Fixing families table selector bug; readme updates

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/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;
 

README.md

@@ -3,6 +3,12 @@ Software for constructing, quantifying, and visualizing proteoform families.
 [![Build status](https://ci.appveyor.com/api/projects/status/qbc3xy4b35otnsxe/branch/master?svg=true)](https://ci.appveyor.com/project/stefanks/proteoform-suite/branch/master)
 [![Coverage Status](https://coveralls.io/repos/github/smith-chem-wisc/proteoform-suite/badge.svg?branch=master)](https://coveralls.io/github/smith-chem-wisc/proteoform-suite?branch=master)
 
+## Papers
+
+* [Proteoform Suite: Software for Constructing, Quantifying, and Visualizing Proteoform Families. (2017, _J. Proteome Res._)](http://pubs.acs.org/doi/10.1021/acs.jproteome.7b00685)
+
+* [Elucidating _Escherichia coli_ Proteoform Families Using Intact-Mass Proteomics and a Global PTM Discovery Database. (2017, _J. Proteome Res._)](http://pubs.acs.org/doi/abs/10.1021/acs.jproteome.7b00516)
+
 ## Latest Release and Vignette
 
 The latest release and vignette can be found [here](https://github.com/smith-chem-wisc/ProteoformSuite/releases/latest).