/// <summary>
/// Finds a list of input files within the folder provided.
/// </summary>
/// <param name="folderPath"></param>
/// <returns></returns>
public static List<InputFile> FindDatasets(string folderPath, List<string> extensions, SearchOption options)
{
var datasetList = new List<InputFile>();
var candidates = new List<string>();
foreach (var extension in extensions)
{
var paths = Directory.GetFiles(folderPath, "*" + extension, options);
candidates.AddRange(paths);
}
foreach (var path in candidates)
{
var type = DatasetInformation.GetInputFileType(path);
if (type == InputFileType.NotRecognized)
{
continue;
}
var file = new InputFile();
file.Path = path;
file.FileType = type;
datasetList.Add(file);
}
return datasetList;
}
/// <summary>
/// Adds datasets from a single file
/// </summary>
private void AddSingleFileDelegate()
{
var fileExists = File.Exists(SingleFilePath);
if (fileExists)
{
var type = DatasetInformation.GetInputFileType(SingleFilePath);
if (type == InputFileType.NotRecognized)
{
ApplicationStatusMediator.SetStatus("The input file was not recognized.");
return;
}
if (type == InputFileType.Scans)
{
ApplicationStatusMediator.SetStatus("The input file was not recognized.");
return;
}
var file = new InputFile {Path = SingleFilePath, FileType = type};
var inputs = new List<InputFile> {file};
AddDatasets(inputs);
}
else
{
ApplicationStatusMediator.SetStatus("The input file does not exist.");
}
}
/// <summary>
/// Reads the input paths file
/// </summary>
/// <param name="path"></param>
/// <returns></returns>
public static InputAnalysisInfo ReadInputFile(string path)
{
var info = new InputAnalysisInfo();
var lines = File.ReadAllLines(path);
var readType = FileReadMode.None;
foreach (var line in lines)
{
var fixedLine = line.ToLower();
fixedLine = fixedLine.Trim();
var containsHeaderOpen = fixedLine.Contains("[");
var containsHeaderClose = fixedLine.Contains("]");
if (containsHeaderClose && containsHeaderOpen)
{
fixedLine = fixedLine.Replace(" ", "");
}
if (string.IsNullOrEmpty(fixedLine) || string.IsNullOrWhiteSpace(fixedLine))
{
continue;
}
// If wasModeChanged = true, then the current
// line is not data, but a tag to say change how read the next section.
var wasModeChanged = false;
switch (fixedLine)
{
case FILE_HEADER:
wasModeChanged = true;
readType = FileReadMode.Files;
break;
case DATABASE_HEADER:
wasModeChanged = true;
readType = FileReadMode.Database;
break;
case RAW_HEADER:
wasModeChanged = true;
readType = FileReadMode.RawFiles;
break;
case SCANS_HEADER:
wasModeChanged = true;
readType = FileReadMode.ScanFiles;
break;
case PEAKS_HEADER:
wasModeChanged = true;
readType = FileReadMode.Peaks;
break;
case SEQUENCE_HEADER:
wasModeChanged = true;
readType = FileReadMode.Sequence;
break;
default:
if (containsHeaderClose && containsHeaderOpen)
{
wasModeChanged = true;
readType = FileReadMode.Unknown;
throw new Exception(fixedLine + " is not a recognized data tag.");
}
wasModeChanged = false;
break;
}
if (!wasModeChanged)
{
switch (readType)
{
case FileReadMode.Files:
var baselineCheck = fixedLine.Split(BASELINE_INDICATOR);
if (baselineCheck.Length == 2 && !string.IsNullOrEmpty(baselineCheck[0]))
{
var newFile = new InputFile();
newFile.Path = baselineCheck[0];
newFile.FileType = InputFileType.Features;
info.BaselineFile = newFile;
info.Files.Add(newFile);
}
else if (!string.IsNullOrEmpty(baselineCheck[0]))
{
var newFile = new InputFile();
newFile.Path = baselineCheck[0];
newFile.FileType = InputFileType.Features;
info.Files.Add(newFile);
}
break;
case FileReadMode.Database:
var keys = fixedLine.Split('=');
if (keys.Length > 1)
{
keys[0] = keys[0].Replace('\t', ' ').Trim();
switch (keys[0].ToLower())
{
case "database":
info.Database.DatabaseFormat = MassTagDatabaseFormat.MassTagSystemSql;
info.Database.DatabaseName = keys[1];
break;
case "server":
info.Database.DatabaseFormat = MassTagDatabaseFormat.MassTagSystemSql;
info.Database.DatabaseServer = keys[1];
break;
case "sqlite":
info.Database.DatabaseFormat = MassTagDatabaseFormat.Sqlite;
info.Database.LocalPath = keys[1];
break;
case "metasample":
info.Database.DatabaseFormat = MassTagDatabaseFormat.DelimitedTextFile;
info.Database.LocalPath = keys[1];
break;
case "ims":
info.Database.DatabaseFormat = MassTagDatabaseFormat.SkipAlignment;
info.Database.LocalPath = keys[1];
break;
}
}
break;
case FileReadMode.RawFiles:
var rawFile = new InputFile();
rawFile.Path = fixedLine;
rawFile.FileType = InputFileType.Raw;
info.Files.Add(rawFile);
break;
case FileReadMode.ScanFiles:
var scanFile = new InputFile();
scanFile.Path = fixedLine;
scanFile.FileType = InputFileType.Scans;
info.Files.Add(scanFile);
break;
case FileReadMode.Unknown:
// do nothing!
break;
case FileReadMode.Sequence:
var sequenceFile = new InputFile();
sequenceFile.Path = fixedLine;
sequenceFile.FileType = InputFileType.Sequence;
info.Files.Add(sequenceFile);
break;
}
}
}
return(info);
}
/// <summary>
/// Reads the input paths file
/// </summary>
/// <param name="path"></param>
/// <returns></returns>
public static InputAnalysisInfo ReadInputFile(string path)
{
var info = new InputAnalysisInfo();
var lines = File.ReadAllLines(path);
var readType = FileReadMode.None;
foreach (var line in lines)
{
var fixedLine = line.ToLower();
fixedLine = fixedLine.Trim();
var containsHeaderOpen = fixedLine.Contains("[");
var containsHeaderClose = fixedLine.Contains("]");
if (containsHeaderClose && containsHeaderOpen)
{
fixedLine = fixedLine.Replace(" ", "");
}
if (string.IsNullOrEmpty(fixedLine) || string.IsNullOrWhiteSpace(fixedLine))
{
continue;
}
// If wasModeChanged = true, then the current
// line is not data, but a tag to say change how read the next section.
var wasModeChanged = false;
switch (fixedLine)
{
case FILE_HEADER:
wasModeChanged = true;
readType = FileReadMode.Files;
break;
case DATABASE_HEADER:
wasModeChanged = true;
readType = FileReadMode.Database;
break;
case RAW_HEADER:
wasModeChanged = true;
readType = FileReadMode.RawFiles;
break;
case SCANS_HEADER:
wasModeChanged = true;
readType = FileReadMode.ScanFiles;
break;
case PEAKS_HEADER:
wasModeChanged = true;
readType = FileReadMode.Peaks;
break;
case SEQUENCE_HEADER:
wasModeChanged = true;
readType = FileReadMode.Sequence;
break;
default:
if (containsHeaderClose && containsHeaderOpen)
{
wasModeChanged = true;
readType = FileReadMode.Unknown;
throw new Exception(fixedLine + " is not a recognized data tag.");
}
wasModeChanged = false;
break;
}
if (!wasModeChanged)
{
switch (readType)
{
case FileReadMode.Files:
var baselineCheck = fixedLine.Split(BASELINE_INDICATOR);
if (baselineCheck.Length == 2 && !string.IsNullOrEmpty(baselineCheck[0]))
{
var newFile = new InputFile();
newFile.Path = baselineCheck[0];
newFile.FileType = InputFileType.Features;
info.BaselineFile = newFile;
info.Files.Add(newFile);
}
else if (!string.IsNullOrEmpty(baselineCheck[0]))
{
var newFile = new InputFile();
newFile.Path = baselineCheck[0];
newFile.FileType = InputFileType.Features;
info.Files.Add(newFile);
}
break;
case FileReadMode.Database:
var keys = fixedLine.Split('=');
if (keys.Length > 1)
{
keys[0] = keys[0].Replace('\t', ' ').Trim();
switch (keys[0].ToLower())
{
case "database":
info.Database.DatabaseFormat = MassTagDatabaseFormat.MassTagSystemSql;
info.Database.DatabaseName = keys[1];
break;
case "server":
info.Database.DatabaseFormat = MassTagDatabaseFormat.MassTagSystemSql;
info.Database.DatabaseServer = keys[1];
break;
case "sqlite":
info.Database.DatabaseFormat = MassTagDatabaseFormat.Sqlite;
info.Database.LocalPath = keys[1];
break;
case "metasample":
info.Database.DatabaseFormat = MassTagDatabaseFormat.DelimitedTextFile;
info.Database.LocalPath = keys[1];
break;
case "ims":
info.Database.DatabaseFormat = MassTagDatabaseFormat.SkipAlignment;
info.Database.LocalPath = keys[1];
break;
}
}
break;
case FileReadMode.RawFiles:
var rawFile = new InputFile();
rawFile.Path = fixedLine;
rawFile.FileType = InputFileType.Raw;
info.Files.Add(rawFile);
break;
case FileReadMode.ScanFiles:
var scanFile = new InputFile();
scanFile.Path = fixedLine;
scanFile.FileType = InputFileType.Scans;
info.Files.Add(scanFile);
break;
case FileReadMode.Unknown:
// do nothing!
break;
case FileReadMode.Sequence:
var sequenceFile = new InputFile();
sequenceFile.Path = fixedLine;
sequenceFile.FileType = InputFileType.Sequence;
info.Files.Add(sequenceFile);
break;
}
}
}
return info;
}