// To match this
// New File 2008/02/06 09:16:49 E:\copytest\src\file2.txt
Modification ParseAddedFile(
string logLine)
{
Match match = ParseAddedFileRegex.Match(logLine);
if (match.Success)
{
if (match.Groups.Count == 3)
{
string date = match.Groups["Date"].Captures[0].ToString();
string path = match.Groups["Path"].Captures[0].ToString();
Modification mod = new Modification();
mod.Type = "added";
mod.FileName = Path.GetFileName(path);
mod.FolderName = Path.GetDirectoryName(path);
mod.ModifiedTime = CreateDate(date);
return mod;
}
}
throw new Exception("Failed to match regex");
}
/// <summary>
/// Setups the modification.
/// </summary>
/// <param name="modifications">The modifications.</param>
/// <remarks></remarks>
public void SetupModification(Modification[] modifications)
{
foreach (IModificationUrlBuilder modificationUrlBuilder in _issueTrackers)
{
modificationUrlBuilder.SetupModification(modifications);
}
}
/// <summary>
/// Construct and return an array of Modifications describing the changes in
/// the AccuRev workspace, based on the output of the "accurev hist" command.
/// </summary>
/// <param name="history">the stream of <code><modifications></code> input</param>
/// <param name="from">the starting date and time for the range of modifications we want.</param>
/// <param name="to">the ending date and time for the range of modifications we want.</param>
/// <returns>the changes in the specified time range.</returns>
public Modification[] Parse(TextReader history, DateTime from, DateTime to)
{
XmlSerializer serializer = new XmlSerializer(typeof (Modification[]));
Modification[] mods = new Modification[0];
try
{
// return 0 modifications if "history" is empty.
if (history.Peek() == -1)
return mods;
mods = (Modification[]) serializer.Deserialize(history);
}
catch (InvalidOperationException e)
{
Log.Error(e);
if (e.InnerException is XmlException)
return mods;
throw;
}
var results = new List<Modification>();
foreach (Modification mod in mods)
{
if ((mod.ModifiedTime >= from) & (mod.ModifiedTime <= to))
results.Add(mod);
}
return results.ToArray();
}
/// <summary>
/// Setups the modification.
/// </summary>
/// <param name="modifications">The modifications.</param>
/// <remarks></remarks>
public void SetupModification(Modification[] modifications)
{
foreach (Modification modification in modifications)
{
modification.Url = Url + "rev/" + modification.Version;
}
}
/// <summary>
/// Gets the modifications from the source control provider
/// </summary>
/// <param name="from"></param>
/// <param name="to"></param>
/// <returns></returns>
public Modification[] GetModifications(IIntegrationResult from, IIntegrationResult to)
{
if (FailGetModifications)
{
throw new System.Exception("Failing GetModifications");
}
else if (AlwaysModified)
{
Modification[] mods = new Modification[1];
Modification mod = new Modification();
mod.FileName = "AlwaysModified";
mod.FolderName = "NullSourceControl";
mod.ModifiedTime = DateTime.Now;
mod.UserName = "******";
mod.ChangeNumber = Guid.NewGuid().ToString("N");
mod.Comment = "Making a change";
mod.Type = "modified";
mods[0] = mod;
return mods;
}
else
{
return new Modification[0];
}
}
/// <summary>
/// Parses the specified input.
/// </summary>
/// <param name="input">The input.</param>
/// <param name="from">From.</param>
/// <param name="to">To.</param>
/// <returns></returns>
/// <remarks></remarks>
public Modification[] Parse(TextReader input, DateTime from, DateTime to)
{
var mods = new List<Modification>();
var filemods = new List<string>();
string line;
while( (line = input.ReadLine()) != null )
{
if( !line.StartsWith(PlasticSCM.DELIMITER.ToString(CultureInfo.CurrentCulture)))
continue;
// path date user changeset
string[] data = line.Split(PlasticSCM.DELIMITER);
Modification mod = new Modification();
string path = data[1];
mod.FileName = Path.GetFileName(path);
mod.FolderName = Path.GetDirectoryName(path);
mod.UserName = data[2];
mod.ModifiedTime = DateTime.ParseExact (data[3], PlasticSCM.DATEFORMAT, CultureInfo.InvariantCulture);
mod.ChangeNumber = data[4];
if (!filemods.Contains(path))
{
filemods.Add(path);
mods.Add(mod);
}
}
return mods.ToArray();
}
public void SetupModification(Modification[] modifications)
{
foreach( Modification mod in modifications )
{
mod.Url = String.Format( _url, mod.FolderName + "/" + mod.FileName, mod.ChangeNumber );
}
}
public void SetupModification(Modification[] modifications)
{
foreach (Modification mod in modifications)
{
mod.Url = String.Format(_url, mod.FolderName.Length == 0 ? mod.FileName : mod.FolderName + "/" + mod.FileName);
}
}
/// <summary>
/// Parse a commit for modifications and returns a list with every modification in the date/time limits.
/// </summary>
/// <param name="commitMatch"></param>
/// <param name="from"></param>
/// <param name="to"></param>
/// <returns></returns>
private static IList<Modification> GetCommitModifications(Match commitMatch, DateTime from, DateTime to)
{
IList<Modification> result = new List<Modification>();
string hash = commitMatch.Groups["Hash"].Value;
DateTime modifiedTime = DateTime.Parse(commitMatch.Groups["Time"].Value);
string username = commitMatch.Groups["Author"].Value;
string emailAddress = commitMatch.Groups["Mail"].Value;
string comment = commitMatch.Groups["Message"].Value.TrimEnd('\r', '\n');
string changes = commitMatch.Groups["Changes"].Value;
if (modifiedTime < from || modifiedTime > to)
{
Log.Debug(string.Concat("[Git] Ignore commit '", hash, "' from '", modifiedTime.ToUniversalTime(),
"' because it is older then '",
from.ToUniversalTime(), "' or newer then '", to.ToUniversalTime(), "'."));
return result;
}
MatchCollection file_matches = changeList.Matches(changes);
if (file_matches.Count != 0)
{
foreach (Match change in file_matches)
{
Modification mod = new Modification();
mod.ChangeNumber = hash;
mod.Comment = comment;
mod.EmailAddress = emailAddress;
mod.ModifiedTime = modifiedTime;
mod.UserName = username;
mod.Type = GetModificationType(change.Groups["Type"].Value);
string fullFilePath = change.Groups["FileName"].Value.TrimEnd('\r', '\n');
mod.FileName = GetFileFromPath(fullFilePath);
mod.FolderName = GetFolderFromPath(fullFilePath);
result.Add(mod);
}
}
else
{
Modification mod = new Modification();
mod.ChangeNumber = hash;
mod.Comment = comment;
mod.EmailAddress = emailAddress;
mod.ModifiedTime = modifiedTime;
mod.UserName = username;
mod.Type = GetModificationType("m");
mod.FileName = "Specific commit. No file changes.";
mod.FolderName = "";
result.Add(mod);
}
return result;
}
private DateTime firstModifiedTime(Modification[] modifications)
{
DateTime subResult = modifications[0].ModifiedTime;
foreach (Modification modification in modifications)
if (modification.ModifiedTime < subResult)
subResult = modification.ModifiedTime;
return subResult;
}
public bool Accept(Modification modification)
{
if (modification.FolderName == null || modification.FileName == null)
{
return false;
}
string path = Path.Combine(modification.FolderName, modification.FileName);
return PathUtils.MatchPath(Pattern, path, caseSensitive);
}
/// <summary>
/// Build the Modification list of what files will be built
/// with this Release
/// </summary>
/// <param name="mods"></param>
/// <returns></returns>
public static Modification[] AnalyzeModifications(IList mods)
{
// Hashtables are used so we can compare on the keys in search of duplicates
Hashtable allFiles = new Hashtable();
foreach (Modification mod in mods)
{
string key = mod.FolderName + mod.FileName;
if (!allFiles.ContainsKey(key))
allFiles.Add(key, mod);
else
{
// If the revision number on the original is larger, then
// do the comparision against the original modification
// in search to see which revision is higher
// example: 1.64.1 < 1.65 but you need to compare against the
// larger string of 1.64.1 because we are splitting the numbers individually
// so 1 is compared to 1 and 64 is compared to 65.
Modification compareMod = allFiles[key] as Modification;
string[] originalVersion = compareMod.Version.Split(char.Parse("."));
string[] currentVersion = mod.Version.Split(char.Parse("."));
int len1 = originalVersion.Length;
int len2 = currentVersion.Length;
int usingLen = -1;
int otherLen = -1;
if (len1 >= len2)
{
usingLen = len1;
otherLen = len2;
}
else
{
usingLen = len2;
otherLen = len1;
}
for (int i = 0; i < usingLen; i++)
{
if (i > otherLen)
continue;
if (Convert.ToInt32(currentVersion[i]) > Convert.ToInt32(originalVersion[i]))
{
allFiles[compareMod.FolderName + compareMod.FileName] = mod;
break;
}
}
}
}
// Convert the Hashtables to Modification arrays
Modification[] validMods = new Modification[allFiles.Count];
int count = 0;
foreach (string key in allFiles.Keys)
{
validMods[count++] = allFiles[key] as Modification;
}
return validMods;
}
public void SendMessageToModifiersWhoCheckedInTheFiles(Modification[] modifications, String Message)
{
foreach (Modification modification in modifications)
{
YahooUser yuser = GetYahooUser(modification.UserName);
if (yuser!=null)
{
YahooWrap.SendYahooMessage(yuser.ID, Message);
}
}
}
public void LastModificationDate()
{
Modification earlierModification = new Modification();
earlierModification.ModifiedTime = new DateTime(0);
Modification laterModification = new Modification();
laterModification.ModifiedTime = new DateTime(1);
result.Modifications = new Modification[] { earlierModification, laterModification };
Assert.AreEqual(laterModification.ModifiedTime, result.LastModificationDate);
}
public void AssignModificationTime( Modification modification, string time )
{
try
{
modification.ModifiedTime = DateTime.Parse( time );
}
catch ( FormatException )
{
modification.ModifiedTime = DateTime.MinValue;
}
}
private static Modification ParseModification(Match revision, string path, DateTime createdDate)
{
Modification mod = new Modification();
mod.Comment = revision.Groups["Comment"].Value.Trim();
mod.FileName = Path.GetFileName(path);
mod.FolderName = Path.GetDirectoryName(path).Trim();
mod.ModifiedTime = Pvcs.GetDate(revision.Groups["CheckIn"].Value.Trim());
mod.UserName = revision.Groups["Author"].Value.Trim();
mod.Version = revision.Groups["Version"].Value.Trim();
mod.Type = (mod.ModifiedTime == createdDate) ? "New" : "Checked in";
return mod;
}
public ModificationPhaseFactory(IPofSerializer pofSerializer, IFileSystemProxy fileSystemProxy, TemporaryFileService temporaryFileService, ExeggutorService exeggutorService, ModificationPhaseManager phaseManager, ModificationLoader modificationLoader, ModificationViewModel viewModel, LeagueBuildUtilities leagueBuildUtilities, Modification modification)
{
this.pofSerializer = pofSerializer;
this.fileSystemProxy = fileSystemProxy;
this.temporaryFileService = temporaryFileService;
this.exeggutorService = exeggutorService;
this.phaseManager = phaseManager;
this.modificationLoader = modificationLoader;
this.viewModel = viewModel;
this.leagueBuildUtilities = leagueBuildUtilities;
this.modification = modification;
}
private string GetModificationsDetectedMessage(Modification[] modifications)
{
switch (modifications.Length)
{
case 0:
return "No modifications detected.";
case 1:
return "1 modification detected.";
default:
return string.Format("{0} modifications detected.", modifications.Length);
}
}
public ModificationForm(Modification modification)
{
InitializeComponent();
RevivalMod = modification;
// Set tab size
int EM_SETTABSTOPS = 0x00CB;
Graphics graphics = releaseNotesTextBox.CreateGraphics();
int characterWidth = (int)graphics.MeasureString("M", releaseNotesTextBox.Font).Width;
int tabWidth = 1;
SendMessage(releaseNotesTextBox.Handle, EM_SETTABSTOPS, 1, new int[] { tabWidth * characterWidth });
}
private Modification GenerateModification(string name, string type)
{
Modification modification = new Modification();
modification.ChangeNumber = "1";
modification.Comment = "A comment";
modification.EmailAddress = "*****@*****.**";
modification.FileName = name;
modification.ModifiedTime = new DateTime(2009, 1, 1);
modification.Type = type;
modification.UserName = "******";
modification.Version = "1.1.1.1";
return modification;
}
public void WriteModifications(Modification[] mods)
{
writer.WriteStartElement(Elements.MODIFICATIONS);
if (mods == null)
{
return;
}
foreach (Modification mod in mods)
{
mod.ToXml(writer);
}
writer.WriteEndElement();
}
/// <summary>
/// Parses output from p4.exe obtained using arguments <code>p4 -s describe -s 123</code>
/// where 123 (etc...) are changelist numbers. This output looks like this:
/// <p>
/// <code>
/// text: Change 123 by user@hostname on 2002/08/21 14:39:52
/// text:
/// text: The checkin comment
/// text:
/// text: Affected files ...
/// text:
/// info1: //view/path/filename.java#1 add
/// text:
/// exit: 0
/// </code>
/// </p>
/// the type appears at the end of the info1 line, and may be add, edit, delete etc...
/// Two regex strings are used to match the first line, and the 'info1:' line.
/// NOTE there's a tab character before comment text.
/// </summary>
/// <param name="reader"></param>
/// <param name="from"></param>
/// <param name="to"></param>
/// <returns></returns>
public Modification[] Parse(TextReader reader, DateTime from, DateTime to)
{
var mods = new List<Modification>();
string line;
string change = null, email = null, user = null, comment = string.Empty;
DateTime date = DateTime.Now;
while((line = reader.ReadLine()) != null)
{
Match modificationMatch = modRegex.Match(line);
if (modificationMatch.Success)
{
// when this line is matched, we're finished with this mod, so add it
Modification mod = new Modification();
mod.ChangeNumber = change;
mod.Version = modificationMatch.Groups["revision"].Value;
mod.FolderName = modificationMatch.Groups["folder"].Value;
mod.FileName = modificationMatch.Groups["file"].Value;
mod.Type = modificationMatch.Groups["type"].Value;
mod.EmailAddress = email;
mod.UserName = user;
mod.ModifiedTime = date;
mod.Comment = comment.Trim();
mods.Add(mod);
}
else
{
Match changeMatch = changeRegex.Match(line);
if (changeMatch.Success)
{
// set these values while they're available
change = changeMatch.Groups["change"].Value;
email = changeMatch.Groups["email"].Value;
user = changeMatch.Groups["user"].Value;
date = DateTime.Parse(changeMatch.Groups["date"].Value, CultureInfo.CurrentCulture);
// TODO this is necessary, could someone explain why?
comment =string.Empty;
}
else
{
string checkinCommentPrefix = "text: \t";
if (line.StartsWith(checkinCommentPrefix))
{
comment += line.Substring(checkinCommentPrefix.Length) + "\r\n";
}
}
}
}
return mods.ToArray();
}
// #CheckInComment#|#Name#|#DbPath#|#SCIT#|#Mime Type#|#LocalPath#|#Changed By#|#NxN_VersionNumber#
public Modification ParseModification(string[] modificationParams)
{
Modification modification = new Modification();
modification.Comment = modificationParams[0];
modification.FileName = modificationParams[1];
modification.FolderName = "ab:/" + modificationParams[2].Replace("/" + modificationParams[1],string.Empty);
modification.ModifiedTime = DateTime.FromFileTime(long.Parse(modificationParams[3]));
modification.Type = modificationParams[4];
modification.Url = modificationParams[5];
modification.UserName = modificationParams[6];
modification.Version = modificationParams[7];
return modification;
}
public void AssignFileInfo( Modification modification, string file )
{
int separatorLocation = file.LastIndexOf( Path.DirectorySeparatorChar.ToString() );
if ( separatorLocation > - 1 )
{
modification.FolderName = file.Substring( 0, separatorLocation );
modification.FileName = file.Substring( separatorLocation + 1 );
}
else
{
modification.FolderName = string.Empty;
modification.FileName = file;
}
}
/// <summary>
/// Setups the modification.
/// </summary>
/// <param name="modifications">The modifications.</param>
/// <remarks></remarks>
public void SetupModification(Modification[] modifications)
{
foreach (Modification mod in modifications)
{
if ((mod != null) && !string.IsNullOrEmpty(mod.Comment) && mod.Comment.Length > 0)
{
if (Regex.IsMatch(mod.Comment, _find))
{
mod.IssueUrl = Regex.Replace(mod.Comment, _find, _replace);
}
}
}
}
private Modification ParseModification(string[] modificationParams)
{
Modification modification = new Modification();
int lastIndexOfBackslash = modificationParams[1].LastIndexOf("\\");
modification.FileName = modificationParams[1].Substring(modificationParams[1].LastIndexOf("\\") + 1);
if (lastIndexOfBackslash > 0)
{
modification.FolderName = modificationParams[1].Substring(0, (modificationParams[1].LastIndexOf("\\")));
}
modification.ChangeNumber = int.Parse(modificationParams[2]);
modification.ModifiedTime = DateTime.Parse(modificationParams[3]);
modification.UserName = modificationParams[4];
modification.Comment = modificationParams[5];
return modification;
}
/// <summary>
/// Construct and return an array of Modifications describing the changes in
/// the AccuRev workspace, based on the output of the "accurev hist" command.
/// </summary>
/// <param name="history">the stream of "accurev hist" command output</param>
/// <param name="from">the starting date and time for the range of modifications we want.</param>
/// <param name="to">the ending date and time for the range of modifications we want.</param>
/// <returns>the changes in the specified time range.</returns>
public Modification[] Parse(TextReader history, DateTime from, DateTime to)
{
string line;
fromDateTime = from;
toDateTime = to;
modificationList = new List<Modification>();
modificationTemplate = null;
Regex firstTokenPattern = new Regex(@"^\s*(\S+)");
Regex absolutePathPrefixPattern = new Regex(@"(\\|/)\.(\\|/)");
Regex commentTextPattern = new Regex(@"^\s*# (.*)$");
while ((line = history.ReadLine()) != null)
{
// Get the first non-whitespace token in the line and decide how to parse based on it:
Match parsed = firstTokenPattern.Match(line);
string firstToken =string.Empty;
if (parsed.Success)
firstToken = parsed.Groups[1].ToString();
switch (firstToken)
{
case "transaction":
ParseTransaction(line);
break;
case "#":
// String together the lines of the comment, with a newline sequence between
// adjacent lines.
if (modificationTemplate.Comment != null)
modificationTemplate.Comment += Environment.NewLine;
Match commentText = commentTextPattern.Match(line);
if (commentText.Groups.Count != 0)
modificationTemplate.Comment += commentText.Groups[1].ToString();
break;
case "ancestor:":
case "type:":
case "":
// Ignore uninteresting lines.
break;
default:
if (absolutePathPrefixPattern.IsMatch(firstToken))
ParseFileLine(line);
else
Log.Error(string.Format(System.Globalization.CultureInfo.CurrentCulture,"Unrecognized line in AccuRev \"accurev hist\" output: {0}", line));
break;
}
}
Log.Debug(string.Format(System.Globalization.CultureInfo.CurrentCulture,"AccuRev reported {0} modifications", modificationList.Count));
return modificationList.ToArray();
}
/// <summary>
/// Accepts the specified m.
/// </summary>
/// <param name="m">The m.</param>
/// <returns></returns>
/// <remarks></remarks>
public bool Accept(Modification m)
{
if (this.Filters.Length == 0)
{
return false;
}
foreach (IModificationFilter mf in Filters)
{
if (!mf.Accept(m))
{
return false;
}
}
return true;
}
public Modification CreateNewModification(
string userName,
string time,
string elementName,
string modificationType,
string comment,
string change )
{
Modification modification = new Modification();
modification.ChangeNumber = change;
modification.UserName = userName;
modification.Type = modificationType;
modification.Comment = ( comment == string.Empty ? null : comment );
AssignFileInfo( modification, elementName );
AssignModificationTime( modification, time );
return modification;
}
/// <summary>
/// Setups the modification.
/// </summary>
/// <param name="modifications">The modifications.</param>
/// <remarks></remarks>
public void SetupModification(Modification[] modifications)
{
if (modifications == null) throw new ArgumentNullException("modifications");
foreach (Modification mod in modifications)
{
//split the comment on a space, take the first part
//this must be the issue ID
//from the last position of this part, go back while the characters are numeric
if ((mod != null) && !string.IsNullOrEmpty(mod.Comment) && mod.Comment.Length > 0)
{
if (mod.Comment.IndexOf(' ') != 0)
{
string searchingComment = mod.Comment.Split(' ')[0];
int endPosition = searchingComment.Length - 1;
char currentChar = searchingComment[endPosition];
string result = string.Empty;
bool numericPartFound = false;
//eliminate non numeric characters at the end (ex type [ccnet-1500])
while (endPosition > 0 && !char.IsNumber(currentChar))
{
endPosition--;
currentChar = searchingComment[endPosition];
}
//while last position is numeric add to result
while (endPosition >= 0 && char.IsNumber(currentChar))
{
result = result.Insert(0, currentChar.ToString(CultureInfo.CurrentCulture));
endPosition--;
if (endPosition >= 0) currentChar = searchingComment[endPosition];
numericPartFound = true;
}
if (numericPartFound)
{
mod.IssueUrl = string.Format(CultureInfo.CurrentCulture, _url, result);
}
}
}
}
}
public void TestFullProteinReadWrite()
{
Modification mod = new Modification("mod1", "modType1");
ModificationMotif.TryGetMotif("E", out ModificationMotif motif);
ModificationWithLocation mod2 = new ModificationWithLocation("mod2", "modType1", motif, TerminusLocalization.Any, null);
ModificationMotif.TryGetMotif("N", out ModificationMotif motif3);
ModificationWithMass mod3 = new ModificationWithMass("mod3", "modType1", motif3, TerminusLocalization.Any, 10, null, null, null);
List <Tuple <string, string> > gene_names = new List <Tuple <string, string> > {
new Tuple <string, string>("a", "b")
};
IDictionary <int, List <Modification> > oneBasedModifications = new Dictionary <int, List <Modification> >
{
{ 3, new List <Modification> {
mod
} },
{ 4, new List <Modification> {
mod2
} },
{ 5, new List <Modification> {
mod3
} }
};
List <ProteolysisProduct> proteolysisProducts = new List <ProteolysisProduct> {
new ProteolysisProduct(1, 2, "propeptide")
};
string name = "testName";
string full_name = "testFullName";
List <DatabaseReference> databaseReferences = new List <DatabaseReference> {
new DatabaseReference("type1", "id1", new List <Tuple <string, string> > {
new Tuple <string, string>("e1", "e2")
})
};
List <SequenceVariation> sequenceVariations = new List <SequenceVariation> {
new SequenceVariation(3, "Q", "N", "replace Q by N"),
new SequenceVariation(3, 4, "QE", "NN", "replace QE by NN")
};
List <DisulfideBond> disulfideBonds = new List <DisulfideBond> {
new DisulfideBond(1, "ds1"), new DisulfideBond(2, 3, "ds2")
};
Protein p1 = new Protein("SEQENCE",
"a1",
gene_names: gene_names,
oneBasedModifications: oneBasedModifications,
proteolysisProducts: proteolysisProducts,
name: name,
full_name: full_name,
isDecoy: false,
isContaminant: true,
databaseReferences: databaseReferences,
sequenceVariations: sequenceVariations,
disulfideBonds: disulfideBonds,
databaseFilePath: Path.Combine(TestContext.CurrentContext.TestDirectory, @"bnueiwhf.xml"));
// Generate data for files
ProteinDbWriter.WriteXmlDatabase(new Dictionary <string, HashSet <Tuple <int, Modification> > >(), new List <Protein> {
p1
}, Path.Combine(TestContext.CurrentContext.TestDirectory, @"bnueiwhf.xml"));
IEnumerable <string> modTypesToExclude = new List <string>();
IEnumerable <Modification> allKnownModifications = new List <Modification>();
List <Protein> ok = ProteinDbLoader.LoadProteinXML(Path.Combine(TestContext.CurrentContext.TestDirectory, @"bnueiwhf.xml"), true, DecoyType.None, allKnownModifications, true, modTypesToExclude, out Dictionary <string, Modification> unknownModifications);
Assert.AreEqual(p1.Accession, ok[0].Accession);
Assert.AreEqual(p1.BaseSequence, ok[0].BaseSequence);
Assert.AreEqual(p1.DatabaseReferences.First().Id, ok[0].DatabaseReferences.First().Id);
Assert.AreEqual(p1.DatabaseReferences.First().Properties.First().Item1, ok[0].DatabaseReferences.First().Properties.First().Item1);
Assert.AreEqual(p1.DatabaseReferences.First().Properties.First().Item2, ok[0].DatabaseReferences.First().Properties.First().Item2);
Assert.AreEqual(p1.DatabaseReferences.First().Type, ok[0].DatabaseReferences.First().Type);
Assert.AreEqual(p1.DisulfideBonds.First().Description, ok[0].DisulfideBonds.First().Description);
Assert.AreEqual(p1.DisulfideBonds.First().OneBasedBeginPosition, ok[0].DisulfideBonds.First().OneBasedBeginPosition);
Assert.AreEqual(p1.DisulfideBonds.First().OneBasedEndPosition, ok[0].DisulfideBonds.First().OneBasedEndPosition);
Assert.AreEqual(p1.DisulfideBonds.Last().Description, ok[0].DisulfideBonds.Last().Description);
Assert.AreEqual(p1.DisulfideBonds.Last().OneBasedBeginPosition, ok[0].DisulfideBonds.Last().OneBasedBeginPosition);
Assert.AreEqual(p1.DisulfideBonds.Last().OneBasedEndPosition, ok[0].DisulfideBonds.Last().OneBasedEndPosition);
Assert.AreEqual(p1.FullDescription, ok[0].FullDescription);
Assert.AreEqual(p1.FullName, ok[0].FullName);
Assert.AreEqual(p1.GeneNames, ok[0].GeneNames);
Assert.AreEqual(p1.IsContaminant, ok[0].IsContaminant);
Assert.AreEqual(p1.IsDecoy, ok[0].IsDecoy);
Assert.AreEqual(p1.Length, ok[0].Length);
Assert.AreEqual(p1.Name, ok[0].Name);
Assert.AreEqual(p1.Organism, ok[0].Organism);
Assert.AreEqual(p1.DatabaseFilePath, ok[0].DatabaseFilePath);
Assert.AreEqual(p1.OneBasedPossibleLocalizedModifications[3][0], ok[0].OneBasedPossibleLocalizedModifications[3][0]);
Assert.AreEqual(p1.OneBasedPossibleLocalizedModifications[3][0].id, ok[0].OneBasedPossibleLocalizedModifications[3][0].id);
Assert.AreEqual(p1.OneBasedPossibleLocalizedModifications[3][0].modificationType, ok[0].OneBasedPossibleLocalizedModifications[3][0].modificationType);
Assert.AreEqual(p1.OneBasedPossibleLocalizedModifications[4][0].id, ok[0].OneBasedPossibleLocalizedModifications[4][0].id);
Assert.AreEqual(p1.OneBasedPossibleLocalizedModifications[4][0].modificationType, ok[0].OneBasedPossibleLocalizedModifications[4][0].modificationType);
Assert.AreEqual((p1.OneBasedPossibleLocalizedModifications[4][0] as ModificationWithLocation).linksToOtherDbs, (ok[0].OneBasedPossibleLocalizedModifications[4][0] as ModificationWithLocation).linksToOtherDbs);
Assert.AreEqual((p1.OneBasedPossibleLocalizedModifications[4][0] as ModificationWithLocation).motif, (ok[0].OneBasedPossibleLocalizedModifications[4][0] as ModificationWithLocation).motif);
Assert.AreEqual((p1.OneBasedPossibleLocalizedModifications[4][0] as ModificationWithLocation).terminusLocalization, (ok[0].OneBasedPossibleLocalizedModifications[4][0] as ModificationWithLocation).terminusLocalization);
Assert.AreEqual((p1.OneBasedPossibleLocalizedModifications[5][0] as ModificationWithMass).diagnosticIons, (ok[0].OneBasedPossibleLocalizedModifications[5][0] as ModificationWithMass).diagnosticIons);
Assert.AreEqual((p1.OneBasedPossibleLocalizedModifications[5][0] as ModificationWithMass).neutralLosses, (ok[0].OneBasedPossibleLocalizedModifications[5][0] as ModificationWithMass).neutralLosses);
Assert.AreEqual((p1.OneBasedPossibleLocalizedModifications[5][0] as ModificationWithMass).monoisotopicMass, (ok[0].OneBasedPossibleLocalizedModifications[5][0] as ModificationWithMass).monoisotopicMass);
Assert.AreEqual(p1.ProteolysisProducts.First().OneBasedBeginPosition, ok[0].ProteolysisProducts.First().OneBasedBeginPosition);
Assert.AreEqual(p1.ProteolysisProducts.First().OneBasedEndPosition, ok[0].ProteolysisProducts.First().OneBasedEndPosition);
Assert.AreEqual(p1.ProteolysisProducts.First().Type, ok[0].ProteolysisProducts.First().Type);
Assert.AreEqual(p1.SequenceVariations.First().Description, ok[0].SequenceVariations.First().Description);
Assert.AreEqual(p1.SequenceVariations.First().OneBasedBeginPosition, ok[0].SequenceVariations.First().OneBasedBeginPosition);
Assert.AreEqual(p1.SequenceVariations.First().OneBasedEndPosition, ok[0].SequenceVariations.First().OneBasedEndPosition);
Assert.AreEqual(p1.SequenceVariations.First().OriginalSequence, ok[0].SequenceVariations.First().OriginalSequence);
Assert.AreEqual(p1.SequenceVariations.First().VariantSequence, ok[0].SequenceVariations.First().VariantSequence);
Assert.AreEqual(p1.SequenceVariations.Last().Description, ok[0].SequenceVariations.Last().Description);
Assert.AreEqual(p1.SequenceVariations.Last().OneBasedBeginPosition, ok[0].SequenceVariations.Last().OneBasedBeginPosition);
Assert.AreEqual(p1.SequenceVariations.Last().OneBasedEndPosition, ok[0].SequenceVariations.Last().OneBasedEndPosition);
Assert.AreEqual(p1.SequenceVariations.Last().OriginalSequence, ok[0].SequenceVariations.Last().OriginalSequence);
Assert.AreEqual(p1.SequenceVariations.Last().VariantSequence, ok[0].SequenceVariations.Last().VariantSequence);
}
/// <summary>
/// Creates the individual label string.
/// </summary>
/// <param name="mod">The mod.</param>
/// <param name="label">The label.</param>
/// <returns></returns>
/// <remarks></remarks>
public string CreateIndividualLabelString(Modification mod, string label)
{
return(string.Format(CultureInfo.CurrentCulture, INDIVIDUAL_LABEL_REVISION_TEMPLATE, GetVersion(mod, label), GetUncPathPrefix(mod), mod.FolderName, mod.FileName));
}
/// <summary>
/// Gets the modifications.
/// </summary>
/// <param name="from">From.</param>
/// <param name="to">To.</param>
/// <returns></returns>
/// <remarks></remarks>
public override Modification[] GetModifications(IIntegrationResult from, IIntegrationResult to)
{
List <NameValuePair> originalSourceControlData = new List <NameValuePair>();
List <NameValuePair> finalSourceControlData = new List <NameValuePair>();
var sourceControlDataType = from.SourceControlData.GetType();
// check that the source control data given to us is in the list of list format
// if not, then convert it now
var fromSourceControlDataCount = from.SourceControlData.Count;
if (fromSourceControlDataCount > 0 &&
(fromSourceControlDataCount != SourceControls.Length ||
!XmlConversionUtil.CanConvertXmlToObject(sourceControlDataType, from.SourceControlData[0].Value)
)
)
{
var conversionList = new List <NameValuePair>();
for (int i = 0; i < SourceControls.Length; i++)
{
originalSourceControlData.Add(new NameValuePair(string.Format("sc{0:d}", i), ""));
}
int scdIndex = fromSourceControlDataCount - 1;
for (int i = originalSourceControlData.Count - 1; i >= 0; i--)
{
conversionList.Clear();
if (scdIndex >= 0)
{
if (!XmlConversionUtil.CanConvertXmlToObject(sourceControlDataType, from.SourceControlData[scdIndex].Value))
{
conversionList.Add(from.SourceControlData[scdIndex]);
}
}
originalSourceControlData[i].Value = XmlConversionUtil.ConvertObjectToXml(conversionList);
scdIndex--;
}
}
else
{
originalSourceControlData.AddRange(from.SourceControlData);
}
var originalSourceControlDataCount = originalSourceControlData.Count;
var modificationSet = new Dictionary <Modification, bool>();
int sourceControlIndex = 0;
foreach (ISourceControl sourceControl in SourceControls)
{
from.SourceControlData.Clear();
if (sourceControlIndex < originalSourceControlDataCount)
{
from.SourceControlData.AddRange((List <NameValuePair>)(XmlConversionUtil.ConvertXmlToObject(sourceControlDataType, originalSourceControlData[sourceControlIndex].Value)));
}
to.SourceControlData.Clear();
Modification[] mods = sourceControl.GetModifications(from, to);
finalSourceControlData.Add(new NameValuePair(string.Format("sc{0:d}", sourceControlIndex), XmlConversionUtil.ConvertObjectToXml(to.SourceControlData)));
if (mods != null && mods.Length > 0)
{
foreach (var mod in mods)
{
modificationSet[mod] = true;
}
}
else if (RequireChangesFromAll)
{
modificationSet.Clear();
break;
}
sourceControlIndex++;
}
to.SourceControlData.Clear();
to.SourceControlData.AddRange(finalSourceControlData);
// reset the from.SourceControlData to its original contents
from.SourceControlData.Clear();
from.SourceControlData.AddRange(originalSourceControlData);
var modArray = new Modification[modificationSet.Count];
modificationSet.Keys.CopyTo(modArray, 0);
return(modArray);
}
public static void TestModificationAnalysis()
{
Ms2ScanWithSpecificMass scan = new Ms2ScanWithSpecificMass(new MsDataScan(new MzSpectrum(new double[, ] {
}), 0, 0, true, Polarity.Positive,
0, new MzLibUtil.MzRange(0, 0), "", MZAnalyzerType.FTICR, 0, null, null, ""), 0, 0, "", new CommonParameters());
ModificationMotif.TryGetMotif("N", out ModificationMotif motif1);
Modification mod1 = new Modification(_originalId: "mod1", _modificationType: "myModType", _target: motif1, _locationRestriction: "Anywhere.", _monoisotopicMass: 10);
ModificationMotif.TryGetMotif("L", out ModificationMotif motif2);
Modification mod2 = new Modification(_originalId: "mod2", _modificationType: "myModType", _target: motif2, _locationRestriction: "Anywhere.", _monoisotopicMass: 10);
IDictionary <int, List <Modification> > oneBasedModifications = new Dictionary <int, List <Modification> >
{
{ 2, new List <Modification> {
mod1
} },
{ 5, new List <Modification> {
mod2
} },
{ 7, new List <Modification> {
mod1
} },
};
Protein protein1 = new Protein("MNLDLDNDL", "prot1", oneBasedModifications: oneBasedModifications);
Dictionary <int, Modification> allModsOneIsNterminus1 = new Dictionary <int, Modification>
{
{ 2, mod1 },
};
PeptideWithSetModifications pwsm1 = new PeptideWithSetModifications(protein1, new DigestionParams(), 2, 9, CleavageSpecificity.Unknown, null, 0, allModsOneIsNterminus1, 0);
Dictionary <int, Modification> allModsOneIsNterminus2 = new Dictionary <int, Modification>
{
{ 2, mod1 },
{ 7, mod1 },
};
PeptideWithSetModifications pwsm2 = new PeptideWithSetModifications(protein1, new DigestionParams(), 2, 9, CleavageSpecificity.Unknown, null, 0, allModsOneIsNterminus2, 0);
Dictionary <int, Modification> allModsOneIsNterminus3 = new Dictionary <int, Modification>
{
{ 7, mod1 },
};
PeptideWithSetModifications pwsm3 = new PeptideWithSetModifications(protein1, new DigestionParams(), 2, 9, CleavageSpecificity.Unknown, null, 0, allModsOneIsNterminus3, 0);
Dictionary <int, Modification> allModsOneIsNterminus4 = new Dictionary <int, Modification>
{
{ 8, mod1 },
};
PeptideWithSetModifications pwsm4 = new PeptideWithSetModifications(protein1, new DigestionParams(), 1, 9, CleavageSpecificity.Unknown, null, 0, allModsOneIsNterminus4, 0);
CommonParameters CommonParameters = new CommonParameters(
digestionParams: new DigestionParams(
maxMissedCleavages: 0,
minPeptideLength: 1,
maxModificationIsoforms: int.MaxValue),
scoreCutoff: 1);
var fsp = new List <(string fileName, CommonParameters fileSpecificParameters)>();
fsp.Add(("", CommonParameters));
var newPsms = new List <PeptideSpectralMatch>
{
new PeptideSpectralMatch(pwsm1, 0, 10, 0, scan, CommonParameters, new List <MatchedFragmentIon>()),
new PeptideSpectralMatch(pwsm1, 0, 10, 0, scan, CommonParameters, new List <MatchedFragmentIon>()),
new PeptideSpectralMatch(pwsm2, 0, 10, 0, scan, CommonParameters, new List <MatchedFragmentIon>()),
new PeptideSpectralMatch(pwsm3, 0, 10, 0, scan, CommonParameters, new List <MatchedFragmentIon>()),
new PeptideSpectralMatch(pwsm4, 0, 10, 0, scan, CommonParameters, new List <MatchedFragmentIon>()),
};
foreach (var psm in newPsms)
{
psm.ResolveAllAmbiguities();
}
MassDiffAcceptor searchMode = new SinglePpmAroundZeroSearchMode(5);
List <Protein> proteinList = new List <Protein> {
protein1
};
FdrAnalysisEngine fdrAnalysisEngine = new FdrAnalysisEngine(newPsms, searchMode.NumNotches, CommonParameters, fsp, new List <string>());
fdrAnalysisEngine.Run();
ModificationAnalysisEngine modificationAnalysisEngine = new ModificationAnalysisEngine(newPsms, new CommonParameters(), fsp, new List <string>());
var res = (ModificationAnalysisResults)modificationAnalysisEngine.Run();
Assert.AreEqual(2, res.CountOfEachModSeenOnProteins.Count());
Assert.AreEqual(2, res.CountOfEachModSeenOnProteins[mod1.IdWithMotif]);
Assert.AreEqual(1, res.CountOfEachModSeenOnProteins[mod2.IdWithMotif]);
Assert.AreEqual(1, res.CountOfModsSeenAndLocalized.Count());
Assert.AreEqual(2, res.CountOfModsSeenAndLocalized[mod1.IdWithMotif]);
Assert.AreEqual(0, res.CountOfAmbiguousButLocalizedModsSeen.Count());
Assert.AreEqual(0, res.CountOfUnlocalizedMods.Count());
Assert.AreEqual(0, res.CountOfUnlocalizedFormulas.Count());
}
protected override void ModifyValue(PropertyReferenceProperty property, object valueToSet, Modification modification, int index)
{
if (this.objects.Length == 0)
{
using (this.ViewModel.ForceDefaultSetValue())
this.parent.SetValue((PropertyReferenceProperty)this.parentProperty, this.parent.GetValue(this.baseReference, PropertyReference.GetValueFlags.Computed));
this.RebuildObjects();
}
bool treeModified = false;
SceneEditTransaction sceneEditTransaction = (SceneEditTransaction)null;
try
{
sceneEditTransaction = this.parent.PrepareTreeForModifyValue(this.parentProperty.Reference.Append(property.Reference), valueToSet, modification, out treeModified);
if (treeModified)
{
this.RebuildObjects();
}
base.ModifyValue(property, valueToSet, modification, index);
}
finally
{
if (sceneEditTransaction != null)
{
sceneEditTransaction.Commit();
sceneEditTransaction.Dispose();
}
}
}
/// <summary>
/// Read results from tsv file into group of objects from PSI_Interface
/// </summary>
/// <param name="idFilePath"></param>
/// <returns></returns>
public static SimpleMZIdentMLReader.SimpleMZIdentMLData ReadResultsFromFileToMzIdData(string idFilePath)
{
var databaseSearchResultData = ReadResultsFromFile(idFilePath);
var simpleMzIdentMLData = new SimpleMZIdentMLReader.SimpleMZIdentMLData(idFilePath);
foreach (var databaseSearchResult in databaseSearchResultData)
{
var peptide = new SimpleMZIdentMLReader.PeptideRef
{
Sequence = databaseSearchResult.Sequence
};
var identification = new SimpleMZIdentMLReader.SpectrumIdItem
{
Peptide = peptide,
Charge = databaseSearchResult.Charge,
ScanNum = databaseSearchResult.ScanNum,
SpecEv = databaseSearchResult.SpecEValue,
};
// Parse modification
var modParts = databaseSearchResult.Modifications.Split(',');
if (modParts.Length > 0)
{
foreach (var part in modParts)
{
var mod = part.Split(' ');
if (mod.Length < 2)
{
continue;
}
var modName = mod[0];
var modIndex = Convert.ToInt32(mod[1]);
var ipMod = Modification.Get(modName);
var modification = new SimpleMZIdentMLReader.Modification
{
Mass = ipMod.Mass,
Tag = modName,
};
peptide.ModsAdd(modIndex, modification);
}
}
var proteinAccessions = databaseSearchResult.ProteinName.Split(',');
foreach (var accession in proteinAccessions)
{
var dbSequence = new SimpleMZIdentMLReader.DatabaseSequence
{
Accession = accession.Trim(),
ProteinDescription = databaseSearchResult.ProteinDescription
};
var peptideEvidence = new SimpleMZIdentMLReader.PeptideEvidence
{
DbSeq = dbSequence,
Pre = databaseSearchResult.Pre,
Post = databaseSearchResult.Post,
PeptideRef = identification.Peptide,
Start = databaseSearchResult.Start,
End = databaseSearchResult.End,
};
identification.PepEvidence.Add(peptideEvidence);
}
simpleMzIdentMLData.Identifications.Add(identification);
}
return(simpleMzIdentMLData);
}
/*============*\
|* Setter *|
\*============*/
public void AddModification(Modification modification)
{
modification.SetModificationTarget(m_modificationObject);
m_modifications.Add(modification);
modAdded?.Invoke(modification);
}
public static Dictionary <Tuple <int, int>, List <Product> > XlLoopGetTheoreticalFragments(DissociationType dissociationType, Modification loopMass,
List <int> modPos, PeptideWithSetModifications peptide)
{
Dictionary <Tuple <int, int>, List <Product> > AllTheoreticalFragmentsLists = new Dictionary <Tuple <int, int>, List <Product> >();
var originalFragments = peptide.Fragment(dissociationType, FragmentationTerminus.Both).ToList();
foreach (int position1 in modPos)
{
foreach (int position2 in modPos)
{
if (position2 <= position1)
{
continue;
}
// add N and C terminal fragments that do not contain the loop
Tuple <int, int> loopPositions = new Tuple <int, int>(position1, position2);
List <Product> loopFragments = originalFragments
.Where(p => p.TerminusFragment.Terminus == FragmentationTerminus.N && p.TerminusFragment.AminoAcidPosition <position1 ||
p.TerminusFragment.Terminus == FragmentationTerminus.C && p.TerminusFragment.AminoAcidPosition> position2).ToList();
// add N-terminal fragments containing the loop
Dictionary <int, Modification> modDict = new Dictionary <int, Modification>();
if (peptide.AllModsOneIsNterminus.Any())
{
double combinedModMass = loopMass.MonoisotopicMass.Value + peptide.AllModsOneIsNterminus.Where(v => v.Key <= position2 + 1).Sum(p => p.Value.MonoisotopicMass.Value);
Modification combined = new Modification(_monoisotopicMass: combinedModMass);
modDict.Add(position1 + 1, combined);
foreach (var mod in peptide.AllModsOneIsNterminus.Where(m => m.Key > position2 + 1))
{
modDict.Add(mod.Key, mod.Value);
}
}
else
{
modDict.Add(position1 + 1, loopMass);
}
PeptideWithSetModifications peptideWithLoop = new PeptideWithSetModifications(peptide.Protein, peptide.DigestionParams,
peptide.OneBasedStartResidueInProtein, peptide.OneBasedEndResidueInProtein, peptide.CleavageSpecificityForFdrCategory,
peptide.PeptideDescription, peptide.MissedCleavages, modDict, peptide.NumFixedMods);
loopFragments.AddRange(peptideWithLoop.Fragment(dissociationType, FragmentationTerminus.Both)
.Where(p => p.TerminusFragment.Terminus == FragmentationTerminus.N && p.TerminusFragment.AminoAcidPosition >= position2));
// add C-terminal fragments containing the loop
modDict.Clear();
if (peptide.AllModsOneIsNterminus.Any())
{
double combinedModMass = loopMass.MonoisotopicMass.Value + peptide.AllModsOneIsNterminus.Where(v => v.Key >= position1 + 1).Sum(p => p.Value.MonoisotopicMass.Value);
Modification combined = new Modification(_monoisotopicMass: combinedModMass);
modDict.Add(position2 + 1, combined);
foreach (var mod in peptide.AllModsOneIsNterminus.Where(m => m.Key < position1 + 1))
{
modDict.Add(mod.Key, mod.Value);
}
}
else
{
modDict.Add(position2 + 1, loopMass);
}
peptideWithLoop = new PeptideWithSetModifications(peptide.Protein, peptide.DigestionParams,
peptide.OneBasedStartResidueInProtein, peptide.OneBasedEndResidueInProtein, peptide.CleavageSpecificityForFdrCategory,
peptide.PeptideDescription, peptide.MissedCleavages, modDict, peptide.NumFixedMods);
loopFragments.AddRange(peptideWithLoop.Fragment(dissociationType, FragmentationTerminus.Both)
.Where(p => p.TerminusFragment.Terminus == FragmentationTerminus.C && p.TerminusFragment.AminoAcidPosition <= position1));
AllTheoreticalFragmentsLists.Add(loopPositions, loopFragments);
}
}
return(AllTheoreticalFragmentsLists);
}
public void FilesLoading()
{
Loaders.LoadElements(Path.Combine(TestContext.CurrentContext.TestDirectory, "elements2.dat"));
var unimodMods = Loaders.LoadUnimod(Path.Combine(TestContext.CurrentContext.TestDirectory, "unimod_tables2.xml")).ToList();
Assert.AreEqual(2639, unimodMods.Count); // UniMod PTM list may be updated at some point, causing the unit test to fail
List <Modification> myList = unimodMods.Where(m => m.OriginalId.Equals("HexNAc(2)")).ToList();
Modification testMod = myList.First();
int neutralLossCount = 0;
if (testMod.NeutralLosses.Count != 0)
{
foreach (KeyValuePair <MassSpectrometry.DissociationType, List <double> > item in testMod.NeutralLosses)
{
foreach (double loss in item.Value)
{
neutralLossCount++;
}
}
}
Assert.AreEqual(2, neutralLossCount);
var psiModDeserialized = Loaders.LoadPsiMod(Path.Combine(TestContext.CurrentContext.TestDirectory, "PSI-MOD.obo2.xml"));
// N6,N6,N6-trimethyllysine
var trimethylLysine = psiModDeserialized.Items.OfType <UsefulProteomicsDatabases.Generated.oboTerm>().First(b => b.id.Equals("MOD:00083"));
Assert.AreEqual("1+", trimethylLysine.xref_analog.First(b => b.dbname.Equals("FormalCharge")).name);
// Phosphoserine
Assert.IsFalse(psiModDeserialized.Items.OfType <UsefulProteomicsDatabases.Generated.oboTerm>().First(b => b.id.Equals("MOD:00046")).xref_analog.Any(b => b.dbname.Equals("FormalCharge")));
Dictionary <string, int> formalChargesDictionary = Loaders.GetFormalChargesDictionary(psiModDeserialized);
var uniprotPtms = Loaders.LoadUniprot(Path.Combine(TestContext.CurrentContext.TestDirectory, "ptmlist2.txt"), formalChargesDictionary).ToList();
Assert.AreEqual(334, uniprotPtms.Count()); // UniProt PTM list may be updated at some point, causing the unit test to fail
using (StreamWriter w = new StreamWriter(Path.Combine(TestContext.CurrentContext.TestDirectory, "test.txt")))
{
foreach (var nice in uniprotPtms)
{
w.WriteLine(nice.ToString());
w.WriteLine("//");
}
foreach (var nice in unimodMods)
{
w.WriteLine(nice.ToString());
w.WriteLine("//");
}
}
var sampleModList = PtmListLoader.ReadModsFromFile(Path.Combine(TestContext.CurrentContext.TestDirectory, "test.txt"), out var errors).ToList();
Assert.AreEqual(2973, sampleModList.Count());
string s = "";
List <Modification> myOtherList = new List <Modification>();
foreach (Modification mod in sampleModList)
{
if (mod.IdWithMotif != null && mod.IdWithMotif.Contains("Acetyl"))
{
myOtherList.Add(mod);
}
}
var thisMod = myOtherList.First();
Assert.IsTrue(thisMod.MonoisotopicMass > 42);
Assert.IsTrue(thisMod.MonoisotopicMass < 43);
}
public void ShouldReturnNullAsLastChangeNumberIfNoModifications()
{
Modification[] modifications = new Modification[0];
Assert.AreEqual(null, Modification.GetLastChangeNumber(modifications), "LastChangeNumer({})");
}
public bool AddModification(Modification modification)
{
var result = ModificationRepository.AddModification(modification);
return(result);
}
public bool UpdateModification(Modification modification)
{
var result = ModificationRepository.UpdateModification(modification);
return(result);
}
private void OptimizationLoop()
{
population = new List <OptimizableStructure>();
scoreList = new List <double>();
if (optimizationMethod == OptimizationMethod.GA)
{
stopWatch.Start();
running = true;
double elapsedOptimizationTime;
SetUpGeneticAlgorithm();
creepMutationRate = 0;
bestScore = double.MinValue;
iterationIndex = 0;
numberOfEvaluatedIndividuals = 0;
double minimumParameterValue = optimizationSettings.MinimumSpeedValue;
double maximumParameterValue = optimizationSettings.MaximumSpeedValue;
double desiredAverageSpeed = optimizationSettings.DesiredAverageSpeed;
while (running)
{
for (int ii = 0; ii < populationSize; ii++)
{
OptimizableStructure individual = population[ii].Copy();
speedProfileEvaluator = new PiecewiseLinearSpeedProfileEvaluator();
speedProfileEvaluator.AssignMetricMap(metricMap);
speedProfileEvaluator.AssignMetricPath(metricPath);
speedProfileEvaluator.MaximumAllowedSpeed = maximumParameterValue;
speedProfileEvaluator.MinimumAllowedSpeed = minimumParameterValue;
speedProfileEvaluator.DesiredAverageSpeed = desiredAverageSpeed;
speedProfileEvaluator.AssignPossibleSpeedList(possibleSpeedList);
double score = speedProfileEvaluator.EvaluateGA(individual);
scoreList[ii] = score;
cumulativeScore += score;
List <int> individualSpeedIndexList = new List <int>();
for (int kk = 0; kk < individual.ParameterList.Count; kk++)
{
individualSpeedIndexList.Add(((IntParameter)individual.ParameterList[kk]).ParameterValue);
}
long speedProfileIndex = ConvertToBase10(individualSpeedIndexList);
OnIndividualEvaluated(individualSpeedIndexList, speedProfileIndex, 0, score, individual.Copy(), ii, iterationIndex, true);
if (score >= bestScore)
{
// MW 20180206
if (score > bestScore)
{
OnNewBestIndividualFound(individualSpeedIndexList, speedProfileIndex, 0, score, individual.Copy(), ii, iterationIndex, true);
}
bestScore = score;
bestIndividualIndex = ii;
// Copy the best individual here, in case the algorithm exits due to maximum time reached.
optimizedSpeedProfile = individual.Copy();
}
numberOfEvaluatedIndividuals++;
elapsedOptimizationTime = stopWatch.ElapsedTicks / (double)Stopwatch.Frequency;
if (elapsedOptimizationTime >= optimizationTime | numberOfEvaluatedIndividuals >= optimizationSettings.NumberOfGenerations * optimizationSettings.PopulationSize)
{
running = false;
OnStopped();
break;
}
if (!running)
{
break;
}
}
// Make new generation:
OptimizableStructure bestIndividual = population[bestIndividualIndex].Copy();
List <OptimizableStructure> oldPopulation = new List <OptimizableStructure>();
foreach (OptimizableStructure individual in population)
{
OptimizableStructure copiedIndividual = individual.Copy();
oldPopulation.Add(copiedIndividual);
}
population = new List <OptimizableStructure>();
int counter = 0;
while (counter < oldPopulation.Count)
{
int firstIndex = TournamentSelection.Select(randomNumberGenerator, scoreList, OptimizationObjective.Maximization,
tournamentSize, tournamentSelectionParameter);
int secondIndex = TournamentSelection.Select(randomNumberGenerator, scoreList, OptimizationObjective.Maximization,
tournamentSize, tournamentSelectionParameter);
double r = randomNumberGenerator.NextDouble();
OptimizableStructure parent1 = oldPopulation[firstIndex];
OptimizableStructure parent2 = oldPopulation[secondIndex];
if (r < crossoverProbability)
{
List <OptimizableStructure> newIndividualsList = null;
newIndividualsList = Crossover.ExecuteSinglePoint(parent1, parent2, unitLength, randomNumberGenerator);
population.Add(newIndividualsList[0]);
population.Add(newIndividualsList[1]);
}
else
{
population.Add(parent1);
population.Add(parent2);
}
counter += 2;
}
if (population.Count > oldPopulation.Count)
{
population.RemoveAt(population.Count - 1);
} // If the population size is odd..
for (int jj = 0; jj < population.Count; jj++)
{
OptimizableStructure individual = population[jj];
OptimizableStructure mutatedIndividual = (OptimizableStructure)Modification.Execute(individual,
mutationRate, creepMutationRate, randomNumberGenerator);
population[jj] = mutatedIndividual;
}
if (useElitism)
{
population[0] = bestIndividual;
}
double bestFitness = bestScore;
double averageFitness = scoreList.Average();
List <int> bestIndividualSpeedIndexList = new List <int>();
for (int kk = 0; kk < bestIndividual.ParameterList.Count; kk++)
{
bestIndividualSpeedIndexList.Add(((IntParameter)bestIndividual.ParameterList[kk]).ParameterValue);
}
long bestSpeedProfileIndex = ConvertToBase10(bestIndividualSpeedIndexList);
List <int> populationAverageIndividual = new List <int>();
OnGenerationEvaluated(bestFitness, averageFitness, iterationIndex, bestIndividualIndex,
numberOfEvaluatedIndividuals, bestIndividualSpeedIndexList, bestSpeedProfileIndex);
iterationIndex++;
if (numberOfEvaluatedIndividuals >= optimizationSettings.NumberOfGenerations * optimizationSettings.PopulationSize)
{
running = false;
OnStopped();
break;
}
}
OnStopped();
}
OnStopped();
}
public void TestParsePtms(double qValueThreshold, int expectedPTMListCount)
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
var resultFilePath = Path.Combine(Utils.DEFAULT_SPEC_FILES_FOLDER, "QC_Shew_Intact_26Sep14_Bane_C2Column3_Excerpt_IcTda.tsv");
var resultFile = Utils.GetTestFile(methodName, resultFilePath);
var parser = new TsvFileParser(resultFile.FullName);
var sequences = parser.GetData("Sequence");
var modifications = parser.GetData("Modifications");
var compositions = parser.GetData("Composition");
var scanNums = parser.GetData("Scan").Select(s => Convert.ToInt32(s)).ToArray();
var qValues = parser.GetData("QValue").Select(s => Convert.ToDouble(s)).ToArray();
var nMacthed = parser.GetData("#MatchedFragments");
var aaSet = new AminoAcidSet();
var ptmList = new List <Tuple <int, double, double> >();
var trimChars = new[] { '"', ' ' };
var filterPassingResults = 0;
for (var i = 0; i < parser.NumData; i++)
{
if (qValues[i] > qValueThreshold)
{
continue;
}
filterPassingResults++;
var seq = new Sequence(sequences[i], aaSet);
var sequenceComp = seq.Composition + Composition.H2O;
var modComposition = Composition.Zero;
var modsStr = modifications[i].Trim(trimChars);
if (modsStr.Length == 0)
{
continue;
}
var mods = modsStr.Split(',');
foreach (var modStr in mods.Where(str => str.Length > 0))
{
var modName = modStr.Split()[0];
var mod = Modification.Get(modName);
modComposition += mod.Composition;
}
if (ptmList.Count < 5)
{
Console.WriteLine("{0}\t{1}\t{2}\t{3}\t{4}\t{5}", scanNums[i], sequenceComp.Mass, modComposition.Mass, nMacthed[i], sequences[i], modsStr);
}
var compFromSeqAndMods = sequenceComp + modComposition;
var expectedComposition = compositions[i];
Assert.AreEqual(expectedComposition, compFromSeqAndMods.ToString(), "Composition Mismatch");
ptmList.Add(new Tuple <int, double, double>(scanNums[i], sequenceComp.Mass, modComposition.Mass));
}
Console.WriteLine();
Console.WriteLine("{0} results with PTMs / {1} total results passing threshold qValue < {2}", ptmList.Count, filterPassingResults, qValueThreshold);
Assert.AreEqual(expectedPTMListCount, ptmList.Count, "Unexpected number of identifications with at least one PTM at qValue < {0}", qValueThreshold);
}
public void RemoveModiciation(Modification modification)
{
m_modifications.Remove(modification);
modRemoved?.Invoke(modification);
}
override public void ApplyModification(Modification mod, Sheet sheet)
{
StaticErrorLogger.AddGenericError("trying to modify a modification component: " + name);
}
public override IEnumerable <ICodeBlockMappingExpression> Map(IModificationMappingExpression expression)
{
Modification modification = expression.CurrentEntity <Modification>();
if (modification.Action == TouchedFileAction.REMOVED)
{
return(SingleExpression(expression
.RemoveCode()));
}
List <CodeBlockMappingExpression> codeBlockExpressions = new List <CodeBlockMappingExpression>();
string revision = expression.CurrentEntity <Commit>().Revision;
CodeFile file = expression.CurrentEntity <CodeFile>();
var blame = vcsData.Blame(revision, file.Path);
if (blame != null)
{
var linesByRevision = blame.Select(x => new
{
Revision = x.Key,
CodeSize = x.Value
}).ToList();
void CopyCode()
{
foreach (var linesForRevision in linesByRevision)
{
var newExp = expression.Code(linesForRevision.CodeSize);
if (linesForRevision.Revision != revision)
{
newExp.CopiedFrom(linesForRevision.Revision);
}
codeBlockExpressions.Add(newExp);
}
};
if ((modification.Action == TouchedFileAction.ADDED) &&
(modification.SourceFile != null))
{
CopyCode();
}
else
{
var addedCode = linesByRevision.SingleOrDefault(x => x.Revision == revision);
if (addedCode != null)
{
linesByRevision.Remove(addedCode);
codeBlockExpressions.Add(
expression.Code(addedCode.CodeSize)
);
}
var isMerge = vcsData.Log(revision).IsMerge;
var updatedCodeExp = expression.UpdateCode((exp, rev, size) =>
{
var linesForRevision = linesByRevision.SingleOrDefault(x => x.Revision == rev);
if (linesForRevision != null)
{
linesByRevision.Remove(linesForRevision);
}
double realCodeSize = linesForRevision == null ? 0 : linesForRevision.CodeSize;
if ((size > realCodeSize) ||
(size < realCodeSize && isMerge))
{
var newExp = expression.Code(realCodeSize - size);
newExp.ForCodeAddedInitiallyInRevision(rev);
return(newExp);
}
return(null);
});
if (isMerge && linesByRevision.Count > 0)
{
CopyCode();
}
if (updatedCodeExp != null)
{
codeBlockExpressions.Add(updatedCodeExp);
}
}
}
if (codeBlockExpressions.Count == 0 && modification.Action == TouchedFileAction.MODIFIED)
{
expression.Revert();
}
return(codeBlockExpressions);
}
protected bool Equals(Modification other)
{
return(ExplicitMod.Equals(other.ExplicitMod) && MonoisotopicMass.Equals(other.MonoisotopicMass) &&
AverageMass.Equals(other.AverageMass));
}
/// <summary>
/// Synergy specific implemtation of <see cref="IHistoryParser.Parse"/>
/// </summary>
/// <remarks>
/// Processes both the task query and the object query to fully populate each
/// <see cref="Modification"/> object in the returned array.
/// </remarks>
/// <param name="newTasks">
/// Standard output stream from the Synergy query command.
/// </param>
/// <param name="newObjects">
/// Standard output stream from the Synergy finduse command.
/// </param>
/// <param name="from">
/// The date since the last successful integration run. Not used, since the finduse
/// query includes this parameter.
/// </param>
/// <returns>
/// <c>null</c> by default.
/// If changes have occurred since the last integration attempt, an array containing
/// each new modification is returned.
/// </returns>
public virtual Modification[] Parse(string newTasks, string newObjects, DateTime from)
{
var modifications = new List <Modification>();
Hashtable tasks = new Hashtable();
// don't bother doing anything if no modified objects were found
if (string.IsNullOrEmpty(newObjects))
{
return(new Modification[0]);
}
// optionally, parse the comments from each associated task
if (!string.IsNullOrEmpty(newTasks))
{
tasks = ParseTasks(newTasks);
}
// look for modifications in the output from the finduse command
Regex grep = new Regex(ObjectFormat, RegexOptions.CultureInvariant);
MatchCollection matches = grep.Matches(newObjects);
// each match is a detected modification
foreach (Match match in matches)
{
Modification modification = new Modification();
modification.FolderName = match.Groups["folder"].Value;
modification.FileName = match.Groups["displayname"].Value;
modification.Type = match.Groups["cvtype"].Value;
modification.EmailAddress = match.Groups["resolver"].Value;
modification.UserName = match.Groups["resolver"].Value;
/* normalize the folder path to resemble other SCM systems
* vis a vis the "$/project/folder/file" format */
if (modification.FolderName.Length > 0)
{
modification.FolderName = String.Concat("$/", modification.FolderName.Replace('\\', '/'));
}
// Retrieve the comment, if available
CaptureCollection captures = match.Groups["task"].Captures;
if (null != captures)
{
foreach (Capture capture in captures)
{
SynergyTaskInfo info = (SynergyTaskInfo)tasks[capture.Value];
if (info == null)
{
modification.ChangeNumber = Regex.Match(capture.Value, @"\d+").Value;
}
else
{
modification.ChangeNumber = info.TaskNumber.ToString(CultureInfo.CurrentCulture);
modification.ModifiedTime = info.CompletionDate;
if (null != info.TaskSynopsis)
{
modification.Comment = info.TaskSynopsis;
}
}
}
}
modifications.Add(modification);
}
return(modifications.ToArray());
}
public static void TestModificationAnalysisWithNonLocalizedPtms()
{
Ms2ScanWithSpecificMass scan = new Ms2ScanWithSpecificMass(new MsDataScan(new MzSpectrum(new double[, ] {
}), 0, 0, true, Polarity.Positive,
0, new MzLibUtil.MzRange(0, 0), "", MZAnalyzerType.FTICR, 0, null, null, ""), 0, 0, "", new CommonParameters());
ModificationMotif.TryGetMotif("N", out ModificationMotif motif1);
Modification mod1 = new Modification(_originalId: "mod1", _modificationType: "mt", _target: motif1, _locationRestriction: "Anywhere.", _monoisotopicMass: 10, _neutralLosses: new Dictionary <DissociationType, List <double> > {
{ MassSpectrometry.DissociationType.AnyActivationType, new List <double> {
10
} }
});
IDictionary <int, List <Modification> > oneBasedModifications = new Dictionary <int, List <Modification> >
{
{ 2, new List <Modification> {
mod1
} },
{ 7, new List <Modification> {
mod1
} },
};
Protein protein1 = new Protein("MNLDLDNDL", "prot1", oneBasedModifications: oneBasedModifications);
Dictionary <int, Modification> allModsOneIsNterminus1 = new Dictionary <int, Modification>
{
{ 2, mod1 },
};
PeptideWithSetModifications pwsm1 = new PeptideWithSetModifications(protein1, new DigestionParams(), 2, 9, CleavageSpecificity.Unknown, null, 0, allModsOneIsNterminus1, 0);
Dictionary <int, Modification> allModsOneIsNterminus3 = new Dictionary <int, Modification>
{
{ 7, mod1 },
};
PeptideWithSetModifications pwsm2 = new PeptideWithSetModifications(protein1, new DigestionParams(), 2, 9, CleavageSpecificity.Unknown, null, 0, allModsOneIsNterminus3, 0);
CommonParameters CommonParameters = new CommonParameters(digestionParams: new DigestionParams(maxMissedCleavages: 0, minPeptideLength: 1), scoreCutoff: 1);
var fsp = new List <(string fileName, CommonParameters fileSpecificParameters)>();
fsp.Add(("", CommonParameters));
PeptideSpectralMatch myPsm = new PeptideSpectralMatch(pwsm1, 0, 10, 0, scan, new CommonParameters(), new List <MatchedFragmentIon>());
myPsm.AddOrReplace(pwsm2, 10, 0, true, new List <MatchedFragmentIon>(), 0);
myPsm.ResolveAllAmbiguities();
MassDiffAcceptor searchMode = new SinglePpmAroundZeroSearchMode(5);
List <Protein> proteinList = new List <Protein> {
protein1
};
FdrAnalysisEngine fdrAnalysisEngine = new FdrAnalysisEngine(new List <PeptideSpectralMatch> {
myPsm
}, searchMode.NumNotches, CommonParameters, fsp, new List <string>());
fdrAnalysisEngine.Run();
ModificationAnalysisEngine modificationAnalysisEngine = new ModificationAnalysisEngine(new List <PeptideSpectralMatch> {
myPsm
}, new CommonParameters(), fsp, new List <string>());
var res = (ModificationAnalysisResults)modificationAnalysisEngine.Run();
Assert.AreEqual(1, res.CountOfEachModSeenOnProteins.Count());
Assert.AreEqual(2, res.CountOfEachModSeenOnProteins[mod1.IdWithMotif]);
Assert.AreEqual(0, res.CountOfModsSeenAndLocalized.Count());
Assert.AreEqual(0, res.CountOfAmbiguousButLocalizedModsSeen.Count);
Assert.AreEqual(1, res.CountOfUnlocalizedMods[mod1.IdWithMotif]); // Saw it, but not sure where!
Assert.AreEqual(0, res.CountOfUnlocalizedFormulas.Count());
}
//Reading in metamopheus excel
public List <TopDownHit> ReadMetamopheusFile(InputFile file)
{
//if neucode labeled, calculate neucode light theoretical AND observed mass! --> better for matching up
//if carbamidomethylated, add 57 to theoretical mass (already in observed mass...)
aaIsotopeMassList = new AminoAcidMasses(Sweet.lollipop.carbamidomethylation, Sweet.lollipop.neucode_labeled).AA_Masses;
List <TopDownHit> td_hits = new List <TopDownHit>();//for one line in excel file
//creates dictionary to find mods
Dictionary <string, Modification> mods = Sweet.lollipop.theoretical_database.all_mods_with_mass.ToDictionary(kv => kv.IdWithMotif, kv => kv);
List <List <string> > cells = ExcelReader.get_cell_strings(file, true);//This returns the entire sheet except for the header. Each row of cells is one List<string>
//get ptms on proteoform -- check for mods. IF not in database, make new topdown mod, show Warning message.
Parallel.ForEach(cells, cellStrings =>
{
bool add_topdown_hit = true; //if PTM or accession not found, will not add (show warning)
if (cellStrings.Count == 55)
{
List <Ptm> new_ptm_list = new List <Ptm>();
//if bad mod itll catch it to add to bad_topdown_ptms
try
{
PeptideWithSetModifications modsIdentifier = new PeptideWithSetModifications(cellStrings[14].Split('|')[0], mods);
var ptm_list = modsIdentifier.AllModsOneIsNterminus;
//for each entry in ptm_list make a new Ptm and add it to the new_ptm_list
foreach (KeyValuePair <int, Proteomics.Modification> entry in ptm_list)
{
Modification mod = Sweet.lollipop.theoretical_database.uniprotModifications.Values.SelectMany(m => m).Where(m => m.IdWithMotif == entry.Value.IdWithMotif).FirstOrDefault();
var Ptm = new Ptm();
if (mod != null)
{
new_ptm_list.Add(new Ptm(entry.Key, entry.Value));
}
else
{
lock (bad_topdown_ptms)
{
//error is somewahre in sequece
bad_topdown_ptms.Add("Mod Name:" + entry.Value.IdWithMotif + " at " + entry.Key);
add_topdown_hit = false;
}
}
}
}
catch (MzLibUtil.MzLibException)
{
lock (bad_topdown_ptms)
{
//error is somewahre in sequece
bad_topdown_ptms.Add("Bad mod at " + cellStrings[0] + " scan " + cellStrings[1]);
add_topdown_hit = false;
}
}
//This is the excel file header:
//cellStrings[0]=File Name
//cellStrings[1]=Scan Number
//cellStrings[2]=Scan Retention Time
//cellStrings[3]=Num Experimental Peaks
//cellStrings[4]=Total Ion Current
//cellStrings[5]=Precursor Scan Number
//cellStrings[6]=Precursor Charge
//cellStrings[7]=Precursor MZ
//cellStrings[8]=Precursor Mass
//cellStrings[9]=Score
//cellStrings[10]=Delta Score
//cellStrings[11]=Notch
//cellStrings[12]=Different Peak Matches
//cellStrings[13]=Base Sequence
//cellStrings[14]=Full Sequence
//cellStrings[15]=Essential Sequence
//cellStrings[16]=PSM Count
//cellStrings[17]=Mods
//cellStrings[18]=Mods Chemical Formulas
//cellStrings[19]=Mods Combined Chemical Formula
//cellStrings[20]=Num Variable Mods
//cellStrings[21]=Missed Cleavages
//cellStrings[22]=Peptide Monoisotopic Mass
//cellStrings[23]=Mass Diff (Da)
//cellStrings[24]=Mass Diff (ppm)
//cellStrings[25]=Protein Accession
//cellStrings[26]=Protein Name
//cellStrings[27]=Gene Name
//cellStrings[28]=Organism Name
//cellStrings[29]=Intersecting Sequence Variations
//cellStrings[30]=Identified Sequence Variations
//cellStrings[31]=Splice Sites
//cellStrings[32]=Contaminant
//cellStrings[33]=Decoy
//cellStrings[34]=Peptide Description
//cellStrings[35]=Start and End Residues In Protein
//cellStrings[36]=Previous Amino Acid
//cellStrings[37]=Next Amino Acid
//cellStrings[38]=All Scores
//cellStrings[39]=Theoreticals Searched
//cellStrings[40]=Decoy/Contaminant/Target
//cellStrings[41]=Matched Ion Series
//cellStrings[42]=Matched Ion Mass-To-Charge Ratios
//cellStrings[43]=Matched Ion Mass Diff (Da)
//cellStrings[44]=Matched Ion Mass Diff (Ppm)
//cellStrings[45]=Matched Ion Intensities
//cellStrings[46]=Matched Ion Counts
//cellStrings[47]=Localized Scores
//cellStrings[48]=Improvement Possible
//cellStrings[49]=Cumulative Target
//cellStrings[50]=Cumulative Decoy
//cellStrings[51]=QValue
//cellStrings[52]=Cumulative Target Notch
//cellStrings[53]=Cumulative Decoy Notch
//cellStrings[54]=QValue Notch
//cellStrings[55]=eValue
//cellStrings[56]=eScore
if (cellStrings[35].Length > 0)
{
string[] ids = cellStrings[35].Split('|');
//splits the string to get the value of starting index
string[] index = ids[0].Split(' ');
string[] startIndexValue = index[0].Split('[');
string startResidues = startIndexValue[1];
//splits string to get value of ending index
string[] endIndexValue = index[2].Split(']');
string endResidues = endIndexValue[0];
if (add_topdown_hit)
{
//if bad mod u want td hit to be false
TopDownHit td_hit = new TopDownHit(aaIsotopeMassList, file, TopDownResultType.TightAbsoluteMass, cellStrings[25], cellStrings[14], cellStrings[25], cellStrings[26], cellStrings[13],
Int32.TryParse(startResidues, out int j) ? j : 0, Int32.TryParse(endResidues, out int i) ? i : 0, new_ptm_list, Double.TryParse(cellStrings[8], out double d) ? d : 0, Double.TryParse(cellStrings[22], out d) ? d : 0,
Int32.TryParse(cellStrings[1], out i) ? i : 0, Double.TryParse(cellStrings[2], out d) ? d : 0, cellStrings[0].Split('.')[0], Double.TryParse(cellStrings[8], out d) ? d : 0, Sweet.lollipop.min_score_td + 1);
if (td_hit.begin > 0 && td_hit.end > 0 && td_hit.theoretical_mass > 0 && td_hit.pscore > 0 && td_hit.reported_mass > 0 && td_hit.score > 0 &&
td_hit.ms2ScanNumber > 0 && td_hit.ms2_retention_time > 0)
{
lock (td_hits) td_hits.Add(td_hit);
}
}
}
}
});
return(td_hits);
}
/// <summary>
/// Parses the parameter file for ascore
/// </summary>
/// <param name="inputFile">name of the xml file</param>
/// <returns>ascore parameters object</returns>
public static AScoreParameters ParseXml(string inputFile)
{
XmlDocument parameterFile = new XmlDocument();
parameterFile.Load(new XmlTextReader(inputFile));
XmlNodeList staticMod = parameterFile.SelectNodes("/Run/Modifications/StaticSeqModifications");
XmlNodeList terminiMod = parameterFile.SelectNodes("/Run/Modifications/TerminiModifications");
XmlNodeList dynamicMod = parameterFile.SelectNodes("/Run/Modifications/DynamicModifications");
XmlNode massTolerance = parameterFile.SelectSingleNode("/Run/MassTolerance");
XmlNode fragmentType = parameterFile.SelectSingleNode("/Run/FragmentType");
FragmentType f = GetFragmentType(fragmentType);
double massTol = double.Parse(massTolerance.InnerText);
List <Modification> stat = new List <Modification>();
List <TerminiModification> termMod = new List <TerminiModification>();
List <DynamicModification> dynam = new List <DynamicModification>();
foreach (XmlNode mod in staticMod)
{
foreach (XmlNode mod2 in mod.ChildNodes)
{
double massMonoIsotopic = 0.0;
char modSymbol = ' ';
List <char> possibleModSites = new List <char>();
int uniqueID = 0;
foreach (XmlNode item in mod2.ChildNodes)
{
if (item.Name == "MassMonoIsotopic")
{
massMonoIsotopic = double.Parse(item.InnerText);
}
else if (item.Name == "PossibleModSites")
{
foreach (XmlNode item2 in item.ChildNodes)
{
possibleModSites.Add(item2.InnerText[0]);
}
}
else if (item.Name == "UniqueID")
{
uniqueID = int.Parse(item.InnerText);
}
}
Modification m = new Modification();
m.MassMonoisotopic = massMonoIsotopic;
m.ModSymbol = modSymbol;
m.PossibleModSites = possibleModSites;
m.UniqueID = uniqueID;
stat.Add(m);
}
}
foreach (XmlNode mod in terminiMod)
{
foreach (XmlNode mod2 in mod.ChildNodes)
{
double massMonoIsotopic = 0.0;
char modSymbol = ' ';
List <char> possibleModSites = new List <char>();
int uniqueID = 0;
bool nTerm = false;
bool cTerm = false;
foreach (XmlNode item in mod2.ChildNodes)
{
if (item.Name == "MassMonoIsotopic")
{
massMonoIsotopic = double.Parse(item.InnerText);
}
else if (item.Name == "UniqueID")
{
uniqueID = int.Parse(item.InnerText);
}
else if (item.Name == "Nterm")
{
nTerm = bool.Parse(item.InnerText);
}
else if (item.Name == "Cterm")
{
cTerm = bool.Parse(item.InnerText);
}
}
TerminiModification m = new TerminiModification();
m.MassMonoisotopic = massMonoIsotopic;
m.ModSymbol = modSymbol;
m.PossibleModSites = possibleModSites;
m.UniqueID = uniqueID;
m.nTerminus = nTerm;
m.cTerminus = cTerm;
termMod.Add(m);
}
}
foreach (XmlNode mod in dynamicMod)
{
foreach (XmlNode mod2 in mod.ChildNodes)
{
double massMonoIsotopic = 0.0;
char modSymbol = ' ';
List <char> possibleModSites = new List <char>();
int uniqueID = 0;
foreach (XmlNode item in mod2.ChildNodes)
{
if (item.Name == "MassMonoIsotopic")
{
massMonoIsotopic = double.Parse(item.InnerText);
}
else if (item.Name == "ModificationSymbol")
{
modSymbol = item.InnerText[0];
}
else if (item.Name == "PossibleModSites")
{
foreach (XmlNode item2 in item.ChildNodes)
{
possibleModSites.Add(item2.InnerText[0]);
}
}
else if (item.Name == "UniqueID")
{
uniqueID = int.Parse(item.InnerText);
}
else if (item.Name == "MaxPerSite")
{
}
}
DynamicModification m = new DynamicModification();
m.MassMonoisotopic = massMonoIsotopic;
m.ModSymbol = modSymbol;
m.PossibleModSites = possibleModSites;
m.UniqueID = uniqueID;
dynam.Add(m);
}
}
AScoreParameters aParams = new AScoreParameters(stat, termMod, dynam, f, massTol);
return(aParams);
}
/// <summary>
/// Accepts the specified m.
/// </summary>
/// <param name="m">The m.</param>
/// <returns></returns>
/// <remarks></remarks>
public bool Accept(Modification m)
{
return(Array.IndexOf(UserNames, m.UserName) >= 0);
}
/// <summary>
/// Creates the individual get string.
/// </summary>
/// <param name="mod">The mod.</param>
/// <param name="fileLocation">The file location.</param>
/// <returns></returns>
/// <remarks></remarks>
public string CreateIndividualGetString(Modification mod, string fileLocation)
{
return(string.Format(CultureInfo.CurrentCulture, INDIVIDUAL_GET_REVISION_TEMPLATE, GetVersion(mod, string.Empty), GetUncPathPrefix(mod), mod.FolderName, mod.FileName, fileLocation));
}
/// <summary>
/// Method calls listeners of the change event
/// </summary>
/// <param name="message">Some sembols that brings info about event</param>
protected void Modified(string message)
{
Modification?.Invoke(message);
}
public ModificationController(Modification modification, ModificationViewModel viewModel)
{
this.modification = modification;
this.viewModel = viewModel;
}
private string GetUncPathPrefix(Modification mod)
{
//Add extract \ for UNC paths
return(mod.FolderName.StartsWith("\\") ? @"\" :string.Empty);
}
/// <summary>
/// Determines whether given modification can be a C-terminal modification
/// </summary>
/// <param name="variableModification"></param>
/// <param name="peptideLength"></param>
/// <returns></returns>
private bool CanBeCTerminalMod(Modification variableModification, int peptideLength)
{
return(ModificationLocalization.ModFits(variableModification, Protein.BaseSequence, peptideLength, peptideLength, OneBasedStartResidueInProtein + peptideLength - 1) &&
(variableModification.LocationRestriction == "C-terminal." || variableModification.LocationRestriction == "Peptide C-terminal."));
}
private string GetVersion(Modification mod, string label)
{
return((label == null || label.Length == 0) ? (mod.Version == null ? "1.0" : mod.Version) : (LabelOrPromotionInput(label)));
}
private void SetUpGeneticAlgorithm()
{
populationSize = optimizationSettings.PopulationSize;
tournamentSelectionParameter = optimizationSettings.TournamentSelectionParameter;
tournamentSize = optimizationSettings.TournamentSize;
// Note: The mutation rate is set below, after the individuals have been generated
crossoverProbability = optimizationSettings.CrossoverProbability;
creepMutationRate = optimizationSettings.CreepMutationRate;
int numberOfLineSegments = optimizationSettings.NumberOfSpeedPoints;
double minimumParameterValue = optimizationSettings.MinimumSpeedValue;
double maximumParameterValue = optimizationSettings.MaximumSpeedValue;
double discretizationStep = optimizationSettings.SpeedIncrement;
double desiredAverageSpeed = optimizationSettings.DesiredAverageSpeed;
possibleSpeedList = new List <double>();
double initialSpeed = minimumParameterValue;
possibleSpeedList.Add(initialSpeed);
while (initialSpeed < maximumParameterValue)
{
initialSpeed += discretizationStep;
initialSpeed = Math.Min(initialSpeed, maximumParameterValue);
possibleSpeedList.Add(initialSpeed);
}
//returns the index of desired average speed from the possible speed list (generated above). Required for optimizaiton.
int desiredAverageSpeedIndex = possibleSpeedList.FindIndex(s => s == desiredAverageSpeed);
OptimizableStructure cruiseControlSpeedProfile = new OptimizableStructure();
IntParameter p0ParameterFirstIndividual = new IntParameter();
p0ParameterFirstIndividual.MaximumValue = possibleSpeedList.Count - 1;
p0ParameterFirstIndividual.MinimumValue = 0;
p0ParameterFirstIndividual.ParameterValue = desiredAverageSpeedIndex;
cruiseControlSpeedProfile.ParameterList.Add(p0ParameterFirstIndividual);
for (int jj = 0; jj < numberOfLineSegments; jj++)
{
IntParameter p0Parameter = new IntParameter();
p0Parameter.MaximumValue = possibleSpeedList.Count - 1;
p0Parameter.MinimumValue = 0;
p0Parameter.ParameterValue = desiredAverageSpeedIndex;
cruiseControlSpeedProfile.ParameterList.Add(p0Parameter);
}
population.Add(cruiseControlSpeedProfile.Copy());
scoreList.Add(double.MinValue);
for (int ii = 1; ii < populationSize; ii++)
{
OptimizableStructure individual = new OptimizableStructure();
IntParameter p0ParameterFirst = new IntParameter();
p0ParameterFirst.MaximumValue = possibleSpeedList.Count - 1;
p0ParameterFirst.MinimumValue = 0;
p0ParameterFirst.ParameterValue = desiredAverageSpeedIndex;
individual.ParameterList.Add(p0ParameterFirst);
for (int jj = 0; jj < numberOfLineSegments; jj++)
{
IntParameter p0Parameter = new IntParameter();
p0Parameter.MaximumValue = possibleSpeedList.Count - 1;
p0Parameter.MinimumValue = 0;
p0Parameter.ParameterValue = desiredAverageSpeedIndex;
individual.ParameterList.Add(p0Parameter);
}
// Randomize all individuals except the first one:
OptimizableStructure mutatedIndividual = (OptimizableStructure)Modification.Execute(individual,
1.0, 1.0, randomNumberGenerator);
population.Add(mutatedIndividual.Copy());
scoreList.Add(double.MinValue);
}
mutationRate = optimizationSettings.RelativeMutationProbability /
(double)population[0].ParameterList.Count;
}
