private string LoadModsFile(string modFilePath)
{
if (string.IsNullOrWhiteSpace(modFilePath))
{
AminoAcidSet = new AminoAcidSet();
Modifications = new List <SearchModification>();
return(string.Empty);
}
if (!File.Exists(modFilePath))
{
return("-mod file not found: " + modFilePath);
}
var parser = new ModFileParser(modFilePath);
Modifications = parser.SearchModifications.ToList();
MaxDynamicModificationsPerSequence = parser.MaxNumDynModsPerSequence;
if (Modifications == null)
{
return("Error while parsing " + modFilePath);
}
AminoAcidSet = new AminoAcidSet(Modifications, MaxDynamicModificationsPerSequence);
return(string.Empty);
}
public void HandleHandshakeReplyReceivedMessage(HandshakeReplyMsgData data)
{
HandshakeReply reply;
string reason;
var modFileData = "";
try
{
reply = data.Response;
reason = data.Reason;
//If we handshook successfully, the mod data will be available to read.
if (reply == HandshakeReply.HANDSHOOK_SUCCESSFULLY)
{
ModSystem.Singleton.ModControl = data.ModControlMode;
if (ModSystem.Singleton.ModControl != ModControlMode.DISABLED)
{
modFileData = Encoding.UTF8.GetString(data.ModFileData);
}
}
}
catch (Exception e)
{
Debug.LogError($"[LMP]: Error handling HANDSHAKE_REPLY Message, exception: {e}");
reply = HandshakeReply.MALFORMED_HANDSHAKE;
reason = "Incompatible HANDSHAKE_REPLY Message";
}
switch (reply)
{
case HandshakeReply.HANDSHOOK_SUCCESSFULLY:
{
if (ModFileParser.ParseModFile(modFileData))
{
Debug.Log("[LMP]: Handshake successful");
MainSystem.Singleton.NetworkState = ClientState.AUTHENTICATED;
}
else
{
Debug.LogError("[LMP]: Failed to pass mod validation");
NetworkConnection.Disconnect("[LMP]: Failed mod validation");
}
}
break;
default:
var disconnectReason = "Handshake failure: " + reason;
//If it's a protocol mismatch, append the client/server version.
if (reply == HandshakeReply.PROTOCOL_MISMATCH)
{
disconnectReason += "\nClient: " + VersionInfo.VersionNumber + ", Server: " + data.Version;
}
Debug.Log(disconnectReason);
NetworkConnection.Disconnect(disconnectReason);
break;
}
}
public void HandleHandshakeReplyReceivedMessage(HandshakeReplyMsgData data)
{
HandshakeReply reply;
string reason;
var modFileData = "";
try
{
reply = data.Response;
reason = data.Reason;
//If we handshook successfully, the mod data will be available to read.
if (reply == HandshakeReply.HandshookSuccessfully)
{
SystemsContainer.Get <ModSystem>().ModControl = data.ModControlMode;
if (SystemsContainer.Get <ModSystem>().ModControl != ModControlMode.Disabled)
{
modFileData = Encoding.UTF8.GetString(data.ModFileData);
}
}
}
catch (Exception e)
{
LunaLog.LogError($"[LMP]: Error handling HANDSHAKE_REPLY Message, exception: {e}");
reply = HandshakeReply.MalformedHandshake;
reason = "Incompatible HANDSHAKE_REPLY Message";
}
switch (reply)
{
case HandshakeReply.HandshookSuccessfully:
{
if (ModFileParser.ParseModFile(modFileData))
{
LunaLog.Log("[LMP]: Handshake successful");
MainSystem.NetworkState = ClientState.Authenticated;
}
else
{
LunaLog.LogError("[LMP]: Failed to pass mod validation");
NetworkConnection.Disconnect("[LMP]: Failed mod validation");
}
}
break;
default:
var disconnectReason = $"Handshake failure: {reason}";
//If it's a protocol mismatch, append the client/server version.
if (reply == HandshakeReply.ProtocolMismatch)
{
disconnectReason += $"\nClient: {VersionInfo.VersionNumber}, Server: {data.Version}";
}
LunaLog.Log(disconnectReason);
NetworkConnection.Disconnect(disconnectReason);
break;
}
}
public static void LoadModProjects()
{
CreateExampleModProject();
// 获取所有得 mod 项目文件夹
DirectoryInfo[] directoryInfos = new DirectoryInfo(ModGlobalData.MOD_PATH_ROOT).GetDirectories();
foreach (DirectoryInfo directoryInfo in directoryInfos)
{
if (File.Exists(directoryInfo.Parent.FullName + @"\" + directoryInfo.Name + ".mod"))
{
// 获取mod配置文件
FileInfo fileInfo = new FileInfo(directoryInfo.Parent.FullName + @"\" + directoryInfo.Name + ".mod");
ModFileParser modFileParser = new ModFileParser();
PdxMod pdxMod = modFileParser.ParseModFile(fileInfo.FullName);
ModProjects.Add(pdxMod);
}
}
}
public void TestReadingModFile()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
var modFilePath = Path.Combine(Utils.DEFAULT_TEST_FILE_FOLDER, @"TopDown\ProductionQCShew\Mods.txt");
var modFile = Utils.GetTestFile(methodName, modFilePath);
var modFileParser = new ModFileParser(modFile.FullName);
Console.WriteLine("MaxNumDynModsPerSequence: {0}", modFileParser.MaxNumDynModsPerSequence);
foreach (var searhMod in modFileParser.SearchModifications)
{
Console.WriteLine("{0}\t{1}\t{2}\t{3}", searhMod.TargetResidue, searhMod.Location, searhMod.IsFixedModification, searhMod.Modification);
}
var aaSet = new AminoAcidSet(modFile.FullName);
aaSet.Display();
}
public void HandleHandshakeReplyReceivedMessage(HandshakeReplyMsgData data)
{
TimeSyncSystem.ServerStartTime = data.ServerStartTime;
switch (data.Response)
{
case HandshakeReply.HandshookSuccessfully:
ModSystem.Singleton.Clear();
ModSystem.Singleton.ModControl = data.ModControl;
if (ModSystem.Singleton.ModControl)
{
if (ModSystem.Singleton.ModFileHandler.ParseModFile(ModFileParser.ReadModFileFromString(data.ModFileData)))
{
LunaLog.Log("[LMP]: Handshake successful");
MainSystem.NetworkState = ClientState.Handshaked;
}
else
{
LunaLog.LogError("[LMP]: Failed to pass mod validation");
NetworkConnection.Disconnect("[LMP]: Failed mod validation");
}
}
else
{
LunaLog.Log("[LMP]: Handshake successful");
MainSystem.NetworkState = ClientState.Handshaked;
}
break;
default:
var disconnectReason = $"Handshake failure: {data.Reason}";
LunaLog.Log(disconnectReason);
NetworkConnection.Disconnect(disconnectReason);
break;
}
}
public void TestReadingModFile()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string modFilePath = @"..\..\..\TestFiles\Mods.txt";
if (!File.Exists(modFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, modFilePath);
}
var modFileParser = new ModFileParser(modFilePath);
Console.WriteLine("MaxNumDynModsPerSequence: {0}", modFileParser.MaxNumDynModsPerSequence);
foreach (var searhMod in modFileParser.SearchModifications)
{
Console.WriteLine("{0}\t{1}\t{2}\t{3}", searhMod.TargetResidue, searhMod.Location, searhMod.IsFixedModification, searhMod.Modification);
}
var aaSet = new AminoAcidSet(modFilePath);
aaSet.Display();
}
/// <summary>
/// Opens parameter file from .PARAM file..
/// </summary>
/// <param name="filePath">The path of the parameter file.</param>
/// <returns>
/// Parsed MSPathFinder parameters. Returns null if file does not exist.
/// Throws exception if file is not formatted correctly.
/// </returns>
public static MsPfParameters Parse(string filePath)
{
if (!File.Exists(filePath))
{
return(null);
}
var file = File.ReadAllLines(filePath);
var param = new MsPfParameters();
foreach (var line in file)
{
var parts = line.Split('\t');
if (parts.Length < 2)
{
continue;
}
switch (parts[0])
{
case "SpecFile":
param.SpecFilePath = parts[1];
break;
case "DatabaseFile":
param.DatabaseFilePath = parts[1];
break;
case "FeatureFile":
param.FeatureFilePath = parts[1];
break;
case "SearchMode":
#pragma warning disable 618
param.SearchModeInt = Convert.ToInt32(parts[1]);
#pragma warning restore 618
break;
case "InternalCleavageMode":
param.InternalCleavageMode = (InternalCleavageType)Enum.Parse(typeof(InternalCleavageType), parts[1]);
break;
case "Tda":
int tda = 0;
tda += Convert.ToInt32(parts[1].Contains("Target"));
tda += Convert.ToInt32(parts[1].Contains("Decoy")) * 2;
param.TargetDecoySearchMode = (DatabaseSearchMode)tda;
break;
case "PrecursorIonTolerancePpm":
param.PrecursorIonTolerance = new Tolerance(Convert.ToDouble(parts[1]), ToleranceUnit.Ppm);
break;
case "ProductIonTolerancePpm":
param.ProductIonTolerance = new Tolerance(Convert.ToDouble(parts[1]), ToleranceUnit.Ppm);
break;
case "MinSequenceLength":
param.MinSequenceLength = Convert.ToInt32(parts[1]);
break;
case "MaxSequenceLength":
param.MaxSequenceLength = Convert.ToInt32(parts[1]);
break;
case "MinPrecursorIonCharge":
param.MinPrecursorIonCharge = Convert.ToInt32(parts[1]);
break;
case "MaxPrecursorIonCharge":
param.MaxPrecursorIonCharge = Convert.ToInt32(parts[1]);
break;
case "MinProductIonCharge":
param.MinProductIonCharge = Convert.ToInt32(parts[1]);
break;
case "MaxProductIonCharge":
param.MaxProductIonCharge = Convert.ToInt32(parts[1]);
break;
case "MinSequenceMass":
param.MinSequenceMass = Convert.ToDouble(parts[1]);
break;
case "MaxSequenceMass":
param.MaxSequenceMass = Convert.ToDouble(parts[1]);
break;
case "MinFeatureProbability":
param.MinFeatureProbablility = Convert.ToDouble(parts[1]);
break;
case "MaxDynamicModificationsPerSequence":
param.MaxDynamicModificationsPerSequence = Convert.ToInt32(parts[1]);
break;
case "Modification":
param.Modifications.AddRange(ModFileParser.ParseModification(parts[1]));
break;
case "ActivationMethod":
param.ActivationMethod = (ActivationMethod)Convert.ToInt32(parts[1]);
break;
}
}
if (param.PrecursorIonTolerance == null && param.ProductIonTolerance != null)
{
param.PrecursorIonTolerance = param.ProductIonTolerance;
}
if (param.PrecursorIonTolerance != null && param.ProductIonTolerance == null)
{
param.ProductIonTolerance = param.PrecursorIonTolerance;
}
return(param);
}
public string Parse(Dictionary <string, string> parameters)
{
var message = CheckIsValid(parameters);
if (message != null)
{
return(message);
}
var specFilePath = parameters["-s"];
if (Directory.Exists(specFilePath)) // Directory
{
SpecFilePaths = Directory.GetFiles(specFilePath, "*.raw");
}
else
{
SpecFilePaths = new[] { specFilePath };
}
DatabaseFilePath = parameters["-d"];
var outputDir = parameters["-o"] ?? Environment.CurrentDirectory;
if (outputDir[outputDir.Length - 1] == Path.DirectorySeparatorChar)
{
outputDir = outputDir.Remove(outputDir.Length - 1);
}
if (!Directory.Exists(outputDir))
{
if (File.Exists(outputDir) && !File.GetAttributes(outputDir).HasFlag(FileAttributes.Directory))
{
return("OutputDir " + outputDir + " is not a directory!");
}
Directory.CreateDirectory(outputDir);
}
OutputDir = outputDir;
var modFilePath = parameters["-mod"];
if (modFilePath != null)
{
var parser = new ModFileParser(modFilePath);
_searchModifications = parser.SearchModifications;
_maxNumDynModsPerSequence = parser.MaxNumDynModsPerSequence;
if (_searchModifications == null)
{
return("Error while parsing " + modFilePath + "!");
}
AminoAcidSet = new AminoAcidSet(_searchModifications, _maxNumDynModsPerSequence);
}
else
{
AminoAcidSet = new AminoAcidSet();
_searchModifications = new SearchModification[0];
}
var enzymeId = Convert.ToInt32(parameters["-e"]);
Enzyme enzyme;
switch (enzymeId)
{
case 0:
enzyme = Enzyme.UnspecificCleavage;
break;
case 1:
enzyme = Enzyme.Trypsin;
break;
case 2:
enzyme = Enzyme.Chymotrypsin;
break;
case 3:
enzyme = Enzyme.LysC;
break;
case 4:
enzyme = Enzyme.LysN;
break;
case 5:
enzyme = Enzyme.GluC;
break;
case 6:
enzyme = Enzyme.ArgC;
break;
case 7:
enzyme = Enzyme.AspN;
break;
case 8:
enzyme = Enzyme.Alp;
break;
case 9:
enzyme = Enzyme.NoCleavage;
break;
default:
return("Invalid enzyme ID (" + enzymeId + ") for parameter -e");
}
Enzyme = enzyme;
NumTolerableTermini = Convert.ToInt32(parameters["-ntt"]);
if (NumTolerableTermini < 0 || NumTolerableTermini > 2)
{
return("Invalid value (" + NumTolerableTermini + ") for parameter -m");
}
PrecursorIonTolerancePpm = Convert.ToDouble(parameters["-t"]);
ProductIonTolerancePpm = Convert.ToDouble(parameters["-f"]);
var tdaVal = Convert.ToInt32(parameters["-tda"]);
if (tdaVal != 0 && tdaVal != 1)
{
return("Invalid value (" + tdaVal + ") for parameter -tda");
}
Tda = (tdaVal == 1);
MinSequenceLength = Convert.ToInt32(parameters["-minLength"]);
MaxSequenceLength = Convert.ToInt32(parameters["-maxLength"]);
if (MinSequenceLength > MaxSequenceLength)
{
return("MinSequenceLength (" + MinSequenceLength + ") is larger than MaxSequenceLength (" + MaxSequenceLength + ")!");
}
MinPrecursorIonCharge = Convert.ToInt32(parameters["-minCharge"]);
MaxPrecursorIonCharge = Convert.ToInt32(parameters["-maxCharge"]);
if (MinSequenceLength > MaxSequenceLength)
{
return("MinPrecursorCharge (" + MinPrecursorIonCharge + ") is larger than MaxPrecursorCharge (" + MaxPrecursorIonCharge + ")!");
}
MinProductIonCharge = Convert.ToInt32(parameters["-minFragCharge"]);
MaxProductIonCharge = Convert.ToInt32(parameters["-maxFragCharge"]);
if (MinSequenceLength > MaxSequenceLength)
{
return("MinFragmentCharge (" + MinProductIonCharge + ") is larger than MaxFragmentCharge (" + MaxProductIonCharge + ")!");
}
return(null);
}
public string Parse(Dictionary <string, string> parameters)
{
var message = CheckIsValid(parameters);
if (message != null)
{
return(message);
}
try
{
var specFilePath = parameters["-s"];
SpecFilePaths = Directory.Exists(specFilePath) ? Directory.GetFiles(specFilePath, "*.raw") : new[] { specFilePath };
}
catch (Exception ex)
{
Console.WriteLine("Exception parsing the file path for parameter -s: " + ex.Message);
throw;
}
DatabaseFilePath = parameters["-d"];
try
{
var outputDir = parameters["-o"] ?? Environment.CurrentDirectory;
if (!Directory.Exists(outputDir))
{
if (File.Exists(outputDir) && !File.GetAttributes(outputDir).HasFlag(FileAttributes.Directory))
{
return("OutputDir is not a directory: " + outputDir);
}
Directory.CreateDirectory(outputDir);
}
OutputDir = outputDir;
}
catch (Exception ex)
{
Console.WriteLine("Exception validating the path for parameter -o: " + ex.Message);
throw;
}
try
{
var modFilePath = parameters["-mod"];
if (modFilePath != null)
{
var parser = new ModFileParser(modFilePath);
_searchModifications = parser.SearchModifications;
_maxNumDynModsPerSequence = parser.MaxNumDynModsPerSequence;
if (_searchModifications == null)
{
return("Error while parsing " + modFilePath);
}
AminoAcidSet = new AminoAcidSet(_searchModifications, _maxNumDynModsPerSequence);
}
else
{
AminoAcidSet = new AminoAcidSet();
_searchModifications = new SearchModification[0];
}
}
catch (Exception ex)
{
Console.WriteLine("Exception parsing the path for parameter -mod: " + ex.Message);
throw;
}
var currentParameter = string.Empty;
try
{
currentParameter = "-feature";
FeatureFilePath = parameters["-feature"];
currentParameter = "-m";
var searchMode = Convert.ToInt32(parameters["-m"]);
if (searchMode < 0 || searchMode > 2)
{
return("Invalid value (" + searchMode + ") for parameter -m");
}
SearchModeInt = searchMode;
currentParameter = "-t";
PrecursorIonTolerancePpm = Convert.ToDouble(parameters["-t"]);
currentParameter = "-f";
ProductIonTolerancePpm = Convert.ToDouble(parameters["-f"]);
currentParameter = "-tda";
var tdaVal = Convert.ToInt32(parameters["-tda"]);
if (tdaVal != 0 && tdaVal != 1 && tdaVal != -1)
{
return("Invalid value (" + tdaVal + ") for parameter -tda");
}
if (tdaVal == 1)
{
Tda = DatabaseSearchMode.Both;
}
else if (tdaVal == -1)
{
Tda = DatabaseSearchMode.Decoy;
}
else
{
Tda = DatabaseSearchMode.Target;
}
currentParameter = "-minLength";
MinSequenceLength = Convert.ToInt32(parameters["-minLength"]);
currentParameter = "-maxLength";
MaxSequenceLength = Convert.ToInt32(parameters["-maxLength"]);
if (MinSequenceLength > MaxSequenceLength)
{
return("MinSequenceLength (" + MinSequenceLength + ") is larger than MaxSequenceLength (" + MaxSequenceLength + ")!");
}
currentParameter = "-feature";
MinPrecursorIonCharge = Convert.ToInt32(parameters["-minCharge"]);
currentParameter = "-feature";
MaxPrecursorIonCharge = Convert.ToInt32(parameters["-maxCharge"]);
if (MinSequenceLength > MaxSequenceLength)
{
return("MinPrecursorCharge (" + MinPrecursorIonCharge + ") is larger than MaxPrecursorCharge (" + MaxPrecursorIonCharge + ")!");
}
currentParameter = "-minFragCharge";
MinProductIonCharge = Convert.ToInt32(parameters["-minFragCharge"]);
currentParameter = "-maxFragCharge";
MaxProductIonCharge = Convert.ToInt32(parameters["-maxFragCharge"]);
if (MinSequenceLength > MaxSequenceLength)
{
return("MinFragmentCharge (" + MinProductIonCharge + ") is larger than MaxFragmentCharge (" + MaxProductIonCharge + ")!");
}
currentParameter = "-minMass";
MinSequenceMass = Convert.ToDouble(parameters["-minMass"]);
currentParameter = "-maxMass";
MaxSequenceMass = Convert.ToDouble(parameters["-maxMass"]);
if (MinSequenceMass > MaxSequenceMass)
{
return("MinSequenceMassInDa (" + MinSequenceMass + ") is larger than MaxSequenceMassInDa (" + MaxSequenceMass + ")!");
}
currentParameter = "-threads";
MaxNumThreads = Convert.ToInt32(parameters["-threads"]);
MaxNumThreads = GetOptimalMaxThreads(MaxNumThreads);
currentParameter = "-tagSearch";
TagBasedSearch = Convert.ToInt32(parameters["-tagSearch"]) == 1;
}
catch (Exception ex)
{
Console.WriteLine("Exception parsing parameter '" + currentParameter + "': " + ex.Message);
throw;
}
return(null);
}
