public Size RenderTip(Graphics g, Size sizeMax, bool draw)
{
var table = new TableDesc();
using (var rt = new RenderTools())
{
if (_row.Peptide != null)
{
table.AddDetailRow(Helpers.PeptideToMoleculeTextMapper.Translate(GroupComparisonStrings.FoldChangeRowTipProvider_RenderTip_Peptide, _row.Peptide.IsSmallMolecule()),
_row.Peptide.ModifiedSequence == null ? _row.Peptide.ToString() : _row.Peptide.ModifiedSequence.ToString(), rt);
}
if (_row.Protein != null)
{
table.AddDetailRow(Helpers.PeptideToMoleculeTextMapper.Translate(GroupComparisonStrings.FoldChangeRowTipProvider_RenderTip_Protein, _row.Protein.IsNonProteomic()),
ProteinMetadataManager.ProteinModalDisplayText(_row.Protein.DocNode), rt);
}
table.AddDetailRow(GroupComparisonStrings.FoldChangeRowTipProvider_RenderTip_Fold_Change, _row.FoldChangeResult.FoldChange.ToString(Formats.FoldChange, CultureInfo.CurrentCulture), rt);
table.AddDetailRow(GroupComparisonStrings.FoldChange_Log2_Fold_Change_, _row.FoldChangeResult.Log2FoldChange.ToString(Formats.FoldChange, CultureInfo.CurrentCulture), rt);
table.AddDetailRow(GroupComparisonStrings.FoldChangeRowTipProvider_RenderTip_P_Value, _row.FoldChangeResult.AdjustedPValue.ToString(Formats.PValue, CultureInfo.CurrentCulture), rt);
table.AddDetailRow(GroupComparisonStrings.FoldChange__Log10_P_Value_, (-Math.Log10(_row.FoldChangeResult.AdjustedPValue)).ToString(Formats.PValue, CultureInfo.CurrentCulture), rt);
var size = table.CalcDimensions(g);
if (draw)
{
table.Draw(g);
}
return(new Size((int)size.Width + 2, (int)size.Height + 2));
}
}
/// <summary>
/// 初始化<see cref="TableDescContext"/>实例
/// </summary>
/// <param name="tableHtml">数据表HTML</param>
public TableDescContext(string tableHtml)
{
this._tableHtml = tableHtml;
//默认初始化，避免为null时操作
_table = new TableDesc();
}
public void AddLine(string description, string data)
{
if (_table == null)
{
_table = new TableDesc();
}
_table.AddDetailRow(description, data, _rt);
}
public static Size RenderTip(TransitionDocNode nodeTran, Graphics g, Size sizeMax, bool draw)
{
var table = new TableDesc();
using (RenderTools rt = new RenderTools())
{
table.AddDetailRow(Resources.TransitionTreeNode_RenderTip_Ion, nodeTran.Transition.FragmentIonName, rt);
table.AddDetailRow(Resources.TransitionTreeNode_RenderTip_Charge, nodeTran.Transition.Adduct.AdductCharge.ToString(LocalizationHelper.CurrentCulture), rt);
table.AddDetailRow(Resources.TransitionTreeNode_RenderTip_Product_m_z, string.Format(@"{0:F04}", nodeTran.Mz), rt);
int?decoyMassShift = nodeTran.Transition.DecoyMassShift;
if (decoyMassShift.HasValue)
{
table.AddDetailRow(Resources.TransitionTreeNode_RenderTip_Decoy_Mass_Shift, decoyMassShift.Value.ToString(LocalizationHelper.CurrentCulture), rt);
}
if (nodeTran.HasLoss)
{
// If there is only one loss, show its full description
var losses = nodeTran.Losses;
if (losses.Losses.Count == 1)
{
table.AddDetailRow(Resources.TransitionTreeNode_RenderTip_Loss, losses.ToStrings()[0], rt);
}
// Otherwise, just show the total mass for multiple losses
// followed by individual losses
else
{
table.AddDetailRow(Resources.TransitionTreeNode_RenderTip_Loss, string.Format(@"{0:F04}", losses.Mass), rt);
table.AddDetailRow(Resources.TransitionTreeNode_RenderTip_Losses, TextUtil.LineSeparate(losses.ToStrings()), rt);
}
}
if (nodeTran.HasLibInfo)
{
table.AddDetailRow(Resources.TransitionTreeNode_RenderTip_Library_rank, nodeTran.LibInfo.Rank.ToString(LocalizationHelper.CurrentCulture), rt);
float intensity = nodeTran.LibInfo.Intensity;
table.AddDetailRow(Resources.TransitionTreeNode_RenderTip_Library_intensity, MathEx.RoundAboveZero(intensity,
(intensity < 10 ? 1 : 0), 4).ToString(LocalizationHelper.CurrentCulture), rt);
}
if (nodeTran.Transition.IsCustom() && !string.IsNullOrEmpty(nodeTran.Transition.CustomIon.Formula))
{
table.AddDetailRow(Resources.TransitionTreeNode_RenderTip_Formula, nodeTran.Transition.CustomIon.Formula + nodeTran.Transition.Adduct.AdductFormula.ToString(LocalizationHelper.CurrentCulture), rt);
}
SizeF size = table.CalcDimensions(g);
if (draw)
{
table.Draw(g);
}
return(new Size((int)size.Width + 2, (int)size.Height + 2));
}
}
public FeatureInformations GetIdentifyFeatureInfos(MapObjects2.Point mousePosition, AxMapObjects2.AxMap mapControl, MapProject.MapStruct mapInfosCollection)
{
FeatureInformations oFeatureInfos = null;
foreach (ILayerStruct oLayerInfos in mapInfosCollection.Layers)
{
if (oLayerInfos.LayerType != (short)LayerTypeConstants.moMapLayer)
{
continue;
}
MapUtil.MapOperation oMapOper = new MapOperation();
MapObjects2.MapLayer oMapLayer = oMapOper.GetLayerByName(mapControl, oLayerInfos.AliasName) as MapObjects2.MapLayer;
if (oMapLayer.Visible == false)
{
continue;
}
Recordset oSelectedRecords = oMapLayer.SearchShape(mousePosition, SearchMethodConstants.moAreaIntersect, "");
if (oSelectedRecords.EOF)
{
continue;
}
oSelectedRecords.MoveFirst();
oFeatureInfos = new FeatureInformations();
oFeatureInfos.CurrentLayerInfos = oLayerInfos;
oFeatureInfos.Geometry = oSelectedRecords.Fields.Item("shape").Value;
TableDesc oTableDesc = oSelectedRecords.TableDesc;
oFeatureInfos.FieldsAndValuesCollection = new Dictionary <string, string>();
int iFieldsCount = oTableDesc.FieldCount;
string sFieldName = "";
string sValue = "";
for (short i = 0; i < iFieldsCount; i++)
{
sFieldName = oTableDesc.get_FieldName(i);
sValue = oSelectedRecords.Fields.Item(sFieldName).ValueAsString;
oFeatureInfos.FieldsAndValuesCollection.Add(sFieldName, sValue);
}
break;
}
return(oFeatureInfos);
}
private void RecreateTable <T>(TableDesc tableDesc, IEnumerable <T> data, Func <T, object[]> getColumnValues)
{
database.CreateTable(tableDesc.tableName, tableDesc.columns);
database.BulkCopy(tableDesc.tableName, tableDesc.columns, data.Select(delegate(T x)
{
var columnValues = getColumnValues(x);
if (columnValues.Length != tableDesc.columns.Length)
{
const string messageFormat = "invalid values, expected length [{0}], actual length [{1}]";
throw new InvalidOperationException(string.Format(messageFormat,
tableDesc.columns.Length, columnValues.Length));
}
return(columnValues);
}));
database.ExecuteNonQuery(tableDesc.createIndexesSql);
}
private static string DoMinTableName(ExpressionSqlBuilder builder, ITableSource parent, TableClause tc1)
{
TableDesc td1 = (TableDesc)tc1.Table;
var arr = parent.GetTables();
bool find = false;
bool findDubName = false;
bool findDubSchema = false;
foreach (var tc in arr)
{
if (tc == tc1)
{
find = true;
}
else
if (string.IsNullOrEmpty(tc.Alias) &&
(tc.Table is TableDesc)
)
{
TableDesc td = (TableDesc)tc.Table;
if (td.PhysicalTableName.ToLower() == td1.PhysicalTableName.ToLower())
{
findDubName = true;
if (td.PhysicalSchema.ToLower() == td1.PhysicalSchema.ToLower())
{
findDubSchema = true;
}
}
}
}
if (!find)
{
return(null);
}
if (!findDubName)
{
return(builder.EncodeTable(td1.PhysicalTableName));
}
if (!findDubSchema)
{
return(builder.EncodeTable(td1.PhysicalSchema) + "." + builder.EncodeTable(td1.PhysicalTableName));
}
throw new Exception("Not unique table " + builder.EncodeTable(td1.PhysicalSchema) + "." + builder.EncodeTable(td1.PhysicalTableName));
}
public Size RenderTip(Graphics g, Size sizeMax, bool draw)
{
var table = new TableDesc();
using (var rt = new RenderTools())
{
table.AddDetailRow(Resources.PeptideRegressionTipProvider_RenderTip_Peptide, DocNode.ModifiedSequence, rt);
table.AddDetailRow(XLabel, Point.X.ToString(CultureInfo.CurrentCulture), rt);
table.AddDetailRow(YLabel, Point.Y.ToString(CultureInfo.CurrentCulture), rt);
var size = table.CalcDimensions(g);
if (draw)
{
table.Draw(g);
}
return(new Size((int)size.Width + 2, (int)size.Height + 2));
}
}
public static Size RenderTip(PeptideDocNode nodePep,
TransitionGroupDocNode nodeGroup,
TransitionDocNode nodeTranSelected,
SrmSettings settings,
Graphics g,
Size sizeMax,
bool draw)
{
if (nodeGroup.TransitionGroup.IsCustomIon)
{
var customTable = new TableDesc();
using (RenderTools rt = new RenderTools())
{
customTable.AddDetailRow(Resources.TransitionGroupTreeNode_RenderTip_Molecule, nodeGroup.CustomIon.Name, rt);
customTable.AddDetailRow(Resources.TransitionGroupTreeNode_RenderTip_Precursor_charge,
nodeGroup.TransitionGroup.PrecursorCharge.ToString(LocalizationHelper.CurrentCulture), rt);
customTable.AddDetailRow(Resources.TransitionGroupTreeNode_RenderTip_Precursor_mz,
string.Format("{0:F04}", nodeGroup.PrecursorMz), rt); // Not L10N
if (nodeGroup.CustomIon.Formula != null)
{
customTable.AddDetailRow(Resources.TransitionTreeNode_RenderTip_Formula,
nodeGroup.CustomIon.Formula, rt);
}
SizeF size = customTable.CalcDimensions(g);
customTable.Draw(g);
return new Size((int) size.Width + 2, (int) size.Height + 2);
}
}
ExplicitMods mods = (nodePep != null ? nodePep.ExplicitMods : null);
IEnumerable<DocNode> choices = GetChoices(nodeGroup, settings, mods, true).ToArray();
HashSet<DocNode> chosen = new HashSet<DocNode>(nodeGroup.Children);
// Make sure all chosen peptides get listed
HashSet<DocNode> setChoices = new HashSet<DocNode>(choices);
setChoices.UnionWith(chosen);
choices = setChoices.ToArray();
Transition tranSelected = (nodeTranSelected != null ? nodeTranSelected.Transition : null);
IFragmentMassCalc calc = settings.GetFragmentCalc(nodeGroup.TransitionGroup.LabelType, mods);
string aa = nodeGroup.TransitionGroup.Peptide.Sequence; // We handled custom ions above, and returned
double[,] masses = calc.GetFragmentIonMasses(aa);
var filter = settings.TransitionSettings.Filter;
// Get charges and type pairs, making sure all chosen charges are included
HashSet<int> setCharges = new HashSet<int>(filter.ProductCharges.Where(charge =>
Math.Abs(charge) <= Math.Abs(nodeGroup.TransitionGroup.PrecursorCharge) &&
Math.Sign(charge) == Math.Sign(nodeGroup.TransitionGroup.PrecursorCharge)));
HashSet<IonType> setTypes = new HashSet<IonType>(filter.IonTypes);
foreach (TransitionDocNode nodTran in chosen)
{
var type = nodTran.Transition.IonType;
if (type == IonType.precursor)
continue;
setCharges.Add(nodTran.Transition.Charge);
setTypes.Add(type);
}
setTypes.Remove(IonType.precursor);
int[] charges = setCharges.ToArray();
Array.Sort(charges);
IonType[] types = Transition.GetTypePairs(setTypes);
var tableDetails = new TableDesc();
var table = new TableDesc();
using (RenderTools rt = new RenderTools())
{
string seqModified = GetModifiedSequence(nodePep, nodeGroup, settings);
if (!Equals(seqModified, nodeGroup.TransitionGroup.Peptide.Sequence))
tableDetails.AddDetailRow(Resources.TransitionGroupTreeNode_RenderTip_Modified, seqModified, rt);
var precursorCharge = nodeGroup.TransitionGroup.PrecursorCharge;
var precursorMz = nodeGroup.PrecursorMz;
tableDetails.AddDetailRow(Resources.TransitionGroupTreeNode_RenderTip_Precursor_charge,
precursorCharge.ToString(LocalizationHelper.CurrentCulture), rt);
tableDetails.AddDetailRow(Resources.TransitionGroupTreeNode_RenderTip_Precursor_mz,
string.Format("{0:F04}", precursorMz), rt); // Not L10N
tableDetails.AddDetailRow(Resources.TransitionGroupTreeNode_RenderTip_Precursor_mh,
string.Format("{0:F04}", nodeGroup.GetPrecursorIonMass()), // Not L10N
rt);
int? decoyMassShift = nodeGroup.TransitionGroup.DecoyMassShift;
if (decoyMassShift.HasValue)
{
tableDetails.AddDetailRow(Resources.TransitionGroupTreeNode_RenderTip_Decoy_Mass_Shift,
decoyMassShift.Value.ToString(LocalizationHelper.CurrentCulture), rt);
}
if (nodeGroup.HasLibInfo)
{
foreach (KeyValuePair<PeptideRankId, string> pair in nodeGroup.LibInfo.RankValues)
tableDetails.AddDetailRow(pair.Key.Label, pair.Value, rt);
}
if (charges.Length > 0 && types.Length > 0)
{
var headers = new RowDesc
{
CreateHead("#", rt), // Not L10N
CreateHead("AA", rt), // Not L10N
CreateHead("#", rt) // Not L10N
};
foreach (int charge in charges)
{
string plusSub = Transition.GetChargeIndicator(charge);
foreach (IonType type in types)
{
CellDesc cell = CreateHead(type.ToString().ToLower() + plusSub, rt);
if (Transition.IsNTerminal(type))
headers.Insert(0, cell);
else
headers.Add(cell);
}
}
table.Add(headers);
int len = aa.Length;
for (int i = 0; i < len; i++)
{
CellDesc cellAA = CreateRowLabel(aa.Substring(i, 1), rt);
cellAA.Align = StringAlignment.Center;
var row = new RowDesc
{
CreateRowLabel(i == len - 1 ? string.Empty : (i + 1).ToString(CultureInfo.InvariantCulture), rt),
cellAA,
CreateRowLabel(i == 0 ? string.Empty : (len - i).ToString(CultureInfo.InvariantCulture), rt)
};
foreach (int charge in charges)
{
foreach (IonType type in types)
{
CellDesc cell;
if (Transition.IsNTerminal(type))
{
if (i == len - 1)
cell = CreateData(string.Empty, rt);
else
{
double massH = masses[(int)type, i];
cell = CreateIon(type, i + 1, massH, charge, choices, chosen, tranSelected, rt);
}
row.Insert(0, cell);
}
else
{
if (i == 0)
cell = CreateData(string.Empty, rt);
else
{
double massH = masses[(int)type, i - 1];
cell = CreateIon(type, len - i, massH, charge, choices, chosen, tranSelected, rt);
}
row.Add(cell);
}
}
}
table.Add(row);
}
}
SizeF sizeDetails = tableDetails.CalcDimensions(g);
sizeDetails.Height += TableDesc.TABLE_SPACING; // Spacing between details and fragments
SizeF size = table.CalcDimensions(g);
if (draw)
{
tableDetails.Draw(g);
g.TranslateTransform(0, sizeDetails.Height);
table.Draw(g);
g.TranslateTransform(0, -sizeDetails.Height);
}
int width = (int) Math.Round(Math.Max(sizeDetails.Width, size.Width));
int height = (int) Math.Round(sizeDetails.Height + size.Height);
return new Size(width + 2, height + 2);
}
}
public override Size RenderTip(Graphics g, Size sizeMax, bool draw)
{
var sizeInitial = base.RenderTip(g, sizeMax, draw);
if (ShowAnnotationTipOnly)
{
return(sizeInitial);
}
g.TranslateTransform(0, sizeInitial.Height);
FastaSequence fastaSeq = DocNode.Id as FastaSequence;
var tableDetails = new TableDesc();
using (RenderTools rt = new RenderTools())
{
SizeF sizeX80 = g.MeasureString(X80, rt.FontNormal);
float widthLine = sizeX80.Width;
float heightLine = sizeX80.Height;
float heightMax = sizeMax.Height;
tableDetails.AddDetailRow(Resources.PeptideGroupTreeNode_RenderTip_Name, DocNode.Name, rt);
// If current name isn't the original, show that.
if (DocNode.PeptideGroup.Name != null && !Equals(DocNode.Name, DocNode.PeptideGroup.Name))
{
tableDetails.AddDetailRow(Resources.PeptideGroupTreeNode_RenderTip_Original_Name, DocNode.OriginalName, rt);
}
if (!String.IsNullOrEmpty(DocNode.ProteinMetadata.Accession))
{
tableDetails.AddDetailRow(Resources.PeptideGroupTreeNode_RenderTip_Accession, DocNode.ProteinMetadata.Accession, rt);
}
if (!String.IsNullOrEmpty(DocNode.ProteinMetadata.PreferredName))
{
tableDetails.AddDetailRow(Resources.PeptideGroupTreeNode_RenderTip_Preferred_Name, DocNode.ProteinMetadata.PreferredName, rt);
}
if (!String.IsNullOrEmpty(DocNode.ProteinMetadata.Gene))
{
tableDetails.AddDetailRow(Resources.PeptideGroupTreeNode_RenderTip_Gene, DocNode.ProteinMetadata.Gene, rt);
}
if (!String.IsNullOrEmpty(DocNode.ProteinMetadata.Species))
{
tableDetails.AddDetailRow(Resources.PeptideGroupTreeNode_RenderTip_Species, DocNode.ProteinMetadata.Species, rt);
}
if (!String.IsNullOrEmpty(DocNode.ProteinMetadata.DisplaySearchHistory()))
{
tableDetails.AddDetailRow(Resources.PeptideGroupTreeNode_RenderTip_Searched, DocNode.ProteinMetadata.DisplaySearchHistory(), rt);
}
if (!String.IsNullOrEmpty(DocNode.ProteinMetadata.Description))
{
tableDetails.AddDetailRowLineWrap(g, Resources.PeptideGroupTreeNode_RenderTip_Description, DocNode.ProteinMetadata.Description, rt);
}
if (DocNode.PeptideGroup.Description != null && !Equals(DocNode.Description, DocNode.PeptideGroup.Description))
{
tableDetails.AddDetailRow(Resources.PeptideGroupTreeNode_RenderTip_Original_Description, DocNode.OriginalDescription, rt);
}
SizeF sizeDetails = tableDetails.CalcDimensions(g);
sizeDetails.Height += TableDesc.TABLE_SPACING; // Spacing between details and fragments
float heightTotal = sizeDetails.Height;
widthLine = Math.Max(widthLine, sizeDetails.Width);
if (draw)
{
tableDetails.Draw(g);
}
if (fastaSeq != null)
{
IList <DocNode> peptidesChoices = GetChoices(true).ToArray();
HashSet <DocNode> peptidesChosen = new HashSet <DocNode>(Chosen);
// Make sure all chosen peptides get listed
HashSet <DocNode> setChoices = new HashSet <DocNode>(peptidesChoices);
setChoices.UnionWith(peptidesChosen);
var arrayChoices = setChoices.ToArray();
Array.Sort(arrayChoices, (choice1, choice2) =>
PeptideFromChoice(choice1).Order - PeptideFromChoice(choice2).Order);
peptidesChoices = arrayChoices;
// Get the selected peptide, if there is one
PeptideTreeNode nodePepTree = SequenceTree.GetNodeOfType <PeptideTreeNode>();
Peptide peptideSelected = (nodePepTree != null ? nodePepTree.DocNode.Peptide : null);
int i = 0;
string aa = fastaSeq.Sequence;
const bool peptideList = false;
while (i < aa.Length)
{
// If this is not the last possible line, just render it.
if (heightTotal + heightLine * 2 <= heightMax)
{
i = RenderAALine(aa, peptideList, i, false, draw,
peptidesChoices, peptidesChosen, peptideSelected,
g, rt, heightTotal, widthLine);
heightTotal += heightLine;
}
// If not drawing, then this is the last possible line, and
// it will have content.
else if (!draw)
{
heightTotal += heightLine;
break;
}
// Otherwise, measure first, and then re-render, with an elipsis
// if the full sequence cannot be shown.
else
{
RenderAALine(aa, peptideList, i, false, false,
peptidesChoices, peptidesChosen, peptideSelected,
g, rt, heightTotal, widthLine);
RenderAALine(aa, peptideList, i, i < aa.Length, true,
peptidesChoices, peptidesChosen, peptideSelected,
g, rt, heightTotal, widthLine);
heightTotal += heightLine;
break;
}
}
}
return(TipSize(Math.Max(widthLine, sizeInitial.Width), heightTotal + sizeInitial.Height));
}
}
public static Size RenderTip(TransitionDocNode nodeTran, Graphics g, Size sizeMax, bool draw)
{
var table = new TableDesc();
using (RenderTools rt = new RenderTools())
{
table.AddDetailRow(Resources.TransitionTreeNode_RenderTip_Ion, nodeTran.Transition.FragmentIonName, rt);
table.AddDetailRow(Resources.TransitionTreeNode_RenderTip_Charge, nodeTran.Transition.Charge.ToString(LocalizationHelper.CurrentCulture), rt);
table.AddDetailRow(Resources.TransitionTreeNode_RenderTip_Product_m_z, string.Format("{0:F04}", nodeTran.Mz), rt); // Not L10N
int? decoyMassShift = nodeTran.Transition.DecoyMassShift;
if (decoyMassShift.HasValue)
table.AddDetailRow(Resources.TransitionTreeNode_RenderTip_Decoy_Mass_Shift, decoyMassShift.Value.ToString(LocalizationHelper.CurrentCulture), rt);
if (nodeTran.HasLoss)
{
// If there is only one loss, show its full description
var losses = nodeTran.Losses;
if (losses.Losses.Count == 1)
table.AddDetailRow(Resources.TransitionTreeNode_RenderTip_Loss, losses.ToStrings()[0], rt);
// Otherwise, just show the total mass for multiple losses
// followed by individual losses
else
{
table.AddDetailRow(Resources.TransitionTreeNode_RenderTip_Loss, string.Format("{0:F04}", losses.Mass), rt); // Not L10N
table.AddDetailRow(Resources.TransitionTreeNode_RenderTip_Losses, TextUtil.LineSeparate(losses.ToStrings()), rt);
}
}
if (nodeTran.HasLibInfo)
{
table.AddDetailRow(Resources.TransitionTreeNode_RenderTip_Library_rank, nodeTran.LibInfo.Rank.ToString(LocalizationHelper.CurrentCulture), rt);
float intensity = nodeTran.LibInfo.Intensity;
table.AddDetailRow(Resources.TransitionTreeNode_RenderTip_Library_intensity, MathEx.RoundAboveZero(intensity,
(intensity < 10 ? 1 : 0), 4).ToString(LocalizationHelper.CurrentCulture), rt);
}
if (nodeTran.Transition.IsCustom() && !string.IsNullOrEmpty(nodeTran.Transition.CustomIon.Formula))
{
table.AddDetailRow(Resources.TransitionTreeNode_RenderTip_Formula, nodeTran.Transition.CustomIon.Formula, rt);
}
SizeF size = table.CalcDimensions(g);
if (draw)
table.Draw(g);
return new Size((int)size.Width + 2, (int)size.Height + 2);
}
}
public override Size RenderTip(Graphics g, Size sizeMax, bool draw)
{
var sizeInitial = base.RenderTip(g, sizeMax, draw);
if (ShowAnnotationTipOnly)
return sizeInitial;
g.TranslateTransform(0, sizeInitial.Height);
FastaSequence fastaSeq = DocNode.Id as FastaSequence;
var tableDetails = new TableDesc();
using (RenderTools rt = new RenderTools())
{
SizeF sizeX80 = g.MeasureString(X80, rt.FontNormal);
float widthLine = sizeX80.Width;
float heightLine = sizeX80.Height;
float heightMax = sizeMax.Height;
tableDetails.AddDetailRow(Resources.PeptideGroupTreeNode_RenderTip_Name, DocNode.Name, rt);
// If current name isn't the original, show that.
if (DocNode.PeptideGroup.Name != null && !Equals(DocNode.Name, DocNode.PeptideGroup.Name))
tableDetails.AddDetailRow(Resources.PeptideGroupTreeNode_RenderTip_Original_Name, DocNode.OriginalName, rt);
if (!String.IsNullOrEmpty(DocNode.ProteinMetadata.Accession))
tableDetails.AddDetailRow(Resources.PeptideGroupTreeNode_RenderTip_Accession, DocNode.ProteinMetadata.Accession, rt);
if (!String.IsNullOrEmpty(DocNode.ProteinMetadata.PreferredName))
tableDetails.AddDetailRow(Resources.PeptideGroupTreeNode_RenderTip_Preferred_Name, DocNode.ProteinMetadata.PreferredName, rt);
if (!String.IsNullOrEmpty(DocNode.ProteinMetadata.Gene))
tableDetails.AddDetailRow(Resources.PeptideGroupTreeNode_RenderTip_Gene, DocNode.ProteinMetadata.Gene, rt);
if (!String.IsNullOrEmpty(DocNode.ProteinMetadata.Species))
tableDetails.AddDetailRow(Resources.PeptideGroupTreeNode_RenderTip_Species, DocNode.ProteinMetadata.Species, rt);
if (!String.IsNullOrEmpty(DocNode.ProteinMetadata.DisplaySearchHistory()))
tableDetails.AddDetailRow(Resources.PeptideGroupTreeNode_RenderTip_Searched, DocNode.ProteinMetadata.DisplaySearchHistory(), rt);
if (!String.IsNullOrEmpty(DocNode.ProteinMetadata.Description))
tableDetails.AddDetailRowLineWrap(g,Resources.PeptideGroupTreeNode_RenderTip_Description, DocNode.ProteinMetadata.Description, rt);
if (DocNode.PeptideGroup.Description != null && !Equals(DocNode.Description, DocNode.PeptideGroup.Description))
tableDetails.AddDetailRow(Resources.PeptideGroupTreeNode_RenderTip_Original_Description, DocNode.OriginalDescription, rt);
SizeF sizeDetails = tableDetails.CalcDimensions(g);
sizeDetails.Height += TableDesc.TABLE_SPACING; // Spacing between details and fragments
float heightTotal = sizeDetails.Height;
widthLine = Math.Max(widthLine, sizeDetails.Width);
if (draw)
{
tableDetails.Draw(g);
}
if (fastaSeq != null)
{
IList<DocNode> peptidesChoices = GetChoices(true).ToArray();
HashSet<DocNode> peptidesChosen = new HashSet<DocNode>(Chosen);
// Make sure all chosen peptides get listed
HashSet<DocNode> setChoices = new HashSet<DocNode>(peptidesChoices);
setChoices.UnionWith(peptidesChosen);
var arrayChoices = setChoices.ToArray();
Array.Sort(arrayChoices, (choice1, choice2) =>
PeptideFromChoice(choice1).Order - PeptideFromChoice(choice2).Order);
peptidesChoices = arrayChoices;
// Get the selected peptide, if there is one
PeptideTreeNode nodePepTree = SequenceTree.GetNodeOfType<PeptideTreeNode>();
Peptide peptideSelected = (nodePepTree != null ? nodePepTree.DocNode.Peptide : null);
int i = 0;
string aa = fastaSeq.Sequence;
const bool peptideList = false;
while (i < aa.Length)
{
// If this is not the last possible line, just render it.
if (heightTotal + heightLine * 2 <= heightMax)
{
i = RenderAALine(aa, peptideList, i, false, draw,
peptidesChoices, peptidesChosen, peptideSelected,
g, rt, heightTotal, widthLine);
heightTotal += heightLine;
}
// If not drawing, then this is the last possible line, and
// it will have content.
else if (!draw)
{
heightTotal += heightLine;
break;
}
// Otherwise, measure first, and then re-render, with an elipsis
// if the full sequence cannot be shown.
else
{
RenderAALine(aa, peptideList, i, false, false,
peptidesChoices, peptidesChosen, peptideSelected,
g, rt, heightTotal, widthLine);
RenderAALine(aa, peptideList, i, i < aa.Length, true,
peptidesChoices, peptidesChosen, peptideSelected,
g, rt, heightTotal, widthLine);
heightTotal += heightLine;
break;
}
}
}
return TipSize(Math.Max(widthLine, sizeInitial.Width), heightTotal + sizeInitial.Height);
}
}
public override ITableDesc GetTableByName(string[] names, bool useCache)
{
if (useCache)
{
var t = Get(names);
if (t != null)
{
return(t);
}
}
string tn;
string sh;
if (names.Length == 2)
{
sh = names[0];
tn = names[1];
}
else
if (names.Length == 1)
{
sh = DefaultSchema();
tn = names[0];
}
else
{
throw new Exception("Incorrect table name");
}
using (var con = GetConnection())
{
con.Open();
string sql = @"SELECT EXISTS (
SELECT 1
FROM pg_catalog.pg_class c
JOIN pg_catalog.pg_namespace n ON n.oid = c.relnamespace
WHERE n.nspname = @schema
AND c.relname = @name
);";
DbCommand cmd = con.CreateCommand();
cmd.CommandText = sql;
ParserDbUtils.AddParam(cmd, "@schema", sh);
ParserDbUtils.AddParam(cmd, "@name", tn);
using (var reader = cmd.ExecuteReader())
{
if (!reader.Read())
{
throw new Exception("Table " + string.Join(".", names) + " is not found");
}
}
}
using (var con = GetConnection())
{
con.Open();
string sql = @"SELECT
attname AS column_name
, atttypid::regtype AS data_type
-- more attributes?
FROM pg_attribute
WHERE attrelid = @schemaTable::regclass -- table name, optionally schema-qualified
AND attnum > 0
AND NOT attisdropped
ORDER BY attnum";
DbCommand cmd = con.CreateCommand();
cmd.CommandText = sql;
string st = "";
if (!string.IsNullOrEmpty(sh))
{
st += "\"" + sh + "\"";
}
if (!string.IsNullOrEmpty(tn))
{
if (st != "")
{
st += ".";
}
st += "\"" + tn + "\"";
}
ParserDbUtils.AddParam(cmd, "@schemaTable", st);
TableDesc td = new TableDesc();
td.PhysicalTableName = tn;
td.LogicalTableName = tn;
td.PhysicalSchema = sh;
td.LogicalSchema = sh;
//td.DbDriver = Driver;
td.TableColumns = new List <Column>();
using (var reader = cmd.ExecuteReader())
{
while (reader.Read())
{
Column ci = new Column(
reader.GetString(reader.GetOrdinal("column_name")),
ColumnSqlTypeToSimpleType(reader.GetString(reader.GetOrdinal("data_type")))
);
td.TableColumns.Add(ci);
}
}
Set(names, td);
return(td);
}
}
public static Size RenderTip(PeptideDocNode nodePep,
TransitionGroupDocNode nodeGroup,
TransitionDocNode nodeTranSelected,
SrmSettings settings,
Graphics g,
Size sizeMax,
bool draw)
{
if (nodeGroup.TransitionGroup.IsCustomIon) // TODO(bspratt) this seems to leave out a lot of detail
{
var customTable = new TableDesc();
using (RenderTools rt = new RenderTools())
{
customTable.AddDetailRow(Resources.TransitionGroupTreeNode_RenderTip_Molecule, nodeGroup.CustomMolecule.Name, rt);
customTable.AddDetailRow(Resources.TransitionGroupTreeNode_RenderTip_Precursor_charge,
nodeGroup.TransitionGroup.PrecursorAdduct.AdductCharge.ToString(LocalizationHelper.CurrentCulture), rt);
customTable.AddDetailRow(Resources.TransitionGroupTreeNode_RenderTip_Precursor_mz,
string.Format(@"{0:F04}", nodeGroup.PrecursorMz), rt);
if (nodeGroup.CustomMolecule.Formula != null)
{
customTable.AddDetailRow(Resources.TransitionTreeNode_RenderTip_Formula,
nodeGroup.CustomMolecule.Formula + nodeGroup.TransitionGroup.PrecursorAdduct.AdductFormula.ToString(LocalizationHelper.CurrentCulture), rt);
}
SizeF size = customTable.CalcDimensions(g);
customTable.Draw(g);
return(new Size((int)size.Width + 2, (int)size.Height + 2));
}
}
ExplicitMods mods = (nodePep != null ? nodePep.ExplicitMods : null);
IEnumerable <DocNode> choices = nodeGroup.GetPrecursorChoices(settings, mods, true).ToArray();
HashSet <DocNode> chosen = new HashSet <DocNode>(nodeGroup.Children);
// Make sure all chosen peptides get listed
HashSet <DocNode> setChoices = new HashSet <DocNode>(choices);
setChoices.UnionWith(chosen);
choices = setChoices.ToArray();
Transition tranSelected = (nodeTranSelected != null ? nodeTranSelected.Transition : null);
IFragmentMassCalc calc = settings.GetFragmentCalc(nodeGroup.TransitionGroup.LabelType, mods);
var aa = nodeGroup.TransitionGroup.Peptide.Target.Sequence; // We handled custom ions above, and returned
var masses = calc.GetFragmentIonMasses(nodeGroup.TransitionGroup.Peptide.Target);
var filter = settings.TransitionSettings.Filter;
// Get charges and type pairs, making sure all chosen charges are included
var setCharges = new HashSet <Adduct>(filter.PeptideProductCharges.Where(charge =>
Math.Abs(charge.AdductCharge) <= Math.Abs(nodeGroup.TransitionGroup.PrecursorCharge) &&
Math.Sign(charge.AdductCharge) == Math.Sign(nodeGroup.TransitionGroup.PrecursorCharge)));
HashSet <IonType> setTypes = new HashSet <IonType>(filter.PeptideIonTypes);
foreach (TransitionDocNode nodTran in chosen)
{
var type = nodTran.Transition.IonType;
if (!Transition.IsPeptideFragment(type))
{
continue;
}
setCharges.Add(nodTran.Transition.Adduct);
setTypes.Add(type);
}
setTypes.RemoveWhere(t => !Transition.IsPeptideFragment(t));
var charges = setCharges.Where(c => c.IsProteomic).ToArray();
Array.Sort(charges);
IonType[] types = Transition.GetTypePairs(setTypes);
var tableDetails = new TableDesc();
var table = new TableDesc();
using (RenderTools rt = new RenderTools())
{
var seqModified = GetModifiedSequence(nodePep, nodeGroup, settings);
if (!Equals(seqModified, nodeGroup.TransitionGroup.Peptide.Target))
{
tableDetails.AddDetailRow(Resources.TransitionGroupTreeNode_RenderTip_Modified, seqModified.Sequence, rt);
}
var precursorCharge = nodeGroup.TransitionGroup.PrecursorAdduct;
var precursorMz = nodeGroup.PrecursorMz;
tableDetails.AddDetailRow(Resources.TransitionGroupTreeNode_RenderTip_Precursor_charge,
precursorCharge.AdductCharge.ToString(LocalizationHelper.CurrentCulture), rt);
tableDetails.AddDetailRow(Resources.TransitionGroupTreeNode_RenderTip_Precursor_mz,
string.Format(@"{0:F04}", precursorMz), rt);
tableDetails.AddDetailRow(Resources.TransitionGroupTreeNode_RenderTip_Precursor_mh,
string.Format(@"{0:F04}", nodeGroup.GetPrecursorIonMass()),
rt);
int?decoyMassShift = nodeGroup.TransitionGroup.DecoyMassShift;
if (decoyMassShift.HasValue)
{
tableDetails.AddDetailRow(Resources.TransitionGroupTreeNode_RenderTip_Decoy_Mass_Shift,
decoyMassShift.Value.ToString(LocalizationHelper.CurrentCulture), rt);
}
if (nodeGroup.HasLibInfo)
{
foreach (KeyValuePair <PeptideRankId, string> pair in nodeGroup.LibInfo.RankValues)
{
tableDetails.AddDetailRow(pair.Key.Label, pair.Value, rt);
}
}
if (charges.Length > 0 && types.Length > 0)
{
var headers = new RowDesc
{
CreateHead(@"#", rt),
CreateHead(@"AA", rt),
CreateHead(@"#", rt)
};
foreach (var charge in charges)
{
string plusSub = Transition.GetChargeIndicator(charge);
foreach (IonType type in types)
{
CellDesc cell = CreateHead(type.ToString().ToLower() + plusSub, rt);
if (Transition.IsNTerminal(type))
{
headers.Insert(0, cell);
}
else
{
headers.Add(cell);
}
}
}
table.Add(headers);
int len = aa.Length;
for (int i = 0; i < len; i++)
{
CellDesc cellAA = CreateRowLabel(aa.Substring(i, 1), rt);
cellAA.Align = StringAlignment.Center;
var row = new RowDesc
{
CreateRowLabel(i == len - 1 ? string.Empty : (i + 1).ToString(CultureInfo.InvariantCulture), rt),
cellAA,
CreateRowLabel(i == 0 ? string.Empty : (len - i).ToString(CultureInfo.InvariantCulture), rt)
};
foreach (var charge in charges)
{
foreach (IonType type in types)
{
CellDesc cell;
if (Transition.IsNTerminal(type))
{
if (i == len - 1)
{
cell = CreateData(string.Empty, rt);
}
else
{
var massH = masses[type, i];
cell = CreateIon(type, i + 1, massH, charge, choices, chosen, tranSelected, rt);
}
row.Insert(0, cell);
}
else
{
if (i == 0)
{
cell = CreateData(string.Empty, rt);
}
else
{
var massH = masses[type, i - 1];
cell = CreateIon(type, len - i, massH, charge, choices, chosen, tranSelected, rt);
}
row.Add(cell);
}
}
}
table.Add(row);
}
}
SizeF sizeDetails = tableDetails.CalcDimensions(g);
sizeDetails.Height += TableDesc.TABLE_SPACING; // Spacing between details and fragments
SizeF size = table.CalcDimensions(g);
if (draw)
{
tableDetails.Draw(g);
g.TranslateTransform(0, sizeDetails.Height);
table.Draw(g);
g.TranslateTransform(0, -sizeDetails.Height);
}
int width = (int)Math.Round(Math.Max(sizeDetails.Width, size.Width));
int height = (int)Math.Round(sizeDetails.Height + size.Height);
return(new Size(width + 2, height + 2));
}
}
public static Size RenderTip(PeptideDocNode nodePep,
TransitionDocNode nodeTranSelected,
SrmSettings settings,
Graphics g,
Size sizeMax,
bool draw)
{
var table = new TableDesc();
using (RenderTools rt = new RenderTools())
{
Peptide peptide = nodePep.Peptide;
SizeF size;
if (peptide.IsCustomIon)
{
table.AddDetailRow(Resources.TransitionGroupTreeNode_RenderTip_Molecule, nodePep.CustomIon.Name, rt);
table.AddDetailRow(Resources.TransitionTreeNode_RenderTip_Formula, nodePep.CustomIon.Formula, rt);
table.AddDetailRow(Resources.PeptideTreeNode_RenderTip_Neutral_Mass,
nodePep.CustomIon.GetMass(settings.TransitionSettings.Prediction.PrecursorMassType).ToString(LocalizationHelper.CurrentCulture), rt);
size = table.CalcDimensions(g);
table.Draw(g);
return new Size((int)Math.Round(size.Width + 2), (int)Math.Round(size.Height + 2));
}
if (nodePep.Children.Count > 1)
{
foreach (var typedModSequence in GetTypedModifiedSequences(nodePep, settings))
table.AddDetailRow(typedModSequence.Key.Title, typedModSequence.Value, rt);
}
if (peptide.Begin.HasValue)
{
// Add a spacing row, if anything was added
if (table.Count > 0)
table.AddDetailRow(" ", " ", rt); // Not L10N
table.AddDetailRow(Resources.PeptideTreeNode_RenderTip_Previous, peptide.PrevAA.ToString(CultureInfo.InvariantCulture), rt);
table.AddDetailRow(Resources.PeptideTreeNode_RenderTip_First, peptide.Begin.Value.ToString(LocalizationHelper.CurrentCulture), rt);
table.AddDetailRow(Resources.PeptideTreeNode_RenderTip_Last, ((peptide.End ?? 1) - 1).ToString(LocalizationHelper.CurrentCulture), rt);
table.AddDetailRow(Resources.PeptideTreeNode_RenderTip_Next, peptide.NextAA.ToString(CultureInfo.InvariantCulture), rt);
}
if (nodePep.Rank.HasValue)
table.AddDetailRow(Resources.PeptideTreeNode_RenderTip_Rank, nodePep.Rank.Value.ToString(LocalizationHelper.CurrentCulture), rt);
size = table.CalcDimensions(g);
if (draw)
table.Draw(g);
// Render group tip, if there is only one, and this node is collapsed
if (nodePep.Children.Count == 1)
{
var nodeGroup = (TransitionGroupDocNode)nodePep.Children[0];
if (size.Height > 0)
size.Height += TableDesc.TABLE_SPACING;
if (draw)
g.TranslateTransform(0, size.Height);
Size sizeMaxGroup = new Size(sizeMax.Width, sizeMax.Height - (int)size.Height);
SizeF sizeGroup = TransitionGroupTreeNode.RenderTip(nodePep, nodeGroup,
nodeTranSelected, settings, g, sizeMaxGroup, draw);
if (draw)
g.TranslateTransform(0, -size.Height);
size.Width = Math.Max(size.Width, sizeGroup.Width);
size.Height += sizeGroup.Height;
}
return new Size((int)Math.Round(size.Width + 2), (int)Math.Round(size.Height + 2));
}
}
/// <summary>
/// 实始化<see cref="MappingResolveContext"/>实例
/// </summary>
/// <param name="template">Mapping类文件模板</param>
/// <param name="table">数据表</param>
public MappingResolveContext(string template, TableDesc table)
{
this._output = template;
this._table = table;
}
public static Size RenderTip(PeptideDocNode nodePep,
TransitionDocNode nodeTranSelected,
SrmSettings settings,
Graphics g,
Size sizeMax,
bool draw)
{
var table = new TableDesc();
using (RenderTools rt = new RenderTools())
{
Peptide peptide = nodePep.Peptide;
SizeF size;
if (peptide.IsCustomMolecule)
{
table.AddDetailRow(Resources.TransitionGroupTreeNode_RenderTip_Molecule, nodePep.CustomMolecule.Name, rt);
table.AddDetailRow(Resources.TransitionTreeNode_RenderTip_Formula, nodePep.CustomMolecule.Formula, rt);
table.AddDetailRow(Resources.PeptideTreeNode_RenderTip_Neutral_Mass,
nodePep.CustomMolecule.GetMass(settings.TransitionSettings.Prediction.PrecursorMassType).ToString(LocalizationHelper.CurrentCulture), rt);
foreach (var id in nodePep.CustomMolecule.AccessionNumbers.AccessionNumbers)
{
table.AddDetailRow(id.Key, id.Value, rt); // Show InChiKey etc as available
}
size = table.CalcDimensions(g);
table.Draw(g);
return(new Size((int)Math.Round(size.Width + 2), (int)Math.Round(size.Height + 2)));
}
if (peptide.IsDecoy)
{
string sourceText = nodePep.SourceTextId
.Replace(@".0]", @"]")
.Replace(@".", LocalizationHelper.CurrentCulture.NumberFormat.NumberDecimalSeparator);
table.AddDetailRow(Resources.PeptideTreeNode_RenderTip_Source, sourceText, rt);
}
if (nodePep.Children.Count > 1)
{
foreach (var typedModSequence in GetTypedModifiedSequences(nodePep, settings))
{
table.AddDetailRow(typedModSequence.Key.Title, typedModSequence.Value, rt);
}
}
if (peptide.Begin.HasValue)
{
// Add a spacing row, if anything was added
if (table.Count > 0)
{
table.AddDetailRow(@" ", @" ", rt);
}
table.AddDetailRow(Resources.PeptideTreeNode_RenderTip_Previous, peptide.PrevAA.ToString(CultureInfo.InvariantCulture), rt);
table.AddDetailRow(Resources.PeptideTreeNode_RenderTip_First, peptide.Begin.Value.ToString(LocalizationHelper.CurrentCulture), rt);
table.AddDetailRow(Resources.PeptideTreeNode_RenderTip_Last, ((peptide.End ?? 1) - 1).ToString(LocalizationHelper.CurrentCulture), rt);
table.AddDetailRow(Resources.PeptideTreeNode_RenderTip_Next, peptide.NextAA.ToString(CultureInfo.InvariantCulture), rt);
}
if (nodePep.Rank.HasValue)
{
table.AddDetailRow(Resources.PeptideTreeNode_RenderTip_Rank, nodePep.Rank.Value.ToString(LocalizationHelper.CurrentCulture), rt);
}
size = table.CalcDimensions(g);
if (draw)
{
table.Draw(g);
}
// Render group tip, if there is only one, and this node is collapsed
if (nodePep.Children.Count == 1)
{
var nodeGroup = (TransitionGroupDocNode)nodePep.Children[0];
if (size.Height > 0)
{
size.Height += TableDesc.TABLE_SPACING;
}
if (draw)
{
g.TranslateTransform(0, size.Height);
}
Size sizeMaxGroup = new Size(sizeMax.Width, sizeMax.Height - (int)size.Height);
SizeF sizeGroup = TransitionGroupTreeNode.RenderTip(nodePep, nodeGroup,
nodeTranSelected, settings, g, sizeMaxGroup, draw);
if (draw)
{
g.TranslateTransform(0, -size.Height);
}
size.Width = Math.Max(size.Width, sizeGroup.Width);
size.Height += sizeGroup.Height;
}
return(new Size((int)Math.Round(size.Width + 2), (int)Math.Round(size.Height + 2)));
}
}
/// <summary>
/// 初始化<see cref="EntityClassResolverContext"/>实例
/// </summary>
/// <param name="entityTemplate">实体类文件模板</param>
/// <param name="tableDesc">数据表描述对象</param>
public EntityClassResolveContext(string entityTemplate, TableDesc tableDesc)
{
this._outputEntityClassContent = entityTemplate;
this._tableDesc = tableDesc;
}
public override ITableDesc GetTableByName(string[] names, bool useCache)
{
if (useCache)
{
var t = Get(names);
if (t != null)
{
return(t);
}
}
string tn;
string sh;
if (names.Length == 2)
{
sh = names[0];
tn = names[1];
}
else
if (names.Length == 1)
{
sh = DefaultSchema();
tn = names[0];
}
else
{
throw new Exception("Incorrect table name");
}
using (var con = GetConnection())
{
con.Open();
string sql = "select TABLE_SCHEMA, TABLE_NAME from INFORMATION_SCHEMA.TABLES where TABLE_SCHEMA = @schema and TABLE_NAME = @name";
DbCommand cmd = con.CreateCommand();
cmd.CommandText = sql;
ParserDbUtils.AddParam(cmd, "@schema", sh);
ParserDbUtils.AddParam(cmd, "@name", tn);
using (var reader = cmd.ExecuteReader())
{
if (!reader.Read())
{
throw new Exception("Table " + string.Join(".", names) + " is not found");
}
}
}
using (var con = GetConnection())
{
con.Open();
string sql = @"select
COLUMN_NAME,
DATA_TYPE
from INFORMATION_SCHEMA.COLUMNS where TABLE_SCHEMA = @schema and TABLE_NAME = @name";
DbCommand cmd = con.CreateCommand();
cmd.CommandText = sql;
ParserDbUtils.AddParam(cmd, "@schema", sh);
ParserDbUtils.AddParam(cmd, "@name", tn);
TableDesc td = new TableDesc();
td.PhysicalTableName = tn;
td.LogicalTableName = tn;
td.PhysicalSchema = sh;
td.LogicalSchema = sh;
td.TableColumns = new List <Column>();
using (var reader = cmd.ExecuteReader())
{
while (reader.Read())
{
Column ci = new Column(
reader.GetString(reader.GetOrdinal("COLUMN_NAME")),
ColumnSqlTypeToSimpleType(reader.GetString(reader.GetOrdinal("DATA_TYPE"))));
td.TableColumns.Add(ci);
}
}
Set(names, td);
return(td);
}
}
