private static IList <Resume> GetResumes(ResumesDataContext dc, IEnumerable <Guid> ids)
{
var resumeIds = new SplitList <Guid>(ids).ToString();
var resumes = GetAllResumesQuery(dc, resumeIds).ToList();
var allJobs = (from e in GetAllJobsQuery(dc, resumeIds)
group e by e.Item1).ToDictionary(g => g.Key, g => (from e in g select e.Item2).ToList());
var allSchools = (from e in GetAllSchoolsQuery(dc, resumeIds)
group e by e.Item1).ToDictionary(g => g.Key, g => (from e in g select e.Item2).ToList());
foreach (var resume in resumes)
{
List <Job> jobs;
if (allJobs.TryGetValue(resume.Id, out jobs))
{
resume.Jobs = jobs;
}
List <School> schools;
if (allSchools.TryGetValue(resume.Id, out schools))
{
resume.Schools = schools;
}
}
return(resumes.ToList());
}
public SampleProcessingParam(SplitList<Lib.Model.Param>[] steps, CVLookUp cv)
: base(null)
{
_cv = cv;
_count = steps.Length;
Value = steps;
Default = steps;
}
public SampleProcessingPanel(SplitList<Lib.Model.Param>[] steps, CVLookUp cv)
{
_cv = cv;
_count = steps.Length;
InitializeComponent();
Value = steps;
}
private IList <Candidate> GetCandidates(CandidatesDataContext dc, IEnumerable <Guid> ids)
{
var candidateIds = new SplitList <Guid>(ids).ToString();
var candidates = GetCandidatesQuery(dc, candidateIds, _industriesQuery).ToList();
GetRelocationLocations(dc, candidateIds, candidates);
GetIndustries(dc, candidateIds, candidates);
return(candidates);
}
protected void lnkRemove_Click(object sender, EventArgs e)
{
SplitList = GetSplitsFromRepeater();
int myindex = Convert.ToInt32(((LinkButton)sender).Attributes[DataIndex]);
SplitList.RemoveAt(myindex);
SplitList = SplitList;
RebindSplitList();
}
JobAdTotalsReport IJobAdReportsRepository.GetJobAdTotalsReport(IEnumerable <Guid> jobAdIds)
{
using (var dc = CreateDataContext(true))
{
var jobAdIdList = new SplitList <Guid>(jobAdIds).ToString();
return(new JobAdTotalsReport
{
Views = GetViewedJobAds(dc, jobAdIdList),
Applications = GetApplications(dc, jobAdIdList),
});
}
}
public void Build(Scene scene)
{
foreach (Primitive p in scene.Primitives) {
Root.Add(p);
}
int prims = scene.Primitives.Count;
AxisAlignedBox sBox = scene.Extends;
_list = null;
_sortedList = null;
Subdivide(Root, sBox, 0, prims);
}
public void AddUpdate(IEnumerable <DeviceConnection> existingConnections, List <DeviceConnection> connections)
{
var splitList = new SplitList <DeviceConnection>();
splitList.Process(existingConnections, connections, (source, target) => target.Id = source.Id);
using (Db.Open())
{
Add(splitList.New, Db);
Update(splitList.Existing, Db);
Db.Commit();
}
}
public (ServerFrame ServerFrame, List <UnitFrame> UnitFrame) GetServerData(Player player)
{
float viewRange = Math.Max(player.ViewZone.ViewRange + 2f, _config.MaxViewRange);
bool FilterRect(Vector2 pos) =>
(pos.X > player.ViewZone.MinX - 1f && pos.X < player.ViewZone.MaxX + 1f) && (pos.Y > player.ViewZone.MinY - 1f && pos.Y < player.ViewZone.MaxY + 1f);
var visiblePlayers = _players.Where((p) => p.Value == player ||
(p.Value.IsAlive && (p.Value.UnitsEffect?.StatsChange.UnitVisible ?? true) &&
(p.Value.AvgPosition - player.AvgPosition).SqrLength() < viewRange * viewRange) &&
FilterRect(p.Value.AvgPosition))
.Select((p) => p.Value.GetPlayerCameraInfo()).ToArray();
var visibleUnits = OverlapUnits(player.AvgPosition, viewRange)
.Where((u) => (u.CurrentStats.UnitVisible || u.Owner == player) && FilterRect(u.Position));
var visibleUnitsData = visibleUnits.Select((u) => u.GetUnitInfo(this, player)).ToList();
int[] visibleUnitsMap = new int[_units.Length / 32 + 1];
foreach (var unit in visibleUnitsData)
{
visibleUnitsMap.SetBit(unit.UnitId);
}
var visibleRunes = _runesTree.Overlap <Rune>(player.AvgPosition, viewRange)
.Select((r) => r.GetRuneInfo()).ToArray();
var sFrame = new ServerFrame()
{
State = _worldState,
PlayTime = _timeToEnd,
ZoneSize = ZoneRadius,
AlivePlayers = _alivePlayers,
Cooldown = player.GetCooldown(),
VisualEffect = player.UnitsEffect?.VisualEffect ?? VisualEffect.None,
VisualEffectTime = (float)((player.UnitsEffect?.EndTime ?? DateTime.Now) - DateTime.Now).TotalSeconds,
PlayerCameras = visiblePlayers,
EnabledUnits = visibleUnitsMap,
UnitKill = player.PlayerStatus.UnitKill,
PlayerUnitCount = player.Units.Count,
Runes = visibleRunes
};
var unitFrames = SplitList.Split(visibleUnitsData, visibleUnitsData.Count < 45 ? 12 : 24)
.Select((lst) => new UnitFrame()
{
Units = lst.ToArray(), PacketId = UnitFrame.UnitsPacketId++
}).ToList();
return(sFrame, unitFrames);
}
public static SplitList<double> ParseDoubleList(string target)
{
SplitList<string> list = ParseStringList(MZTabConstants.BAR, target);
SplitList<double> valueList = new SplitList<double>(MZTabConstants.BAR);
foreach (string listItem in list){
double value = ParseDouble(listItem);
if (value.Equals(double.MinValue)){
valueList.Clear();
break;
}
valueList.Add(value);
}
return valueList;
}
JobAdReport IJobAdReportsRepository.GetJobAdReport(IEnumerable <Guid> posterIds, DateRange dateRange)
{
using (var dc = CreateDataContext(true))
{
var posterIdList = new SplitList <Guid>(posterIds).ToString();
return(new JobAdReport
{
OpenedJobAds = GetOpenedJobAds(dc, posterIdList, dateRange).ToList(),
ClosedJobAds = GetClosedJobAds(dc, posterIdList, dateRange).ToList(),
Totals = new JobAdTotalsReport
{
Views = GetViewedJobAdsByPosters(dc, posterIdList, dateRange),
Applications = GetApplicationsByPosters(dc, posterIdList, dateRange),
},
});
}
}
/**
* A list of '|' separated parameters
*/
public static SplitList<Param> ParseParamList(string target)
{
SplitList<string> list = ParseStringList(MZTabConstants.BAR, target);
SplitList<Param> paramList = new SplitList<Param>(MZTabConstants.BAR);
foreach (string item in list){
Param param = ParseParam(item);
if (param == null){
paramList.Clear();
return paramList;
}
paramList.Add(param);
}
return paramList;
}
/**
* A publication on this unit. PubMed ids must be prefixed by “pubmed:”,
* DOIs by “doi:”. Multiple identifiers MUST be separated by “|”.
*/
public static SplitList<PublicationItem> ParsePublicationItems(string target)
{
SplitList<string> list = ParseStringList(MZTabConstants.BAR, target);
SplitList<PublicationItem> itemList = new SplitList<PublicationItem>(MZTabConstants.BAR);
foreach (string pubList in list){
var pub = ParseString(pubList);
if (pub == null){
itemList.Clear();
break;
}
string[] items = pub.Split(new[]{"" + MZTabConstants.COLON}, StringSplitOptions.None);
PublicationType type;
if (items.Length != 2 || (type = PublicationItem.FindType(items[0].Trim())) == null){
itemList.Clear();
break;
}
string accession = items[1].Trim();
PublicationItem item = new PublicationItem(type, accession);
itemList.Add(item);
}
return itemList;
}
/**
* A '|' delimited list of GO accessions
*/
public static SplitList<string> ParseGoTermList(string target)
{
SplitList<string> list = ParseStringList(MZTabConstants.COMMA, target);
SplitList<string> goList = new SplitList<string>(MZTabConstants.COMMA);
foreach (string listitem in list){
var item = ParseString(listitem);
if (item.StartsWith("GO:")){
goList.Add(item);
}
else{
goList.Clear();
break;
}
}
return goList;
}
public static SplitList<Modification> ParseModificationList(Section section, string target)
{
target = ParseString(target);
if (target == null){
return null;
}
SplitList<Modification> modList = new SplitList<Modification>(MZTabConstants.COMMA);
if (target.Equals("0")){
modList.Add(Modification.CreateNoModification(section));
return modList;
}
target = translateCommaToTab(target);
SplitList<string> list = ParseStringList(MZTabConstants.COMMA, target);
foreach (string item in list){
Modification mod = ParseModification(section, item.Trim());
if (mod == null){
modList.Clear();
break;
}
modList.Add(mod);
}
return modList;
}
public bool AddSearchEngineScore(MsRun msRun, CVParam param)
{
if (param == null){
return false;
}
SplitList<Param> searchparams = getSearchEngineScore(msRun);
if (searchparams == null){
searchparams = new SplitList<Param>(MZTabConstants.BAR);
SetSearchEngineScore(msRun, searchparams);
}
searchparams.Add(param);
return true;
}
public void SetSearchEngineScore(MsRun msRun, SplitList<Param> searchEngineScore)
{
SetSearchEngineScore(getPosition(PeptideColumn.SEARCH_ENGINE_SCORE, msRun), searchEngineScore);
}
public void setSearchEngineScore(MsRun msRun, SplitList<Param> searchEngineScore)
{
setValue(getPosition(SmallMoleculeColumn.SEARCH_ENGINE_SCORE, msRun), searchEngineScore);
}
public Metadata CreateMetadataDefault(IMatrixData parameters, IMatrixData experiment, IMatrixData search)
{
Metadata mtd = new Metadata(new MZTabDescription(MzTabMode.Complete, MzTabType.Quantification));
List<MsRunImpl> runs = null;
List<StudyVariable> studyvariables = null;
List<Assay> assays = null;
List<Sample> samples = null;
List<Instrument> instruments = null;
GetExperminetValues(null, null, experiment, search, ref runs, ref studyvariables, ref assays, ref samples,
ref instruments);
foreach (var msRun in runs){
mtd.MsRunMap.Add(msRun.Id, msRun);
}
foreach (var studyvariable in studyvariables){
mtd.StudyVariableMap.Add(studyvariable.Id, studyvariable);
}
foreach (var sample in samples){
mtd.SampleMap.Add(sample.Id, sample);
}
foreach (var assay in assays){
mtd.AssayMap.Add(assay.Id, assay);
}
foreach (var instrument in instruments){
mtd.InstrumentMap.Add(instrument.Id, instrument);
}
SplitList<Lib.Model.Param> sampleProcessing = new SplitList<Lib.Model.Param>{
cv.GetParam("enzyme digestion", "SEP"),
cv.GetParam("reversed-phase chromatography", "SEP")
};
//sampleProcessing.Add(_cv.GetParam("ion-exchange chromatography", "SEP"));
mtd.SampleProcessingMap.Add(1, sampleProcessing);
var paramDict = MzTabMatrixUtils.ConvertToParamDict(parameters);
string key = Constants.GetKeywordName(Utils.parameters.fixedMod, paramDict.Keys.ToArray());
if (key != null){
string[] values = paramDict[key].Split(';');
foreach (var mod in values.Select(x => BaseLib.Mol.Tables.Modifications[x])){
int id = mtd.FixedModMap.Count + 1;
mtd.AddFixedModParam(id, cv.GetModificationParam(mod));
mtd.AddFixedModPosition(id, mod.Position.ToString());
mtd.AddFixedModSite(id, StringUtils.Concat(", ", mod.GetSiteArray()));
}
}
key = Constants.GetKeywordName(Utils.parameters.variableMod, paramDict.Keys.ToArray());
if (key != null){
string[] values = paramDict[key].Split(';');
foreach (var mod in values.Select(x => BaseLib.Mol.Tables.Modifications[x])){
int id = mtd.VariableModMap.Count + 1;
mtd.AddVariableModParam(id, cv.GetModificationParam(mod));
mtd.AddVariableModPosition(id, mod.Position.ToString());
mtd.AddVariableModSite(id, StringUtils.Concat(", ", mod.GetSiteArray()));
}
}
string version = Constants.GetKeywordName(Utils.parameters.version, paramDict.Keys.ToArray());
Software software = new Software(1){
Param = cv.GetParam("MaxQuant", "MS", GetParameterString(parameters, version, null))
};
mtd.SoftwareMap.Add(software.Id, software);
software = new Software(2){
Param = cv.GetParam("Andromeda", "MS", GetParameterString(parameters, version, null))
};
mtd.SoftwareMap.Add(software.Id, software);
if (assays.Count > 0){
var tmp = ArrayUtils.UniqueValues(assays.Select(x => x.QuantificationReagent.Name).ToArray());
if (tmp.Length == 1 && tmp.First().Equals("Unlabeled sample")){
mtd.QuantificationMethod = cv.GetParam("label-free proteingroup level quantitation", "MS");
}
else if (tmp.Any(x => x.Contains("SILAC"))){
mtd.QuantificationMethod = cv.GetParam("SILAC quantitation analysis", "MS");
}
}
return mtd;
}
public bool addRetentionTime(double rt)
{
if (rt.Equals(double.MinValue)){
return false;
}
SplitList<double> rtList = RetentionTime;
if (rtList == null){
rtList = new SplitList<double>(MZTabConstants.BAR);
RetentionTime = rtList;
}
rtList.Add(rt);
return true;
}
public bool addSearchEngineScore(MsRun msRun, CVParam param)
{
if (param == null){
return false;
}
SplitList<Param> paramList = getSearchEngineScore(msRun);
if (paramList == null){
paramList = new SplitList<Param>(MZTabConstants.BAR);
setSearchEngineScore(msRun, paramList);
}
paramList.Add(param);
return true;
}
public void addIdentifier(string identifier)
{
if (string.IsNullOrEmpty(identifier)){
return;
}
SplitList<string> identifierList = Identifier;
if (identifierList == null){
identifierList = new SplitList<string>(MZTabConstants.BAR);
Identifier = identifierList;
}
identifierList.Add(identifier);
}
public override void Clear()
{
Value = new SplitList<Lib.Model.Param>[_count];
}
public override void ResetDefault()
{
Default = Value;
}
public static SplitList<SpectraRef> ParseSpectraRefList(Metadata metadata, string target)
{
SplitList<string> list = ParseStringList(MZTabConstants.BAR, target);
SplitList<SpectraRef> refList = new SplitList<SpectraRef>(MZTabConstants.BAR);
Regex regex = new Regex("ms_run\\[(\\d+)\\]:(.*)");
foreach (string item in list){
if (regex.IsMatch(item.Trim())){
int ms_file_id = int.Parse(regex.Match(item.Trim()).Groups[1].Value);
string reference = regex.Match(item.Trim()).Groups[2].Value;
MsRun msRun = metadata.MsRunMap[ms_file_id];
SpectraRef sref = msRun == null ? null : new SpectraRef(msRun, reference);
if (sref == null){
refList.Clear();
break;
}
refList.Add(sref);
}
}
return refList;
}
public bool addAmbiguityMembers(string member)
{
if (string.IsNullOrEmpty(member)){
return false;
}
SplitList<string> ambiguityMembers = AmbiguityMembers;
if (ambiguityMembers == null){
ambiguityMembers = new SplitList<string>(MZTabConstants.COMMA);
AmbiguityMembers = ambiguityMembers;
}
ambiguityMembers.Add(member);
return true;
}
/**
* Multiple identifiers MUST be separated by splitChar.
*/
public static SplitList<string> ParseStringList(char splitChar, string target)
{
SplitList<string> list = new SplitList<string>(splitChar);
target = ParseString(target);
if (target == null){
return list;
}
// regular express reserved keywords escape
IList<char> chars = new List<char>();
switch (splitChar){
case '.':
case '$':
case '^':
case '{':
case '}':
case '[':
case ']':
case '(':
case ')':
case '|':
case '*':
case '+':
case '?':
case '\\':
chars.Add(splitChar);
break;
default:
chars.Add(splitChar);
break;
}
string[] items = target.Split(chars.ToArray());
list.AddRange(items);
return list;
}
/**
* @return tab split column header string list.
*/
public SplitList<string> GetHeaderList()
{
SplitList<string> headerList = new SplitList<string>(MZTabConstants.TAB);
foreach (MZTabColumn mzTabColumn in columnMapping.Values){
headerList.Add(mzTabColumn.Header);
}
return headerList;
}
public static void Release(SplitList toRelease) => s_Pool.Release(toRelease);
public bool AddSampleProcessing(int id, SplitList<Param> sampleProcessing)
{
if (_sampleProcessingMap.ContainsKey(id)){
return false;
}
sampleProcessing.Separator = MZTabConstants.BAR;
_sampleProcessingMap.Add(id, sampleProcessing);
return true;
}
public bool addModification(Modification modification)
{
if (modification == null){
return false;
}
SplitList<Modification> modList = Modifications;
if (modList == null){
modList = new SplitList<Modification>(MZTabConstants.COMMA);
Modifications = modList;
}
modList.Add(modification);
return true;
}
public bool AddBestSearchEngineScore(Param param)
{
if (param == null){
return false;
}
SplitList<Param> searchparams = BestSearchEngineScore;
if (searchparams == null){
searchparams = new SplitList<Param>(MZTabConstants.BAR);
BestSearchEngineScore = (searchparams);
}
searchparams.Add(param);
return true;
}
public bool addSearchEngineParam(Param param)
{
if (param == null){
return false;
}
SplitList<Param> paramList = SearchEngine;
if (paramList == null){
paramList = new SplitList<Param>(MZTabConstants.BAR);
SearchEngine = paramList;
}
paramList.Add(param);
return true;
}
public bool AddModification(Modification modification)
{
if (modification == null){
return false;
}
if (Modifications == null){
Modifications = new SplitList<Modification>(MZTabConstants.COMMA);
}
if (Modifications.All(x => x.Accession != modification.Accession)){
Modifications.Add(modification);
}
else{
var m = Modifications.First(x => x.Accession == modification.Accession);
foreach (int key in modification.PositionMap.Keys){
if (m.PositionMap.ContainsKey(key)){
continue;
}
m.AddPosition(key, modification.PositionMap[key]);
}
}
return true;
}
public bool addSpectraRef(SpectraRef specRef)
{
if (specRef == null){
return false;
}
SplitList<SpectraRef> specRefs = SpectraRef;
if (specRefs == null){
specRefs = new SplitList<SpectraRef>(MZTabConstants.BAR);
SpectraRef = specRefs;
}
specRefs.Add(specRef);
return true;
}
public bool AddRetentionTimeWindow(double rtw)
{
SplitList<double> rtwList = RetentionTimeWindow;
if (rtwList == null){
rtwList = new SplitList<double>(MZTabConstants.BAR);
RetentionTimeWindow = rtwList;
}
if (rtw.Equals(double.MinValue) || rtwList.Contains(rtw)){
return false;
}
rtwList.Add(rtw);
return true;
}
public void setSearchEngineScore(string logicalPosition, SplitList<Param> searchEngineScore)
{
setValue(logicalPosition, searchEngineScore);
}
public bool AddSearchEngine(Param param)
{
if (param == null){
return false;
}
SplitList<Param> searchParams = SearchEngine;
if (searchParams == null){
searchParams = new SplitList<Param>(MZTabConstants.BAR);
SearchEngine = searchParams;
searchParams.Add(param);
}
else if (! searchParams.Contains(param)){
searchParams.Add(param);
}
return true;
}
