Merge pull request #479 from acesnik/master

Bug fixes and nice notifications.

ProteoformSuiteGUI/DisplayObjects/DisplayGoTermNumber.cs

@@ -10,6 +10,7 @@ namespace ProteoformSuiteGUI
 {
     public class DisplayGoTermNumber : DisplayObject
     {
+
         #region Public Constructors
 
         public DisplayGoTermNumber(GoTermNumber g)
@@ -48,7 +49,7 @@ public string ID
 
         public double p_value
         {
-            get { return gtn.by; }
+            get { return gtn.p_value; }
         }
 
         public double by //benjamini yekutieli calculated after all p-values are calculated
@@ -138,5 +139,6 @@ private static string number_format(string property_name)
         }
 
         #endregion Private Methods
+
     }
 }

ProteoformSuiteGUI/DisplayUtility.cs

@@ -197,6 +197,16 @@ public static DataTable FormatTable(List<DisplayObject> display_objects, IEnumer
             return dt;
         }
 
+        public static bool CheckForProteinFastas(ComboBox cmb, IEnumerable<string> files)
+        {
+            if (Lollipop.file_filters[cmb.SelectedIndex].Contains(".fasta") && files.Any(x => x.Contains(".fasta")))
+            {
+                MessageBox.Show("Usage of protein fasta files is not yet enabled. Please use a protein XML file for now, e.g. from UniProt. (See this site for more information, and let us know there if this is an issue for you: https://github.com/smith-chem-wisc/ProteoformSuite/issues/477.)", "Load Files Message");
+                return true;
+            }
+            return false;
+        }
+
         #endregion Public Methods
 
     }

ProteoformSuiteGUI/LoadDeconvolutionResults.cs

@@ -205,6 +205,7 @@ private void dgv_quantResults_DragEnter(object sender, DragEventArgs e)
         private void drag_drop(DragEventArgs e, ComboBox cmb, DataGridView dgv)
         {
             string[] files = (string[])e.Data.GetData(DataFormats.FileDrop);
+            if (DisplayUtility.CheckForProteinFastas(cmb, files)) return; // todo: implement protein fasta usage
             Sweet.lollipop.enter_input_files(files, Lollipop.acceptable_extensions[cmb.SelectedIndex], Lollipop.file_types[cmb.SelectedIndex], Sweet.lollipop.input_files, true);
             match_files();
             DisplayUtility.FillDataGridView(dgv, Sweet.lollipop.get_files(Sweet.lollipop.input_files, Lollipop.file_types[cmb.SelectedIndex]).Select(f => new DisplayInputFile(f)));
@@ -295,6 +296,7 @@ private void add_files(ComboBox cmb, DataGridView dgv)
             DialogResult dr = openFileDialog.ShowDialog();
             if (dr == DialogResult.OK)
             {
+                if (DisplayUtility.CheckForProteinFastas(cmb, openFileDialog.FileNames)) return; // todo: implement protein fasta usage
                 Sweet.lollipop.enter_input_files(openFileDialog.FileNames, Lollipop.acceptable_extensions[cmb.SelectedIndex], Lollipop.file_types[cmb.SelectedIndex], Sweet.lollipop.input_files, true);
                 match_files();
             }

ProteoformSuiteGUI/ProteoformFamilies.cs

@@ -16,6 +16,23 @@ public partial class ProteoformFamilies : Form, ISweetForm
         public ProteoformFamilies()
         {
             InitializeComponent();
+
+            //Initialize display options
+            cmbx_colorScheme.Items.AddRange(CytoscapeScript.color_scheme_names);
+            cmbx_nodeLayout.Items.AddRange(Lollipop.node_positioning);
+            cmbx_nodeLabelPositioning.Items.AddRange(CytoscapeScript.node_label_positions);
+            cmbx_edgeLabel.Items.AddRange(Lollipop.edge_labels);
+            cmbx_nodeLabel.Items.AddRange(Lollipop.node_labels);
+            cmbx_geneLabel.Items.AddRange(Lollipop.gene_name_labels.ToArray());
+            cmbx_tableSelector.Items.AddRange(table_names);
+
+            cmbx_colorScheme.SelectedIndex = 1;
+            cmbx_nodeLayout.SelectedIndex = 1;
+            cmbx_nodeLabelPositioning.SelectedIndex = 0;
+            cmbx_edgeLabel.SelectedIndex = 1;
+            cmbx_nodeLabel.SelectedIndex = 1;
+            cmbx_geneLabel.SelectedIndex = 1;
+
             InitializeParameterSet();
             this.AutoScroll = true;
             this.AutoScrollMinSize = this.ClientSize;
@@ -43,21 +60,6 @@ public void initialize_every_time()
 
         public void InitializeParameterSet()
         {
-            //Initialize display options
-            cmbx_colorScheme.Items.AddRange(CytoscapeScript.color_scheme_names);
-            cmbx_nodeLayout.Items.AddRange(Lollipop.node_positioning);
-            cmbx_nodeLabelPositioning.Items.AddRange(CytoscapeScript.node_label_positions);
-            cmbx_edgeLabel.Items.AddRange(Lollipop.edge_labels);
-            cmbx_nodeLabel.Items.AddRange(Lollipop.node_labels);
-            cmbx_geneLabel.Items.AddRange(Lollipop.gene_name_labels.ToArray());
-            cmbx_tableSelector.Items.AddRange(table_names);
-
-            cmbx_colorScheme.SelectedIndex = 1;
-            cmbx_nodeLayout.SelectedIndex = 1;
-            cmbx_nodeLabelPositioning.SelectedIndex = 0;
-            cmbx_edgeLabel.SelectedIndex = 1;
-            cmbx_nodeLabel.SelectedIndex = 1;
-            cmbx_geneLabel.SelectedIndex = 1;
             Lollipop.preferred_gene_label = cmbx_geneLabel.SelectedItem.ToString();
             Lollipop.gene_centric_families = cb_geneCentric.Checked;
 
@@ -123,22 +125,17 @@ public void ClearListsTablesFigures(bool clear_following)
             }
         }
 
+        /// <summary>
+        /// generate report and change selected table names based on # decoy communities
+        /// </summary>
         public void update_figures_of_merit()
         {
             rtb_proteoformFamilyResults.Text = ResultsSummaryGenerator.proteoform_families_report();
-
-            //change selected table names based on # decoy communities
-            int decoy_communities = Sweet.lollipop.decoy_proteoform_communities.Count;
-            for(int i = 0; i < decoy_communities; i++)
-            {
-               if (!cmbx_tableSelector.Items.Contains("Decoy Community " + i)) cmbx_tableSelector.Items.Add("Decoy Community " + i);
-            }
-
-            //if more items than decoy databases, remove later ones //FIX   
-            while(cmbx_tableSelector.Items.Count - 5 - decoy_communities > 0)
-            {
-                cmbx_tableSelector.Items.RemoveAt(5 + decoy_communities);
-            }
+            int selection = cmbx_tableSelector.SelectedIndex;
+            cmbx_tableSelector.Items.Clear();
+            cmbx_tableSelector.Items.AddRange(table_names);
+            cmbx_tableSelector.Items.AddRange(Enumerable.Range(0, Sweet.lollipop.decoy_proteoform_communities.Count).Select(i => "Decoy Community " + i).ToArray());
+            cmbx_tableSelector.SelectedIndex = selection < cmbx_tableSelector.Items.Count ? selection : 0;
         }
 
         #endregion Public Methods

ProteoformSuiteGUI/ProteoformSweet.cs

@@ -210,7 +210,7 @@ private bool load_method()
                 string method_filename = methodFileOpen.FileName;
                 DialogResult d4 = MessageBox.Show("Add files at the listed paths if they still exist?", "Full Run", MessageBoxButtons.YesNoCancel);
                 if (d4 == DialogResult.Cancel) return false;
-                if (!open_method(File.ReadAllLines(method_filename), d4 == DialogResult.Yes))
+                if (!open_method(method_filename, File.ReadAllLines(method_filename), d4 == DialogResult.Yes))
                 {
                     MessageBox.Show("Method file was not loaded succesffully.");
                     return false;
@@ -223,9 +223,9 @@ private bool load_method()
             return false;
         }
 
-        public bool open_method(string[] lines, bool add_files)
+        public bool open_method(string methodFilePath, string[] lines, bool add_files)
         {
-            bool method_file_success = Sweet.open_method(String.Join(Environment.NewLine, lines), add_files, out string warning);
+            bool method_file_success = Sweet.open_method(methodFilePath, String.Join(Environment.NewLine, lines), add_files, out string warning);
             if (warning.Length > 0 && MessageBox.Show("WARNING" + Environment.NewLine + Environment.NewLine + warning, "Open Method", MessageBoxButtons.OKCancel) == DialogResult.Cancel)
                 return false;
             foreach (ISweetForm form in forms) form.InitializeParameterSet();
@@ -246,7 +246,7 @@ public Stopwatch full_run()
                     DialogResult d4 = MessageBox.Show("Add files at the listed paths if they still exist?", "Full Run", MessageBoxButtons.YesNoCancel);
                     if (d4 == DialogResult.Cancel) return null;
 
-                    if (!open_method(File.ReadAllLines(filepath), d4 == DialogResult.Yes))
+                    if (!open_method(filepath, File.ReadAllLines(filepath), d4 == DialogResult.Yes))
                     {
                         MessageBox.Show("Error in method file. Generate a new method file.");
                         return null;

ProteoformSuiteGUI/Quantification.cs

@@ -20,6 +20,25 @@ public Quantification()
             InitializeComponent();
             this.AutoScroll = true;
             this.AutoScrollMinSize = this.ClientSize;
+
+            //Initialize display options
+            cmbx_volcanoChartSelection.Items.AddRange(volcano_selections);
+            cmbx_colorScheme.Items.AddRange(CytoscapeScript.color_scheme_names);
+            cmbx_nodeLayout.Items.AddRange(Lollipop.node_positioning);
+            cmbx_nodeLabelPositioning.Items.AddRange(CytoscapeScript.node_label_positions);
+            cmbx_edgeLabel.Items.AddRange(Lollipop.edge_labels.ToArray());
+            cmbx_nodeLabel.Items.AddRange(Lollipop.node_labels.ToArray());
+            cmbx_geneLabel.Items.AddRange(Lollipop.gene_name_labels.ToArray());
+            cb_redBorder.Checked = true;
+            cb_boldLabel.Checked = true;
+
+            cmbx_volcanoChartSelection.SelectedIndex = 0;
+            cmbx_colorScheme.SelectedIndex = 1;
+            cmbx_nodeLayout.SelectedIndex = 1;
+            cmbx_nodeLabelPositioning.SelectedIndex = 0;
+            cmbx_geneLabel.SelectedIndex = 1;
+            cmbx_nodeLabel.SelectedIndex = 1;
+            cmbx_edgeLabel.SelectedIndex = 1;
         }
 
         #endregion Constructor
@@ -201,29 +220,10 @@ public void InitializeConditionsParameters()
             Sweet.lollipop.numerator_condition = cmbx_ratioNumerator.SelectedItem.ToString();
             Sweet.lollipop.denominator_condition = cmbx_ratioDenominator.SelectedItem.ToString();
             Sweet.lollipop.induced_condition = cmbx_inducedCondition.SelectedItem.ToString();
-            cmbx_edgeLabel.Items.AddRange(Lollipop.edge_labels);
         }
 
         public void InitializeParameterSet()
         {
-            //Initialize display options
-            cmbx_volcanoChartSelection.Items.AddRange(volcano_selections);
-            cmbx_colorScheme.Items.AddRange(CytoscapeScript.color_scheme_names);
-            cmbx_nodeLayout.Items.AddRange(Lollipop.node_positioning);
-            cmbx_nodeLabelPositioning.Items.AddRange(CytoscapeScript.node_label_positions);
-            cmbx_edgeLabel.Items.AddRange(Lollipop.edge_labels.ToArray());
-            cmbx_nodeLabel.Items.AddRange(Lollipop.node_labels.ToArray());
-            cmbx_geneLabel.Items.AddRange(Lollipop.gene_name_labels.ToArray());
-            cb_redBorder.Checked = true;
-            cb_boldLabel.Checked = true;
-
-            cmbx_volcanoChartSelection.SelectedIndex = 0;
-            cmbx_colorScheme.SelectedIndex = 1;
-            cmbx_nodeLayout.SelectedIndex = 1;
-            cmbx_nodeLabelPositioning.SelectedIndex = 0;
-            cmbx_geneLabel.SelectedIndex = 1;
-            cmbx_nodeLabel.SelectedIndex = 1;
-            cmbx_edgeLabel.SelectedIndex = 1;
             Lollipop.preferred_gene_label = cmbx_geneLabel.SelectedItem.ToString();
             Lollipop.gene_centric_families = cb_geneCentric.Checked;
 

ProteoformSuiteGUI/TheoreticalDatabase.cs

@@ -45,11 +45,12 @@ private void TheoreticalDatabase_Load(object sender, EventArgs e)
             initial_load = false;
         }
 
-        private void set_Make_Database_Button()
+        private bool SetMakeDatabaseButton()
         {
             bool ready_to_run = ReadyToRunTheGamut();
             btn_downloadUniProtPtmList.Enabled = !ready_to_run && Sweet.lollipop.get_files(Sweet.lollipop.input_files, Purpose.PtmList).Count() == 0;
             btn_Make_Databases.Enabled = ready_to_run;
+            return ready_to_run;
         }
 
         private void btn_Make_Databases_Click(object sender, EventArgs e)
@@ -278,7 +279,10 @@ private void cb_limitLargePtmSets_CheckedChanged(object sender, EventArgs e)
         private void dgv_loadFiles_DragDrop(object sender, DragEventArgs e)
         {
             drag_drop(e, cmb_loadTable, dgv_loadFiles);
-            set_Make_Database_Button();
+            if (!SetMakeDatabaseButton() && Sweet.lollipop.get_files(Sweet.lollipop.input_files, Purpose.ProteinDatabase).Count() > 0)
+            {
+                MessageBox.Show("You still need a PTM list. Please use the \"Donwload UniProt PTM List\" button.", "Enabling Make Database Button");
+            }
         }
 
         private void dgv_loadFiles_DragEnter(object sender, DragEventArgs e)
@@ -289,6 +293,7 @@ private void dgv_loadFiles_DragEnter(object sender, DragEventArgs e)
         private void drag_drop(DragEventArgs e, ComboBox cmb, DataGridView dgv)
         {
             string[] files = (string[])e.Data.GetData(DataFormats.FileDrop);
+            if (DisplayUtility.CheckForProteinFastas(cmb, files)) return; // todo: implement protein fasta usage
             Sweet.lollipop.enter_input_files(files, Lollipop.acceptable_extensions[cmb.SelectedIndex], Lollipop.file_types[cmb.SelectedIndex], Sweet.lollipop.input_files, true);
             DisplayUtility.FillDataGridView(dgv, Sweet.lollipop.get_files(Sweet.lollipop.input_files, Lollipop.file_types[cmb.SelectedIndex]).Select(f => new DisplayInputFile(f)));
             DisplayInputFile.FormatInputFileTable(dgv, Lollipop.file_types[cmb.SelectedIndex]);
@@ -302,7 +307,10 @@ public void reload_database_list()
             DisplayUtility.FillDataGridView(dgv_loadFiles, Sweet.lollipop.get_files(Sweet.lollipop.input_files, Lollipop.file_types[cmb_loadTable.SelectedIndex]).Select(f => new DisplayInputFile(f)));
             DisplayInputFile.FormatInputFileTable(dgv_loadFiles, Lollipop.file_types[cmb_loadTable.SelectedIndex]);
             initialize_table_bindinglist();
-            set_Make_Database_Button();
+            if (!SetMakeDatabaseButton() && Sweet.lollipop.get_files(Sweet.lollipop.input_files, Purpose.ProteinDatabase).Count() > 0)
+            {
+                MessageBox.Show("You still need a PTM list. Please use the \"Donwload UniProt PTM List\" button.", "Enabling Make Database Button");
+            }
         }
 
         private void tb_tableFilter_TextChanged(object sender, EventArgs e)
@@ -326,6 +334,7 @@ private void btn_downloadUniProtPtmList_Click(object sender, EventArgs e)
             DisplayUtility.FillDataGridView(dgv_loadFiles, Sweet.lollipop.get_files(Sweet.lollipop.input_files, Lollipop.file_types[cmb_loadTable.SelectedIndex]).Select(f => new DisplayInputFile(f)));
             DisplayInputFile.FormatInputFileTable(dgv_loadFiles, Lollipop.file_types[cmb_loadTable.SelectedIndex]);
             btn_downloadUniProtPtmList.Enabled = false;
+            SetMakeDatabaseButton();
         }
 
         #endregion LOAD DATABASES GRID VIEW Private Methods
@@ -341,11 +350,17 @@ private void btn_addFiles_Click(object sender, EventArgs e)
 
             DialogResult dr = openFileDialog.ShowDialog();
             if (dr == DialogResult.OK)
+            {
+                if (DisplayUtility.CheckForProteinFastas(cmb_loadTable, openFileDialog.FileNames)) return; // todo: implement protein fasta usage
                 Sweet.lollipop.enter_input_files(openFileDialog.FileNames, Lollipop.acceptable_extensions[cmb_loadTable.SelectedIndex], Lollipop.file_types[cmb_loadTable.SelectedIndex], Sweet.lollipop.input_files, true);
+            }
 
             DisplayUtility.FillDataGridView(dgv_loadFiles, Sweet.lollipop.get_files(Sweet.lollipop.input_files, Lollipop.file_types[cmb_loadTable.SelectedIndex]).Select(f => new DisplayInputFile(f)));
             DisplayInputFile.FormatInputFileTable(dgv_loadFiles, Lollipop.file_types[cmb_loadTable.SelectedIndex]);
-            set_Make_Database_Button();
+            if (!SetMakeDatabaseButton() && Sweet.lollipop.get_files(Sweet.lollipop.input_files, Purpose.ProteinDatabase).Count() > 0)
+            {
+                MessageBox.Show("You still need a PTM list. Please use the \"Donwload UniProt PTM List\" button.", "Enabling Make Database Button");
+            }
         }
 
         private void btn_clearFiles_Click(object sender, EventArgs e)
@@ -355,7 +370,7 @@ private void btn_clearFiles_Click(object sender, EventArgs e)
             Sweet.lollipop.input_files = Sweet.lollipop.input_files.Except(files_to_remove).ToList();
             DisplayUtility.FillDataGridView(dgv_loadFiles, Sweet.lollipop.get_files(Sweet.lollipop.input_files, Lollipop.file_types[cmb_loadTable.SelectedIndex]).Select(f => new DisplayInputFile(f)));
             DisplayInputFile.FormatInputFileTable(dgv_loadFiles, Lollipop.file_types[cmb_loadTable.SelectedIndex]);
-            set_Make_Database_Button();
+            SetMakeDatabaseButton();
         }
 
         #endregion ADD/CLEAR Private Methods

ProteoformSuiteInternal/ComponentReader.cs

@@ -124,7 +124,10 @@ public List<Component> remove_monoisotopic_duplicates_harmonics_from_same_scan(L
                     foreach (double missedMonoMass in possibleMissedMonoisotopicsList)
                     {
                         double massTolerance = missedMonoMass / 1000000d * Sweet.lollipop.raw_component_mass_tolerance;
-                        List<Component> missedMonoisotopics = scanComps.Where(cp => !removeThese.Contains(cp) && cp.weighted_monoisotopic_mass >= (missedMonoMass - massTolerance) && cp.weighted_monoisotopic_mass <= (missedMonoMass + massTolerance)).ToList(); // this is a list of harmonics to hc
+                        List<Component> missedMonoisotopics = scanComps.Where(cp => 
+                            !removeThese.Contains(cp) 
+                            && cp.weighted_monoisotopic_mass >= (missedMonoMass - massTolerance) 
+                            && cp.weighted_monoisotopic_mass <= (missedMonoMass + massTolerance)).ToList(); // this is a list of harmonics to hc
 
                         foreach (Component c in missedMonoisotopics.Where(m => m.id != sc.id).ToList())
                         {
@@ -164,7 +167,10 @@ public List<Component> remove_monoisotopic_duplicates_harmonics_from_same_scan(L
                     foreach (double harmonicMass in possibleHarmonicList)
                     {
                         double massTolerance = harmonicMass / 1000000d * Sweet.lollipop.raw_component_mass_tolerance;
-                        List<Component> harmonics = scanComps.Where(cp => !removeThese.Contains(cp) && cp.weighted_monoisotopic_mass >= (harmonicMass - massTolerance) && cp.weighted_monoisotopic_mass <= (harmonicMass + massTolerance)).ToList(); // this is a list of harmonics to hc
+                        List<Component> harmonics = scanComps.Where(cp => 
+                            !removeThese.Contains(cp) 
+                            && cp.weighted_monoisotopic_mass >= (harmonicMass - massTolerance) 
+                            && cp.weighted_monoisotopic_mass <= (harmonicMass + massTolerance)).ToList(); // this is a list of harmonics to hc
                         List<Component> someHarmonics = harmonics.Where(harmonicComponent => harmonicComponent.id != hc.id).ToList();
                         foreach (Component h in someHarmonics) // now that we have a list of harmonics to hc, we have to figure out what to do with them
                         {

ProteoformSuiteInternal/CytoscapeScript.cs

@@ -618,7 +618,7 @@ public static void write_styles(List<ProteoformFamily> all_families, string styl
                 writer.WriteEndElement();
 
                 //NODE PROPERTIES
-                double max_total_intensity = quantitative != null ?
+                double max_total_intensity = all_families.Count == 0 ? 0 : quantitative != null ?
                     (double)all_families.SelectMany(f => f.experimental_proteoforms).Max(p => p.quant.intensitySum) :
                     all_families.SelectMany(f => f.experimental_proteoforms).Max(p => p.agg_intensity);
                 writer.WriteStartElement("node");