public static List<SearchResult> ReadSearchResultsViaBiblioSpec(String filename, Func<int, bool> progressMonitor)
{
string tempFile = null;
try
{
tempFile = Path.GetTempFileName();
var blibBuild = new BlibBuild(tempFile, new[] {filename})
{
CompressLevel = 0,
};
var status = new ProgressStatus("");
var progressMonitorImpl = ProgressMonitorImpl.NewProgressMonitorImpl(status, progressMonitor);
string[] ambiguousPeptides;
blibBuild.BuildLibrary(LibraryBuildAction.Create, progressMonitorImpl, ref status, out ambiguousPeptides);
return ReadBiblioSpecDatabase(tempFile, progressMonitor);
}
finally
{
try
{
if (tempFile != null)
{
File.Delete(tempFile);
}
}
catch (Exception exception)
{
Trace.TraceWarning("Exception deleting temp file {0}", exception);
}
}
}
public bool BuildLibrary(IProgressMonitor progress)
{
_ambiguousMatches = null;
ProgressStatus status = new ProgressStatus(Resources.BiblioSpecLiteBuilder_BuildLibrary_Preparing_to_build_library);
progress.UpdateProgress(status);
if (InputFiles.Any(f => f.EndsWith(EXT_PILOT)))
{
try
{
InputFiles = VendorIssueHelper.ConvertPilotFiles(InputFiles, progress, status);
if (progress.IsCanceled)
return false;
}
catch (Exception x)
{
progress.UpdateProgress(status.ChangeErrorException(x));
return false;
}
}
string message = string.Format(Resources.BiblioSpecLiteBuilder_BuildLibrary_Building__0__library,
Path.GetFileName(OutputPath));
progress.UpdateProgress(status = status.ChangeMessage(message));
string redundantLibrary = BiblioSpecLiteSpec.GetRedundantName(OutputPath);
var blibBuilder = new BlibBuild(redundantLibrary, InputFiles, TargetSequences)
{
Authority = Authority,
IncludeAmbiguousMatches = IncludeAmbiguousMatches,
CutOffScore = CutOffScore,
Id = Id,
};
try
{
if (!blibBuilder.BuildLibrary(Action, progress, ref status, out _ambiguousMatches))
{
return false;
}
}
catch (IOException x)
{
progress.UpdateProgress(status.ChangeErrorException(x));
return false;
}
catch (Exception x)
{
Console.WriteLine(x.Message);
progress.UpdateProgress(status.ChangeErrorException(
new Exception(string.Format(Resources.BiblioSpecLiteBuilder_BuildLibrary_Failed_trying_to_build_the_redundant_library__0__,
redundantLibrary))));
return false;
}
var blibFilter = new BlibFilter();
status = new ProgressStatus(message);
progress.UpdateProgress(status);
// Write the non-redundant library to a temporary file first
try
{
using (var saver = new FileSaver(OutputPath))
{
if (!blibFilter.Filter(redundantLibrary, saver.SafeName, progress, ref status))
{
return false;
}
saver.Commit();
}
}
catch (IOException x)
{
progress.UpdateProgress(status.ChangeErrorException(x));
return false;
}
catch
{
progress.UpdateProgress(status.ChangeErrorException(
new Exception(string.Format(Resources.BiblioSpecLiteBuilder_BuildLibrary_Failed_trying_to_build_the_library__0__,
OutputPath))));
return false;
}
finally
{
if (!KeepRedundant)
FileEx.SafeDelete(redundantLibrary, true);
}
return true;
}
