public void reload_database_list()
{
cmb_loadTable.Items.Clear();
cmb_loadTable.Items.AddRange(Lollipop.file_lists);
cmb_loadTable.SelectedIndex = 2;
DisplayUtility.FillDataGridView(dgv_loadFiles, SaveState.lollipop.get_files(SaveState.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();
}
public void FillTablesAndCharts()
{
DisplayUtility.FillDataGridView(dgv_TD_proteoforms, Sweet.lollipop.topdown_proteoforms.Select(t => new DisplayTopDownProteoform(t)));
DisplayTopDownProteoform.FormatTopDownTable(dgv_TD_proteoforms, false);
load_colors();
mods = Sweet.lollipop.topdown_proteoforms.SelectMany(p => p.topdown_ptm_set.ptm_combination).Select(m => m.modification.OriginalId).Distinct().ToList();
tb_tdProteoforms.Text = Sweet.lollipop.topdown_proteoforms.Count(td => td.accepted).ToString();
tb_td_hits.Text = Sweet.lollipop.top_down_hits.Count.ToString();
tb_unique_PFRs.Text = Sweet.lollipop.topdown_proteoforms.Where(td => td.accepted).Select(p => p.pfr_accession).Distinct().Count().ToString();
}
private void drag_drop(DragEventArgs e, ComboBox cmb, DataGridView dgv)
{
int selected_index = Lollipop.file_lists.ToList().IndexOf(cmb.Text);
string[] files = (string[])e.Data.GetData(DataFormats.FileDrop);
Sweet.lollipop.enter_input_files(files, Lollipop.acceptable_extensions[selected_index], Lollipop.file_types[selected_index], Sweet.lollipop.input_files, true);
refresh_dgvs();
DisplayUtility.FillDataGridView(dgv, Sweet.lollipop.get_files(Sweet.lollipop.input_files, Lollipop.file_types[selected_index]).Select(f => new DisplayInputFile(f)));
DisplayInputFile.FormatInputFileTable(dgv, Lollipop.file_types[selected_index]);
}
private void btn_clearFiles_Click(object sender, EventArgs e)
{
List <InputFile> files_to_remove = Sweet.lollipop.get_files(Sweet.lollipop.input_files, Lollipop.file_types[cmb_loadTable.SelectedIndex]).ToList();
Sweet.save_actions.RemoveAll(a => files_to_remove.Any(f => a.Contains(f.complete_path)));
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]);
SetMakeDatabaseButton();
}
public void FillTablesAndCharts()
{
reload_database_list();
DisplayUtility.FillDataGridView(dgv_Database, Sweet.lollipop.target_proteoform_community.theoretical_proteoforms.Select(t => new DisplayTheoreticalProteoform(t)));
initialize_table_bindinglist();
DisplayTheoreticalProteoform.FormatTheoreticalProteoformTable(dgv_Database);
DisplayUtility.FillDataGridView(dgv_unlocalizedModifications, Sweet.lollipop.theoretical_database.unlocalized_lookup.Values.Select(m => new DisplayUnlocalizedModification(m)));
DisplayUnlocalizedModification.FormatUnlocalizedModificationTable(dgv_unlocalizedModifications);
tb_totalTheoreticalProteoforms.Text = Sweet.lollipop.target_proteoform_community.theoretical_proteoforms.Length.ToString();
}
public void FillTablesAndCharts()
{
plotObservedVsExpectedRelativeDifference();
DisplayUtility.FillDataGridView(dgv_quantification_results, SaveState.lollipop.qVals.Select(q => new DisplayQuantitativeValues(q)));
DisplayQuantitativeValues.FormatGridView(dgv_quantification_results);
tb_avgIntensity.Text = Math.Round(SaveState.lollipop.selectAverageIntensity, 1).ToString();
tb_stdevIntensity.Text = Math.Round(SaveState.lollipop.selectStDev, 3).ToString();
volcanoPlot();
plotBiorepIntensities();
updateGoTermsTable();
}
private void clear_files(ComboBox cmb, DataGridView dgv)
{
int selected_index = Lollipop.file_lists.ToList().IndexOf(cmb.Text);
List <InputFile> files_to_remove = Sweet.lollipop.get_files(Sweet.lollipop.input_files, Lollipop.file_types[selected_index]).ToList();
Sweet.save_actions.RemoveAll(a => files_to_remove.Any(f => a.Contains(f.complete_path)));
Sweet.lollipop.input_files = Sweet.lollipop.input_files.Except(files_to_remove).ToList();
refresh_dgvs();
DisplayUtility.FillDataGridView(dgv, Sweet.lollipop.get_files(Sweet.lollipop.input_files, Lollipop.file_types[selected_index]).Select(f => new DisplayInputFile(f)));
DisplayInputFile.FormatInputFileTable(dgv, Lollipop.file_types[selected_index]);
}
public void FillDataBaseTable(string table)
{
if (table == "Target")
{
DisplayUtility.FillDataGridView(dgv_Database, Sweet.lollipop.target_proteoform_community.theoretical_proteoforms.Select(t => new DisplayTheoreticalProteoform(t)));
}
else if (Sweet.lollipop.decoy_proteoform_communities.ContainsKey(table))
{
DisplayUtility.FillDataGridView(dgv_Database, Sweet.lollipop.decoy_proteoform_communities[table].theoretical_proteoforms.Select(t => new DisplayTheoreticalProteoform(t)));
}
DisplayTheoreticalProteoform.FormatTheoreticalProteoformTable(dgv_Database);
}
private void tb_tableFilter_TextChanged(object sender, EventArgs e)
{
List <TheoreticalProteoform> theoreticals_to_display = cmbx_DisplayWhichDB.SelectedItem.ToString() == "Target" ?
Sweet.lollipop.target_proteoform_community.theoretical_proteoforms.ToList()
: Sweet.lollipop.decoy_proteoform_communities[cmbx_DisplayWhichDB.SelectedItem.ToString()].theoretical_proteoforms.ToList();
IEnumerable <object> selected_theoreticals = tb_tableFilter.Text == "" ?
theoreticals_to_display :
ExtensionMethods.filter(theoreticals_to_display, tb_tableFilter.Text);
DisplayUtility.FillDataGridView(dgv_Database, selected_theoreticals.OfType <TheoreticalProteoform>().Select(t => new DisplayTheoreticalProteoform(t)));
DisplayTheoreticalProteoform.FormatTheoreticalProteoformTable(dgv_Database);
}
private void display_family_members(int row_index, int column_index)
{
ProteoformFamily selected_family = (ProteoformFamily)((DisplayObject)this.dgv_main.Rows[row_index].DataBoundItem).display_object;
if (column_index < 0)
{
return;
}
if (new List <string> {
nameof(DisplayProteoformFamily.theoretical_count), nameof(DisplayProteoformFamily.accession_list), nameof(DisplayProteoformFamily.name_list)
}.Contains(dgv_main.Columns[column_index].Name))
{
if (selected_family.theoretical_proteoforms.Count > 0)
{
DisplayUtility.FillDataGridView(dgv_proteoform_family_members, selected_family.theoretical_proteoforms.Select(t => new DisplayTheoreticalProteoform(t)));
DisplayTheoreticalProteoform.FormatTheoreticalProteoformTable(dgv_proteoform_family_members);
}
else
{
dgv_proteoform_family_members.Rows.Clear();
}
}
else if (new List <string> {
nameof(DisplayProteoformFamily.experimental_count), nameof(DisplayProteoformFamily.experimentals_list), nameof(DisplayProteoformFamily.agg_mass_list)
}.Contains(dgv_main.Columns[column_index].Name))
{
if (selected_family.experimental_proteoforms.Count > 0)
{
DisplayUtility.FillDataGridView(dgv_proteoform_family_members, selected_family.experimental_proteoforms.Select(e => new DisplayExperimentalProteoform(e)));
DisplayExperimentalProteoform.FormatAggregatesTable(dgv_proteoform_family_members);
}
else
{
dgv_proteoform_family_members.Rows.Clear();
}
}
else if (dgv_main.Columns[column_index].Name == nameof(DisplayProteoformFamily.relation_count))
{
if (selected_family.relations.Count > 0)
{
DisplayUtility.FillDataGridView(dgv_proteoform_family_members, selected_family.relations.Select(r => new DisplayProteoformRelation(r)));
DisplayProteoformRelation.FormatRelationsGridView(dgv_proteoform_family_members, false, false);
}
else
{
dgv_proteoform_family_members.Rows.Clear();
}
}
}
public void fill_proteoform_families(string filter, int decoyCommunityMinusOneIsTarget)
{
IEnumerable <object> families = filter == "" ?
(decoyCommunityMinusOneIsTarget < 0 ?
Sweet.lollipop.target_proteoform_community.families.OrderByDescending(f => f.relations.Count) :
Sweet.lollipop.decoy_proteoform_communities[Sweet.lollipop.decoy_community_name_prefix + decoyCommunityMinusOneIsTarget].families.OrderByDescending(f => f.relations.Count)) :
(decoyCommunityMinusOneIsTarget < 0 ?
ExtensionMethods.filter(Sweet.lollipop.target_proteoform_community.families.OrderByDescending(f => f.relations.Count), filter)
: ExtensionMethods.filter(Sweet.lollipop.decoy_proteoform_communities[Sweet.lollipop.decoy_community_name_prefix + decoyCommunityMinusOneIsTarget].families.OrderByDescending(f => f.relations.Count), filter));
DisplayUtility.FillDataGridView(dgv_main, families.OfType <ProteoformFamily>().Select(f => new DisplayProteoformFamily(f)));
DisplayProteoformFamily.FormatFamiliesTable(dgv_main);
}
public void reload_database_list()
{
cmb_loadTable.Items.Clear();
cmb_loadTable.Items.AddRange(Lollipop.file_lists);
cmb_loadTable.SelectedIndex = 2;
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();
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 cmbx_DisplayWhichDB_SelectedIndexChanged(object sender, EventArgs e)
{
if (!initial_load)
{
string table = cmbx_DisplayWhichDB.SelectedItem.ToString();
if (table == "Target")
{
DisplayUtility.FillDataGridView(dgv_Database, Sweet.lollipop.target_proteoform_community.theoretical_proteoforms.Select(t => new DisplayTheoreticalProteoform(t)));
}
else
{
DisplayUtility.FillDataGridView(dgv_Database, Sweet.lollipop.decoy_proteoform_communities[table].theoretical_proteoforms.Select(t => new DisplayTheoreticalProteoform(t)));
}
}
DisplayTheoreticalProteoform.FormatTheoreticalProteoformTable(dgv_Database);
}
private void tb_tableFilter_TextChanged(object sender, EventArgs e)
{
IEnumerable <object> filter_experimentals = tb_tableFilter.Text == "" ?
Sweet.lollipop.target_proteoform_community.families.SelectMany(f => f.experimental_proteoforms.Where(p => !p.topdown_id && p.linked_proteoform_references != null && (Sweet.lollipop.count_adducts_as_identifications || !p.adduct))).Select(ep => new DisplayExperimentalProteoform(ep)) :
ExtensionMethods.filter(Sweet.lollipop.target_proteoform_community.families.SelectMany(f => f.experimental_proteoforms.Where(p => !p.topdown_id && p.linked_proteoform_references != null)).Select(ep => new DisplayExperimentalProteoform(ep)), tb_tableFilter.Text);
DisplayUtility.FillDataGridView(dgv_identified_experimentals, filter_experimentals);
DisplayExperimentalProteoform.FormatAggregatesTable(dgv_identified_experimentals);
IEnumerable <object> filter_topdown = tb_tableFilter.Text == "" ?
Sweet.lollipop.target_proteoform_community.families.SelectMany(f => f.experimental_proteoforms.Where(p => p.topdown_id && p.linked_proteoform_references != null)).Select(p => new DisplayTopDownProteoform(p as TopDownProteoform)) :
ExtensionMethods.filter(Sweet.lollipop.target_proteoform_community.families.SelectMany(f => f.experimental_proteoforms.Where(p => p.topdown_id && p.linked_proteoform_references != null)).Select(p => new DisplayTopDownProteoform(p as TopDownProteoform)), tb_tableFilter.Text);
DisplayUtility.FillDataGridView(dgv_td_proteoforms, filter_topdown);
DisplayTopDownProteoform.FormatTopDownTable(dgv_td_proteoforms, true);
}
private void btn_loadModNames_Click(object sender, EventArgs e)
{
OpenFileDialog d = new OpenFileDialog();
d.Title = "Modification Names";
d.Filter = "Modification Names (*.modnames) | *.modnames";
d.Multiselect = false;
if (d.ShowDialog() != DialogResult.OK)
{
return;
}
Sweet.lollipop.theoretical_database.load_unlocalized_names(d.FileName);
DisplayUtility.FillDataGridView(dgv_unlocalizedModifications, Sweet.lollipop.theoretical_database.unlocalized_lookup.Values.Select(m => new DisplayUnlocalizedModification(m)));
DisplayUnlocalizedModification.FormatUnlocalizedModificationTable(dgv_unlocalizedModifications);
}
private void btn_addFiles_Click(object sender, EventArgs e)
{
OpenFileDialog openFileDialog = new OpenFileDialog();
openFileDialog.Title = cmb_loadTable.SelectedItem.ToString();
openFileDialog.Filter = Lollipop.file_filters[cmb_loadTable.SelectedIndex];
openFileDialog.Multiselect = true;
DialogResult dr = openFileDialog.ShowDialog();
if (dr == DialogResult.OK)
{
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]);
}
private void add_files(ComboBox cmb, DataGridView dgv)
{
OpenFileDialog openFileDialog = new OpenFileDialog();
openFileDialog.Title = cmb.SelectedItem.ToString();
openFileDialog.Filter = Lollipop.file_filters[cmb.SelectedIndex];
openFileDialog.Multiselect = true;
DialogResult dr = openFileDialog.ShowDialog();
if (dr == DialogResult.OK)
{
SaveState.lollipop.enter_input_files(openFileDialog.FileNames, Lollipop.acceptable_extensions[cmb.SelectedIndex], Lollipop.file_types[cmb.SelectedIndex], SaveState.lollipop.input_files);
match_files();
}
DisplayUtility.FillDataGridView(dgv, SaveState.lollipop.get_files(SaveState.lollipop.input_files, Lollipop.file_types[cmb.SelectedIndex]).Select(f => new DisplayInputFile(f)));
DisplayInputFile.FormatInputFileTable(dgv, Lollipop.file_types[cmb.SelectedIndex]);
}
private void btn_addFiles_Click(object sender, EventArgs e)
{
OpenFileDialog openFileDialog = new OpenFileDialog();
openFileDialog.Title = cmb_loadTable.SelectedItem.ToString();
openFileDialog.Filter = Lollipop.file_filters[cmb_loadTable.SelectedIndex];
openFileDialog.Multiselect = true;
DialogResult dr = openFileDialog.ShowDialog();
if (dr == DialogResult.OK)
{
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]);
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");
}
}
public void FillTablesAndCharts()
{
dgv_EE_Peaks.CurrentCellDirtyStateChanged -= EE_Peak_List_DirtyStateChanged;//remove event handler on form load and table refresh event
DisplayUtility.FillDataGridView(dgv_EE_Peaks, Sweet.lollipop.ee_peaks.OrderByDescending(p => p.peak_relation_group_count).Select(p => new DisplayDeltaMassPeak(p)));
DisplayUtility.FillDataGridView(dgv_EE_Relations, Sweet.lollipop.ee_relations.Select(r => new DisplayProteoformRelation(r)));
DisplayProteoformRelation.FormatRelationsGridView(dgv_EE_Relations, false, true, false);
DisplayDeltaMassPeak.FormatPeakListGridView(dgv_EE_Peaks, true);
GraphEERelations();
GraphEEPeaks();
if (cb_Graph_lowerThreshold.Checked)
{
ct_EE_Histogram.ChartAreas[0].AxisY.StripLines.Add(new StripLine()
{
BorderColor = Color.Red, IntervalOffset = Convert.ToDouble(nUD_PeakCountMinThreshold.Value)
});
}
else
{
ct_EE_Histogram.ChartAreas[0].AxisY.StripLines.Clear();
}
update_figures_of_merit();
dgv_EE_Peaks.CurrentCellDirtyStateChanged += EE_Peak_List_DirtyStateChanged;//re-instate event handler after form load and table refresh event
}
private void reload_dgvs()
{
DisplayUtility.FillDataGridView(dgv_loadFiles1, Sweet.lollipop.get_files(Sweet.lollipop.input_files, Lollipop.file_types[Lollipop.file_lists.ToList().IndexOf(cmb_loadTable1.Text)]).Select(f => new DisplayInputFile(f)));
DisplayInputFile.FormatInputFileTable(dgv_loadFiles1, Lollipop.file_types[Lollipop.file_lists.ToList().IndexOf(cmb_loadTable1.Text)]);
}
private void cmb_loadTable3_SelectedIndexChanged(object sender, EventArgs e)
{
DisplayUtility.FillDataGridView(dgv_loadFiles3, SaveState.lollipop.get_files(SaveState.lollipop.input_files, Lollipop.file_types[cmb_loadTable3.SelectedIndex]).Select(f => new DisplayInputFile(f)));
DisplayInputFile.FormatInputFileTable(dgv_loadFiles3, Lollipop.file_types[cmb_loadTable3.SelectedIndex]);
lb_filter3.Text = cmb_loadTable1.SelectedItem.ToString();
}
private void tb_filter3_TextChanged(object sender, EventArgs e)
{
DisplayUtility.FillDataGridView(dgv_loadFiles3, ExtensionMethods.filter(SaveState.lollipop.get_files(SaveState.lollipop.input_files, Lollipop.file_types[cmb_loadTable3.SelectedIndex]), tb_filter3.Text).OfType <InputFile>().Select(f => new DisplayInputFile(f)));
DisplayInputFile.FormatInputFileTable(dgv_loadFiles3, Lollipop.file_types[cmb_loadTable3.SelectedIndex]);
}
public void FillTablesAndCharts()
{
DisplayUtility.FillDataGridView(dgv_AggregatedProteoforms, SaveState.lollipop.target_proteoform_community.experimental_proteoforms.Select(e => new DisplayExperimentalProteoform(e)));
DisplayExperimentalProteoform.FormatAggregatesTable(dgv_AggregatedProteoforms);
}
private void FillEERelationsGridView()
{
displayRelations = SaveState.lollipop.ee_relations.Select(r => new DisplayProteoformRelation(r)).ToList();
DisplayUtility.FillDataGridView(dgv_EE_Relations, displayRelations);
}
private void FillEEPeakListTable()
{
DisplayUtility.FillDataGridView(dgv_EE_Peaks, SaveState.lollipop.ee_peaks.OrderByDescending(p => p.peak_relation_group_count).ToList());
}
private void fill_go(Aspect aspect, string filter)
{
DisplayUtility.FillDataGridView(dgv_main, filter == "" ?
Sweet.lollipop.target_proteoform_community.families.SelectMany(f => f.theoretical_proteoforms).SelectMany(t => t.ExpandedProteinList).SelectMany(g => g.GoTerms).Where(g => g.Aspect == aspect) :
ExtensionMethods.filter(Sweet.lollipop.target_proteoform_community.families.SelectMany(f => f.theoretical_proteoforms).SelectMany(t => t.ExpandedProteinList).SelectMany(g => g.GoTerms).Where(g => g.Aspect == aspect), filter));
}
private void fillGoTermsTable()
{
DisplayUtility.FillDataGridView(dgv_goAnalysis, SaveState.lollipop.goTermNumbers.Where(x => x.Aspect.ToString() == cmbx_goAspect.SelectedItem.ToString()).Select(g => new DisplayGoTermNumber(g)));
DisplayGoTermNumber.FormatGridView(dgv_goAnalysis);
}
public void load_dgv()
{
DisplayUtility.FillDataGridView(dgv_Database, Sweet.lollipop.target_proteoform_community.theoretical_proteoforms.Select(t => new DisplayTheoreticalProteoform(t)));
initialize_table_bindinglist();
DisplayTheoreticalProteoform.FormatTheoreticalProteoformTable(dgv_Database);
}
private void FillNeuCodePairsDGV()
{
DisplayUtility.FillDataGridView(dgv_RawExpNeuCodePairs, SaveState.lollipop.raw_neucode_pairs.Select(n => new DisplayNeuCodePair(n)));
DisplayNeuCodePair.FormatNeuCodeTable(dgv_RawExpNeuCodePairs);
}