'****************************************************************************
'* Copyright (C) 2004 Peter Mortensen and Matthias Mann *
'* This file is part of MSQuant. *
'* *
'* MSQuant is distributed under the terms of *
'* the GNU General Public License. See src/COPYING.TXT or *
'* <http://www.gnu.org/licenses/gpl.txt> for details. *
'* *
'* MSQuant is free software; you can redistribute it *
'* and/or modify it under the terms of the GNU *
'* General Public License as published by the Free *
'* Software Foundation; either version 2 of the *
'* License, or (at your option) any later version. *
'* *
'* MSQuant is distributed in the hope that it will be *
'* useful, but WITHOUT ANY WARRANTY; without even the *
'* implied warranty of MERCHANTABILITY or FITNESS FOR *
'* A PARTICULAR PURPOSE. See the GNU General Public *
'* License for more details. *
'* *
'* You should have received a copy of the GNU General *
'* Public License along with MSQuant; if not, write to *
'* the Free Software Foundation, Inc., 59 Temple *
'* Place, Suite 330, Boston, MA 02111-1307 USA *
'* *
'* Purpose: <to be filled in>. *
'* *
'****************************************************************************
'****************************************************************************
'* CEBI *
'* Software Development Group *
'* Peter Mortensen *
'* E-mail: NUKESPAMMERSdrmortensen@get2netZZZZZZ.dk *
'* WWW: http://www.cebi.sdu.dk/ *
'* *
'* Program for post-processing of result from search in mass *
'* spectrometric data. *
'* *
'* FILENAME: frmOptions.vb *
'* TYPE: VISUAL_BASIC *
'* *
'* CREATED: PM 2003-??-?? Vrs 1.0. *
'* UPDATED: PM 2004-xx-xx *
'* *
'****************************************************************************
Option Strict On 'Changed PM_OPTIONSTRICT 2003-02-13
Option Explicit On
Imports System.Collections.Generic 'For Dictionary
Imports App 'For class quantApplication
Imports massSpectrometryBase
Imports massSpectrometryBase.quantitation
Imports MolecularSharedStructures 'For generalisedQuantModeStructure
Imports SDUPrecalibrator 'For recalibDomainEnum
'****************************************************************************
'* <placeholder for header> *
'****************************************************************************
Public Class frmOptions
Inherits System.Windows.Forms.Form
Private mMainForm As frmMainForm
Private mApplication As quantApplication
'Changed PM_RAWFILE_PEPFILTER 2007-11-17
Private mRawFiles() As fileSpecStructure
Private mOptions2 As OptionsStruct2
'Changed PM_CANCEL_ALSO_SAVES_PEPTFILT_BUG 2007-09-06
'Local copies of peptide filters that are used until
'the dialog is OK'ed.
Private mPreselPeptideFilter As peptideFilterStructure
Private mRecalibPeptideFilter As peptideFilterStructure
Private mValPeptideFilter As peptideFilterStructure
'Changed PM_RECALIB_REALITY_CHECK 2008-03-26
'Private mRecalibLimitsStructure As recalibLimitsStructure
'Changed PM_PEPTIDEFILTER_GENERALISED 2007-08-29
Private WithEvents mFilterForm As frmPeptideFilters
'Changed PM_RECALIB_FILTER 2007-09-04
Private WithEvents mRecalibFilterForm As frmPeptideFilters
'Changed PM_VALIDATION_AS_PEPTFILTER 2007-09-05
Private WithEvents mValidationFilterForm As frmPeptideFilters
'Changed PM_HIDE_RECALIBVISUALISATION_WINDOW 2008-01-06
Private WithEvents mParseEndForm As frmEndOfParseAction
'Changed PM_RECALIB_REALITY_CHECK 2008-03-26
Private WithEvents mRecalibRealityCheckForm As frmRecalibRealityCheck
Friend WithEvents cbxTITLElineFormat As System.Windows.Forms.ComboBox
Friend WithEvents Label12 As System.Windows.Forms.Label
Friend WithEvents GroupBox2 As System.Windows.Forms.GroupBox
Friend WithEvents btnPeptideFilter As System.Windows.Forms.Button
Friend WithEvents GroupBox3 As System.Windows.Forms.GroupBox
Friend WithEvents btnRecalibPeptideFilter As System.Windows.Forms.Button
Friend WithEvents lblRecalibPeptideFilterSummary As System.Windows.Forms.Label
Friend WithEvents btnValidationPeptideFilter As System.Windows.Forms.Button
Friend WithEvents lblValidationPeptideFilterSummary As System.Windows.Forms.Label
Friend WithEvents Label5 As System.Windows.Forms.Label
Friend WithEvents cbxRecalibDomains As System.Windows.Forms.ComboBox
Friend WithEvents btnEndOfParseAction As System.Windows.Forms.Button
Friend WithEvents lblRecalibLimitsShortSummary As System.Windows.Forms.Label
Friend WithEvents btnRecalibRealityCheck As System.Windows.Forms.Button
Friend WithEvents lblPeptideFilterSummary As System.Windows.Forms.Label
#Region " Windows Form Designer generated code "
'Note: this function is called by the New() function
'with parameters, below.
'****************************************************************************
'* <placeholder for header> *
'****************************************************************************
Public Sub New()
MyBase.New()
'This call is required by the Windows Form Designer.
InitializeComponent()
'Add any initialization after the InitializeComponent() call
End Sub 'Constructor.
'Form overrides dispose to clean up the component list.
Protected Overloads Overrides Sub Dispose(ByVal disposing As Boolean)
If disposing Then
If Not (components Is Nothing) Then
components.Dispose()
End If
End If
MyBase.Dispose(disposing)
End Sub
'Required by the Windows Form Designer
Private components As System.ComponentModel.IContainer
'NOTE: The following procedure is required by the Windows Form Designer
'It can be modified using the Windows Form Designer.
'Do not modify it using the code editor.
Friend WithEvents Label1 As System.Windows.Forms.Label
Friend WithEvents Label3 As System.Windows.Forms.Label
Friend WithEvents Label4 As System.Windows.Forms.Label
Friend WithEvents GroupBox1 As System.Windows.Forms.GroupBox
Friend WithEvents chkNoIPI As System.Windows.Forms.CheckBox
Friend WithEvents chkNoMosquito As System.Windows.Forms.CheckBox
Friend WithEvents chkNoProteinWithoutABC As System.Windows.Forms.CheckBox
Friend WithEvents btnCancel As System.Windows.Forms.Button
Friend WithEvents btnOK As System.Windows.Forms.Button
Friend WithEvents txtScoreA As System.Windows.Forms.TextBox
Friend WithEvents txtScoreB As System.Windows.Forms.TextBox
Friend WithEvents txtScoreC As System.Windows.Forms.TextBox
Friend WithEvents StatusBar1 As System.Windows.Forms.StatusBar
Friend WithEvents chkAllBoldBlackPepts As System.Windows.Forms.CheckBox
Friend WithEvents chkCheckedRedPeptides As System.Windows.Forms.CheckBox
Friend WithEvents chkBoldRedPeptides As System.Windows.Forms.CheckBox
Friend WithEvents chkLightRedPeptides As System.Windows.Forms.CheckBox
Friend WithEvents chkIncludeParensPeptides As System.Windows.Forms.CheckBox
Friend WithEvents chkBoldBlackCheckedPepts As System.Windows.Forms.CheckBox
Friend WithEvents Label2 As System.Windows.Forms.Label
Friend WithEvents Label6 As System.Windows.Forms.Label
Friend WithEvents cbxQuantMode As System.Windows.Forms.ComboBox
Friend WithEvents ToolTip1 As System.Windows.Forms.ToolTip
Friend WithEvents txtProtAutoValid As System.Windows.Forms.TextBox
Friend WithEvents lblRawFile As System.Windows.Forms.Label
Friend WithEvents cbxRawFileMode As System.Windows.Forms.ComboBox
Friend WithEvents xyz123 As System.Windows.Forms.Label
Friend WithEvents cbxMStypesForQuant As System.Windows.Forms.ComboBox
Friend WithEvents grpIncludeInPreselectedPeptides As System.Windows.Forms.GroupBox
Friend WithEvents CheckBox1 As System.Windows.Forms.CheckBox
<System.Diagnostics.DebuggerStepThrough()> Private Sub InitializeComponent()
Me.components = New System.ComponentModel.Container
Dim resources As System.ComponentModel.ComponentResourceManager = New System.ComponentModel.ComponentResourceManager(GetType(frmOptions))
Me.Label1 = New System.Windows.Forms.Label
Me.txtScoreA = New System.Windows.Forms.TextBox
Me.txtScoreB = New System.Windows.Forms.TextBox
Me.Label3 = New System.Windows.Forms.Label
Me.txtScoreC = New System.Windows.Forms.TextBox
Me.Label4 = New System.Windows.Forms.Label
Me.btnCancel = New System.Windows.Forms.Button
Me.btnOK = New System.Windows.Forms.Button
Me.GroupBox1 = New System.Windows.Forms.GroupBox
Me.chkNoIPI = New System.Windows.Forms.CheckBox
Me.chkNoMosquito = New System.Windows.Forms.CheckBox
Me.chkIncludeParensPeptides = New System.Windows.Forms.CheckBox
Me.chkCheckedRedPeptides = New System.Windows.Forms.CheckBox
Me.chkNoProteinWithoutABC = New System.Windows.Forms.CheckBox
Me.StatusBar1 = New System.Windows.Forms.StatusBar
Me.chkBoldRedPeptides = New System.Windows.Forms.CheckBox
Me.chkBoldBlackCheckedPepts = New System.Windows.Forms.CheckBox
Me.grpIncludeInPreselectedPeptides = New System.Windows.Forms.GroupBox
Me.btnPeptideFilter = New System.Windows.Forms.Button
Me.lblPeptideFilterSummary = New System.Windows.Forms.Label
Me.chkLightRedPeptides = New System.Windows.Forms.CheckBox
Me.chkAllBoldBlackPepts = New System.Windows.Forms.CheckBox
Me.CheckBox1 = New System.Windows.Forms.CheckBox
Me.Label2 = New System.Windows.Forms.Label
Me.Label6 = New System.Windows.Forms.Label
Me.cbxQuantMode = New System.Windows.Forms.ComboBox
Me.ToolTip1 = New System.Windows.Forms.ToolTip(Me.components)
Me.cbxMStypesForQuant = New System.Windows.Forms.ComboBox
Me.txtProtAutoValid = New System.Windows.Forms.TextBox
Me.lblRawFile = New System.Windows.Forms.Label
Me.cbxRawFileMode = New System.Windows.Forms.ComboBox
Me.xyz123 = New System.Windows.Forms.Label
Me.cbxTITLElineFormat = New System.Windows.Forms.ComboBox
Me.Label12 = New System.Windows.Forms.Label
Me.GroupBox2 = New System.Windows.Forms.GroupBox
Me.btnValidationPeptideFilter = New System.Windows.Forms.Button
Me.lblValidationPeptideFilterSummary = New System.Windows.Forms.Label
Me.GroupBox3 = New System.Windows.Forms.GroupBox
Me.lblRecalibLimitsShortSummary = New System.Windows.Forms.Label
Me.btnRecalibRealityCheck = New System.Windows.Forms.Button
Me.Label5 = New System.Windows.Forms.Label
Me.cbxRecalibDomains = New System.Windows.Forms.ComboBox
Me.btnRecalibPeptideFilter = New System.Windows.Forms.Button
Me.lblRecalibPeptideFilterSummary = New System.Windows.Forms.Label
Me.btnEndOfParseAction = New System.Windows.Forms.Button
Me.grpIncludeInPreselectedPeptides.SuspendLayout()
Me.GroupBox2.SuspendLayout()
Me.GroupBox3.SuspendLayout()
Me.SuspendLayout()
'
'Label1
'
Me.Label1.Location = New System.Drawing.Point(456, 48)
Me.Label1.Name = "Label1"
Me.Label1.Size = New System.Drawing.Size(88, 16)
Me.Label1.TabIndex = 56
Me.Label1.Text = "Category A >="
'
'txtScoreA
'
Me.txtScoreA.Location = New System.Drawing.Point(593, 48)
Me.txtScoreA.Name = "txtScoreA"
Me.txtScoreA.Size = New System.Drawing.Size(48, 20)
Me.txtScoreA.TabIndex = 12
Me.txtScoreA.Text = "33"
Me.txtScoreA.TextAlign = System.Windows.Forms.HorizontalAlignment.Center
'
'txtScoreB
'
Me.txtScoreB.Location = New System.Drawing.Point(593, 76)
Me.txtScoreB.Name = "txtScoreB"
Me.txtScoreB.Size = New System.Drawing.Size(48, 20)
Me.txtScoreB.TabIndex = 13
Me.txtScoreB.Text = "25"
Me.txtScoreB.TextAlign = System.Windows.Forms.HorizontalAlignment.Center
'
'Label3
'
Me.Label3.Location = New System.Drawing.Point(456, 76)
Me.Label3.Name = "Label3"
Me.Label3.Size = New System.Drawing.Size(88, 16)
Me.Label3.TabIndex = 57
Me.Label3.Text = "Category B >="
'
'txtScoreC
'
Me.txtScoreC.Location = New System.Drawing.Point(593, 104)
Me.txtScoreC.Name = "txtScoreC"
Me.txtScoreC.Size = New System.Drawing.Size(48, 20)
Me.txtScoreC.TabIndex = 14
Me.txtScoreC.Text = "20"
Me.txtScoreC.TextAlign = System.Windows.Forms.HorizontalAlignment.Center
'
'Label4
'
Me.Label4.Location = New System.Drawing.Point(456, 104)
Me.Label4.Name = "Label4"
Me.Label4.Size = New System.Drawing.Size(88, 16)
Me.Label4.TabIndex = 58
Me.Label4.Text = "Category C >="
'
'btnCancel
'
Me.btnCancel.DialogResult = System.Windows.Forms.DialogResult.Cancel
Me.btnCancel.Location = New System.Drawing.Point(580, 388)
Me.btnCancel.Name = "btnCancel"
Me.btnCancel.Size = New System.Drawing.Size(75, 23)
Me.btnCancel.TabIndex = 22
Me.btnCancel.Text = "&Cancel"
'
'btnOK
'
Me.btnOK.Location = New System.Drawing.Point(497, 388)
Me.btnOK.Name = "btnOK"
Me.btnOK.Size = New System.Drawing.Size(75, 23)
Me.btnOK.TabIndex = 21
Me.btnOK.Text = "&OK"
'
'GroupBox1
'
Me.GroupBox1.Location = New System.Drawing.Point(355, 16)
Me.GroupBox1.Name = "GroupBox1"
Me.GroupBox1.Size = New System.Drawing.Size(303, 178)
Me.GroupBox1.TabIndex = 55
Me.GroupBox1.TabStop = False
Me.GroupBox1.Text = "Classification of PSPs by Mascot score"
'
'chkNoIPI
'
Me.chkNoIPI.Location = New System.Drawing.Point(712, 54)
Me.chkNoIPI.Name = "chkNoIPI"
Me.chkNoIPI.Size = New System.Drawing.Size(184, 24)
Me.chkNoIPI.TabIndex = 53
Me.chkNoIPI.Text = "Do not show IPI protein hits"
Me.chkNoIPI.Visible = False
'
'chkNoMosquito
'
Me.chkNoMosquito.Enabled = False
Me.chkNoMosquito.Location = New System.Drawing.Point(712, 24)
Me.chkNoMosquito.Name = "chkNoMosquito"
Me.chkNoMosquito.Size = New System.Drawing.Size(200, 24)
Me.chkNoMosquito.TabIndex = 51
Me.chkNoMosquito.Text = "Do not show mosquito protein hits"
Me.chkNoMosquito.Visible = False
'
'chkIncludeParensPeptides
'
Me.chkIncludeParensPeptides.Location = New System.Drawing.Point(16, 111)
Me.chkIncludeParensPeptides.Name = "chkIncludeParensPeptides"
Me.chkIncludeParensPeptides.Size = New System.Drawing.Size(144, 16)
Me.chkIncludeParensPeptides.TabIndex = 6
Me.chkIncludeParensPeptides.Text = "Parenthesized"
'
'chkCheckedRedPeptides
'
Me.chkCheckedRedPeptides.Checked = True
Me.chkCheckedRedPeptides.CheckState = System.Windows.Forms.CheckState.Checked
Me.chkCheckedRedPeptides.Location = New System.Drawing.Point(184, 24)
Me.chkCheckedRedPeptides.Name = "chkCheckedRedPeptides"
Me.chkCheckedRedPeptides.Size = New System.Drawing.Size(128, 16)
Me.chkCheckedRedPeptides.TabIndex = 2
Me.chkCheckedRedPeptides.Text = "Checked red only"
'
'chkNoProteinWithoutABC
'
Me.chkNoProteinWithoutABC.Checked = True
Me.chkNoProteinWithoutABC.CheckState = System.Windows.Forms.CheckState.Checked
Me.chkNoProteinWithoutABC.Location = New System.Drawing.Point(712, 84)
Me.chkNoProteinWithoutABC.Name = "chkNoProteinWithoutABC"
Me.chkNoProteinWithoutABC.Size = New System.Drawing.Size(280, 24)
Me.chkNoProteinWithoutABC.TabIndex = 54
Me.chkNoProteinWithoutABC.Text = "Do not show proteins without peptides in A, B or C"
Me.chkNoProteinWithoutABC.Visible = False
'
'StatusBar1
'
Me.StatusBar1.Location = New System.Drawing.Point(0, 415)
Me.StatusBar1.Name = "StatusBar1"
Me.StatusBar1.Size = New System.Drawing.Size(669, 8)
Me.StatusBar1.TabIndex = 100
'
'chkBoldRedPeptides
'
Me.chkBoldRedPeptides.Checked = True
Me.chkBoldRedPeptides.CheckState = System.Windows.Forms.CheckState.Checked
Me.chkBoldRedPeptides.Location = New System.Drawing.Point(16, 24)
Me.chkBoldRedPeptides.Name = "chkBoldRedPeptides"
Me.chkBoldRedPeptides.Size = New System.Drawing.Size(120, 16)
Me.chkBoldRedPeptides.TabIndex = 1
Me.chkBoldRedPeptides.Text = "Bold red"
'
'chkBoldBlackCheckedPepts
'
Me.chkBoldBlackCheckedPepts.Location = New System.Drawing.Point(184, 82)
Me.chkBoldBlackCheckedPepts.Name = "chkBoldBlackCheckedPepts"
Me.chkBoldBlackCheckedPepts.Size = New System.Drawing.Size(136, 16)
Me.chkBoldBlackCheckedPepts.TabIndex = 5
Me.chkBoldBlackCheckedPepts.Text = "Checked bold black"
'
'grpIncludeInPreselectedPeptides
'
Me.grpIncludeInPreselectedPeptides.Controls.Add(Me.btnPeptideFilter)
Me.grpIncludeInPreselectedPeptides.Controls.Add(Me.lblPeptideFilterSummary)
Me.grpIncludeInPreselectedPeptides.Controls.Add(Me.chkLightRedPeptides)
Me.grpIncludeInPreselectedPeptides.Controls.Add(Me.chkAllBoldBlackPepts)
Me.grpIncludeInPreselectedPeptides.Controls.Add(Me.chkBoldBlackCheckedPepts)
Me.grpIncludeInPreselectedPeptides.Controls.Add(Me.chkIncludeParensPeptides)
Me.grpIncludeInPreselectedPeptides.Controls.Add(Me.chkBoldRedPeptides)
Me.grpIncludeInPreselectedPeptides.Controls.Add(Me.chkCheckedRedPeptides)
Me.grpIncludeInPreselectedPeptides.Location = New System.Drawing.Point(8, 16)
Me.grpIncludeInPreselectedPeptides.Name = "grpIncludeInPreselectedPeptides"
Me.grpIncludeInPreselectedPeptides.Size = New System.Drawing.Size(331, 178)
Me.grpIncludeInPreselectedPeptides.TabIndex = 60
Me.grpIncludeInPreselectedPeptides.TabStop = False
Me.grpIncludeInPreselectedPeptides.Text = "Include in preselected peptides (PSPs):"
'
'btnPeptideFilter
'
Me.btnPeptideFilter.Location = New System.Drawing.Point(16, 147)
Me.btnPeptideFilter.Name = "btnPeptideFilter"
Me.btnPeptideFilter.Size = New System.Drawing.Size(94, 23)
Me.btnPeptideFilter.TabIndex = 7
Me.btnPeptideFilter.Text = "&Peptide filter..."
'
'lblPeptideFilterSummary
'
Me.lblPeptideFilterSummary.AutoSize = True
Me.lblPeptideFilterSummary.Location = New System.Drawing.Point(135, 152)
Me.lblPeptideFilterSummary.Name = "lblPeptideFilterSummary"
Me.lblPeptideFilterSummary.Size = New System.Drawing.Size(19, 13)
Me.lblPeptideFilterSummary.TabIndex = 50
Me.lblPeptideFilterSummary.Text = "<>"
'
'chkLightRedPeptides
'
Me.chkLightRedPeptides.Checked = True
Me.chkLightRedPeptides.CheckState = System.Windows.Forms.CheckState.Checked
Me.chkLightRedPeptides.Location = New System.Drawing.Point(16, 53)
Me.chkLightRedPeptides.Name = "chkLightRedPeptides"
Me.chkLightRedPeptides.Size = New System.Drawing.Size(120, 16)
Me.chkLightRedPeptides.TabIndex = 3
Me.chkLightRedPeptides.Text = "Light red"
'
'chkAllBoldBlackPepts
'
Me.chkAllBoldBlackPepts.Location = New System.Drawing.Point(16, 82)
Me.chkAllBoldBlackPepts.Name = "chkAllBoldBlackPepts"
Me.chkAllBoldBlackPepts.Size = New System.Drawing.Size(80, 16)
Me.chkAllBoldBlackPepts.TabIndex = 4
Me.chkAllBoldBlackPepts.Text = "Bold black"
'
'CheckBox1
'
Me.CheckBox1.Enabled = False
Me.CheckBox1.Location = New System.Drawing.Point(712, 114)
Me.CheckBox1.Name = "CheckBox1"
Me.CheckBox1.Size = New System.Drawing.Size(312, 16)
Me.CheckBox1.TabIndex = 52
Me.CheckBox1.Text = "Use mod filter only if no peptide in protein matched"
Me.CheckBox1.Visible = False
'
'Label2
'
Me.Label2.Location = New System.Drawing.Point(458, 136)
Me.Label2.Name = "Label2"
Me.Label2.Size = New System.Drawing.Size(128, 45)
Me.Label2.TabIndex = 59
Me.Label2.Text = "Protein is validated by default if ABC score is greater than or equal to:"
'
'Label6
'
Me.Label6.Location = New System.Drawing.Point(352, 209)
Me.Label6.Name = "Label6"
Me.Label6.Size = New System.Drawing.Size(112, 16)
Me.Label6.TabIndex = 24
Me.Label6.Text = "Quantitation mode"
'
'cbxQuantMode
'
Me.cbxQuantMode.DropDownStyle = System.Windows.Forms.ComboBoxStyle.DropDownList
Me.cbxQuantMode.Location = New System.Drawing.Point(469, 209)
Me.cbxQuantMode.MaxDropDownItems = 20
Me.cbxQuantMode.Name = "cbxQuantMode"
Me.cbxQuantMode.Size = New System.Drawing.Size(192, 21)
Me.cbxQuantMode.TabIndex = 16
Me.ToolTip1.SetToolTip(Me.cbxQuantMode, "Select how the application should quantify the experiment")
'
'cbxMStypesForQuant
'
Me.cbxMStypesForQuant.DropDownStyle = System.Windows.Forms.ComboBoxStyle.DropDownList
Me.cbxMStypesForQuant.Items.AddRange(New Object() {"All MS spectra", "SIM spectra (LTQ-FT only)", "Full scan spectra (LTQFT only)"})
Me.cbxMStypesForQuant.Location = New System.Drawing.Point(469, 314)
Me.cbxMStypesForQuant.Name = "cbxMStypesForQuant"
Me.cbxMStypesForQuant.Size = New System.Drawing.Size(192, 21)
Me.cbxMStypesForQuant.TabIndex = 19
Me.ToolTip1.SetToolTip(Me.cbxMStypesForQuant, "Select how the application should quantify the experiment")
'
'txtProtAutoValid
'
Me.txtProtAutoValid.Location = New System.Drawing.Point(593, 157)
Me.txtProtAutoValid.Name = "txtProtAutoValid"
Me.txtProtAutoValid.Size = New System.Drawing.Size(48, 20)
Me.txtProtAutoValid.TabIndex = 15
Me.txtProtAutoValid.Text = "60"
Me.txtProtAutoValid.TextAlign = System.Windows.Forms.HorizontalAlignment.Center
'
'lblRawFile
'
Me.lblRawFile.Location = New System.Drawing.Point(352, 279)
Me.lblRawFile.Name = "lblRawFile"
Me.lblRawFile.Size = New System.Drawing.Size(88, 16)
Me.lblRawFile.TabIndex = 26
Me.lblRawFile.Text = "Raw file type"
'
'cbxRawFileMode
'
Me.cbxRawFileMode.DropDownStyle = System.Windows.Forms.ComboBoxStyle.DropDownList
Me.cbxRawFileMode.Items.AddRange(New Object() {"LTQ-FT / LTQ Orbitrap (.raw)", "QSTAR (.wiff)", "Qtof (.dat)"})
Me.cbxRawFileMode.Location = New System.Drawing.Point(469, 279)
Me.cbxRawFileMode.Name = "cbxRawFileMode"
Me.cbxRawFileMode.Size = New System.Drawing.Size(192, 21)
Me.cbxRawFileMode.TabIndex = 18
'
'xyz123
'
Me.xyz123.Location = New System.Drawing.Point(352, 314)
Me.xyz123.Name = "xyz123"
Me.xyz123.Size = New System.Drawing.Size(125, 16)
Me.xyz123.TabIndex = 34
Me.xyz123.Text = "Type(s) for quantitation"
'
'cbxTITLElineFormat
'
Me.cbxTITLElineFormat.DropDownStyle = System.Windows.Forms.ComboBoxStyle.DropDownList
Me.cbxTITLElineFormat.Location = New System.Drawing.Point(469, 244)
Me.cbxTITLElineFormat.Name = "cbxTITLElineFormat"
Me.cbxTITLElineFormat.Size = New System.Drawing.Size(192, 21)
Me.cbxTITLElineFormat.TabIndex = 17
'
'Label12
'
Me.Label12.Location = New System.Drawing.Point(352, 244)
Me.Label12.Name = "Label12"
Me.Label12.Size = New System.Drawing.Size(100, 16)
Me.Label12.TabIndex = 36
Me.Label12.Text = "MGF file generator"
'
'GroupBox2
'
Me.GroupBox2.Controls.Add(Me.btnValidationPeptideFilter)
Me.GroupBox2.Controls.Add(Me.lblValidationPeptideFilterSummary)
Me.GroupBox2.Location = New System.Drawing.Point(8, 326)
Me.GroupBox2.Name = "GroupBox2"
Me.GroupBox2.Size = New System.Drawing.Size(331, 55)
Me.GroupBox2.TabIndex = 37
Me.GroupBox2.TabStop = False
Me.GroupBox2.Text = "Validation of PSPs"
'
'btnValidationPeptideFilter
'
Me.btnValidationPeptideFilter.Location = New System.Drawing.Point(16, 22)
Me.btnValidationPeptideFilter.Name = "btnValidationPeptideFilter"
Me.btnValidationPeptideFilter.Size = New System.Drawing.Size(94, 23)
Me.btnValidationPeptideFilter.TabIndex = 11
Me.btnValidationPeptideFilter.Text = "Pep&tide filter..."
'
'lblValidationPeptideFilterSummary
'
Me.lblValidationPeptideFilterSummary.AutoSize = True
Me.lblValidationPeptideFilterSummary.Location = New System.Drawing.Point(135, 27)
Me.lblValidationPeptideFilterSummary.Name = "lblValidationPeptideFilterSummary"
Me.lblValidationPeptideFilterSummary.Size = New System.Drawing.Size(19, 13)
Me.lblValidationPeptideFilterSummary.TabIndex = 63
Me.lblValidationPeptideFilterSummary.Text = "<>"
'
'GroupBox3
'
Me.GroupBox3.Controls.Add(Me.lblRecalibLimitsShortSummary)
Me.GroupBox3.Controls.Add(Me.btnRecalibRealityCheck)
Me.GroupBox3.Controls.Add(Me.Label5)
Me.GroupBox3.Controls.Add(Me.cbxRecalibDomains)
Me.GroupBox3.Controls.Add(Me.btnRecalibPeptideFilter)
Me.GroupBox3.Controls.Add(Me.lblRecalibPeptideFilterSummary)
Me.GroupBox3.Location = New System.Drawing.Point(8, 205)
Me.GroupBox3.Name = "GroupBox3"
Me.GroupBox3.Size = New System.Drawing.Size(331, 115)
Me.GroupBox3.TabIndex = 38
Me.GroupBox3.TabStop = False
Me.GroupBox3.Text = "Recalibration of PSPs (precursor mass)"
'
'lblRecalibLimitsShortSummary
'
Me.lblRecalibLimitsShortSummary.AutoSize = True
Me.lblRecalibLimitsShortSummary.Location = New System.Drawing.Point(135, 86)
Me.lblRecalibLimitsShortSummary.Name = "lblRecalibLimitsShortSummary"
Me.lblRecalibLimitsShortSummary.Size = New System.Drawing.Size(19, 13)
Me.lblRecalibLimitsShortSummary.TabIndex = 62
Me.lblRecalibLimitsShortSummary.Text = "<>"
'
'btnRecalibRealityCheck
'
Me.btnRecalibRealityCheck.Location = New System.Drawing.Point(16, 81)
Me.btnRecalibRealityCheck.Name = "btnRecalibRealityCheck"
Me.btnRecalibRealityCheck.Size = New System.Drawing.Size(94, 23)
Me.btnRecalibRealityCheck.TabIndex = 10
Me.btnRecalibRealityCheck.Text = "Reality &check..."
'
'Label5
'
Me.Label5.Location = New System.Drawing.Point(13, 24)
Me.Label5.Name = "Label5"
Me.Label5.Size = New System.Drawing.Size(52, 16)
Me.Label5.TabIndex = 61
Me.Label5.Text = "Domain:"
'
'cbxRecalibDomains
'
Me.cbxRecalibDomains.DropDownStyle = System.Windows.Forms.ComboBoxStyle.DropDownList
Me.cbxRecalibDomains.ItemHeight = 13
Me.cbxRecalibDomains.Items.AddRange(New Object() {"Mass (classic)", "Frequency, 1/f (LTQ-FT)", "Time/TOF (QSTAR/Qtof)", "Frequency, 1/f^0.5 (Orbitrap)"})
Me.cbxRecalibDomains.Location = New System.Drawing.Point(71, 21)
Me.cbxRecalibDomains.Name = "cbxRecalibDomains"
Me.cbxRecalibDomains.Size = New System.Drawing.Size(167, 21)
Me.cbxRecalibDomains.TabIndex = 8
'
'btnRecalibPeptideFilter
'
Me.btnRecalibPeptideFilter.Location = New System.Drawing.Point(16, 52)
Me.btnRecalibPeptideFilter.Name = "btnRecalibPeptideFilter"
Me.btnRecalibPeptideFilter.Size = New System.Drawing.Size(94, 23)
Me.btnRecalibPeptideFilter.TabIndex = 9
Me.btnRecalibPeptideFilter.Text = "Peptide fi<er..."
'
'lblRecalibPeptideFilterSummary
'
Me.lblRecalibPeptideFilterSummary.AutoSize = True
Me.lblRecalibPeptideFilterSummary.Location = New System.Drawing.Point(135, 57)
Me.lblRecalibPeptideFilterSummary.Name = "lblRecalibPeptideFilterSummary"
Me.lblRecalibPeptideFilterSummary.Size = New System.Drawing.Size(19, 13)
Me.lblRecalibPeptideFilterSummary.TabIndex = 64
Me.lblRecalibPeptideFilterSummary.Text = "<>"
'
'btnEndOfParseAction
'
Me.btnEndOfParseAction.Location = New System.Drawing.Point(355, 348)
Me.btnEndOfParseAction.Name = "btnEndOfParseAction"
Me.btnEndOfParseAction.Size = New System.Drawing.Size(122, 23)
Me.btnEndOfParseAction.TabIndex = 20
Me.btnEndOfParseAction.Text = "&End of parse action..."
'
'frmOptions
'
Me.AcceptButton = Me.btnOK
Me.AutoScaleBaseSize = New System.Drawing.Size(5, 13)
Me.CancelButton = Me.btnCancel
Me.ClientSize = New System.Drawing.Size(669, 423)
Me.Controls.Add(Me.btnEndOfParseAction)
Me.Controls.Add(Me.GroupBox3)
Me.Controls.Add(Me.CheckBox1)
Me.Controls.Add(Me.GroupBox2)
Me.Controls.Add(Me.cbxTITLElineFormat)
Me.Controls.Add(Me.Label12)
Me.Controls.Add(Me.txtProtAutoValid)
Me.Controls.Add(Me.txtScoreC)
Me.Controls.Add(Me.txtScoreB)
Me.Controls.Add(Me.txtScoreA)
Me.Controls.Add(Me.cbxRawFileMode)
Me.Controls.Add(Me.lblRawFile)
Me.Controls.Add(Me.cbxQuantMode)
Me.Controls.Add(Me.Label6)
Me.Controls.Add(Me.Label2)
Me.Controls.Add(Me.StatusBar1)
Me.Controls.Add(Me.chkNoProteinWithoutABC)
Me.Controls.Add(Me.chkNoMosquito)
Me.Controls.Add(Me.chkNoIPI)
Me.Controls.Add(Me.btnOK)
Me.Controls.Add(Me.btnCancel)
Me.Controls.Add(Me.Label4)
Me.Controls.Add(Me.Label3)
Me.Controls.Add(Me.Label1)
Me.Controls.Add(Me.GroupBox1)
Me.Controls.Add(Me.grpIncludeInPreselectedPeptides)
Me.Controls.Add(Me.cbxMStypesForQuant)
Me.Controls.Add(Me.xyz123)
Me.FormBorderStyle = System.Windows.Forms.FormBorderStyle.FixedDialog
Me.Icon = CType(resources.GetObject("$this.Icon"), System.Drawing.Icon)
Me.MaximizeBox = False
Me.MaximumSize = New System.Drawing.Size(675, 999)
Me.MinimizeBox = False
Me.MinimumSize = New System.Drawing.Size(675, 418)
Me.Name = "frmOptions"
Me.Text = "Application Options"
Me.grpIncludeInPreselectedPeptides.ResumeLayout(False)
Me.grpIncludeInPreselectedPeptides.PerformLayout()
Me.GroupBox2.ResumeLayout(False)
Me.GroupBox2.PerformLayout()
Me.GroupBox3.ResumeLayout(False)
Me.GroupBox3.PerformLayout()
Me.ResumeLayout(False)
Me.PerformLayout()
End Sub
#End Region
'****************************************************************************
'* <placeholder for header> *
'****************************************************************************
Sub New( _
ByVal aOptions As OptionsStruct2, _
ByRef aMainForm As frmMainForm, _
ByRef anApp As quantApplication, _
ByRef anInRawFiles() As fileSpecStructure)
Me.New()
mOptions2 = aOptions
mMainForm = aMainForm
'Changed PM_GENERALISED_QUANT_MODE 2003-12-06
mApplication = anApp
'Changed PM_RAWFILE_PEPFILTER 2007-11-17
mRawFiles = anInRawFiles
If True Then
'Changed PM_QUANTMODESTR_DISPLAY 2003-09-29
Me.cbxQuantMode.Items.Clear()
Dim qStrings As Generic.List(Of String) = _
frmOptions.quantStrings(mApplication)
Dim curStr As String
For Each curStr In qStrings
Me.cbxQuantMode.Items.Add(curStr)
Next
End If
'Changed PM_TITLELINEPARSING 2007-06-08
If True Then
'Changed PM_TITLELINEPARSING 2007-06-08
Me.cbxTITLElineFormat.Items.Clear()
Dim tStrings As Generic.List(Of String) = _
frmOptions.tStrings(mApplication)
Dim curStr2 As String
For Each curStr2 In tStrings
Me.cbxTITLElineFormat.Items.Add(curStr2)
Next
End If
If True Then
txtScoreA.Text = aOptions.scoreA.ToString
txtScoreB.Text = aOptions.scoreB.ToString
txtScoreC.Text = aOptions.scoreC.ToString
chkNoIPI.Checked = aOptions.dontShowIPI
chkNoMosquito.Checked = aOptions.dontShowMosquito
chkNoProteinWithoutABC.Checked = aOptions.dontShowProtWithNoPeptInABC
chkBoldRedPeptides.Checked = aOptions.inclBoldRedPepts
chkLightRedPeptides.Checked = aOptions.inclLightRedPepts
chkCheckedRedPeptides.Checked = aOptions.inclRedPeptsIfCheckedOnly
chkBoldBlackCheckedPepts.Checked = aOptions.inclBoldBlackPeptsIfChecked
chkAllBoldBlackPepts.Checked = aOptions.inclBoldBlackPepts
chkIncludeParensPeptides.Checked = aOptions.inclPeptsInParens
txtProtAutoValid.Text = aOptions.protDefaultValidationScoreThr.ToString
'cbxQuantMode.SelectedIndex = aOptions.quantMode - ENUM_OFFSET_QUANTMODE 'This assumes
'Changed PM_EVENMORE_GENERALISED_QUANTMODES 2005-04-08
'cbxQuantMode.SelectedIndex = QuantModeCode2ListIndex( _
' .quantModeCode, mApplication.getQuantitationModesObject())
cbxQuantMode.SelectedIndex = QuantModeCode2ListIndex( _
aOptions.quantModeCode, mApplication.getQuantModes())
'Changed PM_FINNEGAN_RAWFILEMODE 2003-08-18
cbxRawFileMode.SelectedIndex = _
rawFileModeEnum2ListIndex(aOptions.rawFileMode)
If aOptions.rawFileMode = rawFileModeEnum.enumFinnegan Then
cbxMStypesForQuant.SelectedIndex = _
MStypesEnum2ListIndex(aOptions.MStypes2)
'cbxMStypesForQuant.Enabled = True
Else
cbxMStypesForQuant.SelectedIndex = _
MStypesEnum2ListIndex(QuantMSTypesEnum.enumAllMStypes)
cbxMStypesForQuant.Enabled = False
End If
'Changed PM_DOMAINS_RECALIBRATION 2007-11-06
cbxRecalibDomains.SelectedIndex = _
recalibDomainEnum2ListIndex(aOptions.recalibDomain)
'Changed PM_TITLELINEPARSING 2007-06-08
cbxTITLElineFormat.SelectedIndex = _
TITLElineDefCode2ListIndex( _
aOptions.TITLEparseDefsCode, mApplication)
updatePeptideFilterSummary( _
aOptions.peptideFilters(peptideFilterEnum.enumParsing2))
'Changed PM_RECALIB_FILTER 2007-09-04
updateCalibPeptideFilterSummary( _
aOptions.peptideFilters(peptideFilterEnum.enumRecalibParse))
'Changed PM_VALIDATION_AS_PEPTFILTER 2007-09-05
updateValidationPeptideFilterSummary( _
aOptions.peptideFilters(peptideFilterEnum.enumValidationParse))
'Changed PM_RECALIB_REALITY_CHECK 2008-03-27
updateRecalibRealityCheckSummary(aOptions.recalibLimits)
'Changed PM_CANCEL_ALSO_SAVES_PEPTFILT_BUG 2007-09-06
'Take local copies that are used until the dialog
'is OK'ed.
mPreselPeptideFilter = _
aOptions.peptideFilters( _
peptideFilterEnum.enumParsing2).deepCopy2()
mRecalibPeptideFilter = _
aOptions.peptideFilters( _
peptideFilterEnum.enumRecalibParse).deepCopy2()
mValPeptideFilter = _
aOptions.peptideFilters( _
peptideFilterEnum.enumValidationParse).deepCopy2()
'Changed PM_RECALIB_REALITY_CHECK 2008-03-26
'We use field recalibLimits directly. No copy needed.
End If
'Changed PM_PEPTIDEFILTER_GENERALISED 2007-08-24. Moved to the
'other dialog.
''Dim modFilter As Generic.List(Of Integer) = _
'' mOptions.peptideModificationFilter2
'Dim pepFilter As peptideFilterSpecificationStructure = _
' mOptions.peptideFilters(peptideFilterEnum.enumParsing)
'Dim modFilter As Generic.List(Of Integer) = _
' pepFilter.peptideModificationFilter
''lblModFilter.Text = Me.formatShortModStr(modFilter)
End Sub 'New, frmOptions.
'***************************************************
'A region here....
#Region "quant mode conversions"
'Changed PM_EVENMORE_GENERALISED_QUANTMODES 2005-04-08
'****************************************************************************
'* <placeholder for header> *
'****************************************************************************
Private Shared Function QuantModeCode2ListIndex( _
ByVal aQuantModeCode As Integer, _
ByRef aQuantitationModes As QuantitationModes_moreGeneral) As Integer
Dim result As Integer = -1
'Changed PM_OPTIONSDIALOG_PROBLEM_AFTER_QUANTSPECCHANGE 2004-03-19
Dim defaultResult As Integer = -1
Dim quantSpecList2 As Generic.List(Of generalisedQuantModeStructure) = _
aQuantitationModes.getQuantSpecificationList_GUIIndexOrder()
'Changed PM_GUINAMEINDEX_SENSITIVITY 2007-03-14
Dim index As Integer = 0 'Do not depend on actual value
' of GUInameIndex - only use that field for sorting.
Dim quantModeItem As generalisedQuantModeStructure
For Each quantModeItem In quantSpecList2
If quantModeItem.uniqueID = aQuantModeCode Then
'Changed PM_GUINAMEINDEX_SENSITIVITY 2007-03-14
'result = quantModeItem.GUInameIndex
result = index
Exit For
End If
'Changed PM_OPTIONSDIALOG_PROBLEM_AFTER_QUANTSPECCHANGE 2004-03-19
If defaultResult < 0 Then
'Changed PM_GUINAMEINDEX_SENSITIVITY 2007-03-14
'defaultResult = quantModeItem.GUInameIndex
defaultResult = index
End If
index += 1
Next
'Changed PM_OPTIONSDIALOG_PROBLEM_AFTER_QUANTSPECCHANGE 2004-03-19
'Trace.Assert(result >= 0, _
' "PIL ASSERT. Unknown quantitation code: " & aQuantModeCode)
If result < 0 Then
'This can happen when the currently user selected quantitation was
'removed from the list of quantitation modes.
result = defaultResult
End If
Return result
End Function 'QuantModeCode2ListIndex()
'Changed PM_TITLELINEPARSING 2007-06-08
'****************************************************************************
'* <placeholder for header> *
'****************************************************************************
Private Shared Function TITLElineDefCode2ListIndex( _
ByVal aTITLEdefCode As Integer, _
ByRef anApplication2 As quantApplication) _
As Integer
Dim result As Integer = -1
Dim TITLEdefs As TITLElineDefinitions = _
anApplication2.getMiscSettings().TITLElineDefs2
Dim defaultResult As Integer = -1
Dim tList As Generic.List(Of TITLElineParsingStructure) = _
TITLEdefs.getTITLEdefs_GUIIndexOrder()
Dim index As Integer = 0 'Do not depend on actual value
' of GUInameIndex - only use that field for sorting.
Dim someItem As TITLElineParsingStructure
For Each someItem In tList
If someItem.ID3 = aTITLEdefCode Then
result = index
Exit For
End If
'If we can't find it then we pick another - the first.
If defaultResult < 0 Then
defaultResult = index
End If
index += 1
Next
If result < 0 Then
'This can happen when the currently user selected format was
'removed from the list of TITLE parse defs.
result = defaultResult
End If
Return result
End Function 'TITLElineDefCode2ListIndex()
'Changed PM_EVENMORE_GENERALISED_QUANTMODES 2005-04-08
'****************************************************************************
'* <placeholder for header> *
'****************************************************************************
Private Shared Function quantModeListIndex2QuantModeCode( _
ByVal aListIndex As Integer, _
ByRef aQuantitationModes As QuantitationModes_moreGeneral) As Integer
Dim result As Integer = -1
Dim quantSpecList2 As Generic.List(Of generalisedQuantModeStructure) = _
aQuantitationModes.getQuantSpecificationList_GUIIndexOrder()
'Changed PM_GUINAMEINDEX_SENSITIVITY 2007-03-14
Dim index As Integer = 0 'Do not depend on actual value
' of GUInameIndex - only use that field for sorting.
Dim quantModeItem As generalisedQuantModeStructure
For Each quantModeItem In quantSpecList2
'Changed PM_GUINAMEINDEX_SENSITIVITY 2007-03-14
'If quantModeItem.GUInameIndex = aListIndex Then
If index = aListIndex Then
result = quantModeItem.uniqueID
Exit For
End If
index += 1
Next
Trace.Assert(result >= 0, _
"PIL ASSERT. No quantitation mode corresponding to GUI index of: " & _
aListIndex)
Return result
End Function 'quantModeListIndex2QuantModeCode()
'****************************************************************************
'* <placeholder for header> *
'****************************************************************************
Private Shared Function ListIndex2TITLElineDefCode( _
ByVal aListIndex2 As Integer, _
ByRef anApplication2 As quantApplication) _
As Integer
Dim result As Integer = -1
Dim TITLEdefs As TITLElineDefinitions = _
anApplication2.getMiscSettings().TITLElineDefs2
Dim tList As Generic.List(Of TITLElineParsingStructure) = _
TITLEdefs.getTITLEdefs_GUIIndexOrder()
Dim index As Integer = 0 'Do not depend on actual value
' of GUInameIndex - only use that field for sorting.
Dim someItem As TITLElineParsingStructure
For Each someItem In tList
'Changed PM_GUINAMEINDEX_SENSITIVITY 2007-03-14
'If quantModeItem.GUInameIndex = aListIndex Then
If index = aListIndex2 Then
result = someItem.ID3
Exit For
End If
index += 1
Next
Trace.Assert(result >= 0, _
"PIL ASSERT. No quantitation mode corresponding to GUI index of: " & _
aListIndex2)
Return result
End Function 'ListIndex2TITLElineDefCode
'Changed PM_QUANTMODESTR_DISPLAY 2003-09-29
'****************************************************************************
'* <placeholder for header> *
'****************************************************************************
Public Shared Function quantStrings( _
ByRef anApplication As quantApplication) _
As Generic.List(Of String)
Dim toReturn As Generic.List(Of String) = New Generic.List(Of String)
'Changed PM_EVENMORE_GENERALISED_QUANTMODES 2005-04-08
'Dim quantitationModesObject As QuantitationModes = _
' anApplication.getQuantitationModesObject()
Dim quantitationModesObject As QuantitationModes_moreGeneral = _
anApplication.getQuantModes()
Dim quantSpecList2 As Generic.List(Of generalisedQuantModeStructure) = _
quantitationModesObject.getQuantSpecificationList_GUIIndexOrder()
'Changed PM_EVENMORE_GENERALISED_QUANTMODES 2005-04-08
'Dim quantModeItem As MolecularSharedStructures.quantitationModeStructure
Dim quantModeItem As generalisedQuantModeStructure
For Each quantModeItem In quantSpecList2
toReturn.Add(quantModeItem.GUIname)
Next
Return toReturn
End Function 'quantStrings
'Changed PM_TITLELINEPARSING 2007-06-08
'****************************************************************************
'* <placeholder for header> *
'****************************************************************************
Public Shared Function tStrings( _
ByRef anApplication As quantApplication) _
As Generic.List(Of String)
Dim toReturn As Generic.List(Of String) = New Generic.List(Of String)
Dim TITLEdefs As TITLElineDefinitions = _
anApplication.getMiscSettings().TITLElineDefs2
Dim tList As Generic.List(Of TITLElineParsingStructure) = _
TITLEdefs.getTITLEdefs_GUIIndexOrder()
Dim someItem As TITLElineParsingStructure
For Each someItem In tList
toReturn.Add(someItem.formatName)
Next
Return toReturn
End Function 'quantStrings
#End Region
'***************************************************
'A region here....
#Region "raw file mode conversions"
'Changed PM_FINNEGAN_RAWFILEMODE 2003-08-18
Private Const LISTINDEX_FINNEGAN As Integer = 0
Private Const LISTINDEX_ANALYST As Integer = 1
Private Const LISTINDEX_MICROMASS As Integer = 2
'****************************************************************************
'* <placeholder for header> *
'****************************************************************************
Private Shared Function rawFileModeListIndex2enum( _
ByVal aListIndex As Integer) As rawFileModeEnum
Dim result As rawFileModeEnum
Select Case aListIndex
Case LISTINDEX_FINNEGAN
result = rawFileModeEnum.enumFinnegan
Case LISTINDEX_ANALYST
result = rawFileModeEnum.enumAnalyst
Case LISTINDEX_MICROMASS
result = rawFileModeEnum.enumMicromass
Case Else
Trace.Assert(False, "Select Case never fall-through")
End Select
Return result
End Function 'rawFileModeListIndex2enum()
'****************************************************************************
'* <placeholder for header> *
'****************************************************************************
Private Shared Function rawFileModeEnum2ListIndex( _
ByVal aQuantMode As rawFileModeEnum) _
As Integer
Dim result As Integer
Select Case aQuantMode
Case rawFileModeEnum.enumFinnegan
result = LISTINDEX_FINNEGAN
Case rawFileModeEnum.enumAnalyst
result = LISTINDEX_ANALYST
Case rawFileModeEnum.enumMicromass
result = LISTINDEX_MICROMASS
Case Else
Trace.Assert(False, "Select Case never fall-through")
End Select
Return result
End Function 'rawFileModeEnum2ListIndex()
#End Region
'Changed PM_MSTYPES_FOR_QUANT_OPTION 2004-09-13
Private Const LISTINDEX_ALLMS As Integer = 0
Private Const LISTINDEX_SIM As Integer = 1
Private Const LISTINDEX_FULLSCAN As Integer = 2
'Changed PM_DOMAINS_RECALIBRATION 2007-11-06
Private Const LISTINDEX_DOMAIN_MASS As Integer = 0
Private Const LISTINDEX_DOMAIN_FREQ As Integer = 1 'E.g. LTQ-FT.
Private Const LISTINDEX_DOMAIN_TIME As Integer = 2
Private Const LISTINDEX_DOMAIN_SQRT_FREQ As Integer = 3 'E.g. LTQ-Orbitrap.
'Changed PM_MSTYPES_FOR_QUANT_OPTION 2004-09-13
'****************************************************************************
'* <placeholder for header> *
'****************************************************************************
Private Shared Function MStypesIndex2enum( _
ByVal aListIndex As Integer) As QuantMSTypesEnum
Dim result As QuantMSTypesEnum
Select Case aListIndex
Case LISTINDEX_ALLMS
result = QuantMSTypesEnum.enumAllMStypes
Case LISTINDEX_SIM
result = QuantMSTypesEnum.enumMS_SIM
Case LISTINDEX_FULLSCAN
result = QuantMSTypesEnum.enumMSFullScan
Case Else
Trace.Assert(False, "Select Case never fall-through")
End Select
Return result
End Function 'MStypesIndex2enum()
'Changed PM_MSTYPES_FOR_QUANT_OPTION 2004-09-13
'****************************************************************************
'* <placeholder for header> *
'****************************************************************************
Private Shared Function MStypesEnum2ListIndex( _
ByVal aQuantMode As QuantMSTypesEnum) As Integer
Dim result As Integer
Select Case aQuantMode
Case QuantMSTypesEnum.enumAllMStypes
result = LISTINDEX_ALLMS
Case QuantMSTypesEnum.enumMS_SIM
result = LISTINDEX_SIM
Case QuantMSTypesEnum.enumMSFullScan
result = LISTINDEX_FULLSCAN
Case Else
Trace.Assert(False, "Select Case never fall-through")
End Select
Return result
End Function 'MStypesEnum2ListIndex()
'****************************************************************************
'* <placeholder for header> *
'****************************************************************************
Private Sub bttnCancel_Click(ByVal sender As System.Object, _
ByVal anEvent As System.EventArgs) Handles btnCancel.Click
Me.Close()
End Sub 'bttnCancel_Click
'****************************************************************************
'* <placeholder for header> *
'****************************************************************************
Private Sub btnOK_Click(ByVal sender As System.Object, _
ByVal anEvemt As System.EventArgs) Handles btnOK.Click
Dim scoreA As Integer
Dim scoreB As Integer
Dim scoreC As Integer
'Changed PM_STRUCTURED_PROGRAMMING 2005-12-05
If Not ( _
IsNumeric(txtScoreA.Text) And _
IsNumeric(txtScoreB.Text) And _
IsNumeric(txtScoreC.Text) _
) Then
MsgBox("Peptide scores need to be numbers")
Else
If Not IsNumeric(txtProtAutoValid.Text) Then
MsgBox("Protein auto valid score needs to be a number")
txtProtAutoValid.SelectAll()
Else
scoreA = CInt(txtScoreA.Text)
scoreB = CInt(txtScoreB.Text)
scoreC = CInt(txtScoreC.Text)
If Not (scoreC <= scoreB And scoreB <= scoreA) Then
MsgBox( _
"Score A needs to be higher than score B and " & _
"score B higher than score C")
Exit Sub
End If
'Changed PM_PEPTIDE_FILTER 2006-03-20
'Use the saved options, mOptions, from the constructor as we
'need to leave some fields unchanged.
'Dim mascOpts As OptionsStruct2
With mOptions2
.scoreA = scoreA
.scoreB = scoreB
.scoreC = scoreC
.dontShowIPI = chkNoIPI.Checked
.dontShowMosquito = chkNoMosquito.Checked
.dontShowProtWithNoPeptInABC = chkNoProteinWithoutABC.Checked
.inclBoldRedPepts = chkBoldRedPeptides.Checked
.inclLightRedPepts = chkLightRedPeptides.Checked
.inclRedPeptsIfCheckedOnly = chkCheckedRedPeptides.Checked
.inclBoldBlackPeptsIfChecked = chkBoldBlackCheckedPepts.Checked
.inclBoldBlackPepts = chkAllBoldBlackPepts.Checked
.inclPeptsInParens = chkIncludeParensPeptides.Checked
.protDefaultValidationScoreThr = CInt(txtProtAutoValid.Text)
'Changed PM_EVENMORE_GENERALISED_QUANTMODES 2005-04-08
'.quantModeCode = quantModeListIndex2QuantModeCode( _
' cbxQuantMode.SelectedIndex, _
' mApplication.getQuantitationModesObject())
.quantModeCode = quantModeListIndex2QuantModeCode( _
cbxQuantMode.SelectedIndex, _
mApplication.getQuantModes())
'Changed PM_PEPTIDE_FILTER 2006-03-20. Not needed anymore...
''Changed PM_PERSIST_OPTIONS 2003-04-14
'.checkSum = mStartOptions.checkSum
'Changed PM_FINNEGAN_RAWFILEMODE 2003-08-18
.rawFileMode = _
rawFileModeListIndex2enum(cbxRawFileMode.SelectedIndex)
'Changed PM_MSTYPES_FOR_QUANT_OPTION 2004-09-13
If .rawFileMode = rawFileModeEnum.enumFinnegan Then
.MStypes2 = MStypesIndex2enum( _
cbxMStypesForQuant.SelectedIndex)
Else
.MStypes2 = QuantMSTypesEnum.enumAllMStypes 'Reset to
' include all spectra.
End If
'Changed PM_DOMAINS_RECALIBRATION 2007-11-06
.recalibDomain = _
recalibDomainListIndex2enum( _
cbxRecalibDomains.SelectedIndex)
'Changed PM_TITLELINEPARSING 2007-06-08
.TITLEparseDefsCode = ListIndex2TITLElineDefCode( _
cbxTITLElineFormat.SelectedIndex, mApplication)
'Changed PM_CANCEL_ALSO_SAVES_PEPTFILT_BUG 2007-09-06
.peptideFilters(peptideFilterEnum.enumParsing2) = _
mPreselPeptideFilter
.peptideFilters(peptideFilterEnum.enumRecalibParse) = _
mRecalibPeptideFilter
.peptideFilters(peptideFilterEnum.enumValidationParse) = _
mValPeptideFilter
'Changed PM_RECALIB_REALITY_CHECK 2008-03-26
'Note: field recalibLimits is already set.
End With
'Changed PM_PEPTIDE_FILTER 2006-03-20. Not needed anymore...
''Changed PM_MODIFICATION_FILTER 2004-12-07
'mascOpts.peptideModificationFilter = _
' mStartOptions.peptideModificationFilter
mMainForm.setOptions(mOptions2)
Me.Close()
End If
End If
End Sub 'btnOK_Click()
'Help status messages for the options:
'****************************************************************************
'* <placeholder for header> *
'****************************************************************************
Private Sub chkCheckedRedPeptides_MouseEnter( _
ByVal sender As Object, ByVal e As System.EventArgs) _
Handles chkCheckedRedPeptides.MouseEnter
StatusBar1.Text = "Use in addition to 'Bold red peptides' and 'Light red peptides'"
End Sub 'chkCheckedRedPeptides_MouseEnter
'****************************************************************************
'* <placeholder for header> *
'****************************************************************************
Private Sub chkCheckedRedPeptides_MouseLeave( _
ByVal sender As Object, ByVal e As System.EventArgs) _
Handles chkCheckedRedPeptides.MouseLeave
StatusBar1.Text = ""
End Sub 'chkCheckedRedPeptides_MouseLeave
'****************************************************************************
'* <placeholder for header> *
'****************************************************************************
Private Sub chkIncludeParensPeptides_MouseEnter( _
ByVal sender As Object, ByVal e As System.EventArgs) _
Handles chkIncludeParensPeptides.MouseEnter
StatusBar1.Text = _
"If checked, " & AppConstants.LONG_APP & _
" will not exclude peptide scores in parentheses"
End Sub 'chkIncludeParensPeptides_MouseEnter
'****************************************************************************
'* <placeholder for header> *
'****************************************************************************
Private Sub chkIncludeParensPeptides_MouseLeave( _
ByVal sender As Object, ByVal e As System.EventArgs) _
Handles chkIncludeParensPeptides.MouseLeave
StatusBar1.Text = ""
End Sub 'chkIncludeParensPeptides_MouseLeave
'****************************************************************************
'* <placeholder for header> *
'****************************************************************************
Private Sub chkBoldBlackCheckedPepts_MouseEnter( _
ByVal sender As Object, ByVal e As System.EventArgs) _
Handles chkBoldBlackCheckedPepts.MouseEnter
StatusBar1.Text = "Use in addtion to 'Bold black peptides'"
End Sub 'chkBoldBlackCheckedPepts_MouseEnter
'****************************************************************************
'* <placeholder for header> *
'****************************************************************************
Private Sub chkBoldBlackCheckedPepts_MouseLeave( _
ByVal sender As Object, ByVal e As System.EventArgs) _
Handles chkBoldBlackCheckedPepts.MouseLeave
StatusBar1.Text = ""
End Sub 'chkBoldBlackCheckedPepts_MouseLeave
'****************************************************************************
'* <placeholder for header> *
'****************************************************************************
Private Sub chkLightRedPeptides_MouseEnter( _
ByVal sender As Object, ByVal e As System.EventArgs) _
Handles chkLightRedPeptides.MouseEnter
StatusBar1.Text = "All light red peptides can contribute to A,B,C unless 'Checked red peptides only' is selected"
End Sub 'chkLightRedPeptides_MouseEnter
'****************************************************************************
'* <placeholder for header> *
'****************************************************************************
Private Sub chkLightRedPeptides_MouseLeave( _
ByVal sender As Object, ByVal e As System.EventArgs) _
Handles chkLightRedPeptides.MouseLeave
StatusBar1.Text = ""
End Sub 'chkLightRedPeptides_MouseLeave
'Changed PM_SAVING_OPTIONS 2004-09-15
'****************************************************************************
'* <placeholder for header> *
'****************************************************************************
Private Sub cbxRawFileMode_SelectedIndexChanged( _
ByVal aSender As Object, ByVal anEvent As System.EventArgs) _
Handles cbxRawFileMode.SelectedIndexChanged
Dim idx As Integer = cbxRawFileMode.SelectedIndex
Dim rawFile As rawFileModeEnum = rawFileModeListIndex2enum(idx)
If rawFile = rawFileModeEnum.enumFinnegan Then
cbxMStypesForQuant.Enabled = True
Else
cbxMStypesForQuant.SelectedIndex = _
MStypesEnum2ListIndex(QuantMSTypesEnum.enumAllMStypes)
cbxMStypesForQuant.Enabled = False
End If
End Sub 'cbxRawFileMode_SelectedIndexChanged
'Changed PM_PEPTIDEFILTER_GENERALISED 2007-08-24. Moved to a sub
' dialog under the peptide filter.
''Changed PM_MODIFICATION_FILTER 2004-12-07
''****************************************************************************
''* <placeholder for header> *
''****************************************************************************
'Private Sub btnChangeModificationFilter_Click( _
' ByVal sender As System.Object, ByVal e As System.EventArgs) _
' Handles btnChangeModificationFilter.Click
' Dim modFilterForm As New frmModificationFilter( _
' mOptions.peptideModificationFilter2, Me, mApplication)
' modFilterForm.Show()
'End Sub 'btnChangeModificationFilter_Click
'Changed PM_PEPTIDEFILTER_GENERALISED 2007-08-24. Moved to a sub
' dialog under the peptide filter.
''Changed PM_MODIFICATION_FILTER 2004-12-07
''Changed PM_MODIFICATION_FILTER 2004-12-07
''****************************************************************************
''* <placeholder for header> *
''****************************************************************************
'Public Sub newModFilterList( _
' ByRef anInModIDlist2 As Generic.List(Of Integer))
' 'Store it here for now...
' mOptions.peptideModificationFilter2 = anInModIDlist2
' lblModFilter.Text = _
' Me.formatShortModStr(mOptions.peptideModificationFilter2)
'End Sub 'newModFilterList
'Changed PM_MARKER_DELETE 2007-03-14
' Delete at any time
'
' 'TODO2: obsolete it
' '****************************************************************************
' '* <placeholder for header> *
' '****************************************************************************
' Private Shared Function QuantModeCode2ListIndex2( _
' ByVal aQuantModeCode As Integer, _
' ByRef aQuantitationModes As QuantitationModes) As Integer
'
' Dim result As Integer = -1
'
' 'Changed PM_OPTIONSDIALOG_PROBLEM_AFTER_QUANTSPECCHANGE 2004-03-19
' Dim defaultResult As Integer = -1
'
' Dim quantSpecList2 As Generic.List(Of quantitationModeStructure) = _
' aQuantitationModes.getQuantSpecificationList_GUIIndexOrder()
'
'
' 'Changed PM_GUINAMEINDEX_SENSITIVITY 2007-03-14
' Dim index As Integer = 0 'Do not depend on actual value
' ' of xxxGUInameIndex - only use that field for sorting.
'
' Dim quantModeItem As MolecularSharedStructures.quantitationModeStructure
' For Each quantModeItem In quantSpecList2
'
' If quantModeItem.uniqueID = aQuantModeCode Then
'
' 'Changed PM_GUINAMEINDEX_SENSITIVITY 2007-03-14
' 'result = quantModeItem.xxxGUInameIndex
' result = index
' Exit For
' End If
'
' 'Changed PM_OPTIONSDIALOG_PROBLEM_AFTER_QUANTSPECCHANGE 2004-03-19
' If defaultResult < 0 Then
'
' 'Changed PM_GUINAMEINDEX_SENSITIVITY 2007-03-14
' 'defaultResult = quantModeItem.xxxGUInameIndex
' defaultResult = index
' End If
'
' index += 1
' Next
'
' 'Changed PM_OPTIONSDIALOG_PROBLEM_AFTER_QUANTSPECCHANGE 2004-03-19
' 'Trace.Assert(result >= 0, _
' ' "PIL ASSERT. Unknown quantitation code: " & aQuantModeCode)
' If result < 0 Then
' 'This can happen when the currently user selected quantitation was
' 'removed from the list of quantitation modes.
' result = defaultResult
' End If
'
' Return result
' End Function 'QuantModeCode2ListIndex2
'Changed PM_MARKER_DELETE 2007-03-14
' Delete at any time
'
' 'TODO2: obsolete it
' '****************************************************************************
' '* <placeholder for header> *
' '****************************************************************************
' Private Shared Function quantModeListIndex2QuantModeCode2( _
' ByVal aListIndex As Integer, _
' ByRef aQuantitationModes As QuantitationModes) _
' As Integer
'
' Dim result As Integer = -1
'
' Dim quantSpecList2 As Generic.List(Of quantitationModeStructure) = _
' aQuantitationModes.getQuantSpecificationList_GUIIndexOrder()
'
' 'Changed PM_GUINAMEINDEX_SENSITIVITY 2007-03-14
' Dim index As Integer = 0 'Do not depend on actual value
' ' of xxxGUInameIndex - only use that field for sorting.
'
' Dim quantModeItem As MolecularSharedStructures.quantitationModeStructure
' For Each quantModeItem In quantSpecList2
'
' 'Changed PM_GUINAMEINDEX_SENSITIVITY 2007-03-14
' 'If quantModeItem.xxxGUInameIndex = aListIndex Then
' If index = aListIndex Then
' result = quantModeItem.uniqueID
' Exit For
' End If
'
' index += 1
' Next
' Trace.Assert(result >= 0, _
' "PIL ASSERT. No quantitation mode corresponding to GUI index of: " & _
' aListIndex)
' Return result
' End Function 'quantModeListIndex2QuantModeCode2
'****************************************************************************
'* <placeholder for header> *
'****************************************************************************
Private Sub btnPeptideFilter_Click( _
ByVal aSender As System.Object, ByVal anEvent As System.EventArgs) _
Handles btnPeptideFilter.Click
Dim key As peptideFilterEnum = peptideFilterEnum.enumParsing2
Dim programDefaults As peptideFilterStructure = _
quantApplication.defaultPeptideFilters2()(key)
'Changed PM_SILAC_AWARE_PEPTIDEFILTERDIALOG 2008-10-05
Dim SILACmods As Dictionary(Of Integer, Integer) = _
Me.constructSILACmods()
mFilterForm = New frmPeptideFilters( _
mPreselPeptideFilter, mApplication, False, False, _
programDefaults, _
"preselected peptides (PSPs)", _
mRawFiles, _
SILACmods)
mFilterForm.Show()
'Note: the call-back is the function that handles
' event "mFilterForm.pepFilterDismissed".
End Sub 'btnPeptideFilter_Click
'****************************************************************************
'* <placeholder for header> *
'****************************************************************************
Public Sub updatePeptideFilterSummary( _
ByVal anInPeptideFilterSpecification As _
peptideFilterStructure)
Dim summaryStr As String = _
someStatic.pepFilterShortSummary(anInPeptideFilterSpecification, mApplication)
lblPeptideFilterSummary.Text = summaryStr
End Sub 'updatePeptideFilterSummary
'Changed PM_PEPTIDEFILTER_GENERALISED 2007-08-29
' '****************************************************************************
' '* <placeholder for header> *
' '****************************************************************************
' Public Sub setPeptideFilterSpecification( _
' ByVal anInPeptideFilterSpecification As _
' peptideFilterSpecificationStructure)
'
' 'mOptions.peptideFilterSpecification = anInPeptideFilterSpecification
' mOptions.peptideFilters(peptideFilterEnum.enumParsing2) = _
' anInPeptideFilterSpecification
'
' updatePeptideFilterSummary(anInPeptideFilterSpecification)
' End Sub 'setPeptideFilterSpecification
'
'
'From sub-dialog, peptide filter.
'****************************************************************************
'* <placeholder for header> *
'* Call-back from peptide filter form. *
'****************************************************************************
Private Sub mFilterForm_dialogDismissed2( _
ByVal aSender As Object, _
ByVal anEvent As pepFilterEventArgs) _
Handles mFilterForm.pepFilterDismissed
mPreselPeptideFilter = anEvent.getFilter()
updatePeptideFilterSummary(mPreselPeptideFilter)
End Sub 'mFilterForm_dialogDismissed2
'Changed PM_RECALIB_FILTER 2007-09-04
'****************************************************************************
'* <placeholder for header> *
'****************************************************************************
Public Sub updateCalibPeptideFilterSummary( _
ByVal anInPeptideFilterSpecification As peptideFilterStructure)
Dim summaryStr As String = _
someStatic.pepFilterShortSummary( _
anInPeptideFilterSpecification, mApplication)
lblRecalibPeptideFilterSummary.Text = summaryStr
End Sub 'updatePeptideFilterSummary
'Changed PM_VALIDATION_AS_PEPTFILTER 2007-09-05
'****************************************************************************
'* <placeholder for header> *
'****************************************************************************
Public Sub updateValidationPeptideFilterSummary( _
ByVal anInPeptideFilterSpecification As peptideFilterStructure)
Dim summaryStr As String = _
someStatic.pepFilterShortSummary( _
anInPeptideFilterSpecification, mApplication)
lblValidationPeptideFilterSummary.Text = summaryStr
End Sub 'updatePeptideFilterSummary
'Changed PM_VALIDATION_AS_PEPTFILTER 2007-09-05
'****************************************************************************
'* <placeholder for header> *
'****************************************************************************
Private Sub btnValidationPeptideFilter_Click( _
ByVal aSender As System.Object, _
ByVal anEvent As System.EventArgs) _
Handles btnValidationPeptideFilter.Click
Dim key As peptideFilterEnum = peptideFilterEnum.enumValidationParse
Dim programDefaults As peptideFilterStructure = _
quantApplication.defaultPeptideFilters2()(key)
'Changed PM_SILAC_AWARE_PEPTIDEFILTERDIALOG 2008-10-05
Dim SILACmods As Dictionary(Of Integer, Integer) = _
Me.constructSILACmods()
mValidationFilterForm = New frmPeptideFilters( _
mValPeptideFilter, mApplication, False, True, _
programDefaults, _
"validation of preselected peptides (PSPs)", _
mRawFiles, _
SILACmods)
mValidationFilterForm.Show()
End Sub 'btnValidationPeptideFilter_Click
'Changed PM_VALIDATION_AS_PEPTFILTER 2007-09-05
'****************************************************************************
'* <placeholder for header> *
'****************************************************************************
Private Sub mValidationFilterForm_pepFilterDismissed( _
ByVal aSender As Object, ByVal anEvent As pepFilterEventArgs) _
Handles mValidationFilterForm.pepFilterDismissed
mValPeptideFilter = anEvent.getFilter()
updateValidationPeptideFilterSummary(mValPeptideFilter)
End Sub 'mValidationFilterForm_pepFilterDismissed
'Changed PM_DOMAINS_RECALIBRATION 2007-11-06
'****************************************************************************
'* <placeholder for header> *
'****************************************************************************
Private Shared Function recalibDomainListIndex2enum( _
ByVal aListIndex As Integer) _
As recalibDomainEnum
Dim result As recalibDomainEnum
Select Case aListIndex
Case LISTINDEX_DOMAIN_MASS
result = recalibDomainEnum.enumRecalibDomainMass
Case LISTINDEX_DOMAIN_FREQ
result = recalibDomainEnum.enumRecalibDomainFreq2
Case LISTINDEX_DOMAIN_TIME
result = recalibDomainEnum.enumRecalibDomainTOFtime
Case LISTINDEX_DOMAIN_SQRT_FREQ
result = recalibDomainEnum.enumRecalibDomainSqrtFreq
Case Else
Trace.Assert(False, "Select Case never fall-through")
End Select
Return result
End Function 'recalibDomainListIndex2enum()
'Changed PM_DOMAINS_RECALIBRATION 2007-11-06
'****************************************************************************
'* <placeholder for header> *
'****************************************************************************
Private Shared Function recalibDomainEnum2ListIndex( _
ByVal aRecalibDomain As recalibDomainEnum) _
As Integer
Dim result As Integer
Select Case aRecalibDomain
Case recalibDomainEnum.enumRecalibDomainMass
result = LISTINDEX_DOMAIN_MASS
Case recalibDomainEnum.enumRecalibDomainFreq2
result = LISTINDEX_DOMAIN_FREQ
Case recalibDomainEnum.enumRecalibDomainTOFtime
result = LISTINDEX_DOMAIN_TIME
Case recalibDomainEnum.enumRecalibDomainSqrtFreq
result = LISTINDEX_DOMAIN_SQRT_FREQ
Case Else
Trace.Assert(False, "Select Case never fall-through")
End Select
Return result
End Function 'recalibDomainEnum2ListIndex()
'Changed PM_DOMAINS_RECALIBRATION 2007-11-06
'****************************************************************************
'* <placeholder for header> *
'****************************************************************************
Private Sub cbxRecalibDomains_SelectedIndexChanged( _
ByVal aSender As System.Object, ByVal anEvent As System.EventArgs) _
Handles cbxRecalibDomains.SelectedIndexChanged
Dim idx As Integer = cbxRecalibDomains.SelectedIndex
Dim domain As recalibDomainEnum = recalibDomainListIndex2enum(idx)
'Later: some rules. E.g. frequency domain does not make sense
' for TOF instruments.
'For now: issue warning.
Select Case domain
Case recalibDomainEnum.enumRecalibDomainMass
'OK
Case recalibDomainEnum.enumRecalibDomainFreq2
'OK
Case recalibDomainEnum.enumRecalibDomainTOFtime
MsgBox("Sorry, not implemented.")
'Changed PM_ORBI_AWARE_RECALIB 2008-02-14
Case recalibDomainEnum.enumRecalibDomainSqrtFreq
'MsgBox("Sorry, not implemented.")
'OK
Case Else
Trace.Assert(False, "Select Case never fall-through")
End Select 'recalib domain
End Sub 'cbxRecalibDomains_SelectedIndexChanged
'Changed PM_HIDE_RECALIBVISUALISATION_WINDOW 2008-01-06
'****************************************************************************
'* <placeholder for header> *
'****************************************************************************
Private Sub btnEndOfParseAction_Click( _
ByVal aSender As System.Object, ByVal anEvent As System.EventArgs) _
Handles btnEndOfParseAction.Click
mParseEndForm = New frmEndOfParseAction(mOptions2.endOfParseAction)
mParseEndForm.Show()
End Sub 'btnEndOfParseAction_Click
'From sub-dialog, end of parse action settings.
'****************************************************************************
'* <placeholder for header> *
'****************************************************************************
Private Sub mParseEndForm_dialogDismissed( _
ByVal aSender As Object, _
ByVal anEvent As endOfParseActionEventArgs) _
Handles mParseEndForm.endOfParseActionDialogDismissed
mOptions2.endOfParseAction = anEvent.getEndOfParseActionSettings()
End Sub 'mParseEndForm_dialogDismissed
'Changed PM_RECALIB_FILTER 2007-09-04
'****************************************************************************
'* <placeholder for header> *
'****************************************************************************
Private Sub btnRecalibPeptideFilter_Click( _
ByVal aSender As System.Object, _
ByVal anEvent As System.EventArgs) _
Handles btnRecalibPeptideFilter.Click
Dim key As peptideFilterEnum = peptideFilterEnum.enumRecalibParse
Dim programDefaults As peptideFilterStructure = _
quantApplication.defaultPeptideFilters2()(key)
'Changed PM_SILAC_AWARE_PEPTIDEFILTERDIALOG 2008-10-05
Dim SILACmods As Dictionary(Of Integer, Integer) = _
Me.constructSILACmods()
mRecalibFilterForm = New frmPeptideFilters( _
mRecalibPeptideFilter, mApplication, False, False, _
programDefaults, _
"recalibration from preselected peptides (PSPs)", _
mRawFiles, _
SILACmods)
mRecalibFilterForm.Show()
'Note: the call-back is the function that handles
' event "mRecalibFilterForm.pepFilterDismissed".
End Sub 'btnRecalibPeptideFilter_Click
'Changed PM_RECALIB_FILTER 2007-09-04
'****************************************************************************
'* <placeholder for header> *
'****************************************************************************
Private Sub mRecalibFilterForm_pepFilterDismissed( _
ByVal aSender As Object, ByVal anEvent As pepFilterEventArgs) _
Handles mRecalibFilterForm.pepFilterDismissed
mRecalibPeptideFilter = anEvent.getFilter()
updateCalibPeptideFilterSummary(mRecalibPeptideFilter)
End Sub 'mRecalibFilterForm_pepFilterDismissed
'Changed PM_RECALIB_REALITY_CHECK 2008-03-26
'****************************************************************************
'* <placeholder for header> *
'****************************************************************************
Private Sub btnRecalibRealityCheck_Click( _
ByVal aSender As System.Object, ByVal anEvent As System.EventArgs) _
Handles btnRecalibRealityCheck.Click
mRecalibRealityCheckForm = _
New frmRecalibRealityCheck(mOptions2.recalibLimits)
mRecalibRealityCheckForm.Show()
End Sub 'btnRecalibRealityCheck_Click
'****************************************************************************
'* <placeholder for header> *
'****************************************************************************
Public Sub updateRecalibRealityCheckSummary( _
ByVal anInRecalibLimits As recalibLimitsStructure)
Dim summaryStr As String = _
SDUPrecalibrator.recalibLimitsShortSummary(anInRecalibLimits)
lblRecalibLimitsShortSummary.Text = summaryStr
End Sub 'updatePeptideFilterSummary
'Changed PM_RECALIB_REALITY_CHECK 2008-03-27
'****************************************************************************
'* <placeholder for header> *
'****************************************************************************
Private Sub mRecalibRealityCheckForm_realityCheckDialogDismissed( _
ByVal aSender As Object, ByVal anEvent As realityCheckEventArgs) _
Handles mRecalibRealityCheckForm.realityCheckDialogDismissed
'Update immediately. This should be fine as long
'as recalibLimitsStructure does not contain any
'reference members (they are all value types).
mOptions2.recalibLimits = anEvent.getFilter()
updateRecalibRealityCheckSummary(mOptions2.recalibLimits)
End Sub 'mRecalibRealityCheckForm_realityCheckDialogDismissed
'Changed PM_SILAC_AWARE_PEPTIDEFILTERDIALOG 2008-10-05
'****************************************************************************
'* <placeholder for header> *
'****************************************************************************
Private Function constructSILACmods() _
As Dictionary(Of Integer, Integer)
'Note: we can't cache the list of SILAC modifications as it
' should change if the user choses another quantitation
' mode.
Dim quantitationModesObject As QuantitationModes_moreGeneral = _
mApplication.getQuantModes()
'Note: we can not use mOptions2.quantModeCode as it not set only the
' user OKs this dialog. Instead we read the quantitation mode
' of the drop-down box in this dialog.
Dim quantModeCode2 As Integer = quantModeListIndex2QuantModeCode( _
cbxQuantMode.SelectedIndex, _
quantitationModesObject)
Dim SILACmods As Dictionary(Of Integer, Integer) = _
quantitationModesObject.modificationIDsForQuantitationMode( _
quantModeCode2)
Return SILACmods
End Function 'constructSILACmods()
End Class 'frmOptions
Generated by script codePublish.pl at 2009-01-05T15:20:59.