private bool AddProteinRowsToGrid(ILongWaitBroker longWaitBroker)
{
longWaitBroker.Message = Resources.UniquePeptidesDlg_AddProteinRowsToGrid_Adding_rows_to_grid_;
HashSet <Protein> proteinSet = new HashSet <Protein>();
foreach (var proteins in _peptideProteins)
{
proteinSet.UnionWith(proteins);
}
List <Protein> proteinList = new List <Protein>();
proteinList.AddRange(proteinSet);
proteinList.Sort();
var proteinsByPreferredNameCounts = proteinList
.Where(p => !string.IsNullOrEmpty(p.PreferredName))
.ToLookup(p => p.PreferredName, StringComparer.OrdinalIgnoreCase)
.ToDictionary(grouping => grouping.Key, grouping => grouping.Count(), StringComparer.OrdinalIgnoreCase);
var newColumns = new List <DataGridViewColumn>();
foreach (var protein in proteinList)
{
ProteinColumn proteinColumn = new ProteinColumn(_proteinColumns.Count + dataGridView1.ColumnCount, protein);
_proteinColumns.Add(proteinColumn);
var accession = string.IsNullOrEmpty(protein.Accession) ? string.Empty : protein.Accession + "\n"; // Not L10N
var proteinName = protein.Name;
// Isoforms may all get the same preferredname, which is confusing to look at
if (!string.IsNullOrEmpty(protein.PreferredName))
{
int countProteinsWithSameName;
if (proteinsByPreferredNameCounts.TryGetValue(protein.PreferredName, out countProteinsWithSameName) && countProteinsWithSameName == 1)
{
proteinName = protein.PreferredName;
}
}
var gene = string.IsNullOrEmpty(protein.Gene) ? string.Empty : "\n" + protein.Gene; // Not L10N
DataGridViewCheckBoxColumn column = new DataGridViewCheckBoxColumn
{
Name = proteinColumn.Name,
HeaderText = accession + proteinName + gene,
ReadOnly = true,
ToolTipText = protein.ProteinMetadata.DisplayTextWithoutName(),
SortMode = DataGridViewColumnSortMode.Automatic,
FillWeight = 1f,
Tag = proteinColumn,
};
if (longWaitBroker.IsCanceled)
{
return(false);
}
newColumns.Add(column);
}
int actualProteinCount = dataGridView1.AddColumns(newColumns);
if (actualProteinCount < _proteinColumns.Count)
{
_proteinColumns.RemoveRange(actualProteinCount, _proteinColumns.Count - actualProteinCount);
}
for (int i = 0; i < _peptideDocNodes.Count; i++)
{
if (longWaitBroker.IsCanceled)
{
return(false);
}
longWaitBroker.ProgressValue = 100 * i / _peptideDocNodes.Count;
var peptideTag = _peptideDocNodes[i];
var proteins = _peptideProteins[i];
var row = dataGridView1.Rows[dataGridView1.Rows.Add()];
row.Tag = peptideTag;
row.Cells[PeptideIncludedColumn.Index].Value = true;
row.Cells[PeptideColumn.Index].Value = peptideTag.Item2.Peptide.Target;
foreach (var proteinColumn in _proteinColumns)
{
row.Cells[proteinColumn.Index].Value = proteins.Contains(proteinColumn.Protein);
}
}
dataGridView1.EndEdit();
if (dataGridView1.RowCount > 0)
{
// Select the first peptide to populate the other controls in the dialog.
dataGridView1.CurrentCell = dataGridView1.Rows[0].Cells[1];
}
DrawCheckBoxOnPeptideIncludedColumnHeader();
return(true);
}
private void LaunchPeptideProteinsQuery()
{
HashSet <Protein> proteinSet = new HashSet <Protein>();
using (var longWaitDlg = new LongWaitDlg
{
Text = Resources.UniquePeptidesDlg_LaunchPeptideProteinsQuery_Querying_Background_Proteome_Database,
Message = Resources.UniquePeptidesDlg_LaunchPeptideProteinsQuery_Looking_for_proteins_with_matching_peptide_sequences
})
{
try
{
longWaitDlg.PerformWork(this, 1000, QueryPeptideProteins);
}
catch (Exception x)
{
var message = TextUtil.LineSeparate(string.Format(Resources.UniquePeptidesDlg_LaunchPeptideProteinsQuery_Failed_querying_background_proteome__0__,
BackgroundProteome.Name), x.Message);
MessageDlg.ShowWithException(this, message, x);
}
}
if (_peptideProteins == null)
{
Close();
return;
}
foreach (var proteins in _peptideProteins)
{
proteinSet.UnionWith(proteins);
}
List <Protein> proteinList = new List <Protein>();
proteinList.AddRange(proteinSet);
proteinList.Sort();
foreach (var protein in proteinList)
{
ProteinColumn proteinColumn = new ProteinColumn(_proteinColumns.Count, protein);
_proteinColumns.Add(proteinColumn);
DataGridViewCheckBoxColumn column = new DataGridViewCheckBoxColumn
{
Name = proteinColumn.Name,
HeaderText = ((protein.Gene != null) ? String.Format(Resources.UniquePeptidesDlg_LaunchPeptideProteinsQuery_, protein.Name, protein.Gene) : protein.Name), // Not L10N
ReadOnly = true,
ToolTipText = protein.ProteinMetadata.DisplayTextWithoutName(),
SortMode = DataGridViewColumnSortMode.Automatic,
Tag = proteinColumn,
};
dataGridView1.Columns.Add(column);
}
for (int i = 0; i < _peptideDocNodes.Count; i++)
{
var peptide = _peptideDocNodes[i];
var proteins = _peptideProteins[i];
var row = dataGridView1.Rows[dataGridView1.Rows.Add()];
row.Tag = peptide;
row.Cells[PeptideIncludedColumn.Name].Value = true;
row.Cells[PeptideColumn.Name].Value = peptide.Peptide.Sequence;
foreach (var proteinColumn in _proteinColumns)
{
row.Cells[proteinColumn.Name].Value = proteins.Contains(proteinColumn.Protein);
}
}
dataGridView1.EndEdit();
if (dataGridView1.RowCount > 0)
{
// Select the first peptide to populate the other controls in the dialog.
dataGridView1.CurrentCell = dataGridView1.Rows[0].Cells[1];
}
DrawCheckBoxOnPeptideIncludedColumnHeader();
}
private void LaunchPeptideProteinsQuery()
{
HashSet<Protein> proteinSet = new HashSet<Protein>();
using (var longWaitDlg = new LongWaitDlg
{
Text = Resources.UniquePeptidesDlg_LaunchPeptideProteinsQuery_Querying_Background_Proteome_Database,
Message = Resources.UniquePeptidesDlg_LaunchPeptideProteinsQuery_Looking_for_proteins_with_matching_peptide_sequences
})
{
try
{
longWaitDlg.PerformWork(this, 1000, QueryPeptideProteins);
}
catch (Exception x)
{
var message = TextUtil.LineSeparate(string.Format(Resources.UniquePeptidesDlg_LaunchPeptideProteinsQuery_Failed_querying_background_proteome__0__,
BackgroundProteome.Name), x.Message);
MessageDlg.ShowWithException(this, message, x);
}
}
if (_peptideProteins == null)
{
Close();
return;
}
foreach (var proteins in _peptideProteins)
{
proteinSet.UnionWith(proteins);
}
List<Protein> proteinList = new List<Protein>();
proteinList.AddRange(proteinSet);
proteinList.Sort();
foreach (var protein in proteinList)
{
ProteinColumn proteinColumn = new ProteinColumn(_proteinColumns.Count, protein);
_proteinColumns.Add(proteinColumn);
DataGridViewCheckBoxColumn column = new DataGridViewCheckBoxColumn
{
Name = proteinColumn.Name,
HeaderText = ((protein.Gene != null) ? String.Format(Resources.UniquePeptidesDlg_LaunchPeptideProteinsQuery_, protein.Name, protein.Gene) : protein.Name), // Not L10N
ReadOnly = true,
ToolTipText = protein.ProteinMetadata.DisplayTextWithoutName(),
SortMode = DataGridViewColumnSortMode.Automatic,
Tag = proteinColumn,
};
dataGridView1.Columns.Add(column);
}
for (int i = 0; i < _peptideDocNodes.Count; i++)
{
var peptide = _peptideDocNodes[i];
var proteins = _peptideProteins[i];
var row = dataGridView1.Rows[dataGridView1.Rows.Add()];
row.Tag = peptide;
row.Cells[PeptideIncludedColumn.Name].Value = true;
row.Cells[PeptideColumn.Name].Value = peptide.Peptide.Sequence;
foreach (var proteinColumn in _proteinColumns)
{
row.Cells[proteinColumn.Name].Value = proteins.Contains(proteinColumn.Protein);
}
}
dataGridView1.EndEdit();
if (dataGridView1.RowCount > 0)
{
// Select the first peptide to populate the other controls in the dialog.
dataGridView1.CurrentCell = dataGridView1.Rows[0].Cells[1];
}
DrawCheckBoxOnPeptideIncludedColumnHeader();
}
private void LaunchPeptideProteinsQuery()
{
HashSet <Protein> proteinSet = new HashSet <Protein>();
using (var longWaitDlg = new LongWaitDlg
{
Text = Resources.UniquePeptidesDlg_LaunchPeptideProteinsQuery_Querying_Background_Proteome_Database,
Message = Resources.UniquePeptidesDlg_LaunchPeptideProteinsQuery_Looking_for_proteins_with_matching_peptide_sequences
})
{
try
{
longWaitDlg.PerformWork(this, 1000, QueryPeptideProteins);
}
catch (Exception x)
{
var message = TextUtil.LineSeparate(string.Format(Resources.UniquePeptidesDlg_LaunchPeptideProteinsQuery_Failed_querying_background_proteome__0__,
BackgroundProteome.Name), x.Message);
MessageDlg.ShowWithException(this, message, x);
}
}
if (_peptideProteins == null)
{
Close();
return;
}
foreach (var proteins in _peptideProteins)
{
proteinSet.UnionWith(proteins);
}
List <Protein> proteinList = new List <Protein>();
proteinList.AddRange(proteinSet);
proteinList.Sort();
foreach (var protein in proteinList)
{
ProteinColumn proteinColumn = new ProteinColumn(_proteinColumns.Count, protein);
_proteinColumns.Add(proteinColumn);
var accession = string.IsNullOrEmpty(protein.Accession) ? string.Empty : protein.Accession + "\n"; // Not L10N
var proteinName = protein.Name;
// Isoforms may all get the same preferredname, which is confusing to look at
if (!string.IsNullOrEmpty(protein.PreferredName) &&
!proteinList.Any(p => (!ReferenceEquals(p, protein) &&
(string.Compare(p.PreferredName, protein.PreferredName, StringComparison.OrdinalIgnoreCase) == 0))))
{
proteinName = protein.PreferredName;
}
var gene = string.IsNullOrEmpty(protein.Gene) ? string.Empty : "\n" + protein.Gene; // Not L10N
DataGridViewCheckBoxColumn column = new DataGridViewCheckBoxColumn
{
Name = proteinColumn.Name,
HeaderText = accession + proteinName + gene,
ReadOnly = true,
ToolTipText = protein.ProteinMetadata.DisplayTextWithoutName(),
SortMode = DataGridViewColumnSortMode.Automatic,
Tag = proteinColumn,
};
dataGridView1.Columns.Add(column);
}
for (int i = 0; i < _peptideDocNodes.Count; i++)
{
var peptide = _peptideDocNodes[i];
var proteins = _peptideProteins[i];
var row = dataGridView1.Rows[dataGridView1.Rows.Add()];
row.Tag = peptide;
row.Cells[PeptideIncludedColumn.Name].Value = true;
row.Cells[PeptideColumn.Name].Value = peptide.Peptide.Sequence;
foreach (var proteinColumn in _proteinColumns)
{
row.Cells[proteinColumn.Name].Value = proteins.Contains(proteinColumn.Protein);
}
}
dataGridView1.EndEdit();
if (dataGridView1.RowCount > 0)
{
// Select the first peptide to populate the other controls in the dialog.
dataGridView1.CurrentCell = dataGridView1.Rows[0].Cells[1];
}
DrawCheckBoxOnPeptideIncludedColumnHeader();
}
