/// <summary>
/// VAlidates mandatory tags.
/// </summary>
/// <returns>Returns empty string if mandatory tags are present; otherwise error message.</returns>
public string IsValid()
{
if (RecordFields.Count == 0)
{
return(string.Empty);
}
if (RecordFields.Count(RF => RF == null) > 0)
{
return(string.Format(CultureInfo.CurrentCulture, Properties.Resource.HeaderContainsNullValue));
}
List <SAMRecordField> fieldsToValidate = RecordFields.Where(F => MandatoryTagsForFieldTypes.Keys.Contains(F.Typecode,
StringComparer.InvariantCultureIgnoreCase)).ToList();
foreach (SAMRecordField field in fieldsToValidate)
{
foreach (string tag in MandatoryTagsForFieldTypes[field.Typecode])
{
if (field.Tags.FirstOrDefault(T => string.Compare(T.Tag, tag, StringComparison.InvariantCultureIgnoreCase) == 0) == null)
{
return(string.Format(CultureInfo.CurrentCulture, Properties.Resource.MandatoryTagNotFound, tag, field.Typecode));
}
}
}
return(string.Empty);
}
/// <summary>
/// Returns list of reference sequences present in this header.
/// </summary>
public IList <string> GetReferenceSequences()
{
List <string> refSequences = new List <string>();
List <SAMRecordField> fields = RecordFields.Where(R => String.Compare(R.Typecode, "SQ", StringComparison.OrdinalIgnoreCase) == 0).ToList();
foreach (SAMRecordField field in fields)
{
SAMRecordFieldTag tag = field.Tags.FirstOrDefault(F => String.Compare(F.Tag, "SN", StringComparison.OrdinalIgnoreCase) == 0);
if (tag != null)
{
refSequences.Add(tag.Value);
}
}
return(refSequences);
}
/// <summary>
/// Returns list of reference sequences name and length present in SQ header.
/// </summary>
public IList <ReferenceSequenceInfo> GetReferenceSequencesInfoFromSQHeader()
{
List <ReferenceSequenceInfo> refSequencesInfo = new List <ReferenceSequenceInfo>();
List <SAMRecordField> fields = RecordFields.Where(R => String.Compare(R.Typecode, "SQ", StringComparison.OrdinalIgnoreCase) == 0).ToList();
foreach (SAMRecordField field in fields)
{
SAMRecordFieldTag tag = field.Tags.FirstOrDefault(F => String.Compare(F.Tag, "SN", StringComparison.OrdinalIgnoreCase) == 0);
if (tag != null)
{
string refName = tag.Value;
long length;
tag = field.Tags.FirstOrDefault(F => String.Compare(F.Tag, "LN", StringComparison.OrdinalIgnoreCase) == 0);
if (tag != null && long.TryParse(tag.Value, out length))
{
refSequencesInfo.Add(new ReferenceSequenceInfo(refName, length));
}
}
}
return(refSequencesInfo);
}
/// <summary>
/// Returns list of SequenceRanges objects which represents reference sequences present in this header.
/// </summary>
public IList <SequenceRange> GetReferenceSequenceRanges()
{
List <SequenceRange> ranges = new List <SequenceRange>();
List <SAMRecordField> fields = RecordFields.Where(R => String.Compare(R.Typecode, "SQ", StringComparison.OrdinalIgnoreCase) == 0).ToList();
foreach (SAMRecordField field in fields)
{
SAMRecordFieldTag tag = field.Tags.FirstOrDefault(F => String.Compare(F.Tag, "SN", StringComparison.OrdinalIgnoreCase) == 0);
if (tag != null)
{
string refName = tag.Value;
long length;
tag = field.Tags.FirstOrDefault(F => String.Compare(F.Tag, "LN", StringComparison.OrdinalIgnoreCase) == 0);
if (tag != null && long.TryParse(tag.Value, out length))
{
SequenceRange range = new SequenceRange(refName, 0, length);
ranges.Add(range);
}
}
}
return(ranges.OrderBy(S => S.ID).ToList());
}
public override void Init()
{
recordFields = new RecordFields();
timer1 = new System.Timers.Timer();
timer1.Elapsed += new System.Timers.ElapsedEventHandler(this.timer1_Tick);
timer1.Interval = timer_interval;
timer1.Enabled = true;
try
{
if (usingRegistry)
{
if (!reg_flag)
{
if (!Read_Registry())
{
L.Log(LogType.FILE, LogLevel.ERROR, "Error on Reading the Registry ");
return;
}
else
if (!Initialize_Logger())
{
L.Log(LogType.FILE, LogLevel.ERROR, "Error on Intialize Logger on Meyer Recorder functions may not be running");
return;
}
reg_flag = true;
//Database.CreateDatabase();
}
}
else
{
if (!reg_flag)
{
if (!Get_logDir())
{
L.Log(LogType.FILE, LogLevel.ERROR, "Error on Reading the Registry ");
return;
}
else
if (!Initialize_Logger())
{
L.Log(LogType.FILE, LogLevel.ERROR, "Error on Intialize Logger on Meyer Recorder functions may not be running");
return;
}
L.Log(LogType.FILE, LogLevel.INFORM, "Start creating Meyer DAL");
reg_flag = true;
//Database.CreateDatabase();
db_name = "master";
if (Database.AddConnection(db_name, Database.Provider.SQLServer, remote_host, user, password, location))
{
L.Log(LogType.FILE, LogLevel.INFORM, "Successfully create Meyer DAL");
}
else
{
L.Log(LogType.FILE, LogLevel.INFORM, "Failed on creating Meyer DAL");
}
}
}
}
catch (Exception er)
{
EventLog.WriteEntry("Security Manager Meyer Recorder Init", er.ToString(), EventLogEntryType.Error);
}
L.Log(LogType.FILE, LogLevel.DEBUG, "Exit Init Function.");
}