diff --git a/RawToolsGUI/ModificationTable.cs b/RawToolsGUI/ModificationTable.cs index 7a34684..3304bc4 100644 --- a/RawToolsGUI/ModificationTable.cs +++ b/RawToolsGUI/ModificationTable.cs @@ -19,8 +19,19 @@ public class PeptideModifications public PeptideModifications() { KMod.AA = "K"; + KMod.Mass = "229.16293"; + KMod.Use = true; + NMod.AA = "["; + NMod.Mass = "229.16293"; + NMod.Use = true; + FMods = new List<(string Mass, string AA, bool Use)>(); + FMods.Add(("57.02146", "C", true)); + + XMod.AA = "M"; + XMod.Mass = "15.99491"; + XMod.Use = true; } public string KModString { get { return GetModString(KMod); } } diff --git a/RawToolsGUI/RawToolsGUI.Designer.cs b/RawToolsGUI/RawToolsGUI.Designer.cs index 135e18f..713bb8e 100644 --- a/RawToolsGUI/RawToolsGUI.Designer.cs +++ b/RawToolsGUI/RawToolsGUI.Designer.cs @@ -57,7 +57,7 @@ private void InitializeComponent() this.comboBoxMaxCharge = new System.Windows.Forms.ComboBox(); this.checkBoxRefinePrecursor = new System.Windows.Forms.CheckBox(); this.groupBoxQcOptions = new System.Windows.Forms.GroupBox(); - this.label1 = new System.Windows.Forms.Label(); + this.labelPeptideMods = new System.Windows.Forms.Label(); this.buttonPeptideMods = new System.Windows.Forms.Button(); this.textBoxQcDataDirectory = new System.Windows.Forms.TextBox(); this.buttonQcDataDirectory = new System.Windows.Forms.Button(); @@ -87,22 +87,22 @@ private void InitializeComponent() this.checkBoxChroMs2 = new System.Windows.Forms.CheckBox(); this.checkBoxChroMs1 = new System.Windows.Forms.CheckBox(); this.toolTip1 = new System.Windows.Forms.ToolTip(this.components); + this.comboBoxLabelingReagents = new System.Windows.Forms.ComboBox(); + this.textBoxMgfLowMass = new System.Windows.Forms.TextBox(); + this.checkBoxMgfLowMass = new System.Windows.Forms.CheckBox(); + this.buttonGo = new System.Windows.Forms.Button(); this.flowLayoutPanel1 = new System.Windows.Forms.FlowLayoutPanel(); this.groupBoxQuantOpt = new System.Windows.Forms.GroupBox(); this.checkBoxReporterFilterMGF = new System.Windows.Forms.CheckBox(); this.checkBoxReporterFilterMatrix = new System.Windows.Forms.CheckBox(); - this.comboBoxLabelingReagents = new System.Windows.Forms.ComboBox(); this.labelReporterIonFilteringApplyTo = new System.Windows.Forms.Label(); this.groupBoxMgfOpts = new System.Windows.Forms.GroupBox(); this.textBoxMgfFilterWindowSize = new System.Windows.Forms.TextBox(); this.labelMgfIntensityFilterWindow = new System.Windows.Forms.Label(); this.labelMgfFilterRelativeIntensity = new System.Windows.Forms.Label(); this.textBoxMgfFilterRelativeIntensity = new System.Windows.Forms.TextBox(); - this.textBoxMgfLowMass = new System.Windows.Forms.TextBox(); this.checkBoxMgfIntensityFiltering = new System.Windows.Forms.CheckBox(); - this.checkBoxMgfLowMass = new System.Windows.Forms.CheckBox(); this.panel1 = new System.Windows.Forms.Panel(); - this.button1 = new System.Windows.Forms.Button(); this.menuStrip1 = new System.Windows.Forms.MenuStrip(); this.fileStripMenuItem = new System.Windows.Forms.ToolStripMenuItem(); this.toolStripMenuItemNewParameters = new System.Windows.Forms.ToolStripMenuItem(); @@ -156,8 +156,8 @@ private void InitializeComponent() this.checkBoxModeParse.Size = new System.Drawing.Size(67, 21); this.checkBoxModeParse.TabIndex = 0; this.checkBoxModeParse.Text = "Parse"; - this.toolTip1.SetToolTip(this.checkBoxModeParse, "Enables parsing of quant and meta data. Select this\r\nfor options under the \"Data " + - "Output\" section."); + this.toolTip1.SetToolTip(this.checkBoxModeParse, "Enables parsing of quant and meta data. Select this\r\nfor options under the \"Parse" + + " Data Output\" section."); this.checkBoxModeParse.UseVisualStyleBackColor = true; this.checkBoxModeParse.CheckedChanged += new System.EventHandler(this.checkBoxModeParse_CheckedChanged); // @@ -254,12 +254,13 @@ private void InitializeComponent() this.groupBoxDataOutput.Controls.Add(this.ckbxOutputMetrics); this.groupBoxDataOutput.Controls.Add(this.ckbxOutputParse); this.groupBoxDataOutput.Controls.Add(this.ckbxOutputMGF); + this.groupBoxDataOutput.Enabled = false; this.groupBoxDataOutput.Location = new System.Drawing.Point(3, 94); this.groupBoxDataOutput.Name = "groupBoxDataOutput"; this.groupBoxDataOutput.Size = new System.Drawing.Size(333, 145); this.groupBoxDataOutput.TabIndex = 2; this.groupBoxDataOutput.TabStop = false; - this.groupBoxDataOutput.Text = "Data Output"; + this.groupBoxDataOutput.Text = "Parse Data Output"; // // checkBoxDataOutputDirectory // @@ -448,7 +449,7 @@ private void InitializeComponent() // // groupBoxQcOptions // - this.groupBoxQcOptions.Controls.Add(this.label1); + this.groupBoxQcOptions.Controls.Add(this.labelPeptideMods); this.groupBoxQcOptions.Controls.Add(this.buttonPeptideMods); this.groupBoxQcOptions.Controls.Add(this.textBoxQcDataDirectory); this.groupBoxQcOptions.Controls.Add(this.buttonQcDataDirectory); @@ -475,17 +476,19 @@ private void InitializeComponent() this.groupBoxQcOptions.TabStop = false; this.groupBoxQcOptions.Text = "QC Options"; // - // label1 + // labelPeptideMods // - this.label1.AutoSize = true; - this.label1.Location = new System.Drawing.Point(331, 203); - this.label1.Name = "label1"; - this.label1.Size = new System.Drawing.Size(146, 17); - this.label1.TabIndex = 23; - this.label1.Text = "Peptide Modifications:"; + this.labelPeptideMods.AutoSize = true; + this.labelPeptideMods.Enabled = false; + this.labelPeptideMods.Location = new System.Drawing.Point(331, 203); + this.labelPeptideMods.Name = "labelPeptideMods"; + this.labelPeptideMods.Size = new System.Drawing.Size(146, 17); + this.labelPeptideMods.TabIndex = 23; + this.labelPeptideMods.Text = "Peptide Modifications:"; // // buttonPeptideMods // + this.buttonPeptideMods.Enabled = false; this.buttonPeptideMods.Location = new System.Drawing.Point(483, 200); this.buttonPeptideMods.Name = "buttonPeptideMods"; this.buttonPeptideMods.Size = new System.Drawing.Size(247, 23); @@ -796,6 +799,63 @@ private void InitializeComponent() this.toolTip1.SetToolTip(this.checkBoxChroMs1, "Write a MS1 chromatogram to disk. You must also\r\none or more of TIC and BP."); this.checkBoxChroMs1.UseVisualStyleBackColor = true; // + // comboBoxLabelingReagents + // + this.comboBoxLabelingReagents.Enabled = false; + this.comboBoxLabelingReagents.FormattingEnabled = true; + this.comboBoxLabelingReagents.Items.AddRange(new object[] { + "- select -", + "TMT0", + "TMT2", + "TMT6", + "TMT10", + "TMT11", + "iTRAQ4", + "iTRAQ8", + "Custom"}); + this.comboBoxLabelingReagents.Location = new System.Drawing.Point(28, 48); + this.comboBoxLabelingReagents.Name = "comboBoxLabelingReagents"; + this.comboBoxLabelingReagents.Size = new System.Drawing.Size(121, 24); + this.comboBoxLabelingReagents.TabIndex = 17; + this.toolTip1.SetToolTip(this.comboBoxLabelingReagents, "Select a labeling reagent from the drop down list."); + this.comboBoxLabelingReagents.SelectedIndexChanged += new System.EventHandler(this.comboBoxLabelingReagents_SelectedIndexChanged); + this.comboBoxLabelingReagents.Enter += new System.EventHandler(this.comboBoxLabelingReagents_Enter); + // + // textBoxMgfLowMass + // + this.textBoxMgfLowMass.Enabled = false; + this.textBoxMgfLowMass.Location = new System.Drawing.Point(185, 19); + this.textBoxMgfLowMass.Name = "textBoxMgfLowMass"; + this.textBoxMgfLowMass.Size = new System.Drawing.Size(100, 22); + this.textBoxMgfLowMass.TabIndex = 2; + this.textBoxMgfLowMass.Text = "0"; + this.toolTip1.SetToolTip(this.textBoxMgfLowMass, resources.GetString("textBoxMgfLowMass.ToolTip")); + this.textBoxMgfLowMass.TextChanged += new System.EventHandler(this.textBoxMgfLowMass_TextChanged); + this.textBoxMgfLowMass.KeyPress += new System.Windows.Forms.KeyPressEventHandler(this.textBoxMgfLowMass_KeyPress); + // + // checkBoxMgfLowMass + // + this.checkBoxMgfLowMass.AutoSize = true; + this.checkBoxMgfLowMass.Location = new System.Drawing.Point(6, 21); + this.checkBoxMgfLowMass.Name = "checkBoxMgfLowMass"; + this.checkBoxMgfLowMass.Size = new System.Drawing.Size(173, 21); + this.checkBoxMgfLowMass.TabIndex = 0; + this.checkBoxMgfLowMass.Text = "Low Mass Cutoff (m/z):"; + this.toolTip1.SetToolTip(this.checkBoxMgfLowMass, resources.GetString("checkBoxMgfLowMass.ToolTip")); + this.checkBoxMgfLowMass.UseVisualStyleBackColor = true; + this.checkBoxMgfLowMass.CheckedChanged += new System.EventHandler(this.checkBoxMgfLowMass_CheckedChanged); + // + // buttonGo + // + this.buttonGo.Location = new System.Drawing.Point(3, 9); + this.buttonGo.Name = "buttonGo"; + this.buttonGo.Size = new System.Drawing.Size(555, 68); + this.buttonGo.TabIndex = 0; + this.buttonGo.Text = "Go!"; + this.toolTip1.SetToolTip(this.buttonGo, "Start processing!"); + this.buttonGo.UseVisualStyleBackColor = true; + this.buttonGo.Click += new System.EventHandler(this.buttonGo_Click); + // // flowLayoutPanel1 // this.flowLayoutPanel1.AutoScroll = true; @@ -858,28 +918,6 @@ private void InitializeComponent() this.checkBoxReporterFilterMatrix.UseVisualStyleBackColor = true; this.checkBoxReporterFilterMatrix.Visible = false; // - // comboBoxLabelingReagents - // - this.comboBoxLabelingReagents.Enabled = false; - this.comboBoxLabelingReagents.FormattingEnabled = true; - this.comboBoxLabelingReagents.Items.AddRange(new object[] { - "- select -", - "TMT0", - "TMT2", - "TMT6", - "TMT10", - "TMT11", - "iTRAQ4", - "iTRAQ8", - "Custom"}); - this.comboBoxLabelingReagents.Location = new System.Drawing.Point(28, 48); - this.comboBoxLabelingReagents.Name = "comboBoxLabelingReagents"; - this.comboBoxLabelingReagents.Size = new System.Drawing.Size(121, 24); - this.comboBoxLabelingReagents.TabIndex = 17; - this.toolTip1.SetToolTip(this.comboBoxLabelingReagents, "Select a labeling reagent from the drop down list."); - this.comboBoxLabelingReagents.SelectedIndexChanged += new System.EventHandler(this.comboBoxLabelingReagents_SelectedIndexChanged); - this.comboBoxLabelingReagents.Enter += new System.EventHandler(this.comboBoxLabelingReagents_Enter); - // // labelReporterIonFilteringApplyTo // this.labelReporterIonFilteringApplyTo.AutoSize = true; @@ -952,18 +990,6 @@ private void InitializeComponent() this.textBoxMgfFilterRelativeIntensity.Visible = false; this.textBoxMgfFilterRelativeIntensity.KeyPress += new System.Windows.Forms.KeyPressEventHandler(this.textBoxMgfFilterRelativeIntensity_KeyPress); // - // textBoxMgfLowMass - // - this.textBoxMgfLowMass.Enabled = false; - this.textBoxMgfLowMass.Location = new System.Drawing.Point(185, 19); - this.textBoxMgfLowMass.Name = "textBoxMgfLowMass"; - this.textBoxMgfLowMass.Size = new System.Drawing.Size(100, 22); - this.textBoxMgfLowMass.TabIndex = 2; - this.textBoxMgfLowMass.Text = "0"; - this.toolTip1.SetToolTip(this.textBoxMgfLowMass, resources.GetString("textBoxMgfLowMass.ToolTip")); - this.textBoxMgfLowMass.TextChanged += new System.EventHandler(this.textBoxMgfLowMass_TextChanged); - this.textBoxMgfLowMass.KeyPress += new System.Windows.Forms.KeyPressEventHandler(this.textBoxMgfLowMass_KeyPress); - // // checkBoxMgfIntensityFiltering // this.checkBoxMgfIntensityFiltering.AutoSize = true; @@ -976,37 +1002,14 @@ private void InitializeComponent() this.checkBoxMgfIntensityFiltering.Visible = false; this.checkBoxMgfIntensityFiltering.CheckedChanged += new System.EventHandler(this.checkBoxMgfIntensityFiltering_CheckedChanged); // - // checkBoxMgfLowMass - // - this.checkBoxMgfLowMass.AutoSize = true; - this.checkBoxMgfLowMass.Location = new System.Drawing.Point(6, 21); - this.checkBoxMgfLowMass.Name = "checkBoxMgfLowMass"; - this.checkBoxMgfLowMass.Size = new System.Drawing.Size(173, 21); - this.checkBoxMgfLowMass.TabIndex = 0; - this.checkBoxMgfLowMass.Text = "Low Mass Cutoff (m/z):"; - this.toolTip1.SetToolTip(this.checkBoxMgfLowMass, resources.GetString("checkBoxMgfLowMass.ToolTip")); - this.checkBoxMgfLowMass.UseVisualStyleBackColor = true; - this.checkBoxMgfLowMass.CheckedChanged += new System.EventHandler(this.checkBoxMgfLowMass_CheckedChanged); - // // panel1 // - this.panel1.Controls.Add(this.button1); + this.panel1.Controls.Add(this.buttonGo); this.panel1.Location = new System.Drawing.Point(192, 636); this.panel1.Name = "panel1"; this.panel1.Size = new System.Drawing.Size(561, 80); this.panel1.TabIndex = 8; // - // button1 - // - this.button1.Location = new System.Drawing.Point(3, 9); - this.button1.Name = "button1"; - this.button1.Size = new System.Drawing.Size(555, 68); - this.button1.TabIndex = 0; - this.button1.Text = "Go!"; - this.toolTip1.SetToolTip(this.button1, "Start processing!"); - this.button1.UseVisualStyleBackColor = true; - this.button1.Click += new System.EventHandler(this.buttonGo_Click); - // // menuStrip1 // this.menuStrip1.ImageScalingSize = new System.Drawing.Size(20, 20); @@ -1069,7 +1072,7 @@ private void InitializeComponent() // aboutToolStripMenuItem // this.aboutToolStripMenuItem.Name = "aboutToolStripMenuItem"; - this.aboutToolStripMenuItem.Size = new System.Drawing.Size(216, 26); + this.aboutToolStripMenuItem.Size = new System.Drawing.Size(192, 26); this.aboutToolStripMenuItem.Text = "About RawTools"; this.aboutToolStripMenuItem.Click += new System.EventHandler(this.aboutToolStripMenuItem_Click); // @@ -1163,7 +1166,7 @@ private void InitializeComponent() private System.Windows.Forms.CheckBox checkBoxChroMs2; private System.Windows.Forms.CheckBox checkBoxChroMs1; private System.Windows.Forms.Panel panel1; - private System.Windows.Forms.Button button1; + private System.Windows.Forms.Button buttonGo; private System.Windows.Forms.TextBox textBoxReporterNumberMissingFilter; private System.Windows.Forms.TextBox textBoxReporterIntensityFilter; private System.Windows.Forms.Label labelReporterIonIntensityFilter; @@ -1181,7 +1184,7 @@ private void InitializeComponent() private System.Windows.Forms.TextBox textBoxMgfFilterRelativeIntensity; private System.Windows.Forms.TextBox textBoxQcDataDirectory; private System.Windows.Forms.Button buttonQcDataDirectory; - private System.Windows.Forms.Label label1; + private System.Windows.Forms.Label labelPeptideMods; private System.Windows.Forms.Button buttonPeptideMods; private PeptideModifications peptideModifications; diff --git a/RawToolsGUI/RawToolsGUI.cs b/RawToolsGUI/RawToolsGUI.cs index 8f1f2fb..b0264b9 100644 --- a/RawToolsGUI/RawToolsGUI.cs +++ b/RawToolsGUI/RawToolsGUI.cs @@ -148,6 +148,9 @@ private void radioButtonSearchNone_CheckedChanged(object sender, EventArgs e) textBoxNumSpectra.Enabled = false; checkBoxAutoSearchIdentipy.Enabled = false; + + labelPeptideMods.Enabled = false; + buttonPeptideMods.Enabled = false; } } @@ -169,6 +172,9 @@ private void radioButtonSearchXTandem_CheckedChanged(object sender, EventArgs e) textBoxNumSpectra.Enabled = true; checkBoxAutoSearchIdentipy.Enabled = false; + + labelPeptideMods.Enabled = true; + buttonPeptideMods.Enabled = true; } } @@ -195,6 +201,9 @@ private void radioButtonSearchIdentipy_CheckedChanged(object sender, EventArgs e textBoxPythonExe.Enabled = true; textBoxIdentipyScript.Enabled = true; } + + labelPeptideMods.Enabled = true; + buttonPeptideMods.Enabled = true; } } @@ -218,6 +227,15 @@ private void checkBoxAutoSearchIdentipy_CheckedChanged(object sender, EventArgs private void checkBoxModeParse_CheckedChanged(object sender, EventArgs e) { + if (checkBoxModeParse.Checked) + { + groupBoxDataOutput.Enabled = true; + } + else + { + groupBoxDataOutput.Enabled = false; + } + } private void checkBoxModeQC_CheckedChanged(object sender, EventArgs e)