public void FillTablesAndCharts()
{
DisplayUtility.FillDataGridView(dgv_fileList, Sweet.lollipop.get_files(Sweet.lollipop.input_files, new Purpose[] { Purpose.Identification, Purpose.Quantification }).Select(c => new DisplayInputFile(c)));
DisplayInputFile.FormatInputFileTable(dgv_fileList, new Purpose[] { Purpose.Identification, Purpose.Quantification });
dgv_fileList.ReadOnly = true;
if (rb_displayIdentificationComponents.Checked && Sweet.lollipop.raw_experimental_components.Count > 0)
{
DisplayUtility.FillDataGridView(dgv_rawComponents, Sweet.lollipop.raw_experimental_components.Select(c => new DisplayComponent(c)));
}
if (rb_displayQuantificationComponents.Checked && Sweet.lollipop.raw_quantification_components.Count > 0)
{
DisplayUtility.FillDataGridView(dgv_rawComponents, Sweet.lollipop.raw_quantification_components.Select(c => new DisplayComponent(c)));
}
DisplayComponent.FormatComponentsTable(dgv_rawComponents);
rtb_raw_components_counts.Text = ResultsSummaryGenerator.raw_components_report();
NeuCodePairs pairs_form = (MdiParent as ProteoformSweet).neuCodePairs;
if (Sweet.lollipop.neucode_labeled && pairs_form.ReadyToRunTheGamut())
{
pairs_form.RunTheGamut(false);
}
}
private void dgv_ET_Peak_List_CellClick(object sender, MouseEventArgs e)
{
int clickedRow = dgv_ET_Peak_List.HitTest(e.X, e.Y).RowIndex;
int clickedCol = dgv_ET_Peak_List.HitTest(e.X, e.Y).ColumnIndex;
if (clickedRow < Sweet.lollipop.et_relations.Count && clickedRow >= 0 && clickedCol >= 0 && clickedCol < dgv_ET_Peak_List.ColumnCount)
{
if (e.Button == MouseButtons.Left)
{
ct_ET_peakList.ChartAreas[0].AxisX.StripLines.Clear();
DeltaMassPeak selected_peak = (dgv_ET_Peak_List.Rows[clickedRow].DataBoundItem as DisplayObject).display_object as DeltaMassPeak;
DisplayUtility.GraphSelectedDeltaMassPeak(ct_ET_peakList, selected_peak, Sweet.lollipop.et_relations);
}
else
{
if (e.Button == MouseButtons.Right && clickedRow >= 0 && clickedRow < Sweet.lollipop.et_relations.Count)
{
ContextMenuStrip ET_peak_List_Menu = new ContextMenuStrip();
int position_xy_mouse_row = dgv_ET_Peak_List.HitTest(e.X, e.Y).RowIndex;
DisplayDeltaMassPeak selected_peak = dgv_ET_Peak_List.Rows[clickedRow].DataBoundItem as DisplayDeltaMassPeak;
if (position_xy_mouse_row > 0)
{
ET_peak_List_Menu.Items.Add("Increase Experimental Mass " + Lollipop.MONOISOTOPIC_UNIT_MASS + " Da").Name = "IncreaseMass";
ET_peak_List_Menu.Items.Add("Decrease Experimental Mass " + Lollipop.MONOISOTOPIC_UNIT_MASS + " Da").Name = "DecreaseMass";
}
ET_peak_List_Menu.Show(dgv_ET_Peak_List, new Point(e.X, e.Y));
//event menu click
ET_peak_List_Menu.ItemClicked += new ToolStripItemClickedEventHandler((s, ev) => ET_peak_List_Menu_ItemClicked(s, ev, selected_peak));
}
}
}
}
private void tb_filter1_TextChanged(object sender, EventArgs e)
{
int selected_index = Lollipop.file_lists.ToList().IndexOf(cmb_loadTable1.Text);
DisplayUtility.FillDataGridView(dgv_loadFiles1, ExtensionMethods.filter(Sweet.lollipop.get_files(Sweet.lollipop.input_files, Lollipop.file_types[selected_index]), tb_filter1.Text).OfType <InputFile>().Select(f => new DisplayInputFile(f)));
DisplayInputFile.FormatInputFileTable(dgv_loadFiles1, Lollipop.file_types[selected_index]);
}
private void clear_files(ComboBox cmb, DataGridView dgv)
{
SaveState.lollipop.input_files = SaveState.lollipop.input_files.Except(SaveState.lollipop.get_files(SaveState.lollipop.input_files, Lollipop.file_types[cmb.SelectedIndex])).ToList();
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 add_files(ComboBox cmb, DataGridView dgv)
{
int selected_index = Lollipop.file_lists.ToList().IndexOf(cmb.Text);
OpenFileDialog openFileDialog = new OpenFileDialog();
openFileDialog.Title = cmb.SelectedItem.ToString();
openFileDialog.Filter = Lollipop.file_filters[selected_index];
openFileDialog.Multiselect = true;
DialogResult dr = openFileDialog.ShowDialog();
if (dr == DialogResult.OK)
{
Sweet.lollipop.enter_input_files(openFileDialog.FileNames, Lollipop.acceptable_extensions[selected_index], Lollipop.file_types[selected_index], Sweet.lollipop.input_files, true);
refresh_dgvs();
if (openFileDialog.FileNames.Any(f => Path.GetExtension(f) == ".raw"))
{
ValidateThermoMsFileReaderVersion();
}
}
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]);
}
void ct_LysineCount_MouseClick(object sender, MouseEventArgs e)
{
if (e.Button == MouseButtons.Left)
{
DisplayUtility.tooltip_graph_display(ct_LysineCount_tt, e, ct_LysineCount, ct_LysineCount_prevPosition);
}
}
void ct_IntensityRatio_MouseClick(object sender, MouseEventArgs e)
{
if (e.Button == MouseButtons.Left)
{
DisplayUtility.tooltip_graph_display(ct_intensityRatio_tt, e, ct_IntensityRatio, ct_intensityRatio_prevPosition);
}
}
private void ct_EE_peakList_MouseClick(object sender, MouseEventArgs e)
{
if (e.Button == MouseButtons.Left)
{
DisplayUtility.tooltip_graph_display(ct_EE_peakList_tt, e, ct_EE_peakList, ct_EE_peakList_prevPosition);
}
}
private void btn_clearFiles_Click(object sender, EventArgs e)
{
SaveState.lollipop.input_files = SaveState.lollipop.input_files.Except(SaveState.lollipop.get_files(SaveState.lollipop.input_files, Lollipop.file_types[cmb_loadTable.SelectedIndex])).ToList();
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]);
set_Make_Database_Button();
}
//Special histogram counting relations of mass difference from unmodified
private void cb_discoveryHistogram_CheckedChanged(object sender, EventArgs e)
{
if (cb_discoveryHistogram.Checked)
{
Cursor = Cursors.WaitCursor;
if (et_histogram_from_unmod.Count == 0)
{
ProteoformCommunity community = new ProteoformCommunity();
et_histogram_from_unmod = community.relate(Sweet.lollipop.target_proteoform_community.experimental_proteoforms.Where(ex => ex.accepted).ToArray(), Sweet.lollipop.target_proteoform_community.theoretical_proteoforms.Where(t => t.ptm_set.mass == 0).ToArray(), ProteoformComparison.ExperimentalTheoretical, false, Environment.CurrentDirectory, false);
}
DisplayUtility.GraphRelationsChart(ct_ET_Histogram, et_histogram_from_unmod, "relations", true);
// Show the raw relations in the table
tb_relationTableFilter.TextChanged -= tb_relationTableFilter_TextChanged;
tb_relationTableFilter.Text = "";
tb_relationTableFilter.TextChanged += tb_relationTableFilter_TextChanged;
DisplayUtility.FillDataGridView(dgv_ET_Relations, et_histogram_from_unmod.Select(r => new DisplayProteoformRelation(r)));
// Get rid of the stripline by default
cb_Graph_lowerThreshold.Checked = false;
Cursor = Cursors.Default;
}
else
{
DisplayUtility.GraphRelationsChart(ct_ET_Histogram, Sweet.lollipop.et_relations, "relations", true);
DisplayUtility.FillDataGridView(dgv_ET_Relations, Sweet.lollipop.et_relations.Select(r => new DisplayProteoformRelation(r)).ToList());
cb_Graph_lowerThreshold.Checked = true;
tb_relationTableFilter.TextChanged -= tb_relationTableFilter_TextChanged;
tb_relationTableFilter.Text = "";
tb_relationTableFilter.TextChanged += tb_relationTableFilter_TextChanged;
}
}
private void display_light_proteoforms()
{
List <IAggregatable> components = selected_pf == null ? new List <IAggregatable>() :
rb_displayIdentificationComponents.Checked ?
selected_pf.aggregated :
rb_displayLightQuantificationComponents.Checked ?
selected_pf.lt_quant_components.ToList <IAggregatable>() :
selected_pf.hv_quant_components.ToList <IAggregatable>();
if (Sweet.lollipop.neucode_labeled && rb_displayIdentificationComponents.Checked)
{
DisplayUtility.FillDataGridView(dgv_AcceptNeuCdLtProteoforms, components.Select(c => new DisplayNeuCodePair(c as NeuCodePair)));
}
else if (rb_displayIdentificationComponents.Checked && selected_pf != null && selected_pf.topdown_id)
{
DisplayUtility.FillDataGridView(dgv_AcceptNeuCdLtProteoforms, (selected_pf as TopDownProteoform).topdown_hits.Select(h => new DisplayTopDownHit(h)));
}
else
{
DisplayUtility.FillDataGridView(dgv_AcceptNeuCdLtProteoforms, components.Select(c => new DisplayComponent(c as Component)));
}
if (Sweet.lollipop.neucode_labeled && rb_displayIdentificationComponents.Checked)
{
DisplayNeuCodePair.FormatNeuCodeTable(dgv_AcceptNeuCdLtProteoforms);
}
else if (rb_displayIdentificationComponents.Checked && selected_pf != null && selected_pf.topdown_id)
{
DisplayTopDownHit.FormatTopDownHitsTable(dgv_AcceptNeuCdLtProteoforms);
}
else
{
DisplayComponent.FormatComponentsTable(dgv_AcceptNeuCdLtProteoforms);
}
}
private void btn_inclusion_list_selected_families_Click(object sender, EventArgs e)
{
object[] selected = DisplayUtility.get_selected_objects(dgv_main);
List <ProteoformFamily> families = selected.OfType <ProteoformFamily>().ToList();
write_inclusion_list(families.SelectMany(f => f.experimental_proteoforms).ToList());
}
private void btn_downloadUniProtPtmList_Click(object sender, EventArgs e)
{
SaveState.lollipop.enter_uniprot_ptmlist();
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]);
btn_downloadUniProtPtmList.Enabled = false;
}
private void drag_drop(DragEventArgs e, ComboBox cmb, DataGridView dgv)
{
string[] files = (string[])e.Data.GetData(DataFormats.FileDrop);
SaveState.lollipop.enter_input_files(files, Lollipop.acceptable_extensions[cmb.SelectedIndex], Lollipop.file_types[cmb.SelectedIndex], SaveState.lollipop.input_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_downloadUniProtPtmList_Click(object sender, EventArgs e)
{
Lollipop.enter_uniprot_ptmlist(Environment.CurrentDirectory);
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();
}
private void tb_relationTableFilter_TextChanged(object sender, EventArgs e)
{
IEnumerable <object> selected_relations = tb_relationTableFilter.Text == "" ?
(cb_discoveryHistogram.Checked ? et_histogram_from_unmod.OfType <ProteoformRelation>().Select(p => new DisplayProteoformRelation(p)) : Sweet.lollipop.et_relations.OfType <ProteoformRelation>().Select(p => new DisplayProteoformRelation(p)))
: (ExtensionMethods.filter((cb_discoveryHistogram.Checked ? et_histogram_from_unmod.OfType <ProteoformRelation>().Select(p => new DisplayProteoformRelation(p)) : Sweet.lollipop.et_relations.OfType <ProteoformRelation>().Select(p => new DisplayProteoformRelation(p))), tb_relationTableFilter.Text));
DisplayUtility.FillDataGridView(dgv_ET_Relations, selected_relations);
DisplayProteoformRelation.FormatRelationsGridView(dgv_ET_Relations, true, false, cb_discoveryHistogram.Checked);
}
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]);
}
private void tb_peakTableFilter_TextChanged(object sender, EventArgs e)
{
IEnumerable <object> selected_peaks = tb_peakTableFilter.Text == "" ?
SaveState.lollipop.ee_peaks :
ExtensionMethods.filter(SaveState.lollipop.ee_peaks, tb_peakTableFilter.Text);
DisplayUtility.FillDataGridView(dgv_EE_Peaks, selected_peaks.OfType <DeltaMassPeak>());
DisplayUtility.FormatPeakListGridView(dgv_EE_Peaks, true);
}
public void FillTablesAndCharts()
{
reload_database_list();
DisplayUtility.FillDataGridView(dgv_Database, SaveState.lollipop.target_proteoform_community.theoretical_proteoforms.Select(t => new DisplayTheoreticalProteoform(t)));
initialize_table_bindinglist();
DisplayTheoreticalProteoform.FormatTheoreticalProteoformTable(dgv_Database);
DisplayUtility.FillDataGridView(dgv_unlocalizedModifications, SaveState.lollipop.theoretical_database.unlocalized_lookup.Values.Select(m => new DisplayUnlocalizedModification(m)));
DisplayUnlocalizedModification.FormatUnlocalizedModificationTable(dgv_unlocalizedModifications);
}
private void fill_theoreticals(string filter)
{
IEnumerable <object> theoreticals = filter == "" ?
Sweet.lollipop.target_proteoform_community.families.SelectMany(f => f.theoretical_proteoforms) :
ExtensionMethods.filter(Sweet.lollipop.target_proteoform_community.families.SelectMany(f => f.theoretical_proteoforms), filter);
DisplayUtility.FillDataGridView(dgv_main, theoreticals.OfType <TheoreticalProteoform>().Select(t => new DisplayTheoreticalProteoform(t)));
DisplayTheoreticalProteoform.FormatTheoreticalProteoformTable(dgv_main);
}
private void tb_tableFilter_TextChanged(object sender, EventArgs e)
{
IEnumerable <object> selected_theoreticals = tb_tableFilter.Text == "" ?
SaveState.lollipop.target_proteoform_community.theoretical_proteoforms :
ExtensionMethods.filter(SaveState.lollipop.target_proteoform_community.theoretical_proteoforms, tb_tableFilter.Text);
DisplayUtility.FillDataGridView(dgv_Database, selected_theoreticals.OfType <TheoreticalProteoform>().Select(t => new DisplayTheoreticalProteoform(t)));
DisplayTheoreticalProteoform.FormatTheoreticalProteoformTable(dgv_Database);
}
private void tb_tableFilter_TextChanged(object sender, EventArgs e)
{
IEnumerable <object> selected_aggregates = tb_tableFilter.Text == "" ?
SaveState.lollipop.target_proteoform_community.experimental_proteoforms :
ExtensionMethods.filter(SaveState.lollipop.target_proteoform_community.experimental_proteoforms, tb_tableFilter.Text);
DisplayUtility.FillDataGridView(dgv_AggregatedProteoforms, selected_aggregates.OfType <ExperimentalProteoform>().Select(ep => new DisplayExperimentalProteoform(ep)));
DisplayExperimentalProteoform.FormatAggregatesTable(dgv_AggregatedProteoforms);
}
private void tb_relationTableFilter_TextChanged(object sender, EventArgs e)
{
IEnumerable <object> selected_peaks = tb_relationTableFilter.Text == "" ?
displayRelations :
ExtensionMethods.filter(displayRelations.ToList(), tb_relationTableFilter.Text);
DisplayUtility.FillDataGridView(dgv_EE_Relations, selected_peaks);
DisplayProteoformRelation.FormatRelationsGridView(dgv_EE_Relations, false, true);
}
private void tb_tableFilter_TextChanged(object sender, EventArgs e)
{
IEnumerable <object> selected_td = tb_tableFilter.Text == "" ?
Sweet.lollipop.topdown_proteoforms :
ExtensionMethods.filter(Sweet.lollipop.topdown_proteoforms, tb_tableFilter.Text);
DisplayUtility.FillDataGridView(dgv_TD_proteoforms, selected_td.OfType <TopDownProteoform>().Select(t => new DisplayTopDownProteoform(t)));
DisplayTopDownProteoform.FormatTopDownTable(dgv_TD_proteoforms, false);
}
private void reload_dgvs()
{
DisplayUtility.FillDataGridView(dgv_loadFiles1, SaveState.lollipop.get_files(SaveState.lollipop.input_files, Lollipop.file_types[cmb_loadTable1.SelectedIndex]).Select(f => new DisplayInputFile(f)));
DisplayUtility.FillDataGridView(dgv_loadFiles2, SaveState.lollipop.get_files(SaveState.lollipop.input_files, Lollipop.file_types[cmb_loadTable2.SelectedIndex]).Select(f => new DisplayInputFile(f)));
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_loadFiles1, Lollipop.file_types[cmb_loadTable1.SelectedIndex]);
DisplayInputFile.FormatInputFileTable(dgv_loadFiles2, Lollipop.file_types[cmb_loadTable2.SelectedIndex]);
DisplayInputFile.FormatInputFileTable(dgv_loadFiles3, Lollipop.file_types[cmb_loadTable3.SelectedIndex]);
}
private void dgv_RawQuantComp_MI_masses_CellContentClick(object sender, DataGridViewCellEventArgs e)
{
if (e.RowIndex >= 0)
{
Component c = ((Component)((DisplayComponent)this.dgv_rawComponents.Rows[e.RowIndex].DataBoundItem).display_object);
DisplayUtility.FillDataGridView(dgv_chargeStates, c.charge_states.Select(cs => new DisplayChargeState(cs)));
DisplayChargeState.FormatChargeStateTable(dgv_chargeStates);
}
}
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();
}
private void tb_peakTableFilter_TextChanged(object sender, EventArgs e)
{
IEnumerable <object> selected_peaks = tb_peakTableFilter.Text == "" ?
Sweet.lollipop.et_peaks :
ExtensionMethods.filter(Sweet.lollipop.et_peaks, tb_peakTableFilter.Text);
DisplayUtility.FillDataGridView(dgv_ET_Peak_List, selected_peaks.OfType <DeltaMassPeak>().Select(p => new DisplayDeltaMassPeak(p)));
DisplayDeltaMassPeak.FormatPeakListGridView(dgv_ET_Peak_List, false);
}
private void tb_modTableFilter_TextChanged(object sender, EventArgs e)
{
IEnumerable <object> selected_unmods = tb_modTableFilter.Text == "" ?
Sweet.lollipop.theoretical_database.unlocalized_lookup.Values :
ExtensionMethods.filter(Sweet.lollipop.theoretical_database.unlocalized_lookup.Values, tb_modTableFilter.Text);
DisplayUtility.FillDataGridView(dgv_unlocalizedModifications, selected_unmods.OfType <UnlocalizedModification>().Select(u => new DisplayUnlocalizedModification(u)));
DisplayUnlocalizedModification.FormatUnlocalizedModificationTable(dgv_unlocalizedModifications);
}
public void FillTablesAndCharts()
{
plotObservedVsExpectedRelativeDifference();
DisplayUtility.FillDataGridView(dgv_quantification_results, SaveState.lollipop.qVals.Select(q => new DisplayQuantitativeValues(q)));
DisplayQuantitativeValues.FormatGridView(dgv_quantification_results);
volcanoPlot();
plotBiorepIntensities();
updateGoTermsTable();
}