Merge pull request #399 from acesnik/master

Modifiable PTM ranks, used in pf assignment. CH2/HPO3 for no-mans-land calculations

ProteoformSuiteGUI/AggregatedProteoforms.cs

@@ -62,11 +62,14 @@ private void nUD_Missed_Ks_ValueChanged(object sender, EventArgs e)
         {
             SaveState.lollipop.missed_lysines = nUD_Missed_Ks.Value;
         }
+
         private void bt_aggregate_Click(object sender, EventArgs e)
         {
-            if (SaveState.lollipop.neucode_labeled && SaveState.lollipop.raw_neucode_pairs.Count > 0 || SaveState.lollipop.raw_experimental_components.Count > 0)
+            if (ReadyToRunTheGamut())
             {
+                Cursor = Cursors.WaitCursor;
                 RunTheGamut();
+                Cursor = Cursors.Default;
             }
             else if (SaveState.lollipop.target_proteoform_community.experimental_proteoforms.Length <= 0)
             {
@@ -110,25 +113,16 @@ private void nUD_min_num_bioreps_ValueChanged(object sender, EventArgs e)
 
         public bool ReadyToRunTheGamut()
         {
-            return SaveState.lollipop.target_proteoform_community.experimental_proteoforms.Length <= 0
-                && (SaveState.lollipop.neucode_labeled && SaveState.lollipop.raw_neucode_pairs.Count > 0 || SaveState.lollipop.raw_experimental_components.Count > 0);
+            return SaveState.lollipop.neucode_labeled && SaveState.lollipop.raw_neucode_pairs.Count > 0 || SaveState.lollipop.raw_experimental_components.Count > 0;
         }
 
         public void RunTheGamut()
         {
-            Cursor = Cursors.WaitCursor;
-            ClearListsTablesFigures();
+            ClearListsTablesFigures(true);
             SaveState.lollipop.aggregate_proteoforms(SaveState.lollipop.validate_proteoforms, SaveState.lollipop.raw_neucode_pairs, SaveState.lollipop.raw_experimental_components, SaveState.lollipop.raw_quantification_components, SaveState.lollipop.min_num_CS);
+            SaveState.lollipop.assign_best_components_for_manual_validation(SaveState.lollipop.target_proteoform_community.experimental_proteoforms);
             FillTablesAndCharts();
-            if (SaveState.lollipop.neucode_labeled && SaveState.lollipop.target_proteoform_community.theoretical_proteoforms.Length > 0)
-            {
-                ((ProteoformSweet)MdiParent).experimentalTheoreticalComparison.RunTheGamut();
-                ((ProteoformSweet)MdiParent).experimentExperimentComparison.RunTheGamut();
-                if (((ProteoformSweet)MdiParent).quantification.ReadyToRunTheGamut()) ((ProteoformSweet)MdiParent).quantification.perform_calculations();
-            }
-
             updateFiguresOfMerit();
-            Cursor = Cursors.Default;
         }
 
         public List<DataGridView> GetDGVs()
@@ -158,16 +152,21 @@ public void InitializeParameterSet()
             tb_tableFilter.TextChanged += tb_tableFilter_TextChanged;
         }
 
-        public void ClearListsTablesFigures()
+        public void ClearListsTablesFigures(bool clear_following)
         {
+            if (clear_following)
+            {
+                for (int i = ((ProteoformSweet)MdiParent).forms.IndexOf(this) + 1; i < ((ProteoformSweet)MdiParent).forms.Count; i++)
+                {
+                    ISweetForm sweet = ((ProteoformSweet)MdiParent).forms[i];
+                    if (sweet as TheoreticalDatabase == null)
+                        sweet.ClearListsTablesFigures(false);
+                }
+            }
+
             SaveState.lollipop.clear_aggregation();
             dgv_AcceptNeuCdLtProteoforms.DataSource = null;
             dgv_AcceptNeuCdLtProteoforms.Rows.Clear();
-
-            ((ProteoformSweet)MdiParent).experimentalTheoreticalComparison.ClearListsTablesFigures();
-            ((ProteoformSweet)MdiParent).quantification.ClearListsTablesFigures();
-            ((ProteoformSweet)MdiParent).experimentExperimentComparison.ClearListsTablesFigures();
-            ((ProteoformSweet)MdiParent).proteoformFamilies.ClearListsTablesFigures();
         }
 
         #endregion Public Methods

ProteoformSuiteGUI/DGVExcelWriter.cs

@@ -1,49 +1,70 @@
-using System;
+using ClosedXML.Excel;
+using System;
 using System.Collections.Generic;
-using System.Linq;
-using System.Text;
-using System.Threading.Tasks;
-using Microsoft.Office.Interop.Excel;
-using Excel = Microsoft.Office.Interop.Excel;
-using System.Windows.Forms;
-using ClosedXML.Excel;
 using System.Data;
-
+using System.Windows.Forms;
 
 namespace ProteoformSuiteInternal
 {
     class DGVExcelWriter
     {
-        public void ExportToExcel(List<DataGridView> dgvs, string filename)
+
+        private XLWorkbook workbook = new XLWorkbook();
+
+        public void ExportToExcel(List<DataGridView> dgvs, string sheet_prefix)
         {
-            var workbook = new XLWorkbook();
+            if (dgvs == null)
+                return;
+
             foreach (DataGridView dgv in dgvs)
             {
-                System.Data.DataTable dt = new System.Data.DataTable();
+                DataTable dt = new DataTable();
                 foreach (DataGridViewColumn col in dgv.Columns)
                 {
                     dt.Columns.Add(col.HeaderText);
-
                 }
+
                 foreach(DataGridViewRow row in dgv.Rows)
                 {
                     DataRow new_row = dt.NewRow();
                     foreach (DataGridViewCell cell in row.Cells)
                     {
-                        if (dgv.Columns[cell.ColumnIndex].Visible) new_row[cell.ColumnIndex] = (cell.Value == null  || cell.Value.ToString() == "NaN")? "" : cell.Value;
+                        if (dgv.Columns[cell.ColumnIndex].Visible)
+                            new_row[cell.ColumnIndex] = cell.Value == null || cell.Value.ToString() == "NaN" ? "" : cell.Value;
                     }
                     lock (dt) dt.Rows.Add(new_row);
                 }
-                foreach (DataGridViewColumn col in dgv.Columns) { if (!col.Visible) dt.Columns.Remove(col.HeaderText); }
 
-                var worksheet = workbook.Worksheets.Add(dt, dgv.Name);
-                foreach (var col in worksheet.Columns())
+                foreach (DataGridViewColumn col in dgv.Columns)
                 {
-                    double is_number;
-                    col.Cells(2, worksheet.LastRowUsed().RowNumber()).DataType = Double.TryParse(worksheet.Row(2).Cell(col.ColumnNumber()).Value.ToString(), out is_number) ? XLCellValues.Number : XLCellValues.Text;
+                    if (!col.Visible)
+                        dt.Columns.Remove(col.HeaderText);
                 }
 
+                IXLWorksheet worksheet = null;
+                lock (workbook)
+                {
+                    worksheet = workbook.Worksheets.Add(dt, sheet_prefix.Substring(0, Math.Min(sheet_prefix.Length, 30 - dgv.Name.Length)) + "_" + dgv.Name);
+                }
+
+                foreach (var col in worksheet.Columns())
+                {
+                    try
+                    {
+                        col.Cells(2, worksheet.LastRowUsed().RowNumber()).DataType = Double.TryParse(worksheet.Row(2).Cell(col.ColumnNumber()).Value.ToString(), out double is_number) ?
+                            XLCellValues.Number :
+                            XLCellValues.Text;
+                    }
+                    catch
+                    {
+                        col.Cells(2, worksheet.LastRowUsed().RowNumber()).DataType = XLCellValues.Text;
+                    }
+                }
             }
+        }
+
+        public void SaveToExcel(string filename)
+        {
             workbook.SaveAs(filename);
         }
     }

ProteoformSuiteGUI/DisplayObjects/DisplayExperimentalProteoform.cs

@@ -5,6 +5,7 @@ namespace ProteoformSuiteGUI
 {
     public class DisplayExperimentalProteoform : DisplayObject
     {
+
         #region Public Constructors
 
         public DisplayExperimentalProteoform(ExperimentalProteoform e)
@@ -63,6 +64,16 @@ public int observation_count
             get { return e.aggregated_components.Count; }
         }
 
+        public int light_verification_count
+        {
+            get { return e.lt_verification_components.Count; }
+        }
+
+        public int heavy_verification_count
+        {
+            get { return e.hv_verification_components.Count; }
+        }
+
         public int light_observation_count
         {
             get { return e.lt_quant_components.Count; }
@@ -87,6 +98,21 @@ public string gene_name
                     "";
             }
         }
+
+        public string manual_validation_id
+        {
+            get { return e.manual_validation_id; }
+        }
+
+        public string manual_validation_verification
+        {
+            get { return e.manual_validation_verification; }
+        }
+
+        public string manual_validation_quant
+        {
+            get { return e.manual_validation_quant; }
+        }
 
         #endregion Public Properties
 
@@ -110,17 +136,23 @@ public static void FormatAggregatesTable(DataGridView dgv)
             dgv.Columns[nameof(agg_intensity)].HeaderText = "Aggregated Intensity";
             dgv.Columns[nameof(agg_rt)].HeaderText = "Aggregated RT";
             dgv.Columns[nameof(observation_count)].HeaderText = "Aggregated Component Count for Identification";
+            dgv.Columns[nameof(heavy_verification_count)].HeaderText = "Heavy Verification Component Count";
+            dgv.Columns[nameof(light_verification_count)].HeaderText = "Light Verification Component Count";
             dgv.Columns[nameof(heavy_observation_count)].HeaderText = "Heavy Quantitative Component Count";
             dgv.Columns[nameof(light_observation_count)].HeaderText = "Light Quantitative Component Count";
             dgv.Columns[nameof(lysine_count)].HeaderText = "Lysine Count";
             dgv.Columns[nameof(mass_shifted)].HeaderText = "Manually Shifted Mass";
             dgv.Columns[nameof(ptm_description)].HeaderText = "PTM Description";
             dgv.Columns[nameof(gene_name)].HeaderText = "Gene Name";
+            dgv.Columns[nameof(manual_validation_id)].HeaderText = "Abundant Component for Manual Validation of Identification";
+            dgv.Columns[nameof(manual_validation_verification)].HeaderText = "Abundant Component for Manual Validation of Identification Verification";
+            dgv.Columns[nameof(manual_validation_quant)].HeaderText = "Abundant Component for Manual Validation of Quantification";
 
             //VISIBILITY
             dgv.Columns[nameof(lysine_count)].Visible = SaveState.lollipop.neucode_labeled; 
         }
 
         #endregion
+
     }
 }

ProteoformSuiteGUI/DisplayObjects/DisplayProteoformRelation.cs

@@ -140,6 +140,16 @@ public string accession_1
             }
         }
 
+        public string manual_validation_id_1
+        {
+            get
+            {
+                return connected_proteoforms[0] as ExperimentalProteoform != null ?
+                    ((ExperimentalProteoform)connected_proteoforms[0]).manual_validation_id :
+                    "";
+            }
+        }
+
 
         // For DataGridView display of proteform2
         public double proteoform_mass_2
@@ -190,6 +200,16 @@ public string accession_2
             }
         }
 
+        public string manual_validation_id_2
+        {
+            get
+            {
+                return connected_proteoforms[1] as ExperimentalProteoform != null ?
+                    ((ExperimentalProteoform)connected_proteoforms[1]).manual_validation_id :
+                    "";
+            }
+        }
+
         public string Name
         {
             get
@@ -272,9 +292,11 @@ public static void FormatRelationsGridView(DataGridView dgv, bool mask_experimen
                 dgv.Columns[nameof(proteoform_mass_1)].HeaderText = "Experimental Aggregated Proteoform Mass";
                 dgv.Columns[nameof(agg_intensity_1)].HeaderText = "Experimental Aggregated Intensity";
                 dgv.Columns[nameof(agg_RT_1)].HeaderText = "Experimental Aggregated RT";
+                dgv.Columns[nameof(manual_validation_id_1)].HeaderText = "Abundant Exp. Component for Manual Validation";
                 dgv.Columns[nameof(agg_intensity_2)].Visible = false;
                 dgv.Columns[nameof(agg_RT_2)].Visible = false;
                 dgv.Columns[nameof(num_observations_2)].Visible = false;
+                dgv.Columns[nameof(manual_validation_id_2)].Visible = false;
                 dgv.Columns[nameof(RelationType)].Visible = false;
             }
 
@@ -291,16 +313,35 @@ public static void FormatRelationsGridView(DataGridView dgv, bool mask_experimen
                 dgv.Columns[nameof(accession_2)].HeaderText = "Light Experimental Accession";
                 dgv.Columns[nameof(proteoform_mass_1)].HeaderText = "Heavy Experimental Aggregated Mass";
                 dgv.Columns[nameof(proteoform_mass_2)].HeaderText = "Light Experimental Aggregated Mass";
+                dgv.Columns[nameof(manual_validation_id_1)].HeaderText = "Heavy Abundant Exp. Component for Manual Validation";
+                dgv.Columns[nameof(manual_validation_id_2)].HeaderText = "Light Abundant Exp. Component for Manual Validation";
+                dgv.Columns[nameof(RelationType)].Visible = false;
                 dgv.Columns[nameof(Name)].Visible = false;
                 dgv.Columns[nameof(Fragment)].Visible = false;
             }
 
             //ProteoformFamilies formatting
-            dgv.Columns[nameof(RelationType)].HeaderText = "Relation Type";
+            if (!mask_experimental && !mask_theoretical)
+            {
+                dgv.Columns[nameof(num_observations_2)].HeaderText = "Number Observations #2";
+                dgv.Columns[nameof(num_observations_1)].HeaderText = "Number Observations #1";
+                dgv.Columns[nameof(agg_intensity_2)].HeaderText = "Intensity #2";
+                dgv.Columns[nameof(agg_intensity_1)].HeaderText = "Intensity #1";
+                dgv.Columns[nameof(agg_RT_1)].HeaderText = "Aggregated RT #1";
+                dgv.Columns[nameof(agg_RT_2)].HeaderText = "Aggregated RT #2";
+                dgv.Columns[nameof(accession_1)].HeaderText = "Accession #1";
+                dgv.Columns[nameof(accession_2)].HeaderText = "Accession #2";
+                dgv.Columns[nameof(proteoform_mass_1)].HeaderText = "Proteoform Mass #1";
+                dgv.Columns[nameof(proteoform_mass_2)].HeaderText = "Proteoform Mass #2";
+                dgv.Columns[nameof(manual_validation_id_1)].HeaderText = "Abundant Exp. Component for Manual Validation #1";
+                dgv.Columns[nameof(manual_validation_id_2)].HeaderText = "Abundant Exp. Component for Manual Validation #2";
+                dgv.Columns[nameof(RelationType)].HeaderText = "Relation Type";
+            }
 
             //making these columns invisible
             dgv.Columns[nameof(LysineCount)].Visible = SaveState.lollipop.neucode_labeled;
         } 
         #endregion
+
     }
 }

ProteoformSuiteGUI/DisplayObjects/DisplayQuantitativeValues.cs

@@ -81,6 +81,11 @@ public decimal TestStatistic
             get { return qval.testStatistic; }
         }
 
+        public string manual_validation_quant
+        {
+            get { return qval.proteoform.manual_validation_quant; }
+        }
+
         #endregion Public Properties
 
         #region Public Methods
@@ -108,7 +113,8 @@ public static void FormatGridView(DataGridView dgv)
             dgv.Columns[nameof(LogFoldChange)].HeaderText = "Log2 Fold Change";
             dgv.Columns[nameof(pValue)].HeaderText = "p-value (by randomization test)";
             dgv.Columns[nameof(TestStatistic)].HeaderText = "Student's t-Test Statistic";
-        } 
+            dgv.Columns[nameof(manual_validation_quant)].HeaderText = "Abundant Component for Manual Validation of Quantification";
+        }
 
         #endregion
 

ProteoformSuiteGUI/DisplayObjects/DisplayUnlocalizedModification.cs

@@ -30,9 +30,9 @@ public string OriginalID
             get { return m.original_modification.id; }
         }
 
-        public string Mass
+        public double Mass
         {
-            get { return m.mass.ToString(); }
+            get { return m.mass; }
         }
 
         public string ID
@@ -47,6 +47,18 @@ public int PtmCount
             set { m.ptm_count = value; }
         }
 
+        public bool require_proteoform_without_mod
+        {
+            get { return m.require_proteoform_without_mod; }
+            set { m.require_proteoform_without_mod = value; }
+        }
+
+        public int PtmRank
+        {
+            get { return m.ptm_rank; }
+            set { m.ptm_rank = value; }
+        }
+
         #endregion Public Properties
 
         #region Public Methods
@@ -61,6 +73,8 @@ public static void FormatUnlocalizedModificationTable(DataGridView dgv)
             dgv.Columns[nameof(OriginalID)].HeaderText = "Original ID";
             dgv.Columns[nameof(ID)].HeaderText = "New ID";
             dgv.Columns[nameof(PtmCount)].HeaderText = "Num. PTMs Represented";
+            dgv.Columns[nameof(require_proteoform_without_mod)].HeaderText = "Require Proteoform Without This Modification";
+            dgv.Columns[nameof(PtmRank)].HeaderText = "Frequency-Based Rank of PTM Mass";
 
             //EDITABILITY
             dgv.Columns[nameof(OriginalID)].ReadOnly = true;