public RefineDlg(SrmDocument document)
{
_document = document;
_settings = document.Settings;
InitializeComponent();
Icon = Resources.Skyline;
// Fill label type combo box
comboRefineLabelType.Items.Add(string.Empty);
comboRefineLabelType.Items.Add(IsotopeLabelType.LIGHT_NAME);
foreach (var typedMods in _settings.PeptideSettings.Modifications.GetHeavyModifications())
comboRefineLabelType.Items.Add(typedMods.LabelType.Name);
comboRefineLabelType.SelectedIndex = 0;
comboReplicateUse.SelectedIndex = 0;
var settings = document.Settings;
if (!settings.HasResults)
{
tabControl1.TabPages.Remove(tabResults);
}
if (settings.PeptideSettings.Libraries.HasLibraries)
{
labelMinDotProduct.Enabled = textMinDotProduct.Enabled = groupLibCorr.Enabled = true;
}
if (settings.TransitionSettings.FullScan.IsHighResPrecursor)
{
labelMinIdotProduct.Enabled = textMinIdotProduct.Enabled = groupLibCorr.Enabled = true;
}
}
public ChromatogramExporter(SrmDocument document)
{
Document = document;
_settings = Document.Settings;
_measuredResults = _settings.MeasuredResults;
_matchTolerance = (float)_settings.TransitionSettings.Instrument.MzMatchTolerance;
_chromatogramSets = _measuredResults.Chromatograms;
}
public static PeptideQuantifier GetPeptideQuantifier(SrmSettings srmSettings, PeptideGroupDocNode peptideGroup, PeptideDocNode peptide)
{
var mods = srmSettings.PeptideSettings.Modifications;
// Quantify on all label types which are not internal standards.
ICollection<IsotopeLabelType> labelTypes = ImmutableList.ValueOf(mods.GetModificationTypes()
.Except(mods.InternalStandardTypes));
return new PeptideQuantifier(peptideGroup, peptide, srmSettings.PeptideSettings.Quantification)
{
MeasuredLabelTypes = labelTypes
};
}
public static Configuration GetConfiguration(String path, SrmSettings settings)
{
Configuration configuration = new Configuration()
.SetProperty("dialect", typeof(NHibernate.Dialect.SQLiteDialect).AssemblyQualifiedName) // Not L10N
.SetProperty("connection.connection_string", new SQLiteConnectionStringBuilder // Not L10N
{
DataSource = path
}.ToString())
.SetProperty("connection.driver_class", typeof(NHibernate.Driver.SQLite20Driver).AssemblyQualifiedName); // Not L10N
Assembly assembly = typeof(SessionFactoryFactory).Assembly;
configuration.SetProperty("connection.provider", typeof(NHibernate.Connection.DriverConnectionProvider).AssemblyQualifiedName); // Not L10N
configuration.AddInputStream(assembly.GetManifestResourceStream(typeof(SessionFactoryFactory).Namespace + ".mapping.xml")); // Not L10N
if (settings != null)
AddRatioColumns(configuration, settings);
AddAnnotations(configuration, settings, AnnotationDef.AnnotationTarget.protein, typeof(DbProtein));
AddAnnotations(configuration, settings, AnnotationDef.AnnotationTarget.peptide, typeof(DbPeptide));
AddAnnotations(configuration, settings, AnnotationDef.AnnotationTarget.precursor, typeof(DbPrecursor));
AddAnnotations(configuration, settings, AnnotationDef.AnnotationTarget.transition, typeof(DbTransition));
AddAnnotations(configuration, settings, AnnotationDef.AnnotationTarget.replicate, typeof(DbProteinResult));
AddAnnotations(configuration, settings, AnnotationDef.AnnotationTarget.precursor_result, typeof(DbPrecursorResult));
AddAnnotations(configuration, settings, AnnotationDef.AnnotationTarget.transition_result, typeof(DbTransitionResult));
return configuration;
}
public bool Accept(SrmSettings settings, Peptide peptide, ExplicitMods explicitMods, out bool allowVariableMods)
{
return PeptideFilter.UNFILTERED.Accept(settings, peptide, explicitMods, out allowVariableMods);
}
internal void InitMatcherSettings(SrmSettings settings,
MappedList<string, StaticMod> defSetStatic, MappedList<string, StaticMod> defSetHeavy)
{
DefSetStatic = defSetStatic;
DefSetHeavy = defSetHeavy;
Settings = settings;
var modifications = settings.PeptideSettings.Modifications;
UserDefinedTypedMods = new Dictionary<StaticMod, IsotopeLabelType>();
// First add modifications found in document settings, then add modifications found in the global settings.
foreach (var type in settings.PeptideSettings.Modifications.GetModificationTypes())
{
// Set the default heavy type to the first heavy type encountered.
if (!ReferenceEquals(type, IsotopeLabelType.light) && DocDefHeavyLabelType == null)
DocDefHeavyLabelType = type;
InitUserDefTypedModDict(modifications.GetModificationsByName(type.Name), false);
}
InitUserDefTypedModDict(new TypedModifications(IsotopeLabelType.light, DefSetStatic), true);
InitUserDefTypedModDict(new TypedModifications(DocDefHeavyLabelType, DefSetHeavy), true);
Matches = new Dictionary<AAModKey, AAModMatch>();
UnmatchedSequences = new List<string>();
_foundHeavyLabels = new List<StaticMod>();
while (MoveNextSequence())
{
InitModMatches();
}
CleanUpMatches();
Initialized = true;
}
public static TextSequence[] CreateTextSequences(PeptideDocNode nodePep,
SrmSettings settings, string label, IDeviceContext g, ModFontHolder fonts)
{
// Store text and font information for all label types
bool heavyMods = false;
var listTypeSequences = new List<TextSequence> { CreateTypeTextSequence(nodePep, settings, IsotopeLabelType.light, fonts) };
foreach (var labelType in settings.PeptideSettings.Modifications.GetHeavyModificationTypes())
{
// Only color for the label types actually measured in this peptide
if (!nodePep.HasChildType(labelType))
continue;
var textSequence = CreateTypeTextSequence(nodePep, settings, labelType, fonts);
listTypeSequences.Add(textSequence);
heavyMods = (heavyMods || textSequence != null);
}
// Calculate text sequence values for the peptide display string
var listTextSequences = new List<TextSequence>();
if (nodePep.Peptide.IsCustomIon)
listTextSequences.Add(CreatePlainTextSequence(nodePep.CustomIon.DisplayName, fonts));
// If no modifications, use a single plain text sequence
else if (!heavyMods && !listTypeSequences[0].Text.Contains("[")) // Not L10N: For identifying modifications
listTextSequences.Add(CreatePlainTextSequence(label, fonts));
else
{
string pepSequence = nodePep.Peptide.Sequence;
int startPep = label.IndexOf(pepSequence, StringComparison.Ordinal);
int endPep = startPep + pepSequence.Length;
// Add prefix plain-text if necessary
if (startPep > 0)
{
string prefix = label.Substring(0, startPep);
listTextSequences.Add(CreatePlainTextSequence(prefix, fonts));
}
// Enumerate amino acid characters coallescing their font information
// into text sequences.
var prevCharFont = new CharFont('.', fonts.Plain, Color.Black); // Not L10N: Amino acid format
var indexes = new int[listTypeSequences.Count];
CharFont charFont;
var sb = new StringBuilder();
while ((charFont = GetCharFont(indexes, listTypeSequences, fonts)) != null)
{
if (!charFont.IsSameDisplay(prevCharFont) && sb.Length > 0)
{
listTextSequences.Add(CreateTextSequence(sb, prevCharFont));
sb.Remove(0, sb.Length);
}
sb.Append(charFont.Character);
prevCharFont = charFont;
}
// Add the last segment
if (sb.Length > 0)
listTextSequences.Add(CreateTextSequence(sb, prevCharFont));
// Add suffix plain-text if necessary
if (endPep < label.Length)
{
string suffix = label.Substring(endPep);
listTextSequences.Add(CreatePlainTextSequence(suffix, fonts));
}
}
if (g != null)
{
// Calculate placement for each text sequence
int textRectWidth = 0;
foreach (var textSequence in listTextSequences)
{
Size sizeMax = new Size(int.MaxValue, int.MaxValue);
textSequence.Position = textRectWidth;
textSequence.Width = TextRenderer.MeasureText(g, textSequence.Text,
textSequence.Font, sizeMax, FORMAT_TEXT_SEQUENCE).
Width;
textRectWidth += textSequence.Width;
}
}
return listTextSequences.ToArray();
}
public bool Equals(SrmSettings obj)
{
if (ReferenceEquals(null, obj)) return false;
if (ReferenceEquals(this, obj)) return true;
return base.Equals(obj) &&
Equals(obj.PeptideSettings, PeptideSettings) &&
Equals(obj.TransitionSettings, TransitionSettings) &&
Equals(obj.DataSettings, DataSettings) &&
Equals(obj.MeasuredResults, MeasuredResults) &&
Equals(obj.DocumentRetentionTimes, DocumentRetentionTimes);
}
public bool Accept(SrmSettings settings, Peptide peptide, ExplicitMods explicitMods, out bool allowVariableMods)
{
return Accept(settings,
peptide,
explicitMods,
TransitionSettings.Filter.PrecursorCharges,
PeptideFilterType.fasta,
out allowVariableMods);
}
/// <summary>
/// Calculates the differences between the settings for two document states.
/// </summary>
/// <param name="settingsOld">The previous document settings</param>
/// <param name="settingsNew">New document settings to chage to</param>
public SrmSettingsDiff(SrmSettings settingsOld, SrmSettings settingsNew)
: this(settingsOld, settingsNew, false)
{
}
private static void AddRatioColumns(Configuration configuration, SrmSettings settings)
{
var mappingPeptide = configuration.GetClassMapping(typeof(DbPeptideResult));
var mappingPrec = configuration.GetClassMapping(typeof(DbPrecursorResult));
var mappingTran = configuration.GetClassMapping(typeof(DbTransitionResult));
var mods = settings.PeptideSettings.Modifications;
var standardTypes = mods.RatioInternalStandardTypes;
var labelTypes = mods.GetModificationTypes().ToArray();
if (labelTypes.Length > 2)
{
foreach (var standardType in standardTypes)
{
foreach (var labelType in labelTypes)
{
if (ReferenceEquals(labelType, standardType))
continue;
AddColumn(mappingPeptide,
RatioPropertyAccessor.PeptideRatioProperty(labelType, standardType).ColumnName,
typeof (RatioPropertyAccessor));
AddColumn(mappingPeptide,
RatioPropertyAccessor.PeptideRdotpProperty(labelType, standardType).ColumnName,
typeof (RatioPropertyAccessor));
}
// Only add TotalAreaRatioTo<label type> and AreaRatioTo<label type> columns
// when there is more than one internal standard label type, because that
// is the only time that data is added to these columns in the database.
if (standardTypes.Count > 1)
{
AddColumn(mappingPrec, RatioPropertyAccessor.PrecursorRatioProperty(standardType).ColumnName,
typeof (RatioPropertyAccessor));
AddColumn(mappingPrec, RatioPropertyAccessor.PrecursorRdotpProperty(standardType).ColumnName,
typeof (RatioPropertyAccessor));
AddColumn(mappingTran, RatioPropertyAccessor.TransitionRatioProperty(standardType).ColumnName,
typeof (RatioPropertyAccessor));
}
}
}
if (settings.HasGlobalStandardArea)
{
foreach (var labelType in labelTypes)
{
AddColumn(mappingPeptide, RatioPropertyAccessor.PeptideRatioProperty(labelType, null).ColumnName, typeof(RatioPropertyAccessor));
}
AddColumn(mappingPrec, RatioPropertyAccessor.PrecursorRatioProperty(null).ColumnName, typeof(RatioPropertyAccessor));
AddColumn(mappingTran, RatioPropertyAccessor.TransitionRatioProperty(null).ColumnName, typeof(RatioPropertyAccessor));
}
}
public PickTransitionGroupTip(PeptideDocNode nodePep,
TransitionGroupDocNode nodeGroup, SrmSettings settings)
{
_nodePep = nodePep;
_nodeGroup = nodeGroup;
_settings = settings;
}
private static IEnumerable<KeyValuePair<IsotopeLabelType, string>> GetTypedModifiedSequences(
PeptideDocNode nodePep, SrmSettings settings)
{
foreach (var labelType in settings.PeptideSettings.Modifications.GetModificationTypes())
{
if (nodePep.Peptide.IsCustomIon)
continue;
// Only return the modified sequence, if the peptide actually as a child
// of this type.
if (!nodePep.HasChildType(labelType))
continue;
var calc = settings.TryGetPrecursorCalc(labelType, nodePep.ExplicitMods);
if (calc == null)
continue;
string modSequence = calc.GetModifiedSequence(nodePep.Peptide.Sequence, true); // Never have to worry about this being a custom ion, we already checked
// Only return if the modified sequence contains modifications
if (modSequence.Contains('[')) // Not L10N
yield return new KeyValuePair<IsotopeLabelType, string>(labelType, modSequence);
}
}
/// <summary>
/// Creates a text sequence with the fully modified peptide sequence text
/// and font information for a given label type.
/// </summary>
private static TextSequence CreateTypeTextSequence(PeptideDocNode nodePep, SrmSettings settings,
IsotopeLabelType labelType, ModFontHolder fonts)
{
var calc = settings.TryGetPrecursorCalc(labelType, nodePep.ExplicitMods);
if (calc == null)
return null;
return new TextSequence
{
Text = nodePep.IsProteomic
? calc.GetModifiedSequence(nodePep.Peptide.Sequence, true)
: nodePep.CustomIon.DisplayName,
Font = fonts.GetModFont(labelType),
Color = ModFontHolder.GetModColor(labelType)
};
}
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));
}
}
public static bool HasPeptideTip(PeptideDocNode nodePep, SrmSettings settings)
{
return nodePep.Peptide.Begin.HasValue ||
nodePep.Rank.HasValue ||
nodePep.Note != null ||
// With one child, its tip detail will be appended
nodePep.Children.Count == 1 ||
// With multiple children, modification sequences may be shown
GetTypedModifiedSequences(nodePep, settings).Any();
}
public static void DrawPeptideText(PeptideDocNode nodePep,
SrmSettings settings,
IEnumerable<TextSequence> textSequences,
Graphics g,
Rectangle bounds,
ModFontHolder fonts,
Color foreColor,
Color backColor)
{
if (textSequences == null)
textSequences = CreateTextSequences(nodePep, settings, GetLabel(nodePep, string.Empty), g, fonts);
Rectangle rectDraw = new Rectangle(0, bounds.Y, 0, bounds.Height);
foreach (var textSequence in textSequences)
{
rectDraw.X = textSequence.Position + bounds.X + TreeViewMS.PADDING;
rectDraw.Width = textSequence.Width;
// Use selection highlight color, if the background is highlight.
if (backColor != SystemColors.Highlight)
foreColor = textSequence.Color;
TextRenderer.DrawText(g, textSequence.Text, textSequence.Font, rectDraw,
foreColor, backColor, FORMAT_TEXT_SEQUENCE);
}
}
private bool Accept(SrmSettings settings,
Peptide peptide,
ExplicitMods mods,
IList<int> precursorCharges,
PeptideFilterType filterType,
out bool allowVariableMods)
{
// Assume variable modifications are not allowed until proven otherwise
allowVariableMods = false;
// Only filter user specified peptides based on the heuristic
// filter when explicitly requested.
bool useFilter = filterType == PeptideFilterType.full;
if (filterType == PeptideFilterType.fasta)
useFilter = peptide.Begin.HasValue;
var libraries = PeptideSettings.Libraries;
if (!libraries.HasLibraries || libraries.Pick == PeptidePick.filter)
{
if (!useFilter)
{
allowVariableMods = true;
return true;
}
return PeptideSettings.Filter.Accept(settings, peptide, mods, out allowVariableMods);
}
// Check if the peptide is in the library for one of the
// acceptable precursor charges.
bool inLibrary = false;
// If the libraries are not fully loaded, then act like nothing
// could be found in the libraries. This will be corrected when
// the libraries are loaded.
if (libraries.IsLoaded &&
// Only check the library, if this is a custom ion or a peptide that already has
// a variable modification, or the library contains some form of the peptide.
// This is a performance improvement over checking every variable modification
// of a peptide when it is not even in the library.
(peptide.IsCustomIon || (mods != null && mods.IsVariableStaticMods) || LibrariesContainAny(peptide.Sequence)))
{
// Only allow variable modifications, if the peptide has no modifications
// or already checking variable modifications, and there is reason to check
// the library. Failing to do this check profiled as a performance bottleneck.
allowVariableMods = mods == null || mods.IsVariableStaticMods;
inLibrary = LibrariesContainMeasurablePeptide(peptide, precursorCharges, mods);
}
switch (libraries.Pick)
{
case PeptidePick.library:
return inLibrary;
case PeptidePick.both:
return inLibrary && (!useFilter || PeptideSettings.Filter.Accept(settings, peptide, mods, out allowVariableMods));
default:
return inLibrary || (!useFilter || PeptideSettings.Filter.Accept(settings, peptide, mods, out allowVariableMods));
}
}
/// <summary>
/// Used for changes that involve only results changes. Usually used to force recalculation of
/// all results information.
/// </summary>
/// <param name="settingsCurrent">The current settings which are used as <see cref="SettingsOld"/></param>
/// <param name="allResults">True if all results information should be recalculated</param>
public SrmSettingsDiff(SrmSettings settingsCurrent, bool allResults)
{
SettingsOld = settingsCurrent;
DiffResults = true;
DiffResultsAll = allResults;
}
private static void AddAnnotations(Configuration configuration, SrmSettings settings, AnnotationDef.AnnotationTarget annotationTarget, Type persistentClass)
{
var mapping = configuration.GetClassMapping(persistentClass);
foreach (var annotationDef in settings.DataSettings.AnnotationDefs)
{
if (!annotationDef.AnnotationTargets.Contains(annotationTarget))
{
continue;
}
string columnName = AnnotationDef.GetColumnName(annotationDef.Name);
Type accessorType;
switch (annotationDef.Type)
{
case AnnotationDef.AnnotationType.number:
accessorType = typeof (NumberAnnotationPropertyAccessor);
break;
case AnnotationDef.AnnotationType.true_false:
accessorType = typeof (BoolAnnotationPropertyAccessor);
break;
default:
accessorType = typeof (AnnotationPropertyAccessor);
break;
}
AddColumn(mapping, columnName, accessorType);
}
}
/// <summary>
/// Calculates the differences between the settings for two document states.
/// </summary>
/// <param name="settingsOld">The previous document settings</param>
/// <param name="settingsNew">New document settings to chage to</param>
/// <param name="isUnexplainedExplicitModificationAllowed">True if this settings change should not check
/// explicit modifications against the global settings to make sure they are present</param>
public SrmSettingsDiff(SrmSettings settingsOld, SrmSettings settingsNew,
bool isUnexplainedExplicitModificationAllowed)
{
_isUnexplainedExplicitModificationAllowed = isUnexplainedExplicitModificationAllowed;
SettingsOld = settingsOld;
PeptideSettings newPep = settingsNew.PeptideSettings;
PeptideSettings oldPep = settingsOld.PeptideSettings;
TransitionSettings newTran = settingsNew.TransitionSettings;
TransitionSettings oldTran = settingsOld.TransitionSettings;
// Figure out whether precursor charges differ for determining
// both peptide and transition group changes.
bool precursorsDiff = !ArrayUtil.EqualsDeep(newTran.Filter.PrecursorCharges,
oldTran.Filter.PrecursorCharges) ||
// Also changing auto-select could change precursors
newTran.Filter.AutoSelect != oldTran.Filter.AutoSelect ||
// And changing DIA isolation scheme could change precursors
!Equals(newTran.FullScan.IsolationScheme, oldTran.FullScan.IsolationScheme);
// Change peptides if enzyme, digestion or filter settings changed
DiffPeptides = !newPep.Enzyme.Equals(oldPep.Enzyme) ||
!newPep.DigestSettings.Equals(oldPep.DigestSettings) ||
!newPep.Filter.Equals(oldPep.Filter) ||
// If precursors differ, and peptide picks depend on the library
(precursorsDiff && newPep.Libraries.HasLibraries && newPep.Libraries.Pick != PeptidePick.filter) ||
// If variable modifications changed
newPep.Modifications.MaxVariableMods != oldPep.Modifications.MaxVariableMods ||
!ArrayUtil.EqualsDeep(newPep.Modifications.VariableModifications.ToArray(),
oldPep.Modifications.VariableModifications.ToArray());
// Peptide standard types can change with iRT calculator
DiffPeptideProps = !ReferenceEquals(newPep.Prediction.RetentionTime,
oldPep.Prediction.RetentionTime);
var oldLib = oldPep.Libraries;
var newLib = newPep.Libraries;
bool libraryChange = !ReferenceEquals(newLib, oldLib);
bool diffLibraries = libraryChange && !EquivalentLibraries(newLib, oldLib);
if (!DiffPeptides && libraryChange)
{
// If libraries have been removed, update peptides, if picking algorithm
// allowed peptides outside the filter.
if (!newLib.HasLibraries)
{
DiffPeptides = oldLib.Pick == PeptidePick.library ||
oldLib.Pick == PeptidePick.either;
}
// If the libraries are not loaded, wait until they are to make any changes
else if (newLib.IsLoaded)
{
// If no libraries were used before, or the picking algorithm has changed,
// or the peptide ranking ID has changed, or the peptide count limit has change,
// or the picking algorithm relies on the libraries, and the libraries have changed
DiffPeptides = (!oldLib.HasLibraries ||
newLib.Pick != oldLib.Pick ||
!Equals(newLib.RankId, oldLib.RankId) ||
!Equals(newLib.PeptideCount, oldLib.PeptideCount) ||
(newLib.Pick != PeptidePick.filter && diffLibraries));
}
}
// Calculate changes in global implicit modifications
var oldMods = oldPep.Modifications;
var newMods = newPep.Modifications;
bool diffStaticMods = !StaticMod.EquivalentImplicitMods(newMods.StaticModifications,
oldMods.StaticModifications);
bool diffHeavyMods = false;
var enumNewHeavyMods = newMods.GetHeavyModifications().GetEnumerator();
foreach (var oldTypedMods in oldMods.GetHeavyModifications())
{
if (!enumNewHeavyMods.MoveNext()) // synch with foreach
{
// If fewer heavy label types
diffHeavyMods = true;
break;
}
var newTypedMods = enumNewHeavyMods.Current;
if (newTypedMods == null || // ReSharper
!Equals(newTypedMods.LabelType, oldTypedMods.LabelType) ||
!StaticMod.EquivalentImplicitMods(newTypedMods.Modifications,
oldTypedMods.Modifications))
{
// If label types or implicit modifications differ
diffHeavyMods = true;
break;
}
}
// If not different yet, then make sure nothing was added
if (!diffHeavyMods)
diffHeavyMods = enumNewHeavyMods.MoveNext();
// Set explicit differences, if no differences in the global implicit modifications,
// but the modifications have changed.
if (!diffStaticMods && !diffHeavyMods && !ReferenceEquals(oldPep.Modifications, newPep.Modifications))
DiffExplicit = true;
// Change transition groups if precursor charges or heavy group
// existence changed, or if the IsolationScheme range changed
var isolationRangesNew = newTran.FullScan.IsolationScheme == null ? null : newTran.FullScan.IsolationScheme.PrespecifiedIsolationWindows;
var isolationRangesOld = oldTran.FullScan.IsolationScheme == null ? null : oldTran.FullScan.IsolationScheme.PrespecifiedIsolationWindows;
bool diffInstrumentRange = newTran.Instrument.MinMz != oldTran.Instrument.MinMz ||
newTran.Instrument.MaxMz != oldTran.Instrument.MaxMz ||
!Equals(isolationRangesNew, isolationRangesOld);
bool diffIsolationScheme = !Equals(newTran.FullScan.IsolationScheme, oldTran.FullScan.IsolationScheme);
DiffTransitionGroups = precursorsDiff || diffHeavyMods || diffInstrumentRange || diffIsolationScheme;
// If libraries changed, then transition groups should change whenever
// peptides change also.
if (!DiffTransitionGroups && libraryChange)
DiffTransitionGroups = DiffPeptides;
// Any change in modifications or precursor mass-type forces a recalc
// of precursor m/z values, as
bool enrichmentsChanged = !Equals(newTran.FullScan.IsotopeEnrichments, oldTran.FullScan.IsotopeEnrichments);
DiffTransitionGroupProps = diffStaticMods || diffHeavyMods ||
!newTran.Prediction.PrecursorMassType.Equals(oldTran.Prediction.PrecursorMassType) ||
// Or changes to MS1 filtering that change the expected isotope distribution
!newTran.FullScan.PrecursorMassAnalyzer.Equals(oldTran.FullScan.PrecursorMassAnalyzer) ||
!Equals(newTran.FullScan.PrecursorRes, oldTran.FullScan.PrecursorRes) ||
!Equals(newTran.FullScan.PrecursorResMz, oldTran.FullScan.PrecursorResMz) ||
// Or isotope enrichments
enrichmentsChanged
;
if (!DiffTransitionGroupProps && libraryChange)
{
// Make sure transition group library properties are updated, as long as the
// libraries are loaded and have changed.
DiffTransitionGroupProps = !newLib.HasLibraries || (newLib.IsLoaded && diffLibraries);
}
// Change transitions if anything in the transition filter changes.
DiffTransitions = !newTran.Filter.Equals(oldTran.Filter) ||
!newTran.Libraries.Equals(oldTran.Libraries) ||
// Or libraries changed, and picking based on libraries
(libraryChange && DiffTransitionGroupProps &&
newTran.Libraries.Pick != TransitionLibraryPick.none) ||
// If instrument min or max m/z changed
diffInstrumentRange ||
newTran.Instrument.IsDynamicMin != oldTran.Instrument.IsDynamicMin ||
// If loss modifications changed
newPep.Modifications.MaxNeutralLosses != oldPep.Modifications.MaxNeutralLosses ||
!ArrayUtil.EqualsDeep(newPep.Modifications.NeutralLossModifications.ToArray(),
oldPep.Modifications.NeutralLossModifications.ToArray()) ||
// MS1 filtering changed select peaks
newTran.FullScan.PrecursorIsotopes != oldTran.FullScan.PrecursorIsotopes ||
newTran.FullScan.PrecursorIsotopeFilter != oldTran.FullScan.PrecursorIsotopeFilter ||
(newTran.FullScan.PrecursorIsotopes != FullScanPrecursorIsotopes.None && enrichmentsChanged)
;
// If the library loded state has changed, make sure the library properties are up to date,
// but avoid changing the chosen transitions.
// CONSIDER: The way library transition ranking is currently implemented makes this too slow
// if (!DiffTransitionGroupProps && libraryChange && newLib.IsLoaded && !oldLib.IsLoaded)
// DiffTransitionGroupProps = true;
// Any change in modifications or fragment mass-type forces a recalc
// of transition m/z values, as
DiffTransitionProps = diffStaticMods || diffHeavyMods ||
!newTran.Prediction.FragmentMassType.Equals(oldTran.Prediction.FragmentMassType) ||
(libraryChange && DiffTransitionGroupProps) ||
// Any change in transitions can change transition rankings
// if a library is in use.
(newLib.HasLibraries && DiffTransitions) ||
// If using MS1 isotopes, an enrichment change can change transition masses
(newTran.FullScan.PrecursorIsotopes != FullScanPrecursorIsotopes.None && enrichmentsChanged)
;
// If the results changed, then update the results information which has changed
DiffResults = !EqualExceptAnnotations(settingsNew.MeasuredResults, settingsOld.MeasuredResults);
// If the integration strategy has changed, then force a full update of all results
if (newTran.Integration.IsIntegrateAll != oldTran.Integration.IsIntegrateAll)
DiffResults = DiffResultsAll = true;
// If the match tolerance has changed, then force a full update of all results
if (newTran.Instrument.MzMatchTolerance != oldTran.Instrument.MzMatchTolerance)
DiffResults = DiffResultsAll = true;
// If internal standard type or all types changed, update all results to recalculate ratios.
if (!ArrayUtil.EqualsDeep(newMods.InternalStandardTypes, oldMods.InternalStandardTypes) ||
!ArrayUtil.EqualsDeep(newMods.GetModificationTypes().ToArray(), oldMods.GetModificationTypes().ToArray()))
{
DiffResults = true;
}
// Results handler is temporary. Any time the document has one, it means the results
// must be updated and reintegration applied.
if (newPep.Integration.ResultsHandler != null)
DiffResults = true;
// Avoid updating results while in a bulk import operation without UI
if (settingsNew.IsResultsJoiningDisabled)
DiffResults = false;
// Force update if the bulk import has just completed
else if (settingsOld.HasResults && settingsOld.MeasuredResults.IsResultsUpdateRequired)
DiffResults = true;
}
private void UpdateGraphUI(SrmSettings settingsOld, bool docIdChanged)
{
SrmSettings settingsNew = DocumentUI.Settings;
if (ReferenceEquals(settingsNew, settingsOld))
{
// Just about any change could potentially change the list
// or retention times or peak areas.
if (settingsNew.HasResults)
{
// UpdateGraphPanes can handle null values in the list, but
// only call it when at least one of the graphs is present.
if (_graphRetentionTime != null || _graphPeakArea != null)
UpdateGraphPanes(new List<IUpdatable> {_graphRetentionTime, _graphPeakArea});
}
return;
}
var listUpdateGraphs = new List<IUpdatable>();
var filterNew = settingsNew.TransitionSettings.Filter;
var filterOld = settingsOld.TransitionSettings.Filter;
if (!ReferenceEquals(filterNew, filterOld))
{
// If ion types or charges changed, make sure the new
// ones are on and the old ones are off by default.
bool refresh = false;
if (!ArrayUtil.EqualsDeep(filterNew.IonTypes, filterOld.IonTypes))
{
// Only turn off old ion types, if new settings are not MS1-only full-scan
var fullScan = settingsNew.TransitionSettings.FullScan;
if (!fullScan.IsEnabled || fullScan.IsEnabledMsMs)
CheckIonTypes(filterOld.IonTypes, false);
CheckIonTypes(filterNew.IonTypes, true);
refresh = true;
}
if (!ArrayUtil.EqualsDeep(filterNew.ProductCharges, filterOld.ProductCharges))
{
CheckIonCharges(filterOld.ProductCharges, false);
CheckIonCharges(filterNew.ProductCharges, true);
refresh = true;
}
if (refresh && _graphSpectrum != null)
listUpdateGraphs.Add(_graphSpectrum);
}
using (var layoutLock = new DockPanelLayoutLock(dockPanel))
{
bool deserialized = false;
string layoutFile = GetViewFile(DocumentFilePath);
if (docIdChanged && File.Exists(layoutFile))
{
layoutLock.EnsureLocked();
try
{
using (var layoutReader = new StreamReader(layoutFile))
{
LoadLayout(layoutReader.BaseStream);
}
deserialized = true;
}
catch (Exception x)
{
var message = TextUtil.LineSeparate(string.Format(Resources.SkylineWindow_UpdateGraphUI_Failure_attempting_to_load_the_window_layout_file__0__, layoutFile),
Resources.SkylineWindow_UpdateGraphUI_Rename_or_delete_this_file_to_restore_the_default_layout,
Resources.SkylineWindow_UpdateGraphUI_Skyline_may_also_need_to_be_restarted);
throw new IOException(message, x);
}
}
bool enable = DocumentUI.Settings.PeptideSettings.Libraries.HasLibraries;
if (graphsToolStripMenuItem.Enabled != enable)
{
graphsToolStripMenuItem.Enabled = enable;
ionTypesMenuItem.Enabled = enable;
chargesMenuItem.Enabled = enable;
ranksMenuItem.Enabled = enable;
if (!deserialized)
{
layoutLock.EnsureLocked();
ShowGraphSpectrum(enable && Settings.Default.ShowSpectra);
}
}
enable = DocumentUI.Settings.HasResults;
bool enableSchedule = enable || DocumentUI.Settings.PeptideSettings.Prediction.RetentionTime != null;
if (retentionTimesMenuItem.Enabled != enableSchedule || replicateComparisonMenuItem.Enabled != enable)
{
retentionTimesMenuItem.Enabled = enableSchedule;
replicateComparisonMenuItem.Enabled = enable;
timePeptideComparisonMenuItem.Enabled = enable;
linearRegressionMenuItem.Enabled = enable;
schedulingMenuItem.Enabled = enableSchedule;
if (!deserialized)
{
layoutLock.EnsureLocked();
ShowGraphRetentionTime(enable && Settings.Default.ShowRetentionTimeGraph);
}
}
if (resultsGridMenuItem.Enabled != enable)
{
resultsGridMenuItem.Enabled = enable;
if (!deserialized)
{
layoutLock.EnsureLocked();
ShowResultsGrid(enable && Settings.Default.ShowResultsGrid);
}
}
if (peakAreasMenuItem.Enabled != enable)
{
peakAreasMenuItem.Enabled = enable;
areaReplicateComparisonMenuItem.Enabled = enable;
areaPeptideComparisonMenuItem.Enabled = enable;
if (!deserialized)
{
layoutLock.EnsureLocked();
ShowGraphPeakArea(enable && Settings.Default.ShowPeakAreaGraph);
}
}
if (_graphFullScan != null && _graphFullScan.Visible && !enable)
{
layoutLock.EnsureLocked();
DestroyGraphFullScan();
}
if (!ReferenceEquals(settingsNew.MeasuredResults, settingsOld.MeasuredResults))
{
// First hide all graph windows for results that no longer exist in the document
foreach (var graphChromatogram in _listGraphChrom.ToArray())
{
string name = graphChromatogram.NameSet;
// Look for mathcing chromatogram sets across the documents
ChromatogramSet chromSetOld;
ChromatogramSet chromSetNew;
int index;
if (settingsOld.HasResults &&
settingsOld.MeasuredResults.TryGetChromatogramSet(name, out chromSetOld, out index) &&
settingsNew.HasResults &&
settingsNew.MeasuredResults.TryGetChromatogramSet(chromSetOld.Id.GlobalIndex, out chromSetNew, out index))
{
// If matching chromatogram found, but name has changed, then
// update the graph pane
if (!Equals(chromSetNew.Name, chromSetOld.Name))
name = graphChromatogram.NameSet = chromSetNew.Name;
}
var results = settingsNew.MeasuredResults;
if (results == null || !results.Chromatograms.Contains(chrom => Equals(chrom.Name, name)))
{
layoutLock.EnsureLocked();
ShowGraphChrom(graphChromatogram.NameSet, false);
// If changed to a new document, destroy unused panes
if (docIdChanged)
{
var graphChrom = GetGraphChrom(name);
_listGraphChrom.Remove(graphChrom);
if (graphChrom != null)
DestroyGraphChrom(graphChrom);
}
}
}
// Next show any graph windows for results that were not previously part of
// the document.
if (settingsNew.MeasuredResults != null && !deserialized)
{
// Keep changes in graph panes from stealing the focus
var focusStart = User32.GetFocusedControl();
_inGraphUpdate = true;
try
{
string nameFirst = null;
string nameLast = SelectedGraphChromName;
foreach (var chromatogram in settingsNew.MeasuredResults.Chromatograms)
{
string name = chromatogram.Name;
var graphChrom = GetGraphChrom(name);
if (graphChrom == null)
{
layoutLock.EnsureLocked();
CreateGraphChrom(name, nameLast, false);
nameFirst = nameFirst ?? name;
nameLast = name;
}
// If the pane is not showing a tab for this graph, than add one.
else if (graphChrom.Pane == null ||
!graphChrom.Pane.DisplayingContents.Contains(graphChrom))
{
layoutLock.EnsureLocked();
ShowGraphChrom(name, true);
nameFirst = nameFirst ?? name;
nameLast = name;
}
}
// Put the first set on top, since it will get populated with data first
if (nameFirst != null)
{
layoutLock.EnsureLocked();
ShowGraphChrom(nameFirst, true);
}
}
finally
{
_inGraphUpdate = false;
}
if (focusStart != null)
focusStart.Focus();
}
// Update displayed graphs, which are no longer valid
var listGraphUpdate = from graph in _listGraphChrom
where graph.Visible
where !graph.IsCurrent(settingsOld, settingsNew)
select graph;
listUpdateGraphs.AddRange(listGraphUpdate.ToArray());
// Make sure view menu is correctly enabled
bool enabled = settingsNew.HasResults;
chromatogramsMenuItem.Enabled = enabled;
transitionsMenuItem.Enabled = enabled;
transformChromMenuItem.Enabled = enabled;
autoZoomMenuItem.Enabled = enabled;
arrangeGraphsToolStripMenuItem.Enabled = enabled;
// UpdateReplicateMenuItems(enabled);
// CONSIDER: Enable/disable submenus too?
}
else if (!ReferenceEquals(settingsNew.PeptideSettings.Prediction.RetentionTime,
settingsOld.PeptideSettings.Prediction.RetentionTime))
{
// If retention time regression changed, and retention prediction is showing
// update all displayed graphs
if (Settings.Default.ShowRetentionTimePred)
listUpdateGraphs.AddRange(_listGraphChrom.ToArray());
}
} // layoutLock.Dispose()
// Do this after layout is unlocked, because it messes up the selected graph otherwise
if (_sequenceTreeForm == null)
{
ShowSequenceTreeForm(true);
}
// Just about any change could potentially change these panes.
if (settingsNew.HasResults)
{
if (_graphRetentionTime != null)
listUpdateGraphs.Add(_graphRetentionTime);
if (_graphPeakArea != null)
listUpdateGraphs.Add(_graphPeakArea);
}
UpdateGraphPanes(listUpdateGraphs);
FoldChangeForm.CloseInapplicableForms(this);
}
/// <summary>
/// This version of Accept is used to select transition groups after the peptide
/// itself has already been screened. For this reason, it only applies library
/// filtering.
/// </summary>
public bool Accept(SrmSettings settings, Peptide peptide, ExplicitMods mods, int charge)
{
bool allowVariableMods;
return Accept(settings, peptide, mods, new[] { charge }, PeptideFilterType.library, out allowVariableMods);
}
public void CreateMatches(SrmSettings settings, IEnumerable<LibKey> libKeys,
MappedList<string, StaticMod> defSetStatic, MappedList<string, StaticMod> defSetHeavy)
{
_dictAAMassPairs = new Dictionary<AATermKey, List<byte[]>>();
_libKeys = libKeys.GetEnumerator();
InitMatcherSettings(settings, defSetStatic, defSetHeavy);
MatcherPepMods = CreateMatcherPeptideSettings();
}
public DataRow(SrmSettings settings, RetentionTimeSource target, RetentionTimeSource timesToAlign)
: this()
{
DocumentRetentionTimes = settings.DocumentRetentionTimes;
Target = target;
Source = timesToAlign;
Assume.IsNotNull(target, "target"); // Not L10N
Assume.IsNotNull(DocumentRetentionTimes.FileAlignments, "DocumentRetentionTimes.FileAlignments"); // Not L10N
var fileAlignment = DocumentRetentionTimes.FileAlignments.Find(target.Name);
if (fileAlignment != null)
{
Assume.IsNotNull(fileAlignment.RetentionTimeAlignments, "fileAlignment.RetentionTimeAlignments"); // Not L10N
Assume.IsNotNull(Source, "Source"); // Not L10N
Alignment = fileAlignment.RetentionTimeAlignments.Find(Source.Name);
}
TargetTimes = GetFirstRetentionTimes(settings, target);
SourceTimes = GetFirstRetentionTimes(settings, timesToAlign);
}
/// <summary>
/// For creating at the Molecule level (create molecule and first transition group) or modifying at the transition level
/// Null values imply "don't ask user for this"
/// </summary>
public EditCustomMoleculeDlg(SkylineWindow parent, string title, Identity initialId, IEnumerable<Identity> existingIds, int minCharge, int maxCharge,
SrmSettings settings, string defaultName, string defaultFormula, int? defaultCharge, ExplicitTransitionGroupValues explicitAttributes,
ExplicitRetentionTimeInfo explicitRetentionTime,
IsotopeLabelType defaultIsotopeLabelType, bool enableFormulaEditing = true)
{
Text = title;
_parent = parent;
_initialId = initialId;
_existingIds = existingIds;
_minCharge = minCharge;
_maxCharge = maxCharge;
_transitionSettings = settings != null ? settings.TransitionSettings : null;
_peptideSettings = settings != null ? settings.PeptideSettings : null;
InitializeComponent();
NameText = defaultName;
var needOptionalValuesBox = explicitRetentionTime != null || explicitAttributes != null;
var heightDelta = 0;
if (explicitAttributes == null)
{
ResultExplicitTransitionGroupValues = null;
labelCollisionEnergy.Visible = false;
textCollisionEnergy.Visible = false;
labelSLens.Visible = false;
textSLens.Visible = false;
labelCompensationVoltage.Visible = false;
textCompensationVoltage.Visible = false;
labelConeVoltage.Visible = false;
textConeVoltage.Visible = false;
labelDriftTimeHighEnergyOffsetMsec.Visible = false;
textDriftTimeHighEnergyOffsetMsec.Visible = false;
labelDriftTimeMsec.Visible = false;
textDriftTimeMsec.Visible = false;
if (needOptionalValuesBox)
{
// We blanked out everything but the retention time
var vmargin = labelRetentionTime.Location.Y;
var newHeight = textRetentionTime.Location.Y + textRetentionTime.Height + vmargin;
heightDelta = groupBoxOptionalValues.Height - newHeight;
groupBoxOptionalValues.Height = newHeight;
}
}
else
{
ResultExplicitTransitionGroupValues = new ExplicitTransitionGroupValues(explicitAttributes);
}
string labelAverage = defaultCharge.HasValue
? Resources.EditCustomMoleculeDlg_EditCustomMoleculeDlg_A_verage_m_z_
: Resources.EditCustomMoleculeDlg_EditCustomMoleculeDlg_A_verage_mass_;
string labelMono = defaultCharge.HasValue
? Resources.EditCustomMoleculeDlg_EditCustomMoleculeDlg__Monoisotopic_m_z_
: Resources.EditCustomMoleculeDlg_EditCustomMoleculeDlg__Monoisotopic_mass_;
_formulaBox =
new FormulaBox(Resources.EditMeasuredIonDlg_EditMeasuredIonDlg_Ion__chemical_formula_,
labelAverage,
labelMono,
defaultCharge)
{
Formula = defaultFormula,
Location = new Point(textName.Left, textName.Bottom + 12)
};
Controls.Add(_formulaBox);
_formulaBox.TabIndex = 2;
_formulaBox.Enabled = enableFormulaEditing;
bool needCharge = defaultCharge.HasValue;
textCharge.Visible = labelCharge.Visible = needCharge;
Charge = defaultCharge ?? 0;
if (needOptionalValuesBox && !needCharge)
{
heightDelta += groupBoxOptionalValues.Location.Y - labelCharge.Location.Y;
groupBoxOptionalValues.Location = new Point(groupBoxOptionalValues.Location.X, labelCharge.Location.Y);
}
if (explicitRetentionTime == null)
{
// Don't ask user for retetention times
RetentionTime = null;
RetentionTimeWindow = null;
labelRetentionTime.Visible = false;
labelRetentionTimeWindow.Visible = false;
textRetentionTime.Visible = false;
textRetentionTimeWindow.Visible = false;
if (needOptionalValuesBox)
{
var rtHeight = labelCollisionEnergy.Location.Y - labelRetentionTimeWindow.Location.Y;
groupBoxOptionalValues.Height -= rtHeight;
heightDelta += rtHeight;
}
}
else
{
RetentionTime = explicitRetentionTime.RetentionTime;
RetentionTimeWindow = explicitRetentionTime.RetentionTimeWindow;
}
if (!needOptionalValuesBox)
{
groupBoxOptionalValues.Visible = false;
heightDelta = groupBoxOptionalValues.Height;
}
// Initialize label
if (settings != null && defaultIsotopeLabelType != null)
{
_driverLabelType = new PeptideSettingsUI.LabelTypeComboDriver(comboIsotopeLabelType,
settings.PeptideSettings.Modifications, null, null, null, null)
{
SelectedName = defaultIsotopeLabelType.Name
};
}
else
{
comboIsotopeLabelType.Visible = false;
labelIsotopeLabelType.Visible = false;
}
Height -= heightDelta;
}
public EditPepModsDlg(SrmSettings settings, PeptideDocNode nodePeptide)
{
DocSettings = settings;
NodePeptide = nodePeptide;
ExplicitMods = nodePeptide.ExplicitMods;
InitializeComponent();
Icon = Resources.Skyline;
SuspendLayout();
ComboBox comboStaticLast = null;
List<ComboBox> listComboHeavyLast = null;
List<Label> listLabelHeavyLast = null;
Label labelAALast = null;
string seq = nodePeptide.Peptide.Sequence;
var modsDoc = DocSettings.PeptideSettings.Modifications;
_listLabelTypeHeavy.AddRange(from typedMods in modsDoc.GetHeavyModifications()
select typedMods.LabelType);
for (int i = 0; i < seq.Length; i++)
{
char aa = seq[i];
int row = i + 1;
if (comboStaticLast == null || listComboHeavyLast == null) // ReSharper
{
labelAALast = labelAA1;
comboStaticLast = comboStatic1;
foreach (var labelType in _listLabelTypeHeavy)
{
if (listComboHeavyLast == null)
{
listComboHeavyLast = new List<ComboBox> { comboHeavy1_1 };
listLabelHeavyLast = new List<Label> { labelHeavy1 };
labelHeavy1.Text = GetIsotopeLabelText(labelType);
}
else
{
var comboHeavyLast = listComboHeavyLast[listComboHeavyLast.Count - 1];
panelMain.Controls.Add(comboHeavyLast = new ComboBox
{
Name = GetHeavyName(row, labelType.SortOrder),
Left = comboHeavyLast.Right + HSPACE,
Top = comboHeavyLast.Top,
Size = comboHeavyLast.Size,
TabIndex = comboHeavyLast.TabIndex + 1
});
listComboHeavyLast.Add(comboHeavyLast);
var labelHeavyLast = listLabelHeavyLast[listLabelHeavyLast.Count - 1];
panelMain.Controls.Add(labelHeavyLast = new Label
{
Text = GetIsotopeLabelText(labelType),
Name = GetIsotopeLabelName(labelType.SortOrder),
Left = comboHeavyLast.Left,
Top = labelHeavyLast.Top,
TabIndex = labelHeavyLast.TabIndex + 1
});
listLabelHeavyLast.Add(labelHeavyLast);
}
}
}
else
{
int controlsPerRow = 2 + listComboHeavyLast.Count;
int top = Top = comboStaticLast.Bottom + VSPACE;
panelMain.Controls.Add(labelAALast = new Label
{
Name = ("labelAA" + row), // Not L10N
AutoSize = true,
Font = labelAA1.Font,
Left = labelAA1.Left,
Top = top + (labelAALast.Top - comboStaticLast.Top),
Size = labelAA1.Size,
TabIndex = labelAALast.TabIndex + controlsPerRow
});
panelMain.Controls.Add(comboStaticLast = new ComboBox
{
Name = GetStaticName(row),
Left = comboStaticLast.Left,
Top = top,
Size = comboStaticLast.Size,
TabIndex = comboStaticLast.TabIndex + controlsPerRow
});
foreach (var labelType in _listLabelTypeHeavy)
{
int col = labelType.SortOrder - 1;
var comboHeavyLast = listComboHeavyLast[col];
panelMain.Controls.Add(comboHeavyLast = new ComboBox
{
Name = GetHeavyName(row, labelType.SortOrder),
Left = comboHeavyLast.Left,
Top = top,
Size = comboHeavyLast.Size,
TabIndex = comboHeavyLast.TabIndex + controlsPerRow
});
listComboHeavyLast[col] = comboHeavyLast;
}
}
// Store static modification combos and selected indexes
_listSelectedIndexStatic.Add(-1);
_listComboStatic.Add(InitModificationCombo(comboStaticLast, i, IsotopeLabelType.light));
// Store heavy moficiation combos and selected indexes
if (listComboHeavyLast != null) // ReSharper
{
for (int j = 0; j < _listLabelTypeHeavy.Count; j++)
{
while (_listListComboHeavy.Count <= j)
{
_listListSelectedIndexHeavy.Add(new List<int>());
_listListComboHeavy.Add(new List<ComboBox>());
}
var comboHeavyLast = listComboHeavyLast[j];
var labelType = _listLabelTypeHeavy[j];
_listListSelectedIndexHeavy[j].Add(-1);
_listListComboHeavy[j].Add(InitModificationCombo(comboHeavyLast, i, labelType));
}
}
// Store amino acid labels
labelAALast.Text = aa.ToString(CultureInfo.InvariantCulture);
_listLabelAA.Add(labelAALast);
}
for (int i = 0; i < _listLabelAA.Count; i++)
{
UpdateAminoAcidLabel(i);
}
if (comboStaticLast != null && comboStaticLast != comboStatic1)
{
// Increase width by the delta from the left edges of the first and last
// heavy combo box columns
int widthDiff = _listListComboHeavy[_listListComboHeavy.Count - 1][0].Left -
_listListComboHeavy[0][0].Left;
Width += widthDiff;
// Increase height by the delta from the bottom edges of the first and last
// amino acid labels
if (comboStatic1 != null) // ReSharper
{
int heightDiff = comboStaticLast.Bottom - comboStatic1.Bottom;
heightDiff += comboStatic1.Bottom - panelMain.Height;
Height += heightDiff;
}
if (listComboHeavyLast != null) // ReSharper
btnOk.TabIndex = listComboHeavyLast[listComboHeavyLast.Count - 1].TabIndex + 1;
btnCancel.TabIndex = btnOk.TabIndex + 1;
}
ResumeLayout(true);
}
private static IDictionary<string, double> GetFirstRetentionTimes(
SrmSettings settings, RetentionTimeSource retentionTimeSource)
{
var libraryRetentionTimes = settings.GetRetentionTimes(MsDataFileUri.Parse(retentionTimeSource.Name));
if (null == libraryRetentionTimes)
{
return new Dictionary<string, double>();
}
return libraryRetentionTimes.GetFirstRetentionTimes();
}
public PeptideDocNode GetModifiedNode(LibKey key, string seqUnmod, SrmSettings settings, SrmSettingsDiff diff)
{
if (string.IsNullOrEmpty(seqUnmod))
return null;
var peptide = new Peptide(null, seqUnmod, null, null,
settings.PeptideSettings.Enzyme.CountCleavagePoints(seqUnmod));
// First try and create the match from the settings created to match the library explorer.
Settings = HasMatches
? settings.ChangePeptideModifications(mods => MatcherPepMods)
: settings;
TransitionGroupDocNode nodeGroup;
var nodePep = CreateDocNodeFromSettings(key.Sequence, peptide, diff, out nodeGroup);
if (nodePep != null)
{
if (diff == null)
{
nodePep = (PeptideDocNode)nodePep.ChangeAutoManageChildren(false);
}
else
{
// Keep only the matching transition group, so that modifications
// will be highlighted differently for light and heavy forms.
// Only performed when getting peptides for display in the explorer.
nodePep = (PeptideDocNode)nodePep.ChangeChildrenChecked(
new DocNode[] { nodeGroup });
}
return nodePep;
}
else if (Matches == null)
return null;
bool hasHeavy;
// Create explicit mods from the found matches.
nodePep = CreateDocNodeFromMatches(new PeptideDocNode(peptide),
EnumerateSequenceInfos(key.Key, true), false, out hasHeavy);
if (nodePep == null)
return null;
// Call change settings with the matched modification settings to enumerate the children.
nodePep = nodePep.ChangeSettings(settings.ChangePeptideModifications(mods =>
!HasMatches ? settings.PeptideSettings.Modifications : MatcherPepMods), diff ?? SrmSettingsDiff.ALL);
if (nodePep.Children.Count == 0)
return null;
// Select the correct child, only for use with the library explorer.
if (diff != null && nodePep.Children.Count > 1)
{
nodePep =
(PeptideDocNode)
nodePep.ChangeChildrenChecked(new List<DocNode> { nodePep.Children[hasHeavy ? 1 : 0] });
}
if (diff == null)
{
nodePep = (PeptideDocNode)nodePep.ChangeAutoManageChildren(false);
}
return nodePep;
}
public void UpdateResultsUI(SrmSettings settingsNew, SrmSettings settingsOld)
{
if (_updateLockCountDoc > 0)
return;
var results = settingsNew.MeasuredResults;
if (settingsOld == null || !ReferenceEquals(results, settingsOld.MeasuredResults))
{
if (results == null || results.Chromatograms.Count < 2)
{
if (toolBarResults.Visible)
toolBarResults.Visible = false;
// Make sure the combo contains the results name, if one is
// available, because graph handling depends on this.
if (results != null && results.Chromatograms.Count > 0)
{
string resultsName = results.Chromatograms[0].Name;
if (ComboResults.Items.Count != 1 || !Equals(ComboResults.SelectedItem, resultsName))
{
ComboResults.Items.Clear();
ComboResults.Items.Add(resultsName);
ComboResults.SelectedIndex = 0;
}
}
}
else
{
// Check to see if the list of files has changed.
var listNames = new List<string>();
foreach (var chromSet in results.Chromatograms)
listNames.Add(chromSet.Name);
var listExisting = new List<string>();
foreach (var item in ComboResults.Items)
listExisting.Add(item.ToString());
if (!ArrayUtil.EqualsDeep(listNames, listExisting))
{
// If it has, update the list, trying to maintain selection, if possible.
object selected = ComboResults.SelectedItem;
ComboResults.Items.Clear();
foreach (string name in listNames)
ComboResults.Items.Add(name);
if (selected == null || ComboResults.Items.IndexOf(selected) == -1)
ComboResults.SelectedIndex = 0;
else
ComboResults.SelectedItem = selected;
ComboHelper.AutoSizeDropDown(ComboResults);
}
// Show the toolbar after updating the files
if (!toolBarResults.Visible)
{
toolBarResults.Visible = true;
EnsureResultsComboSize();
}
}
}
}