public void TestFindModificationByPrimaryIndex()
{
TextFile primary = new TextFile();
primary.AddLines(new[] { "a", "b", "c", "d", "e", "f" });
TextFile secondary = new TextFile();
secondary.AddLines(new[] { "1", "2", "3", "4", "5", "6" });
ModificationCollection modifications = new ModificationCollection(primary, secondary);
modifications.AddNoChanged(0, 2);
modifications.AddReplaced(2, 0, 2);
modifications.AddNoChanged(4, 2);
Modification wanted = modifications.FindModificationByPrimaryIndex(1);
Assert.AreEqual(wanted.Index, 0);
wanted = modifications.FindModificationByPrimaryIndex(3);
Assert.AreEqual(wanted.Index, 1);
wanted = modifications.FindModificationByPrimaryIndex(4);
Assert.AreEqual(wanted.Index, 2);
wanted = modifications.FindModificationByPrimaryIndex(5);
Assert.AreEqual(wanted.Index, 2);
}
public void TestStartIndex()
{
Modification modification = Modification.CreateNoChanged(new List<string> {"aaa", "bbb", "ccc"});
Assert.AreEqual(modification.Primary.StartIndex, 0);
Assert.AreEqual(modification.Secondary.StartIndex, 0);
ModificationCollection modifications = new ModificationCollection();
modifications.Add(modification);
modification = Modification.CreateAdded(new List<string> { "ddd", "eee", "fff" });
modifications.Add(modification);
Assert.AreEqual(modification.Primary.StartIndex, 3);
Assert.AreEqual(modification.Primary.Length, 0);
Assert.AreEqual(modification.Secondary.StartIndex, 3);
Assert.AreEqual(modification.Secondary.Length, 3);
modification = Modification.CreateAdded(new List<string> { "ggg", "hhh", "iii" });
modifications.Add(modification);
Assert.AreEqual(modification.Primary.StartIndex, 3);
Assert.AreEqual(modification.Primary.Length, 0);
Assert.AreEqual(modification.Secondary.StartIndex, 6);
Assert.AreEqual(modification.Secondary.Length, 3);
}
public void ModificationCollectionScrambledEquals()
{
ModificationCollection a = new ModificationCollection(new OldSchoolModification(1, "Mod1"), new OldSchoolModification(2, "Mod2"));
ModificationCollection b = new ModificationCollection(new OldSchoolModification(1, "Mod1"), new OldSchoolModification(3, "Mod3"));
Assert.IsFalse(a.Equals(b));
}
public void TestSplit()
{
TextFile primary = new TextFile();
primary.AddLines(new[] { "a", "b", "c", "d", "e", "f" });
TextFile secondary = new TextFile();
secondary.AddLines(new[] { "1", "2", "3", "4", "5", "6" });
ModificationCollection modifications = new ModificationCollection(primary, secondary);
modifications.AddNoChanged(0, 2);
modifications.AddReplaced(2, 0, 2);
modifications.AddAdded(4, 2);
Modification[] splited = modifications[1].Split(1); // неверный индекс
Assert.AreEqual(splited.Length, 1);
Assert.AreSame(splited[0], modifications[1]);
splited = modifications[1].Split(2); // граничный индекс
Assert.AreEqual(splited.Length, 1);
Assert.AreSame(splited[0], modifications[1]);
splited = modifications[1].Split(3); // индекс в середине
Assert.AreEqual(splited.Length, 2);
}
public void TestFindModificationByPrimaryIndex()
{
TextFile primary = new TextFile();
primary.AddLines(new[] {"a","b","c","d","e","f"});
TextFile secondary = new TextFile();
secondary.AddLines(new[] { "1", "2", "3", "4", "5", "6" });
ModificationCollection modifications = new ModificationCollection(primary, secondary);
modifications.AddNoChanged(0, 2);
modifications.AddReplaced(2, 0, 2);
modifications.AddNoChanged(4, 2);
Modification wanted = modifications.FindModificationByPrimaryIndex(1);
Assert.AreEqual(wanted.Index, 0);
wanted = modifications.FindModificationByPrimaryIndex(3);
Assert.AreEqual(wanted.Index, 1);
wanted = modifications.FindModificationByPrimaryIndex(4);
Assert.AreEqual(wanted.Index, 2);
wanted = modifications.FindModificationByPrimaryIndex(5);
Assert.AreEqual(wanted.Index, 2);
}
public void ModificationCollectionTest()
{
ModificationCollection a = new ModificationCollection(new OldSchoolModification(1, "Mod1"), new OldSchoolModification(2, "Mod2"));
double lala = 0;
IEnumerable aasdf = a;
foreach (var jadfk in aasdf)
{
lala += (jadfk as IHasMass).MonoisotopicMass;
}
Assert.AreEqual(3, lala);
Assert.AreEqual("Mod1 | Mod2", a.ToString());
a.Add(new OldSchoolModification(3, "Mod3"));
Assert.AreEqual("Mod1 | Mod2 | Mod3", a.ToString());
Assert.IsTrue(a.Contains(new OldSchoolModification(2, "Mod2")));
IHasMass[] myArray = new IHasMass[4];
a.CopyTo(myArray, 1);
Assert.AreEqual(3, myArray.Sum(b => b == null ? 0 : 1));
Assert.AreEqual(3, a.Count());
Assert.IsFalse(a.IsReadOnly);
a.Remove(new OldSchoolModification(2, "Mod2"));
Assert.AreEqual("Mod1 | Mod3", a.ToString());
double ok = 0;
foreach (var b in a)
{
ok += b.MonoisotopicMass;
}
Assert.AreEqual(4, ok);
a.Clear();
Assert.AreEqual("", a.ToString());
}
private static string GetLocalizedString(LocalizedHit hit)
{
StringBuilder sb = new StringBuilder();
IMass[] mods = hit.LocalizedIsoform.GetModifications();
bool first = false;
for (int resNumber = 1; resNumber < mods.Length - 1; resNumber++)
{
IMass mod = mods[resNumber];
if (mod == null)
{
continue;
}
ModificationCollection modCollection = mod as ModificationCollection;
if (modCollection != null)
{
IMass trueMod = mod;
bool passes = false;
foreach (IMass mod2 in modCollection)
{
if (Lotor.QuantifiedModifications.Contains(mod2))
{
trueMod = mod2;
passes = true;
break;
}
}
if (!passes)
{
continue;
}
mod = trueMod;
}
else
{
if (Lotor.FixedModifications.Contains(mod) || !Lotor.QuantifiedModifications.Contains(mod))
{
continue;
}
}
int fullResidueNumber = hit.PSM.StartResidue + resNumber - 1;
char res = hit.LocalizedIsoform.Sequence[resNumber - 1];
if (first)
{
sb.Append(" & ");
}
sb.Append(res);
sb.Append(fullResidueNumber);
sb.Append("[" + mod + "]");
first = true;
}
return(sb.ToString());
}
public Merger()
{
ServerFile = new TextFile();
User1File = new TextFile();
User2File = new TextFile();
ServerUser1Modifications = new ModificationCollection(ServerFile, User1File);
ServerUser2Modifications = new ModificationCollection(ServerFile, User2File);
MergedModifications = new ModificationCollection();
}
public Merger()
{
ServerFile = new TextFile();
User1File = new TextFile();
User2File = new TextFile();
ServerUser1Modifications = new ModificationCollection(ServerFile, User1File);
ServerUser2Modifications = new ModificationCollection(ServerFile, User2File);
MergedModifications = new ModificationCollection();
}
public void ExecuteComapare()
{
FileComparer fileComparer = new FileComparer();
ServerUser1Modifications = fileComparer.Compare(ServerFile, User1File);
ServerUser2Modifications = fileComparer.Compare(ServerFile, User2File);
MergedModifications = new ModificationCollection();
RaiseStateChanged();
}
public void ExecuteComapare()
{
FileComparer fileComparer = new FileComparer();
ServerUser1Modifications = fileComparer.Compare(ServerFile, User1File);
ServerUser2Modifications = fileComparer.Compare(ServerFile, User2File);
MergedModifications = new ModificationCollection();
RaiseStateChanged();
}
public void ModificationCollectionTestTest()
{
OldSchoolModification mod1 = new OldSchoolModification(10, "mass 10 modification");
OldSchoolModification mod2 = new OldSchoolModification(100, "mass 100 modification");
OldSchoolModification mod3 = new OldSchoolModification(1000, "mass 1000 modification");
ModificationCollection a = new ModificationCollection(mod1, mod2, mod3, mod1);
ModificationCollection b = new ModificationCollection(mod1, mod3, mod1, mod2);
Assert.IsTrue(a.Equals(b));
ModificationCollection c = new ModificationCollection(mod1);
Assert.IsFalse(c.Equals(b));
}
private void miDelete_Click(object sender, EventArgs e)
{
#if CHECKERS
if (IsSelectionEmpty)
{
throw new InvalidOperationException();
}
#endif
var b = new StringBuilder();
bool isFirst = true;
foreach (var c in _selectionList)
{
if (!isFirst)
{
b.Append(", ");
}
else
{
isFirst = false;
}
b.Append(c.Owner.Title);
}
if (Extenders.ConfirmDelete(b.ToString()))
{
var list = _selectionList.ToArray();
UnSelectAll();
var mg = new ModificationCollection <HtmlControlModification>();
foreach (var c in list)
{
FreeResources(c.Owner);
HtmlDesignMovableControl owner = c.Owner;
owner.NotifyDelete();
mg.Add(HtmlControlModification.GetRemoved(owner));
owner.Parent = null;
}
if (mg.Count > 0)
{
HtmlPage.AddUndoOperation(mg.Count == 1 ? (IModification)mg[0] : mg);
}
else
{
throw new InvalidOperationException();
}
UpdateUndoRedoState();
}
}
public void TestSplit()
{
TextFile primary = new TextFile();
primary.AddLines(new[] { "a", "b", "c", "d", "e", "f" });
TextFile secondary = new TextFile();
secondary.AddLines(new[] { "1", "2", "3", "4", "5", "6" });
ModificationCollection modifications = new ModificationCollection(primary, secondary);
modifications.AddNoChanged(0, 2);
modifications.AddReplaced(2, 0, 2);
modifications.AddAdded(4, 2);
modifications.Split(3); // индекс в середине
Assert.AreEqual(modifications.Count, 4);
}
public void TestReplaced2()
{
TextFile file1 = new TextFile();
file1.AddLine("1");
file1.AddLine("4");
file1.AddLine("3");
TextFile file2 = new TextFile();
file2.AddLine("2");
FileComparer fileComparer = new FileComparer();
ModificationCollection report = fileComparer.Compare(file1, file2);
ModificationAreEqual(report[0], "Replaced", 0, 0, 1);
ModificationAreEqual(report[1], "Removed", 1, -1, 2);
}
private bool IsFirstMoreSecond(ModificationCollection first, ModificationCollection second)
{
if (first.Count == 0)
{
return(second.Count == 0);
}
if (second.Count == 0)
{
return(true);
}
Modification firstLast = first.Last();
Modification secondLast = second.Last();
return(firstLast.Secondary.StartIndex + firstLast.Secondary.Length >
secondLast.Secondary.StartIndex + secondLast.Secondary.Length);
}
public void TestSplit()
{
TextFile primary = new TextFile();
primary.AddLines(new[] { "a", "b", "c", "d", "e", "f" });
TextFile secondary = new TextFile();
secondary.AddLines(new[] { "1", "2", "3", "4", "5", "6" });
ModificationCollection modifications = new ModificationCollection(primary, secondary);
modifications.AddNoChanged(0, 2);
modifications.AddReplaced(2, 0, 2);
modifications.AddAdded(4, 2);
modifications.Split(3); // индекс в середине
Assert.AreEqual(modifications.Count, 4);
}
public void ExecuteMerge()
{
MergedModifications = new ModificationCollection(new TextFile(ServerFile.Name), new TextFile("Merged"));
MergedModifications.Initialize(ServerUser1Modifications);
MergedModifications.Split(ServerUser2Modifications);
ModificationCollection temporary = new ModificationCollection(ServerUser2Modifications);
temporary.Split(MergedModifications);
ICollection <Modification> processed = new List <Modification>();
for (int mergedIndex = 0; mergedIndex < MergedModifications.Count; mergedIndex++)
{
Modification currentMerged = MergedModifications[mergedIndex];
Modification currentUser2 = temporary.FindModificationByPrimaryIndex(processed, currentMerged.Primary.StartIndex);
if (currentUser2 == null)
{
continue;
}
processed.Add(currentUser2);
Modification[] merged = currentMerged.Merge(currentUser2);
currentMerged.Remove();
foreach (Modification mergedModification in merged)
{
MergedModifications.Insert(mergedIndex, mergedModification);
mergedIndex++;
}
mergedIndex--;
}
MergedModifications.GenerateFiles();
RaiseStateChanged();
}
public void TestAdded()
{
TextFile file1 = new TextFile();
file1.AddLine("1");
file1.AddLine("3");
TextFile file2 = new TextFile();
file2.AddLine("1");
file2.AddLine("2");
file2.AddLine("3");
FileComparer fileComparer = new FileComparer();
ModificationCollection report = fileComparer.Compare(file1, file2);
ModificationAreEqual(report[0], "NoChanged", 0, 0, 1);
ModificationAreEqual(report[1], "Added", -1, 1, 1);
ModificationAreEqual(report[2], "NoChanged", 1, 2, 1);
}
public void Initialize(ModificationCollection modifications)
{
primaryListView.Items.Clear();
secondaryListView.Items.Clear();
primaryTextBox.Text = modifications.Primary.Name;
secondaryTextBox.Text = modifications.Secondary.Name;
int rowNumber = 1;
foreach (var modification in modifications)
{
for (int index = 0; index < modification.Length; index++)
{
var primaryItem = new ListViewItem(rowNumber.ToString("00000"));
primaryItem.BackColor = modification.Primary.Color;
string primaryLine = string.Empty;
if (index < modification.Primary.Length)
{
primaryLine = modification.Primary.Lines[index];
}
primaryItem.SubItems.Add(primaryLine);
primaryListView.Items.Add(primaryItem);
var secondaryItem = new ListViewItem(rowNumber.ToString("00000"));
secondaryItem.BackColor = modification.Secondary.Color;
string secondaryLine = string.Empty;
if (index < modification.Secondary.Length)
{
secondaryLine = modification.Secondary.Lines[index];
}
secondaryItem.SubItems.Add(secondaryLine);
secondaryListView.Items.Add(secondaryItem);
rowNumber++;
}
}
}
public void ExecuteMerge()
{
MergedModifications = new ModificationCollection(new TextFile(ServerFile.Name), new TextFile("Merged"));
MergedModifications.Initialize(ServerUser1Modifications);
MergedModifications.Split(ServerUser2Modifications);
ModificationCollection temporary = new ModificationCollection(ServerUser2Modifications);
temporary.Split(MergedModifications);
ICollection<Modification> processed = new List<Modification>();
for (int mergedIndex = 0; mergedIndex < MergedModifications.Count; mergedIndex++)
{
Modification currentMerged = MergedModifications[mergedIndex];
Modification currentUser2 = temporary.FindModificationByPrimaryIndex(processed, currentMerged.Primary.StartIndex);
if (currentUser2 == null)
{
continue;
}
processed.Add(currentUser2);
Modification[] merged = currentMerged.Merge(currentUser2);
currentMerged.Remove();
foreach (Modification mergedModification in merged)
{
MergedModifications.Insert(mergedIndex, mergedModification);
mergedIndex++;
}
mergedIndex--;
}
MergedModifications.GenerateFiles();
RaiseStateChanged();
}
public void Initialize(ModificationCollection modifications)
{
primaryListView.Items.Clear();
secondaryListView.Items.Clear();
primaryTextBox.Text = modifications.Primary.Name;
secondaryTextBox.Text = modifications.Secondary.Name;
int rowNumber = 1;
foreach (var modification in modifications)
{
for (int index = 0; index < modification.Length; index++)
{
var primaryItem = new ListViewItem(rowNumber.ToString("00000"));
primaryItem.BackColor = modification.Primary.Color;
string primaryLine = string.Empty;
if (index < modification.Primary.Length)
{
primaryLine = modification.Primary.Lines[index];
}
primaryItem.SubItems.Add(primaryLine);
primaryListView.Items.Add(primaryItem);
var secondaryItem = new ListViewItem(rowNumber.ToString("00000"));
secondaryItem.BackColor = modification.Secondary.Color;
string secondaryLine = string.Empty;
if (index < modification.Secondary.Length)
{
secondaryLine = modification.Secondary.Lines[index];
}
secondaryItem.SubItems.Add(secondaryLine);
secondaryListView.Items.Add(secondaryItem);
rowNumber++;
}
}
}
public void TestEmptyFiles()
{
TextFile emptyFile = new TextFile();
TextFile file2 = new TextFile();
file2.AddLine("public class MyClass");
file2.AddLine("{");
file2.AddLine("}");
FileComparer fileComparer = new FileComparer();
ModificationCollection report = fileComparer.Compare(emptyFile, file2);
ModificationAreEqual(report[0], "Added", -1, 0, 3);
report = fileComparer.Compare(file2, emptyFile);
ModificationAreEqual(report[0], "Removed", 0, -1, 3);
report = fileComparer.Compare(emptyFile, emptyFile);
Assert.AreEqual(report.Count, 0);
}
public void TestMethod1()
{
TextFile file1 = new TextFile();
file1.AddLine("public class MyClass");
file1.AddLine("{");
file1.AddLine(" public MyClass()");
file1.AddLine(" { }");
file1.AddLine();
file1.AddLine(" public string StringProperty");
file1.AddLine(" {");
file1.AddLine(" get;");
file1.AddLine(" set;");
file1.AddLine(" }");
file1.AddLine("}");
TextFile file2 = new TextFile();
file2.AddLine("public class MyClass");
file2.AddLine("{");
file2.AddLine(" public MyClass()");
file2.AddLine(" { }");
file2.AddLine();
file2.AddLine(" public int MyMethod(int value)");
file2.AddLine(" {");
file2.AddLine(" Console.WriteLine(value);");
file2.AddLine(" }");
file2.AddLine("}");
FileComparer fileComparer = new FileComparer();
ModificationCollection report = fileComparer.Compare(file1, file2);
ModificationAreEqual(report[0], "NoChanged", 0, 0, 5);
ModificationAreEqual(report[1], "Replaced", 5, 5, 1);
ModificationAreEqual(report[2], "NoChanged", 6, 6, 1);
ModificationAreEqual(report[3], "Replaced", 7, 7, 1);
ModificationAreEqual(report[4], "Removed", 8, -1, 1);
ModificationAreEqual(report[5], "NoChanged", 9, 8, 2);
}
private void Control_EndMove(HtmlDesignMovableControl c)
{
IModification m;
if (_selectionList.Count == 1)
{
HtmlDesignMovableControl o = _selectionList[0].Owner;
Point previousLocation = _PreviousLocations[o];
m = previousLocation != o.Control.Location ? HtmlControlModification.GetMoved(o, previousLocation) : (IModification)null;
}
else
{
var list = new ModificationCollection <HtmlControlModification>();
foreach (var bc in _selectionList)
{
HtmlDesignMovableControl o = bc.Owner;
Point previousLocation = _PreviousLocations[o];
if (previousLocation != o.Control.Location)
{
list.Add(HtmlControlModification.GetMoved(o, previousLocation));
}
}
if (list.Count == 1)
{
m = list[0];
}
else
{
m = list.Count > 0 ? list : null;
}
}
if (m != null)
{
HtmlPage.AddUndoOperation(m);
UpdateUndoRedoState();
}
c.Control.LocationChanged -= Control_LocationChanged;
}
private void miDelete_Click(object sender, EventArgs e)
{
#if CHECKERS
if (IsSelectionEmpty)
{
throw new InvalidOperationException();
}
#endif
var b = new StringBuilder();
bool isFirst = true;
foreach (var c in _selectionList)
{
if (!isFirst)
{
b.Append(", ");
}
else
{
isFirst = false;
}
b.Append(c.Owner.Title);
}
if (Extenders.ConfirmDelete(b.ToString()))
{
var list = _selectionList.ToArray();
UnSelectAll();
var mg = new ModificationCollection<HtmlControlModification>();
foreach (var c in list)
{
FreeResources(c.Owner);
HtmlDesignMovableControl owner = c.Owner;
owner.NotifyDelete();
mg.Add(HtmlControlModification.GetRemoved(owner));
owner.Parent = null;
}
if (mg.Count > 0)
{
HtmlPage.AddUndoOperation(mg.Count == 1 ? (IModification)mg[0] : mg);
}
else
{
throw new InvalidOperationException();
}
UpdateUndoRedoState();
}
}
private bool IsFirstMoreSecond(ModificationCollection first, ModificationCollection second)
{
if (first.Count == 0)
{
return second.Count == 0;
}
if (second.Count == 0)
{
return true;
}
Modification firstLast = first.Last();
Modification secondLast = second.Last();
return firstLast.Secondary.StartIndex + firstLast.Secondary.Length >
secondLast.Secondary.StartIndex + secondLast.Secondary.Length;
}
public static IEnumerable <Peptide> GetUniquePeptides(Peptide peptide)
{
HashSet <QuantitationChannelSet> sets = new HashSet <QuantitationChannelSet>();
Dictionary <IQuantitationChannel, HashSet <int> > locations = new Dictionary <IQuantitationChannel, HashSet <int> >();
IMass[] mods = peptide.Modifications;
int modLength = mods.Length;
for (int i = 0; i < modLength; i++)
{
if (mods[i] != null)
{
IMass mod = mods[i];
List <QuantitationChannelSet> channelsets = new List <QuantitationChannelSet>();
QuantitationChannelSet quantSetMod;
ModificationCollection modCol;
if ((modCol = mod as ModificationCollection) != null)
{
foreach (IMass mod2 in modCol)
{
if ((quantSetMod = mod2 as QuantitationChannelSet) != null)
{
channelsets.Add(quantSetMod);
}
}
}
else if ((quantSetMod = mod as QuantitationChannelSet) != null)
{
channelsets.Add(quantSetMod);
}
foreach (QuantitationChannelSet channelset in channelsets)
{
sets.Add(channelset);
foreach (IQuantitationChannel channel in channelset.GetChannels())
{
HashSet <int> residues;
if (locations.TryGetValue(channel, out residues))
{
residues.Add(i);
}
else
{
residues = new HashSet <int> {
i
};
locations.Add(channel, residues);
}
}
}
}
}
if (sets.Count == 0)
{
yield return(new Peptide(peptide, true));
}
else if (sets.Count == 1)
{
foreach (QuantitationChannelSet set in sets)
{
foreach (IQuantitationChannel channel in set.GetChannels())
{
Peptide toReturn = new Peptide(peptide, true);
foreach (int residue in locations[channel])
{
toReturn.SetModification(channel, residue);
}
yield return(toReturn);
}
}
}
else
{
List <HashSet <IQuantitationChannel> > quantChannels = new List <HashSet <IQuantitationChannel> >();
GetUniquePeptides_helper(sets.ToList(), 0, new HashSet <IQuantitationChannel>(), quantChannels);
foreach (HashSet <IQuantitationChannel> channelset in quantChannels)
{
Peptide toReturn = new Peptide(peptide, true);
Dictionary <int, IMass> modsToAdd = new Dictionary <int, IMass>();
foreach (IQuantitationChannel channel in channelset)
{
foreach (int residue in locations[channel])
{
IMass modToAdd;
if (modsToAdd.TryGetValue(residue, out modToAdd))
{
ModificationCollection col = new ModificationCollection(channel, modToAdd);
modsToAdd[residue] = col;
}
else
{
modsToAdd.Add(residue, channel);
}
}
}
foreach (KeyValuePair <int, IMass> kvp in modsToAdd)
{
toReturn.SetModification(kvp.Value, kvp.Key);
}
yield return(toReturn);
}
}
}
public static IEnumerable<Peptide> GetUniquePeptides(Peptide peptide)
{
QuantitationChannelSet quantSetMod;
IMass mod;
ModificationCollection modCol;
HashSet<QuantitationChannelSet> sets = new HashSet<QuantitationChannelSet>();
Dictionary<IQuantitationChannel, HashSet<int>> locations = new Dictionary<IQuantitationChannel, HashSet<int>>();
HashSet<int> residues;
IMass[] mods = peptide.Modifications;
int modLength = mods.Length;
for (int i = 0; i < modLength; i++)
{
if (mods[i] != null)
{
mod = mods[i];
List<QuantitationChannelSet> channelsets = new List<QuantitationChannelSet>();
if ((modCol = mod as ModificationCollection) != null)
{
foreach (IMass mod2 in modCol)
{
if ((quantSetMod = mod2 as QuantitationChannelSet) != null)
{
channelsets.Add(quantSetMod);
}
}
}
else if ((quantSetMod = mod as QuantitationChannelSet) != null)
{
channelsets.Add(quantSetMod);
}
foreach (QuantitationChannelSet channelset in channelsets)
{
sets.Add(channelset);
foreach (IQuantitationChannel channel in channelset.GetChannels())
{
if (locations.TryGetValue(channel, out residues))
{
residues.Add(i);
}
else
{
residues = new HashSet<int>() { i };
locations.Add(channel, residues);
}
}
}
}
}
if (sets.Count == 0)
{
yield return new Peptide(peptide, true);
}
else if (sets.Count == 1)
{
foreach (QuantitationChannelSet set in sets)
{
foreach (IQuantitationChannel channel in set.GetChannels())
{
Peptide toReturn = new Peptide(peptide, true);
foreach (int residue in locations[channel])
{
toReturn.SetModification(channel, residue);
}
yield return toReturn;
}
}
}
else
{
List<HashSet<IQuantitationChannel>> quantChannels = new List<HashSet<IQuantitationChannel>>();
GetUniquePeptides_helper(sets.ToList(), 0, new HashSet<IQuantitationChannel>(), quantChannels);
foreach (HashSet<IQuantitationChannel> channelset in quantChannels)
{
Peptide toReturn = new Peptide(peptide, true);
Dictionary<int, IMass> modsToAdd = new Dictionary<int, IMass>();
IMass modToAdd;
foreach (IQuantitationChannel channel in channelset)
{
foreach (int residue in locations[channel])
{
if (modsToAdd.TryGetValue(residue, out modToAdd))
{
ModificationCollection col = new ModificationCollection(channel, modToAdd);
col.Add(channel);
col.Add(modToAdd);
modsToAdd[residue] = col;
}
else
{
modsToAdd.Add(residue, channel);
}
}
}
foreach (KeyValuePair<int, IMass> kvp in modsToAdd)
{
toReturn.SetModification(kvp.Value, kvp.Key);
}
yield return toReturn;
}
}
yield break;
}
private bool DetermineModification(int primaryStart, int primaryEnd, int secondaryStart, int secondaryEnd, ModificationCollection modifications)
{
bool result = false;
int primaryLength = primaryEnd - primaryStart;
int secondaryLength = secondaryEnd - secondaryStart;
if (secondaryLength > 0)
{
if (primaryLength > 0)
{
var minLength = Math.Min(secondaryLength, primaryLength);
modifications.AddReplaced(primaryStart, secondaryStart, minLength);
if (secondaryLength > primaryLength)
{
secondaryStart += minLength;
modifications.AddAdded(secondaryStart, secondaryLength - primaryLength);
}
else
{
if (primaryLength > secondaryLength)
{
primaryStart += minLength;
modifications.AddRemoved(primaryStart, primaryLength - secondaryLength);
}
}
}
else
{
modifications.AddAdded(secondaryStart, secondaryLength);
}
result = true;
}
else
{
if (primaryLength > 0)
{
modifications.AddRemoved(primaryStart, primaryLength);
result = true;
}
}
return(result);
}
public ModificationCollection Compare(TextFile primary, TextFile secondary)
{
_primary = primary;
_secondary = secondary;
ModificationCollection result = new ModificationCollection(primary, secondary);
if (primary.LineCount == 0 && secondary.LineCount == 0)
{
// два пустых файла
_primary = null;
_secondary = null;
return(result);
}
if (primary.LineCount == 0)
{
if (secondary.LineCount > 0)
{
// первый файл пустой, а второй имеет строки
result.AddAdded(0, secondary.LineCount);
}
_primary = null;
_secondary = null;
return(result);
}
if (secondary.LineCount == 0)
{
if (primary.LineCount > 0)
{
// первый файл имеет строки, а второй пустой
result.AddRemoved(0, primary.LineCount);
}
_primary = null;
_secondary = null;
return(result);
}
List <Area> areas = new List <Area>();
DivideIntoAreas(0, primary.LineCount - 1, 0, secondary.LineCount - 1, areas);
areas.Sort(Area.SecondaryIndexComparer);
int primaryIndex = 0;
int secondaryIndex = 0;
Area last = null;
foreach (Area area in areas)
{
if (DetermineModification(primaryIndex, area.PrimaryIndex, secondaryIndex, area.SecondaryIndex, result) ||
last == null)
{
result.AddNoChanged(area.PrimaryIndex, area.Length);
}
primaryIndex = area.PrimaryIndex + area.Length;
secondaryIndex = area.SecondaryIndex + area.Length;
last = area;
}
// этот вызов решает проблему, когда файлы совершенно разные
// это граничная ситуация, областей пересечения нет
DetermineModification(primaryIndex, primary.LineCount, secondaryIndex, secondary.LineCount, result);
return(result);
}
public void ModificationCollectionTest2()
{
ModificationCollection a = new ModificationCollection(new OldSchoolModification(1, "Mod1"), new OldSchoolModification(2, "Mod2"));
Assert.IsFalse(a.Remove(new OldSchoolModification(3, "Mod3")));
}
public ModificationCollection Compare(TextFile primary, TextFile secondary)
{
_primary = primary;
_secondary = secondary;
ModificationCollection result = new ModificationCollection(primary, secondary);
if (primary.LineCount == 0 && secondary.LineCount == 0)
{
// два пустых файла
_primary = null;
_secondary = null;
return result;
}
if (primary.LineCount == 0)
{
if (secondary.LineCount > 0)
{
// первый файл пустой, а второй имеет строки
result.AddAdded(0, secondary.LineCount);
}
_primary = null;
_secondary = null;
return result;
}
if (secondary.LineCount == 0)
{
if (primary.LineCount > 0)
{
// первый файл имеет строки, а второй пустой
result.AddRemoved(0, primary.LineCount);
}
_primary = null;
_secondary = null;
return result;
}
List<Area> areas = new List<Area>();
DivideIntoAreas(0, primary.LineCount - 1, 0, secondary.LineCount - 1, areas);
areas.Sort(Area.SecondaryIndexComparer);
int primaryIndex = 0;
int secondaryIndex = 0;
Area last = null;
foreach (Area area in areas)
{
if (DetermineModification(primaryIndex, area.PrimaryIndex, secondaryIndex, area.SecondaryIndex, result) ||
last == null)
{
result.AddNoChanged(area.PrimaryIndex, area.Length);
}
primaryIndex = area.PrimaryIndex + area.Length;
secondaryIndex = area.SecondaryIndex + area.Length;
last = area;
}
// этот вызов решает проблему, когда файлы совершенно разные
// это граничная ситуация, областей пересечения нет
DetermineModification(primaryIndex, primary.LineCount, secondaryIndex, secondary.LineCount, result);
return result;
}
private bool DetermineModification(int primaryStart, int primaryEnd, int secondaryStart, int secondaryEnd, ModificationCollection modifications)
{
bool result = false;
int primaryLength = primaryEnd - primaryStart;
int secondaryLength = secondaryEnd - secondaryStart;
if (secondaryLength > 0)
{
if (primaryLength > 0)
{
var minLength = Math.Min(secondaryLength, primaryLength);
modifications.AddReplaced(primaryStart, secondaryStart, minLength);
if (secondaryLength > primaryLength)
{
secondaryStart += minLength;
modifications.AddAdded(secondaryStart, secondaryLength - primaryLength);
}
else
{
if (primaryLength > secondaryLength)
{
primaryStart += minLength;
modifications.AddRemoved(primaryStart, primaryLength - secondaryLength);
}
}
}
else
{
modifications.AddAdded(secondaryStart, secondaryLength);
}
result = true;
}
else
{
if (primaryLength > 0)
{
modifications.AddRemoved(primaryStart, primaryLength);
result = true;
}
}
return result;
}
private void Control_EndMove(HtmlDesignMovableControl c)
{
IModification m;
if (_selectionList.Count == 1)
{
HtmlDesignMovableControl o = _selectionList[0].Owner;
Point previousLocation = _PreviousLocations[o];
m = previousLocation != o.Control.Location ? HtmlControlModification.GetMoved(o, previousLocation) : (IModification)null;
}
else
{
var list = new ModificationCollection<HtmlControlModification>();
foreach (var bc in _selectionList)
{
HtmlDesignMovableControl o = bc.Owner;
Point previousLocation = _PreviousLocations[o];
if (previousLocation != o.Control.Location)
{
list.Add(HtmlControlModification.GetMoved(o, previousLocation));
}
}
if (list.Count == 1)
{
m = list[0];
}
else
{
m = list.Count > 0 ? list : null;
}
}
if(m != null)
{
HtmlPage.AddUndoOperation(m);
UpdateUndoRedoState();
}
c.Control.LocationChanged -= Control_LocationChanged;
}
