/// <summary>
/// Fills subsequences calculation data dictionary.
/// </summary>
/// <param name="minSelectedMatters">
/// The minimum Selected Matters.
/// </param>
/// <param name="maxSelectedMatters">
/// The maximum Selected Matters.
/// </param>
/// <param name="submitName">
/// The submit button name.
/// </param>
/// <returns>
/// The <see cref="Dictionary{String, Object}"/>.
/// </returns>
public Dictionary <string, object> FillSubsequencesViewData(int minSelectedMatters, int maxSelectedMatters, string submitName)
{
var sequenceIds = db.Subsequence.Select(s => s.SequenceId).Distinct();
var matterIds = db.DnaSequence.Where(c => sequenceIds.Contains(c.Id)).Select(c => c.MatterId).ToList();
Dictionary <string, object> data = GetMattersData(minSelectedMatters, maxSelectedMatters, m => matterIds.Contains(m.Id));
var geneticNotations = EnumExtensions.ToArray <Notation>().Where(n => n.GetNature() == Nature.Genetic);
var sequenceTypes = EnumExtensions.ToArray <SequenceType>().Where(st => st.GetNature() == Nature.Genetic);
var groups = EnumExtensions.ToArray <Group>().Where(g => g.GetNature() == Nature.Genetic);
var features = EnumExtensions.ToArray <Feature>().Where(f => f.GetNature() == Nature.Genetic).ToArray();
var selectedFeatures = features.Where(f => f != Feature.NonCodingSequence);
Dictionary <string, object> characteristicsData = GetCharacteristicsData(CharacteristicCategory.Full);
foreach ((string key, object value) in characteristicsData)
{
data.Add(key, value);
}
data.Add("submitName", submitName);
data.Add("notations", geneticNotations.ToSelectListWithNature());
data.Add("nature", ((byte)Nature.Genetic).ToString());
data.Add("features", features.ToSelectListWithNature(selectedFeatures));
data.Add("sequenceTypes", sequenceTypes.ToSelectListWithNature(true));
data.Add("groups", groups.ToSelectListWithNature(true));
return(data);
}
/// <summary>
/// Fills view data.
/// </summary>
/// <param name="minSelectedMatters">
/// The minimum selected matters.
/// </param>
/// <param name="maxSelectedMatters">
/// The maximum selected matters.
/// </param>
/// <returns>
/// The <see cref="Dictionary{String, Object}"/>.
/// </returns>
public Dictionary <string, object> FillViewData(int minSelectedMatters, int maxSelectedMatters)
{
Dictionary <string, object> data = GetMattersData(minSelectedMatters, maxSelectedMatters, m => true);
IEnumerable <SelectListItem> natures;
IEnumerable <SequenceType> sequenceTypes;
IEnumerable <Group> groups;
if (AccountHelper.IsAdmin())
{
natures = EnumHelper.GetSelectList(typeof(Nature));
sequenceTypes = EnumExtensions.ToArray <SequenceType>();
groups = EnumExtensions.ToArray <Group>();
}
else
{
natures = new[] { Nature.Genetic }.ToSelectList();
sequenceTypes = EnumExtensions.ToArray <SequenceType>().Where(st => st.GetNature() == Nature.Genetic);
groups = EnumExtensions.ToArray <Group>().Where(g => g.GetNature() == Nature.Genetic);
}
data.Add("natures", natures);
data.Add("sequenceTypes", sequenceTypes.ToSelectListWithNature(true));
data.Add("groups", groups.ToSelectListWithNature(true));
return(data);
}
/// <summary>
/// Fills matter creation data.
/// </summary>
/// <returns>
/// The <see cref="Dictionary{String, Object}"/>.
/// </returns>
public Dictionary <string, object> FillMatterCreationData()
{
IEnumerable <SelectListItem> natures;
IEnumerable <Notation> notations;
IEnumerable <RemoteDb> remoteDbs = EnumExtensions.ToArray <RemoteDb>();
IEnumerable <SequenceType> sequenceTypes = EnumExtensions.ToArray <SequenceType>();
IEnumerable <Group> groups = EnumExtensions.ToArray <Group>();
if (AccountHelper.IsAdmin())
{
natures = EnumHelper.GetSelectList(typeof(Nature));
notations = EnumExtensions.ToArray <Notation>();
}
else
{
natures = new[] { Nature.Genetic }.ToSelectList();
notations = new[] { Notation.Nucleotides };
remoteDbs = EnumExtensions.ToArray <RemoteDb>().Where(rd => rd.GetNature() == Nature.Genetic);
sequenceTypes = EnumExtensions.ToArray <SequenceType>().Where(st => st.GetNature() == Nature.Genetic);
groups = EnumExtensions.ToArray <Group>().Where(g => g.GetNature() == Nature.Genetic);
}
return(new Dictionary <string, object>
{
{ "matters", matterRepository.GetMatterSelectList() },
{ "natures", natures },
{ "notations", notations.ToSelectListWithNature() },
{ "remoteDbs", remoteDbs.ToSelectListWithNature() },
{ "sequenceTypes", sequenceTypes.ToSelectListWithNature() },
{ "groups", groups.ToSelectListWithNature() },
{ "languages", EnumHelper.GetSelectList(typeof(Language)) },
{ "translators", EnumHelper.GetSelectList(typeof(Translator)) }
});
}
/// <summary>
/// Fills view data.
/// </summary>
/// <param name="minSelectedMatters">
/// The minimum selected matters.
/// </param>
/// <param name="maxSelectedMatters">
/// The maximum selected matters.
/// </param>
/// <param name="filter">
/// The matters filter.
/// </param>
/// <param name="submitName">
/// The submit button name.
/// </param>
/// <returns>
/// The <see cref="Dictionary{String, Object}"/>.
/// </returns>
public Dictionary <string, object> FillViewData(int minSelectedMatters, int maxSelectedMatters, Func <Matter, bool> filter, string submitName)
{
Dictionary <string, object> data = GetMattersData(minSelectedMatters, maxSelectedMatters, filter);
IEnumerable <SelectListItem> natures;
IEnumerable <Notation> notations;
IEnumerable <SequenceType> sequenceTypes;
IEnumerable <Group> groups;
if (AccountHelper.IsAdmin())
{
natures = EnumHelper.GetSelectList(typeof(Nature));
notations = EnumExtensions.ToArray <Notation>();
sequenceTypes = EnumExtensions.ToArray <SequenceType>();
groups = EnumExtensions.ToArray <Group>();
}
else
{
natures = new[] { Nature.Genetic }.ToSelectList();
notations = new[] { Notation.Nucleotides };
sequenceTypes = EnumExtensions.ToArray <SequenceType>().Where(st => st.GetNature() == Nature.Genetic);
groups = EnumExtensions.ToArray <Group>().Where(g => g.GetNature() == Nature.Genetic);
}
data.Add("submitName", submitName);
data.Add("natures", natures);
data.Add("notations", notations.ToSelectListWithNature());
data.Add("languages", EnumHelper.GetSelectList(typeof(Language)));
data.Add("translators", EnumHelper.GetSelectList(typeof(Translator)));
data.Add("pauseTreatments", EnumHelper.GetSelectList(typeof(PauseTreatment)));
data.Add("sequenceTypes", sequenceTypes.ToSelectListWithNature(true));
data.Add("groups", groups.ToSelectListWithNature(true));
return(data);
}
private void TransformOrders()
{
// TODO: get rid of IndexOf here.
int[] ordersIds = Orders.Select(o => Orders.IndexOf(o)).ToArray();
TransformationsData = ordersIds.AsParallel().AsOrdered().Select(el => new OrderTransformationData
{
ResultTransformation = EnumExtensions.ToArray <OrderTransformation>().AsParallel().AsOrdered().Select(t => TransformOrder(t, el)).ToArray()
}).ToArray();
List <OrderTransformationData> resultData = ordersIds.AsParallel().AsOrdered().Select(el => new OrderTransformationData
{
ResultTransformation = TransformationsData[el].ResultTransformation,
UniqueFinalOrdersCount = CalculateUniqueOrdersCount(el)
}).ToList();
TransformationsData = resultData.ToArray();
}
private int CalculateUniqueOrdersCount(int id)
{
OrderTransformation[] transformationTypes = EnumExtensions.ToArray <OrderTransformation>();
bool completed = false;
var ordersForChecking = new List <int> {
id
};
var checkedOrders = new List <int> {
id
};
while (!completed)
{
var newOrders = new List <int>();
foreach (int order in ordersForChecking)
{
for (int i = 0; i < transformationTypes.Length; i++)
{
if (!checkedOrders.Contains(TransformationsData[order].ResultTransformation[i].OrderId))
{
checkedOrders.Add(TransformationsData[order].ResultTransformation[i].OrderId);
newOrders.Add(TransformationsData[order].ResultTransformation[i].OrderId);
}
}
}
if (newOrders.Count > 0)
{
ordersForChecking = newOrders;
}
else
{
completed = true;
}
}
return(checkedOrders.Count);
}
public ActionResult Index(long[] matterIds, short characteristicLinkId, short[] characteristicLinkIds, Feature[] features)
{
return(CreateTask(() =>
{
matterIds = matterIds.OrderBy(m => m).ToArray();
var matterNames = new string[matterIds.Length];
var remoteIds = new string[matterIds.Length];
var subsequencesCharacteristicsNames = new string[characteristicLinkIds.Length];
var subsequencesCharacteristicsList = new SelectListItem[characteristicLinkIds.Length];
var attributeValuesCache = new AttributeValueCacheManager();
long[] sequenceIds;
using (var db = new LibiadaWebEntities())
{
DnaSequence[] parentSequences = db.DnaSequence.Include(s => s.Matter)
.Where(s => s.Notation == Notation.Nucleotides && matterIds.Contains(s.MatterId))
.OrderBy(s => s.MatterId)
.ToArray();
for (int n = 0; n < parentSequences.Length; n++)
{
matterNames[n] = parentSequences[n].Matter.Name;
remoteIds[n] = parentSequences[n].RemoteId;
}
var geneticSequenceRepository = new GeneticSequenceRepository(db);
sequenceIds = geneticSequenceRepository.GetNucleotideSequenceIds(matterIds);
}
var characteristicTypeLinkRepository = FullCharacteristicRepository.Instance;
string sequenceCharacteristicName = characteristicTypeLinkRepository.GetCharacteristicName(characteristicLinkId);
for (int k = 0; k < characteristicLinkIds.Length; k++)
{
subsequencesCharacteristicsNames[k] = characteristicTypeLinkRepository.GetCharacteristicName(characteristicLinkIds[k]);
subsequencesCharacteristicsList[k] = new SelectListItem
{
Value = k.ToString(),
Text = subsequencesCharacteristicsNames[k],
Selected = false
};
}
double[] characteristics = SequencesCharacteristicsCalculator.Calculate(sequenceIds, characteristicLinkId);
var sequencesData = new SequenceData[matterIds.Length];
for (int i = 0; i < matterIds.Length; i++)
{
// all subsequence calculations
SubsequenceData[] subsequencesData = CalculateSubsequencesCharacteristics(
characteristicLinkIds,
features,
sequenceIds[i]);
attributeValuesCache.FillAttributeValues(subsequencesData);
sequencesData[i] = new SequenceData(matterIds[i], matterNames[i], remoteIds[i], characteristics[i], subsequencesData);
}
// sorting organisms by their characteristic
sequencesData = sequencesData.OrderBy(r => r.Characteristic).ToArray();
List <AttributeValue> allAttributeValues = attributeValuesCache.AllAttributeValues;
var result = new Dictionary <string, object>
{
{ "result", sequencesData },
{ "subsequencesCharacteristicsNames", subsequencesCharacteristicsNames },
{ "subsequencesCharacteristicsList", subsequencesCharacteristicsList },
{ "sequenceCharacteristicName", sequenceCharacteristicName },
{ "features", features.ToSelectList(features).ToDictionary(f => f.Value) },
{ "attributes", EnumExtensions.ToArray <Attribute>().ToDictionary(a => (byte)a, a => a.GetDisplayValue()) },
{ "attributeValues", allAttributeValues.Select(sa => new { attribute = sa.AttributeId, value = sa.Value }) }
};
return new Dictionary <string, string> {
{ "data", JsonConvert.SerializeObject(result) }
};
}));
}
