadyPresent = 0;
var rowsSkipped = 0;
foreach (var dataLine in dataLines)
{