Reaggregation now runs through the rest of the pipeline.

smith-chem-wisc · Mar 6, 2017 · aeb2542 · aeb2542
1 parent e78ebe7
commit aeb2542
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Showing 7 changed files with 41 additions and 21 deletions.
diff --git a/ProteoformSuiteGUI/AggregatedProteoforms.cs b/ProteoformSuiteGUI/AggregatedProteoforms.cs
@@ -42,6 +42,14 @@ private void run_the_gamut()
             this.Cursor = Cursors.WaitCursor;
             Lollipop.aggregate_proteoforms(Lollipop.validate_proteoforms, Lollipop.raw_neucode_pairs, Lollipop.raw_experimental_components, Lollipop.raw_quantification_components, Lollipop.min_rel_abundance, Lollipop.min_num_CS);
             FillAggregatesTable();
+            ((ProteoformSweet)MdiParent).experimentalTheoreticalComparison.ClearListsAndTables();
+            ((ProteoformSweet)MdiParent).experimentalTheoreticalComparison.run_the_gamut();
+            ((ProteoformSweet)MdiParent).experimentExperimentComparison.ClearListsAndTables();
+            ((ProteoformSweet)MdiParent).experimentExperimentComparison.run_the_gamut();
+            ((ProteoformSweet)MdiParent).proteoformFamilies.ClearListsAndTables();
+            ((ProteoformSweet)MdiParent).proteoformFamilies.run_the_gamut();
+            ((ProteoformSweet)MdiParent).quantification.ClearListsAndTables();
+            ((ProteoformSweet)MdiParent).quantification.perform_calculations();
             updateFiguresOfMerit();
             this.Cursor = Cursors.Default;
         }

diff --git a/ProteoformSuiteGUI/ExperimentExperimentComparison.cs b/ProteoformSuiteGUI/ExperimentExperimentComparison.cs
@@ -42,7 +42,7 @@ public void compare_ee()
             else if (Lollipop.ee_relations.Count == 0) MessageBox.Show("Go back and aggregate experimental proteoforms.");
         }
 
-        private  void run_the_gamut()
+        public void run_the_gamut()
         {
             this.Cursor = Cursors.WaitCursor;
             Lollipop.make_ee_relationships();
@@ -61,7 +61,7 @@ public DataGridView GetEEPeaksDGV()
             return dgv_EE_Peaks;
         }
 
-        private void ClearListsAndTables()
+        public void ClearListsAndTables()
         {
             Lollipop.ee_relations.Clear();
             Lollipop.ee_peaks.Clear();

diff --git a/ProteoformSuiteGUI/ExperimentTheoreticalComparison.cs b/ProteoformSuiteGUI/ExperimentTheoreticalComparison.cs
@@ -43,7 +43,7 @@ public void compare_et()
             else if (Lollipop.et_relations.Count == 0) MessageBox.Show("Go back and aggregate experimental proteoforms.");
         }
 
-        private void run_the_gamut()
+        public void run_the_gamut()
         {
             this.Cursor = Cursors.WaitCursor;
             Lollipop.make_et_relationships();
@@ -75,7 +75,7 @@ public DataGridView GetETPeaksDGV()
             return dgv_ET_Peak_List;
         }
 
-        private void ClearListsAndTables()
+        public void ClearListsAndTables()
         {
             Lollipop.et_relations.Clear();
             Lollipop.et_peaks.Clear();

diff --git a/ProteoformSuiteGUI/LoadDeconvolutionResults.Designer.cs b/ProteoformSuiteGUI/LoadDeconvolutionResults.Designer.cs
diff --git a/ProteoformSuiteGUI/ProteoformFamilies.cs b/ProteoformSuiteGUI/ProteoformFamilies.cs
@@ -66,7 +66,7 @@ public DataGridView GetDGV()
             return dgv_main;
         }
 
-        private void run_the_gamut()
+        public void run_the_gamut()
         {
             this.Cursor = Cursors.WaitCursor;
             initialize_settings();
@@ -76,6 +76,11 @@ private void run_the_gamut()
             this.Cursor = Cursors.Default;
         }
 
+        public void ClearListsAndTables()
+        {
+            Lollipop.proteoform_community.families.Clear();
+        }
+
         private void update_figures_of_merit()
         {
             this.tb_TotalFamilies.Text = Lollipop.proteoform_community.families.Count(f => f.proteoforms.Count > 1).ToString();

diff --git a/ProteoformSuiteGUI/ProteoformSweet.cs b/ProteoformSuiteGUI/ProteoformSweet.cs
@@ -16,16 +16,16 @@ namespace ProteoformSuite
     public partial class ProteoformSweet : Form
     {
         //  Initialize Forms START
-        private LoadDeconvolutionResults loadDeconvolutionResults = new LoadDeconvolutionResults();
-        private RawExperimentalComponents rawExperimentalComponents = new RawExperimentalComponents();
+        public LoadDeconvolutionResults loadDeconvolutionResults = new LoadDeconvolutionResults();
+        public RawExperimentalComponents rawExperimentalComponents = new RawExperimentalComponents();
         public NeuCodePairs neuCodePairs = new NeuCodePairs();
-        private AggregatedProteoforms aggregatedProteoforms = new AggregatedProteoforms();
+        public AggregatedProteoforms aggregatedProteoforms = new AggregatedProteoforms();
         public TheoreticalDatabase theoreticalDatabase = new TheoreticalDatabase();
-        private ExperimentTheoreticalComparison experimentalTheoreticalComparison = new ExperimentTheoreticalComparison();
-        private ExperimentExperimentComparison experimentExperimentComparison = new ExperimentExperimentComparison();
-        private ProteoformFamilies proteoformFamilies = new ProteoformFamilies();
-        private Quantification quantification = new Quantification();
-        private ResultsSummary resultsSummary = new ResultsSummary();
+        public ExperimentTheoreticalComparison experimentalTheoreticalComparison = new ExperimentTheoreticalComparison();
+        public ExperimentExperimentComparison experimentExperimentComparison = new ExperimentExperimentComparison();
+        public ProteoformFamilies proteoformFamilies = new ProteoformFamilies();
+        public Quantification quantification = new Quantification();
+        public ResultsSummary resultsSummary = new ResultsSummary();
         List<Form> forms;
         //  Initialize Forms END
 
@@ -57,11 +57,14 @@ public void InitializeForms()
                 theoreticalDatabase, experimentalTheoreticalComparison, experimentExperimentComparison,
                 proteoformFamilies, quantification
             });
+            foreach (Form form in forms)
+            {
+                form.MdiParent = this;
+            }
         }
 
         private void showForm(Form form)
         {
-            form.MdiParent = this;
             form.Show();
             form.WindowState = FormWindowState.Maximized;
             current_form = form;
@@ -193,15 +196,10 @@ public bool full_run()
             }
 
             this.Cursor = Cursors.WaitCursor;
-            rawExperimentalComponents.MdiParent = this;
             rawExperimentalComponents.load_raw_components(); //also loads the theoretical database, now
             rawExperimentalComponents.preloaded = true;
             neuCodePairs.preloaded = true;
             aggregatedProteoforms.aggregate_proteoforms();
-            experimentalTheoreticalComparison.compare_et();
-            experimentExperimentComparison.compare_ee();
-            if (Lollipop.neucode_labeled) proteoformFamilies.construct_families();
-            quantification.perform_calculations();
             this.enable_neuCodeProteoformPairsToolStripMenuItem(Lollipop.neucode_labeled);
             this.Cursor = Cursors.Default;
             return true;

diff --git a/ProteoformSuiteGUI/Quantification.cs b/ProteoformSuiteGUI/Quantification.cs
@@ -46,6 +46,17 @@ public void perform_calculations() //this is the first thing that gets run on fo
             }
         }
 
+        public void ClearListsAndTables()
+        {
+            Lollipop.logIntensityHistogram.Clear();
+            Lollipop.logSelectIntensityHistogram.Clear();
+            Lollipop.satisfactoryProteoforms.Clear();
+            Lollipop.qVals.Clear();
+            Lollipop.observedProteins.Clear();
+            Lollipop.inducedOrRepressedProteins.Clear();
+            Lollipop.goTermNumbers.Clear();
+        }
+
         public void fillGuiTablesAndGraphs()
         {
             plotObservedVsExpectedRelativeDifference();