public Transcript(IChromosome chromosome, int start, int end, ICompactId id, ITranslation translation,
BioType bioType, IGene gene, int totalExonLength, byte startExonPhase, bool isCanonical,
ITranscriptRegion[] transcriptRegions, ushort numExons, IInterval[] microRnas, int siftIndex,
int polyPhenIndex, Source source, bool cdsStartNotFound, bool cdsEndNotFound, int[] selenocysteines,
IRnaEdit[] rnaEdits)
{
Chromosome = chromosome;
Start = start;
End = end;
Id = id;
Translation = translation;
BioType = bioType;
Gene = gene;
TotalExonLength = totalExonLength;
StartExonPhase = startExonPhase;
IsCanonical = isCanonical;
TranscriptRegions = transcriptRegions;
NumExons = numExons;
MicroRnas = microRnas;
SiftIndex = siftIndex;
PolyPhenIndex = polyPhenIndex;
Source = source;
CdsStartNotFound = cdsStartNotFound;
CdsEndNotFound = cdsEndNotFound;
Selenocysteines = selenocysteines;
RnaEdits = rnaEdits;
}
/// <summary>
/// 魚のリソースを読み込んでいます。
/// このコードは処理が重いため、改修予定です。
/// </summary>
/// <param name="Type">魚の種類を指定します。</param>
/// <param name="fish_name">魚の名前です。</param>
/// <returns>読み込まれたリソースを返します。</returns>
private GameObject LoadRecource(BioType type, string fish_name)
{
string[] folderName = { "Fish", "Leaf", "Accessory", "Terrain" };
var str = "Prefub/" + folderName[(int)type] + "/" + fish_name;
Debug.Log("Load : " + str);
return(Resources.Load(str) as GameObject);
}
public static EncodedTranscriptData GetEncodedTranscriptData(BioType bioType, bool cdsStartNotFound,
bool cdsEndNotFound, Source source, bool isCanonical, bool hasSift, bool hasPolyPhen, bool hasMicroRnas,
bool hasRnaEdits, bool hasSelenocysteines, bool hasTranscriptRegions, bool hasTranslation,
byte startExonPhase)
{
ushort info = (ushort)bioType;
if (cdsStartNotFound)
{
info |= CdsStartNotFoundMask;
}
if (cdsEndNotFound)
{
info |= CdsEndNotFoundMask;
}
if (isCanonical)
{
info |= CanonicalMask;
}
if (hasRnaEdits)
{
info |= RnaEditsMask;
}
if (hasSelenocysteines)
{
info |= SelenocysteinesMask;
}
info |= (ushort)((ushort)source << TranscriptSourceShift);
byte contents = startExonPhase;
if (hasSift)
{
contents |= SiftMask;
}
if (hasPolyPhen)
{
contents |= PolyPhenMask;
}
if (hasMicroRnas)
{
contents |= MirnasMask;
}
if (hasTranscriptRegions)
{
contents |= TranscriptRegionsMask;
}
if (hasTranslation)
{
contents |= TranslationMask;
}
return(new EncodedTranscriptData(info, contents));
}
private static DataStructures.VEP.Transcript GetTranscript(BioType bioType, DataStructures.VEP.Transcript prev, DataStructures.VEP.Transcript curr)
{
if (prev.BioType == bioType)
{
return(prev);
}
if (curr.BioType == bioType)
{
return(curr);
}
return(null);
}
public void EncodedTranscriptData_EndToEnd()
{
const BioType expectedBiotype = BioType.Y_RNA;
const bool expectedCdsStartNotFound = true;
const bool expectedCdsEndNotFound = true;
const Source expectedSource = Source.BothRefSeqAndEnsembl;
const bool expectedCanonical = true;
const bool expectedSift = true;
const bool expectedPolyPhen = true;
const bool expectedMirnas = true;
const bool expectedRnaEdits = true;
const bool expectedSelenocysteines = true;
const bool expectedTranscriptRegions = true;
const bool expectedTranslation = true;
const byte expectedStartExonPhase = 3;
// ReSharper disable ConditionIsAlwaysTrueOrFalse
var encodedData = EncodedTranscriptData.GetEncodedTranscriptData(expectedBiotype, expectedCdsStartNotFound,
expectedCdsEndNotFound, expectedSource, expectedCanonical, expectedSift, expectedPolyPhen,
expectedMirnas, expectedRnaEdits, expectedSelenocysteines, expectedTranscriptRegions,
expectedTranslation, expectedStartExonPhase);
// ReSharper restore ConditionIsAlwaysTrueOrFalse
EncodedTranscriptData observedEncodedTranscriptData;
using (var ms = new MemoryStream())
{
using (var writer = new ExtendedBinaryWriter(ms, Encoding.UTF8, true))
{
encodedData.Write(writer);
}
ms.Position = 0;
using (var reader = new BufferedBinaryReader(ms))
{
observedEncodedTranscriptData = EncodedTranscriptData.Read(reader);
}
}
Assert.NotNull(observedEncodedTranscriptData);
Assert.Equal(expectedBiotype, observedEncodedTranscriptData.BioType);
Assert.Equal(expectedSource, observedEncodedTranscriptData.TranscriptSource);
Assert.Equal(expectedCanonical, observedEncodedTranscriptData.IsCanonical);
Assert.Equal(expectedSift, observedEncodedTranscriptData.HasSift);
Assert.Equal(expectedPolyPhen, observedEncodedTranscriptData.HasPolyPhen);
Assert.Equal(expectedMirnas, observedEncodedTranscriptData.HasMirnas);
Assert.Equal(expectedTranscriptRegions, observedEncodedTranscriptData.HasTranscriptRegions);
Assert.Equal(expectedTranslation, observedEncodedTranscriptData.HasTranslation);
Assert.Equal(expectedStartExonPhase, observedEncodedTranscriptData.StartExonPhase);
}
/// <summary>
/// 配列の値を初期化する
/// </summary>
/// <param name="fish">データを追加したい配列</param>
/// <param name="type">設定する生体型</param>
/// <param name="en">設定する英語名</param>
/// <param name="jp">設定する日本語名</param>
private void ArrayInit(ArrayList fish, BioType type, string[] en, string[] jp)
{
for (int i = 0; i < en.Length; i++)
{
BioData data = new BioData()
.SetType(type)
.SetNameEn(en[i])
.SetNameJp(jp[i]);
fish.Add(data);
}
BioData blank = new BioData().SetType(type);
int pageData = 8;
int fillSize = pageData - (en.Length % pageData);
ArrayListUtil <BioData> .Fill(fish, blank, fillSize);
}
/// <summary>
/// 魚のインスタンスを増やす関数です。
/// </summary>
/// <param name="type">魚の種類です</param>
/// <param name="fish_name">魚の名前です</param>
public void FishCreate(BioType type, string fish_name)
{
var frame1 = new System.Diagnostics.StackFrame(1);
var frame0 = new System.Diagnostics.StackFrame(0);
Debug.LogFormat(" {0} <= {1} : {2} ", frame0.GetMethod().Name, frame1.GetType().Name, frame1.GetMethod().Name);
DictionaryFix(fish_name);
Vector3 waterScale = _water.transform.localScale;
GameObject objResource = LoadRecource(type, fish_name);
GameObject obj = GameObject.Instantiate(objResource);
obj.transform.position = FirstPosition(waterScale);
obj.transform.rotation = _firstDirection;
obj.name = fish_name;
_fishDictionary[fish_name].Push(obj);
}
/// <summary>
/// 获取某多模态生物最大数量
/// </summary>
/// <param name="BioType">多模态生物类型</param>
/// <returns></returns>
public int GetMaxBioPhotoCount(BioType BioType)
{
int count = 0;
if (string.IsNullOrEmpty(MaxMultiBioPhotoCount))
{
return(count);
}
string[] arr = MaxMultiBioPhotoCount.Split(':');
if (arr.Length != 10 || (int)BioType >= arr.Length)
{
return(count);
}
count = Tools.TryConvertToInt32(arr[(int)BioType]);
return(count);
}
/// <summary>
/// 获取支持某多模态生物版本
/// </summary>
/// <param name="BioType">多模态生物类型</param>
/// <returns></returns>
public string GetBioVersion(BioType BioType)
{
string version = "";
if (string.IsNullOrEmpty(MultiBioVersion))
{
return(version);
}
string[] arr = MultiBioVersion.Split(':');
if (arr.Length != 10 || (int)BioType >= arr.Length)
{
return(version);
}
version = arr[(int)BioType];
return(version);
}
/// <summary>
/// 是否支持某多模态生物图片
/// </summary>
/// <param name="BioType">多模态生物类型</param>
/// <returns></returns>
public bool IsBioPhotoSupport(BioType BioType)
{
if (string.IsNullOrEmpty(MultiBioPhotoSupport))
{
return(false);
}
string[] arr = MultiBioDataSupport.Split(':');
if (arr.Length != 10 || (int)BioType >= arr.Length)
{
return(false);
}
if (arr[(int)BioType] == "0" || arr[(int)BioType] == "")
{
return(false);
}
return(true);
}
public Transcript(BioType biotype, Exon[] transExons, Gene gene, Translation translation, VariantEffectFeatureCache cache, Slice slice,
bool onReverseStrand, bool isCanonical, int cdnaCodingStart, int cdnaCodingEnd, ushort referenceIndex, int start, int end,
string ccdsId, string databaseId, string proteinId, string refSeqId, string geneStableId, string stableId, string geneSymbol,
GeneSymbolSource geneSymbolSource, int hgncId, byte version, SimpleInterval[] microRnas)
: base(referenceIndex, start, end)
{
BioType = biotype;
CcdsId = ccdsId;
CompDnaCodingEnd = cdnaCodingEnd;
CompDnaCodingStart = cdnaCodingStart;
DatabaseId = databaseId;
Gene = gene;
GeneStableId = geneStableId;
GeneSymbol = geneSymbol;
GeneSymbolSource = geneSymbolSource;
HgncId = hgncId;
IsCanonical = isCanonical;
MicroRnas = microRnas;
OnReverseStrand = onReverseStrand;
ProteinId = proteinId;
RefSeqId = refSeqId;
Slice = slice;
StableId = stableId;
TransExons = transExons;
Translation = translation;
VariantEffectCache = cache;
Version = version;
var entrezId = ImportDataStore.TranscriptSource == TranscriptDataSource.Ensembl
? CompactId.Empty
: CompactId.Convert(geneStableId);
var ensemblId = ImportDataStore.TranscriptSource == TranscriptDataSource.Ensembl
? CompactId.Convert(geneStableId)
: CompactId.Empty;
FinalGene = new VariantAnnotation.DataStructures.Gene(referenceIndex, start, end, onReverseStrand,
geneSymbol, hgncId, entrezId, ensemblId, -1);
GenerateHashCode();
}
/// <summary>
/// constructor
/// </summary>
public Transcript(ushort referenceIndex, int start, int end, CompactId id, byte version,
Translation translation, BioType bioType, Gene gene, int totalExonLength, byte startExonPhase,
bool isCanonical, SimpleInterval[] introns, SimpleInterval[] microRnas, CdnaCoordinateMap[] cdnaMaps,
int siftIndex, int polyPhenIndex, TranscriptDataSource transcriptSource) : base(referenceIndex, start, end)
{
Id = id;
Version = version;
Translation = translation;
BioType = bioType;
Gene = gene;
TotalExonLength = totalExonLength;
StartExonPhase = startExonPhase;
IsCanonical = isCanonical;
Introns = introns;
MicroRnas = microRnas;
CdnaMaps = cdnaMaps;
SiftIndex = siftIndex;
PolyPhenIndex = polyPhenIndex;
TranscriptSource = transcriptSource;
TotalExonLength = TranscriptUtilities.GetTotalExonLength(cdnaMaps);
}
/// <summary>
/// constructor
/// </summary>
public EncodedTranscriptData(BioType bioType, byte version, TranscriptDataSource transcriptSource,
bool isCanonical, bool hasSift, bool hasPolyPhen, bool hasMicroRnas, bool hasIntrons, bool hasCdnaMaps,
bool hasTranslation, byte startExonPhase)
{
_info = (ushort)bioType;
_info |= (ushort)(version << VersionShift);
_info |= (ushort)((ushort)transcriptSource << TranscriptSourceShift);
if (isCanonical)
{
_info |= CanonicalMask;
}
_contents = (byte)(startExonPhase << StartExonShift);
if (hasSift)
{
_contents |= SiftMask;
}
if (hasPolyPhen)
{
_contents |= PolyPhenMask;
}
if (hasMicroRnas)
{
_contents |= MirnasMask;
}
if (hasIntrons)
{
_contents |= IntronsMask;
}
if (hasCdnaMaps)
{
_contents |= CdnaMapsMask;
}
if (hasTranslation)
{
_contents |= TranslationMask;
}
}
public MutableTranscript(IChromosome chromosome, int start, int end, string id, byte version, string ccdsId,
string refSeqId, BioType bioType, bool isCanonical, ICodingRegion codingRegion, string proteinId,
byte proteinVersion, string peptideSequence, Source source, MutableGene gene, MutableExon[] exons,
int startExonPhase, int totalExonLength, IInterval[] introns, MutableTranscriptRegion[] cdnaMaps,
string siftData, string polyphenData, string translateableSequence, IInterval[] microRnas,
bool cdsStartNotFound, bool cdsEndNotFound, int[] selenocysteinePositions, IRnaEdit[] rnaEdits,
string bamEditStatus)
{
Chromosome = chromosome;
Start = start;
End = end;
Id = id;
Version = version;
CcdsId = ccdsId;
RefSeqId = refSeqId;
BioType = bioType;
IsCanonical = isCanonical;
CodingRegion = codingRegion;
ProteinId = proteinId;
ProteinVersion = proteinVersion;
PeptideSequence = peptideSequence;
Source = source;
Gene = gene;
Exons = exons;
StartExonPhase = startExonPhase;
TotalExonLength = totalExonLength;
Introns = introns;
CdnaMaps = cdnaMaps;
SiftData = siftData;
PolyphenData = polyphenData;
TranslateableSequence = translateableSequence;
MicroRnas = microRnas;
CdsStartNotFound = cdsStartNotFound;
CdsEndNotFound = cdsEndNotFound;
SelenocysteinePositions = selenocysteinePositions;
RnaEdits = rnaEdits;
BamEditStatus = bamEditStatus;
}
private void radioButton3_CheckedChanged(object sender, EventArgs e)
{
_bioType = BioType.ZK;
toolStripStatusLabel1.Text = @"Source: ZKTech Bio-device";
}
public static string GetBioType(BioType bioType) => bioType == BioType.three_prime_overlapping_ncRNA
? "3prime_overlapping_ncRNA"
: bioType.ToString();
public static string GetBiotypeDescription(BioType biotype)
{
string description;
return(!BioTypeToString.TryGetValue(biotype, out description) ? null : description);
}
private void radioButton4_CheckedChanged(object sender, EventArgs e)
{
_bioType = BioType.Realand;
toolStripStatusLabel1.Text = @"Source: Realand Bio-device";
}
/// <summary>
/// adds the biotype to both dictionaries
/// </summary>
private static void AddBioType(string s, BioType bioType)
{
StringToBioType[s] = bioType;
BioTypeToString[bioType] = s;
}
private void radioButton3_CheckedChanged(object sender, EventArgs e)
{
_bioType = BioType.ZK;
}
public void Transcript_EndToEnd()
{
IChromosome expectedChromosome = new Chromosome("chrBob", "Bob", 1);
const int expectedStart = int.MaxValue;
const int expectedEnd = int.MinValue;
const string expectedId = "ENST00000540021";
const byte expectedVersion = 7;
const BioType expectedBioType = BioType.IG_J_pseudogene;
const bool expectedCanonical = true;
const Source expectedSource = Source.BothRefSeqAndEnsembl;
const bool expectedCdsStartNotFound = true;
const bool expectedCdsEndNotFound = true;
var expectedIdAndVersion = expectedId + "." + expectedVersion;
ICodingRegion expectedCodingRegion = new CodingRegion(10001, 10200, 1, 200, 200);
ITranscriptRegion[] expectedTranscriptRegions = GetTranscriptRegions();
const byte expectedNumExons = 3;
const int expectedTotalExonLength = 300;
const byte expectedStartExonPhase = 3;
const int expectedSiftIndex = 11;
const int expectedPolyPhenIndex = 13;
IInterval[] expectedMicroRnas = GetMicroRnas();
ITranslation expectedTranslation = new Translation(expectedCodingRegion, CompactId.Convert("ENSP00000446475", 17), "VEIDSD");
IGene expectedGene = new Gene(expectedChromosome, 100, 200, true, "TP53", 300, CompactId.Convert("7157"),
CompactId.Convert("ENSG00000141510"));
var genes = new IGene[1];
genes[0] = expectedGene;
var peptideSeqs = new string[1];
peptideSeqs[0] = expectedTranslation.PeptideSeq;
var geneIndices = CreateIndices(genes);
var transcriptRegionIndices = CreateIndices(expectedTranscriptRegions);
var microRnaIndices = CreateIndices(expectedMicroRnas);
var peptideIndices = CreateIndices(peptideSeqs);
var indexToChromosome = new Dictionary <ushort, IChromosome>
{
[expectedChromosome.Index] = expectedChromosome
};
// ReSharper disable ConditionIsAlwaysTrueOrFalse
var transcript = new Transcript(expectedChromosome, expectedStart, expectedEnd,
CompactId.Convert(expectedId, expectedVersion), expectedTranslation, expectedBioType, expectedGene,
expectedTotalExonLength, expectedStartExonPhase, expectedCanonical, expectedTranscriptRegions,
expectedNumExons, expectedMicroRnas, expectedSiftIndex, expectedPolyPhenIndex,
expectedSource, expectedCdsStartNotFound, expectedCdsEndNotFound, null, null);
// ReSharper restore ConditionIsAlwaysTrueOrFalse
ITranscript observedTranscript;
using (var ms = new MemoryStream())
{
using (var writer = new ExtendedBinaryWriter(ms, Encoding.UTF8, true))
{
transcript.Write(writer, geneIndices, transcriptRegionIndices, microRnaIndices, peptideIndices);
}
ms.Position = 0;
using (var reader = new ExtendedBinaryReader(ms))
{
observedTranscript = Transcript.Read(reader, indexToChromosome, genes, expectedTranscriptRegions, expectedMicroRnas, peptideSeqs);
}
}
Assert.NotNull(observedTranscript);
Assert.Equal(expectedStart, observedTranscript.Start);
Assert.Equal(expectedEnd, observedTranscript.End);
Assert.Equal(expectedIdAndVersion, observedTranscript.Id.WithVersion);
Assert.Equal(expectedBioType, observedTranscript.BioType);
Assert.Equal(expectedCanonical, observedTranscript.IsCanonical);
Assert.Equal(expectedSource, observedTranscript.Source);
Assert.Equal(expectedTotalExonLength, observedTranscript.TotalExonLength);
Assert.Equal(expectedStartExonPhase, observedTranscript.StartExonPhase);
Assert.Equal(expectedSiftIndex, observedTranscript.SiftIndex);
Assert.Equal(expectedPolyPhenIndex, observedTranscript.PolyPhenIndex);
Assert.Equal(expectedChromosome.Index, observedTranscript.Chromosome.Index);
Assert.Equal(expectedGene.Symbol, observedTranscript.Gene.Symbol);
Assert.Equal(expectedTranslation.PeptideSeq, observedTranscript.Translation.PeptideSeq);
Assert.Equal(expectedTranscriptRegions.Length, observedTranscript.TranscriptRegions.Length);
Assert.Equal(expectedMicroRnas.Length, observedTranscript.MicroRnas.Length);
}
/// <summary>
/// 生体型を設定する関数
/// </summary>
/// <param name="type">設定するs生体型</param>
/// <returns>自分のインスタンスを返す</returns>
public BioData SetType(BioType type)
{
_type = type; return(this);
}
private void radioButton4_CheckedChanged(object sender, EventArgs e)
{
_bioType = BioType.Realand;
}
