Found 2665 results in 306 files, showing top 50 files (show more).
| chromstaR:src/logging.h: [ ] |
|---|
101: inline FILE*& Output2FILE::Stream()
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97: static FILE*& Stream();
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109: FILE* pStream = Stream();
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137: else if (level > FILELog::ReportingLevel() || !Output2FILE::Stream()) ; \
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103: static FILE* pStream = stderr;
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104: return pStream;
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110: if (!pStream)
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112: fprintf(pStream, "%s", msg.c_str());
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113: fflush(pStream);
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| iBMQ:src/RngStream.c: [ ] |
|---|
307: RngStream RngStream_CreateStream (const char name[])
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337: void RngStream_DeleteStream (RngStream g)
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348: void RngStream_ResetStartStream (RngStream g)
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357: void RngStream_ResetNextSubstream (RngStream g)
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368: void RngStream_ResetStartSubstream (RngStream g)
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377: int RngStream_SetPackageSeed (unsigned long seed[6])
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389: int RngStream_SetSeed (RngStream g, unsigned long seed[6])
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401: void RngStream_AdvanceState (RngStream g, long e, long c)
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432: void RngStream_GetState (RngStream g, unsigned long seed[6])
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441: void RngStream_WriteState (RngStream g)
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459: void RngStream_WriteStateFull (RngStream g)
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491: void RngStream_IncreasedPrecis (RngStream g, int incp)
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498: void RngStream_SetAntithetic (RngStream g, int a)
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505: double RngStream_RandU01 (RngStream g)
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515: int RngStream_RandInt (RngStream g, int i, int j)
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3: * File: RngStream.c for multiple streams of Random Numbers
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14: #include "RngStream.h"
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213: static double U01 (RngStream g)
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246: static double U01d (RngStream g)
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310: RngStream g;
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313: g = (RngStream) malloc (sizeof (struct RngStream_InfoState));
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315: Rprintf ("RngStream_CreateStream: No more memory\n\n");
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316: error("RngStream allocation failed. Exiting.");
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464: Rprintf ("The RngStream");
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517: return i + (int) ((j - i + 1.0) * RngStream_RandU01 (g));
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| velociraptor:R/plotVelocityStream.R: [ ] |
|---|
81: plotVelocityStream <- function(sce, embedded, use.dimred = 1,
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3: #' Plot velocities embedded into low-dimensional space as a stream plot. Stream
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48: #' Streamlines are computed by simple integration with a forward Euler method,
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70: #' plotVelocityStream(out, em)
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71: #' plotVelocityStream(out, em, color.streamlines = TRUE)
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112: stop("'plotVelocityStream' requires the package 'ggplot2'.")
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| iBMQ:src/RngStream.h: [ ] |
|---|
19: typedef struct RngStream_InfoState * RngStream;
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21: struct RngStream_InfoState {
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2: RngStream.h for ANSI C
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29: int RngStream_SetPackageSeed (unsigned long seed[6]);
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32: RngStream RngStream_CreateStream (const char name[]);
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35: void RngStream_DeleteStream (RngStream g);
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38: void RngStream_ResetStartStream (RngStream g);
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41: void RngStream_ResetStartSubstream (RngStream g);
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44: void RngStream_ResetNextSubstream (RngStream g);
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47: void RngStream_SetAntithetic (RngStream g, int a);
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50: void RngStream_IncreasedPrecis (RngStream g, int incp);
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53: int RngStream_SetSeed (RngStream g, unsigned long seed[6]);
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56: void RngStream_AdvanceState (RngStream g, long e, long c);
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59: void RngStream_GetState (RngStream g, unsigned long seed[6]);
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62: void RngStream_WriteState (RngStream g);
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65: void RngStream_WriteStateFull (RngStream g);
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68: double RngStream_RandU01 (RngStream g);
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71: int RngStream_RandInt (RngStream g, int i, int j);
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| netboost:src/mcupgma/clustering_round/myutils/StreamFromFileNameGenerator.hpp: [ ] |
|---|
10: RCPtr<istream> InputStream(string const & filename) {
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30: RCPtr<ostream> OutputStream(string const & filename) {
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2: #define __StreamFromFileNameGenerator_hpp
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1: #ifndef __StreamFromFileNameGenerator_hpp
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| enhancerHomologSearch:src/ClustalW/fileInput/InFileStream.cpp: [ ] |
|---|
34: InFileStream::InFileStream() :
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41: InFileStream::InFileStream(const char *filename) :
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7: * InFileStream subclasses std::ifstream, adding a check for the end-of-line
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28: #include "InFileStream.h"
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38: //Rcpp::Rcout << "InFileStream() constructor 1" << endl;
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44: //Rcpp::Rcout << "InFileStream(f) constructor 2" << endl;
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49: //- InFileStream::InFileStream(const InFileStream ©) :
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52: //- Rcpp::Rcout << "InFileStream() constructor 3" << endl;
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56: void InFileStream::open(const char *filename)
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67: void InFileStream::close()
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74: std::istream& InFileStream::getline(char *s, streamsize n)
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80: std::istream& InFileStream::getline(char *s, streamsize n, char delim)
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93: * 09-02-07,Nigel Brown(EMBL): moved member into new InFileStream subclassed
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95: * that uses InFileStream in place of std::ifstream. Replaced if/then/else
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98: char InFileStream::findDelimiter()
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| enhancerHomologSearch:src/ClustalW/fileInput/InFileStream.h: [ ] |
|---|
22: class InFileStream : public std::ifstream
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7: * InFileStream subclasses std::ifstream, adding a check for the end-of-line
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25: InFileStream();
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26: InFileStream(const char *filename);
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27: //- InFileStream(const InFileStream ©);
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45: InFileStream(const InFileStream ©);
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| gdsfmt:src/CoreArray/dFile.cpp: [ ] |
|---|
278: static const char *ERR_GDSStream = "%s: GDSStream should not be NULL.";
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427: void CdGDSObj::GetOwnBlockStream(vector<const CdBlockStream*> &Out) const
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432: void CdGDSObj::GetOwnBlockStream(vector<CdStream*> &Out)
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477: void CdGDSObj::SaveToBlockStream()
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504: void CdGDSObj::_CheckGDSStream()
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583: CdStream *fStream;
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584: CLASS *fPStream;
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616: CdStream *fStream;
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617: CLASS *fPStream;
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732: virtual void LoadStream(CdReader &Reader, TdVersion Version)
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778: virtual void SaveStream(CdWriter &Writer)
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1032: void CdPipeMgrItem::LoadStream(CdReader &Reader, TdVersion Version) { }
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1034: void CdPipeMgrItem::SaveStream(CdWriter &Writer) { }
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2493: void CdGDSStreamContainer::GetOwnBlockStream(vector<const CdBlockStream*> &Out) const
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2499: void CdGDSStreamContainer::GetOwnBlockStream(vector<CdStream*> &Out)
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2634: void CdGDSFile::LoadStream(CdStream *Stream, bool ReadOnly, bool AllowError)
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2690: void CdGDSFile::SaveStream(CdStream *Stream)
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679: virtual bool GetStreamInfo(CdBufStream *buf)
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723: virtual void UpdateStreamInfo(CdStream &Stream)
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1026: void CdPipeMgrItem::UpdateStreamSize()
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1155: CdStreamPipeMgr CoreArray::dStreamPipeMgr;
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1157: CdStreamPipeMgr::CdStreamPipeMgr(): CdAbstractManager()
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1171: CdStreamPipeMgr::~CdStreamPipeMgr()
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2231: CdGDSStreamContainer::CdGDSStreamContainer(): CdGDSObjPipe()
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2241: CdGDSStreamContainer::~CdGDSStreamContainer()
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543: // Stream Manage Pipe
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590: fStream = BufStream->Stream();
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624: fStream = BufStream->Stream();
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670: return (dynamic_cast<CLASS*>(buf.Stream()) != NULL);
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675: CLASS *s = dynamic_cast<CLASS*>(buf.Stream());
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684: CLASS *s = dynamic_cast<CLASS*>(buf->Stream());
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727: BYTE_LE<CdStream> S(Stream);
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865: typedef CdWritePipe2<CdLZ4Encoder, CdBaseLZ4Stream::TLZ4Chunk> CdLZ4WritePipe;
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875: public CdPipe<CdBaseLZ4Stream::bsLast, CdBaseLZ4Stream::bsDefault,
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876: CdBaseLZ4Stream::TLZ4Chunk, CdLZ4Encoder, CdPipeLZ4>
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2255: return "Stream";
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2645: Stream->ReadData((void*)&buf[0], L);
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2650: fVersion = Stream->R8b();
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2651: fVersion |= Stream->R8b() << 8;
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2660: BYTE_LE<CdStream>(Stream) >> Entry;
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2663: CdBlockCollection::LoadStream(Stream, ReadOnly, AllowError, &Log());
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2699: Stream->WriteData((void*)GDSFilePrefix(), L);
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2702: Stream->W8b(fVersion & 0xFF);
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2703: Stream->W8b(fVersion >> 8);
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2705: SIZE64 _EntryPos = Stream->Position();
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2706: BYTE_LE<CdStream>(Stream) << TdGDSBlockID(0);
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2708: CdBlockCollection::WriteStream(Stream);
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2711: SIZE64 _NewPos = Stream->Position();
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2713: Stream->SetPosition(_EntryPos);
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2714: BYTE_LE<CdStream>(Stream) << fRoot.fGDSStream->ID();
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2715: Stream->SetPosition(_NewPos);
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288: fGDSStream = NULL;
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294: if (fGDSStream)
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295: fGDSStream->Release();
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393: if (fGDSStream && folder.GDSStream() && fFolder)
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395: CdBlockCollection *n1 = &fGDSStream->Collection();
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396: CdBlockCollection *n2 = &folder.GDSStream()->Collection();
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424: SaveToBlockStream();
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439: if (fGDSStream)
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441: CdBlockCollection *collect = &fGDSStream->Collection();
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479: _CheckGDSStream();
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480: if (fGDSStream)
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482: CdWriter Writer(fGDSStream, &GDSFile()->Log());
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506: if (!fGDSStream)
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507: throw ErrGDSObj(ERR_GDSStream, "CdGDSObj");
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537: static_cast<CdGDSObj*>(Obj)->fGDSStream = (CdBlockStream*)Data;
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552: static const CdRecodeStream::TLevel CompressionLevels[] =
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554: CdRecodeStream::clMin,
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555: CdRecodeStream::clFast,
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556: CdRecodeStream::clDefault,
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557: CdRecodeStream::clMax,
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558: CdRecodeStream::clUltra, // ultra (LZMA 512MiB)
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559: CdRecodeStream::clUltraMax, // ultra_max (LZMA 1536MiB)
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560: CdRecodeStream::clDefault
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575: CdWritePipe(CdRecodeStream::TLevel vLevel,
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585: CdRecodeStream::TLevel fLevel;
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588: virtual CdStream *InitPipe(CdBufStream *BufStream)
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591: fPStream = new CLASS(*fStream, fLevel);
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592: fPStream->PtrExtRec = &fRemainder;
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593: return fPStream;
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595: virtual CdStream *FreePipe()
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597: if (fPStream) { fPStream->Release(); fPStream = NULL; }
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598: return fStream;
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607: CdWritePipe2(CdRecodeStream::TLevel vLevel, BSIZE bs,
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618: CdRecodeStream::TLevel fLevel;
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622: virtual CdStream *InitPipe(CdBufStream *BufStream)
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625: fPStream = new CLASS(*fStream, fLevel, fBSize);
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626: fPStream->PtrExtRec = &fRemainder;
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627: return fPStream;
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629: virtual CdStream *FreePipe()
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631: if (fPStream) { fPStream->Release(); fPStream = NULL; }
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632: return fStream;
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648: fLevel = CdRecodeStream::clDefault;
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663: virtual void PopPipe(CdBufStream &buf)
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668: virtual bool WriteMode(CdBufStream &buf) const
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673: virtual void ClosePipe(CdBufStream &buf)
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703: CdRecodeStream::TLevel fLevel;
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758: fLevel = (CdRecodeStream::TLevel)I;
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760: fLevel = CdRecodeStream::clUnknown;
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814: virtual void PushReadPipe(CdBufStream &buf)
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816: virtual void PushWritePipe(CdBufStream &buf)
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847: virtual void PushReadPipe(CdBufStream &buf)
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849: virtual void PushWritePipe(CdBufStream &buf)
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889: virtual void PushReadPipe(CdBufStream &buf)
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891: virtual void PushWritePipe(CdBufStream &buf)
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928: virtual void PushReadPipe(CdBufStream &buf)
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930: virtual void PushWritePipe(CdBufStream &buf)
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964: virtual void PushReadPipe(CdBufStream &buf)
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966: virtual void PushWritePipe(CdBufStream &buf)
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997: virtual void PushReadPipe(CdBufStream &buf)
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999: virtual void PushWritePipe(CdBufStream &buf)
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1250: fPipeInfo->LoadStream(Reader, Version);
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1261: fPipeInfo->SaveStream(Writer);
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1304: StreamID = 0;
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1367: _CheckGDSStream();
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1376: rv->fGDSStream = fGDSStream->Collection().NewBlockStream();
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1377: rv->fGDSStream->AddRef();
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1383: I.StreamID = rv->fGDSStream->ID();
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1408: _CheckGDSStream();
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1436: if (val->fGDSStream == NULL)
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1438: val->fGDSStream = fGDSStream->Collection().NewBlockStream();
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1439: val->fGDSStream->AddRef();
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1440: I.StreamID = val->fGDSStream->ID();
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1442: val->SaveToBlockStream();
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1533: CdBlockStream *stream = it->Obj->fGDSStream;
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1535: vector<const CdBlockStream*> BL;
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1536: it->Obj->GetOwnBlockStream(BL);
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1558: if (fGDSStream)
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1561: fGDSStream->Collection().DeleteBlockStream(stream->ID());
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1563: vector<const CdBlockStream*>::iterator it;
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1566: fGDSStream->Collection().DeleteBlockStream((*it)->ID());
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1749: Reader[VAR_DIR_ID] >> I.StreamID;
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1777: Writer[VAR_DIR_ID] << it->StreamID;
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1844: _CheckGDSStream();
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1845: CdBlockStream *IStream = fGDSStream->Collection()[I.StreamID];
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1846: CdReader Reader(IStream, &GDSFile()->Log());
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1860: vObj->fGDSStream = IStream;
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1861: IStream->AddRef();
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1875: vObj->fGDSStream = IStream;
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1876: IStream->AddRef();
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1890: vObj->fGDSStream = IStream;
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1891: IStream->AddRef();
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1901: vObj->fGDSStream = IStream;
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1902: IStream->AddRef();
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1913: obj = fGDSStream->Collection().ClassMgr()->
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1914: ToObj(Reader, _GDSObjInitProc, fGDSStream, false);
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1928: I.Obj->fGDSStream = IStream;
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1929: IStream->AddRef();
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1943: SaveToBlockStream();
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2233: fBufStream = new CdBufStream(new CdMemoryStream);
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2234: fBufStream->AddRef();
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2235: vAllocStream = NULL;
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2244: if (fBufStream)
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2245: fBufStream->Release();
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2250: return "dStream";
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2273: S->CopyTo(*BufStream());
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2283: if (fGDSStream)
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2289: if (fBufStream)
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2290: fBufStream->Release();
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2291: fBufStream = new CdBufStream(fGDSStream->Collection()[vAllocID]);
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2292: fBufStream->AddRef();
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2295: fPipeInfo->PushReadPipe(*fBufStream);
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2297: throw ErrGDSStreamContainer(ERR_GDSStream, "CdGDSStreamContainer");
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2305: if (fGDSStream)
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2307: if (vAllocStream == NULL)
|
2309: _CheckGDSStream();
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2310: vAllocStream = fGDSStream->Collection().NewBlockStream();
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2312: if (fBufStream) fBufStream->Release();
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2313: fBufStream = new CdBufStream(vAllocStream);
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2314: fBufStream->AddRef();
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2316: fPipeInfo->PushWritePipe(*fBufStream);
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2318: TdGDSBlockID Entry = vAllocStream->ID();
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2322: throw ErrGDSStreamContainer(ERR_GDSStream, "CdGDSStreamContainer");
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2329: return fPipeInfo->StreamTotalIn();
|
2331: return fBufStream->GetSize();
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2343: if (vAllocStream && fGDSStream && (vAllocStream->GetSize()>0))
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2357: CdStream *TmpStream = new CdTempStream;
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2358: TdAutoRef<CdBufStream> Output(new CdBufStream(TmpStream));
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2371: vAllocStream->SetPosition(0);
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2372: vAllocStream->SetSizeOnly(0);
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2373: vAllocStream->CopyFrom(*TmpStream, 0, -1);
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2376: vAllocStream->SetPosition(0);
|
2377: if (fBufStream)
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2378: fBufStream->Release();
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2379: fBufStream = new CdBufStream(vAllocStream);
|
2380: fBufStream->AddRef();
|
2382: fPipeInfo->PushReadPipe(*fBufStream);
|
2385: SaveToBlockStream();
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2398: fBufStream->OnFlush.Clear();
|
2399: fBufStream->FlushWrite();
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2400: if (fPipeInfo && vAllocStream)
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2402: if (fPipeInfo->WriteMode(*fBufStream))
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2404: fPipeInfo->ClosePipe(*fBufStream);
|
2405: if (_GetStreamPipeInfo(fBufStream, false))
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2406: _UpdateStreamPipeInfo(*fGDSStream);
|
2408: if (fBufStream)
|
2409: fBufStream->Release();
|
2410: vAllocStream->SetPosition(0);
|
2411: fBufStream = new CdBufStream(vAllocStream);
|
2412: fBufStream->AddRef();
|
2414: fPipeInfo->PushReadPipe(*fBufStream);
|
2419: void CdGDSStreamContainer::CopyFromBuf(CdBufStream &Source, SIZE64 Count)
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2432: fBufStream->WriteData((void*)Buffer, N);
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2437: void CdGDSStreamContainer::CopyFrom(CdStream &Source, SIZE64 Count)
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2450: fBufStream->WriteData((void*)Buffer, N);
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2455: void CdGDSStreamContainer::CopyTo(CdBufStream &Dest, SIZE64 Count)
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2461: fBufStream->SetPosition(0);
|
2468: fBufStream->ReadData((void*)Buffer, N);
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2474: void CdGDSStreamContainer::CopyTo(CdStream &Dest, SIZE64 Count)
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2480: fBufStream->SetPosition(0);
|
2487: fBufStream->ReadData((void*)Buffer, N);
|
2496: if (vAllocStream) Out.push_back(vAllocStream);
|
2502: if (vAllocStream) Out.push_back(vAllocStream);
|
2673: fRoot.fGDSStream = (*this)[Entry];
|
2674: fRoot.fGDSStream->AddRef();
|
2679: (double)fRoot.fGDSStream->Size());
|
2682: CdReader Reader(fRoot.fGDSStream, &Log());
|
2693: if (fStream != NULL)
|
2709: fRoot.fGDSStream = NewBlockStream();
|
2710: fRoot.fGDSStream->AddRef();
|
2717: fRoot.SaveToBlockStream();
|
2722: TdAutoRef<CdStream> F(new CdFileStream(RawText(fn).c_str(),
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2723: ReadOnly ? CdFileStream::fmOpenRead : CdFileStream::fmOpenReadWrite));
|
2724: LoadStream(F.get(), ReadOnly, AllowError);
|
2730: TdAutoRef<CdStream> F(new CdFileStream(fn,
|
2731: ReadOnly ? CdFileStream::fmOpenRead : CdFileStream::fmOpenReadWrite));
|
2732: LoadStream(F.get(), ReadOnly, AllowError);
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2738: TdAutoRef<CdStream> F(new CdForkFileStream(fn,
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2739: ReadOnly ? CdFileStream::fmOpenRead : CdFileStream::fmOpenReadWrite));
|
2740: LoadStream(F.get(), ReadOnly, AllowError);
|
2746: if (fStream == NULL)
|
2753: TdAutoRef<CdStream> F(new CdFileStream(RawText(fn).c_str(),
|
2754: CdFileStream::fmCreate));
|
2756: SaveStream(F.get());
|
2761: TdAutoRef<CdStream> F(new CdFileStream(fn, CdFileStream::fmCreate));
|
2763: SaveStream(F.get());
|
2774: TdAutoRef<CdStream> F(new CdFileStream(RawText(fn).c_str(),
|
2775: CdFileStream::fmCreate));
|
2786: BYTE_LE<CdStream>(*F) << fRoot.fGDSStream->ID();
|
2793: CdBlockStream::TBlockInfo::HEAD_SIZE + bSize) |
|
2796: BYTE_LE<CdStream>(*F) <<
|
2810: if (fStream)
|
2818: if (fRoot.fGDSStream)
|
2821: fRoot.fGDSStream->Release();
|
2822: fRoot.fGDSStream = NULL;
|
2879: return (dynamic_cast<CdForkFileStream*>(fStream) != NULL);
|
572: class COREARRAY_DLL_DEFAULT CdWritePipe: public CdStreamPipe
|
577: CdStreamPipe(), fRemainder(vRemainder)
|
604: class COREARRAY_DLL_DEFAULT CdWritePipe2: public CdStreamPipe
|
609: CdStreamPipe(), fRemainder(vRemainder)
|
693: if ((in!=fStreamTotalIn) || (out!=fStreamTotalOut))
|
695: fStreamTotalIn = in;
|
696: fStreamTotalOut = out;
|
729: S << fStreamTotalIn << fStreamTotalOut;
|
740: fStreamTotalIn = Ary[0];
|
741: fStreamTotalOut = Ary[1];
|
744: fStreamTotalIn = fStreamTotalOut = -1;
|
780: UpdateStreamSize();
|
781: C_Int64 Ary[2] = { fStreamTotalIn, fStreamTotalOut };
|
798: typedef CdStreamPipe2<CdZDecoder> CdZIPReadPipe;
|
829: typedef CdStreamPipe2<CdZDecoder_RA> CdZRAReadPipe;
|
864: typedef CdStreamPipe2<CdLZ4Decoder> CdLZ4ReadPipe;
|
904: typedef CdStreamPipe2<CdLZ4Decoder_RA> CdLZ4RAReadPipe;
|
947: typedef CdStreamPipe2<CdXZDecoder> CdXZReadPipe;
|
979: typedef CdStreamPipe2<CdXZDecoder_RA> CdXZReadPipe_RA;
|
1021: fStreamTotalIn = fStreamTotalOut = -1;
|
1153: // CdStreamPipeMgr
|
1178: void CdStreamPipeMgr::Register(CdPipeMgrItem *vNewPipe)
|
1185: CdPipeMgrItem *CdStreamPipeMgr::Match(CdGDSObjPipe &Obj, const char *Mode)
|
1247: fPipeInfo = dStreamPipeMgr.Match(*this, RawText(Coder).c_str());
|
1429: } else if (dynamic_cast<CdGDSStreamContainer*>(val))
|
1896: CdGDSStreamContainer *vObj = new CdGDSStreamContainer;
|
2227: // CdGDSStreamContainer
|
2248: const char *CdGDSStreamContainer::dName()
|
2253: const char *CdGDSStreamContainer::dTraitName()
|
2258: CdGDSObj *CdGDSStreamContainer::NewObject()
|
2260: return (new CdGDSStreamContainer)->AssignPipe(*this);
|
2263: void CdGDSStreamContainer::Assign(CdGDSObj &Source, bool Full)
|
2265: if (dynamic_cast<CdGDSStreamContainer*>(&Source))
|
2271: CdGDSStreamContainer *S = static_cast<CdGDSStreamContainer*>(&Source);
|
2276: RaiseInvalidAssign("CdGDSStreamContainer", &Source);
|
2279: void CdGDSStreamContainer::Loading(CdReader &Reader, TdVersion Version)
|
2301: void CdGDSStreamContainer::Saving(CdWriter &Writer)
|
2326: SIZE64 CdGDSStreamContainer::GetSize()
|
2334: void CdGDSStreamContainer::SetPackedMode(const char *Mode)
|
2351: fPipeInfo = dStreamPipeMgr.Match(*this, Mode);
|
2353: throw ErrGDSStreamContainer(ERR_PACKED_MODE, Mode);
|
2367: fPipeInfo->GetStreamInfo(Output.get());
|
2389: fPipeInfo = dStreamPipeMgr.Match(*this, Mode);
|
2391: throw ErrGDSStreamContainer(ERR_PACKED_MODE, Mode);
|
2396: void CdGDSStreamContainer::CloseWriter()
|
2869: return fStreamSize;
|
| R453Plus1Toolbox:R/methods-AVASet.R: [ ] |
|---|
1078: upDownStream = max(width(dnaSet))
|
1088: seqType="gene_exon_intron", upstream=upDownStream, mart=ensembl)
|
1093: seqType="gene_exon_intron", downstream=upDownStream, mart=ensembl)
|
1122: pos[refName] = geneInfo$start_position[ind] - upDownStream + start(m) - 1
|
| ChemmineR:R/AllClasses.R: [ ] |
|---|
2427: sdfStream <- function(input, output, append=FALSE, fct, Nlines=10000, startline=1, restartNlines=10000, silen...(15 bytes skipped)...
|
2420: ## (6.8) Streaming Through SD Files ##
|
2422: ## Streaming function to compute descriptors for large SD Files without consuming much memory.
|
2433: ## For restarting sdfStream at specific line assigned to startline argument. If assigned
|
2535: # sdfStream(input="test.sdf", output="matrix.xls", fct=desc, Nlines=1000)
|
2544: ## as character strings to APset or FPset objects (e.g. generated by sdfStream).
|
2575: ## Extracts specific molecules from SD File based on a line position index computed by the sdfStream function
|
2606: ## Usage: see sdfStream()
|
| Director:inst/www/js/d3.v3.js: [ ] |
|---|
4246: function d3_geo_pathProjectStream(project) {
|
3878: var lower48Stream = lower48.stream(stream), alaskaStream = alaska.stream(stream), hawaiiStream = hawaii.stream(stream);
|
3881: lower48Stream.point(x, y);
|
3886: lower48Stream.sphere();
|
3891: lower48Stream.lineStart();
|
3896: lower48Stream.lineEnd();
|
3901: lower48Stream.polygonStart();
|
3906: lower48Stream.polygonEnd();
|
3862: var point, pointStream = {
|
3882: alaskaStream.point(x, y);
|
3883: hawaiiStream.point(x, y);
|
3887: alaskaStream.sphere();
|
3888: hawaiiStream.sphere();
|
3892: alaskaStream.lineStart();
|
3893: hawaiiStream.lineStart();
|
3897: alaskaStream.lineEnd();
|
3898: hawaiiStream.lineEnd();
|
3902: alaskaStream.polygonStart();
|
3903: hawaiiStream.polygonStart();
|
3907: alaskaStream.polygonEnd();
|
3908: hawaiiStream.polygonEnd();
|
3929: ...(33 bytes skipped)...slate(_).clipExtent([ [ x - .455 * k, y - .238 * k ], [ x + .455 * k, y + .238 * k ] ]).stream(pointStream).point;
|
3930: ...(79 bytes skipped)...([ [ x - .425 * k + ε, y + .12 * k + ε ], [ x - .214 * k - ε, y + .234 * k - ε ] ]).stream(pointStream).point;
|
3931: ...(80 bytes skipped)...[ [ x - .214 * k + ε, y + .166 * k + ε ], [ x - .115 * k - ε, y + .234 * k - ε ] ]).stream(pointStream).point;
|
4200: var pointRadius = 4.5, projection, context, projectStream, contextStream, cacheStream;
|
4203: if (typeof pointRadius === "function") contextStream.pointRadius(+pointRadius.apply(this, arguments));
|
4204: if (!cacheStream || !cacheStream.valid) cacheStream = projectStream(contextStream);
|
4205: d3.geo.stream(object, cacheStream);
|
4207: return contextStream.result();
|
4211: d3.geo.stream(object, projectStream(d3_geo_pathArea));
|
4216: d3.geo.stream(object, projectStream(d3_geo_pathCentroid));
|
4221: d3.geo.stream(object, projectStream(d3_geo_pathBounds));
|
4226: projectStream = (projection = _) ? _.stream || d3_geo_pathProjectStream(_) : d3_identity;
|
4231: contextStream = (context = _) == null ? new d3_geo_pathBuffer() : new d3_geo_pathContext(_);
|
4232: if (typeof pointRadius !== "function") contextStream.pointRadius(pointRadius);
|
4237: pointRadius = typeof _ === "function" ? _ : (contextStream.pointRadius(+_), +_);
|
4241: cacheStream = null;
|
| Rmmquant:src/mmquant.h: [ ] |
|---|
658: std::ostream &getOutputStream () {
|
662: std::ostream &getStatsStream () {
|
1814: parameters.getOutputStream() << "# Program:mmquant v" << VERSION << "; Command:";
|
1816: parameters.getOutputStream() << " \"" << arg << "\"";
|
1818: parameters.getOutputStream() << "\nGeneid\tChr\tStart\tEnd\tStrand\tLength";
|
1821: parameters.getOutputStream() << "Gene";
|
1824: parameters.getOutputStream() << "\t" << sample;
|
1826: parameters.getOutputStream() << "\n";
|
1828: parameters.getOutputStream() << line.first;
|
1830: parameters.getOutputStream() << "\t" << i;
|
1832: parameters.getOutputStream() << "\n";
|
1923: dumpStats(parameters.getStatsStream(), parameters.names, stats);
|
| Rarr:src/compression_tools/zstd/compress/zstd_compress.c: [ ] |
|---|
213: size_t ZSTD_sizeof_CStream(const ZSTD_CStream* zcs)
|
5687: ZSTD_CStream* ZSTD_createCStream(void)
|
5693: ZSTD_CStream* ZSTD_initStaticCStream(void *workspace, size_t workspaceSize)
|
5703: size_t ZSTD_freeCStream(ZSTD_CStream* zcs)
|
5729: size_t ZSTD_resetCStream(ZSTD_CStream* zcs, unsigned long long pss)
|
5837: size_t ZSTD_initCStream(ZSTD_CStream* zcs, int compressionLevel)
|
6060: size_t ZSTD_compressStream(ZSTD_CStream* zcs, ZSTD_outBuffer* output, ZSTD_inBuffer* input)
|
6846: size_t ZSTD_flushStream(ZSTD_CStream* zcs, ZSTD_outBuffer* output)
|
6854: size_t ZSTD_endStream(ZSTD_CStream* zcs, ZSTD_outBuffer* output)
|
5698: ZSTD_CStream* ZSTD_createCStream_advanced(ZSTD_customMem customMem)
|
5746: size_t ZSTD_initCStream_internal(ZSTD_CStream* zcs,
|
5768: size_t ZSTD_initCStream_usingCDict_advanced(ZSTD_CStream* zcs,
|
5782: size_t ZSTD_initCStream_usingCDict(ZSTD_CStream* zcs, const ZSTD_CDict* cdict)
|
5795: size_t ZSTD_initCStream_advanced(ZSTD_CStream* zcs,
|
5813: size_t ZSTD_initCStream_usingDict(ZSTD_CStream* zcs, const void* dict, size_t dictSize, int compressionLevel)
|
5822: size_t ZSTD_initCStream_srcSize(ZSTD_CStream* zcs, int compressionLevel, unsigned long long pss)
|
5863: static size_t ZSTD_compressStream_generic(ZSTD_CStream* zcs,
|
6103: static size_t ZSTD_CCtx_init_compressStream2(ZSTD_CCtx* cctx,
|
6201: size_t ZSTD_compressStream2( ZSTD_CCtx* cctx,
|
6300: size_t ZSTD_compressStream2_simpleArgs (
|
1755: size_t ZSTD_estimateCStreamSize_usingCCtxParams(const ZSTD_CCtx_params* params)
|
1775: size_t ZSTD_estimateCStreamSize_usingCParams(ZSTD_compressionParameters cParams)
|
1792: static size_t ZSTD_estimateCStreamSize_internal(int compressionLevel)
|
1798: size_t ZSTD_estimateCStreamSize(int compressionLevel)
|
5712: size_t ZSTD_CStreamInSize(void) { return ZSTD_BLOCKSIZE_MAX; }
|
5714: size_t ZSTD_CStreamOutSize(void)
|
3679: U32 singleStream = litSize < 256;
|
3688: if (!singleStream) cLitSizeEstimate += 6; /* multi-stream huffman uses 6-byte jump table */
|
5684: * Streaming
|
5689: DEBUGLOG(3, "ZSTD_createCStream");
|
5690: return ZSTD_createCStream_advanced(ZSTD_defaultCMem);
|
5699: { /* CStream and CCtx are now same object */
|
5727: /* ZSTD_resetCStream():
|
5736: DEBUGLOG(4, "ZSTD_resetCStream: pledgedSrcSize = %u", (unsigned)pledgedSrcSize);
|
5742: /*! ZSTD_initCStream_internal() :
|
5751: DEBUGLOG(4, "ZSTD_initCStream_internal");
|
5766: /* ZSTD_initCStream_usingCDict_advanced() :
|
5767: * same as ZSTD_initCStream_usingCDict(), with control over frame parameters */
|
5773: DEBUGLOG(4, "ZSTD_initCStream_usingCDict_advanced");
|
5784: DEBUGLOG(4, "ZSTD_initCStream_usingCDict");
|
5791: /* ZSTD_initCStream_advanced() :
|
5804: DEBUGLOG(4, "ZSTD_initCStream_advanced");
|
5815: DEBUGLOG(4, "ZSTD_initCStream_usingDict");
|
5829: DEBUGLOG(4, "ZSTD_initCStream_srcSize");
|
5839: DEBUGLOG(4, "ZSTD_initCStream");
|
5860: /** ZSTD_compressStream_generic():
|
5861: * internal function for all *compressStream*() variants
|
5877: DEBUGLOG(5, "ZSTD_compressStream_generic, flush=%i, srcSize = %zu", (int)flushMode, input->size - input->pos);
|
5903: RETURN_ERROR(init_missing, "call ZSTD_initCStream() first!");
|
6062: FORWARD_IF_ERROR( ZSTD_compressStream2(zcs, output, input, ZSTD_e_continue) , "");
|
6119: DEBUGLOG(4, "ZSTD_compressStream2 : transparent init stage");
|
6155: DEBUGLOG(4, "ZSTD_compressStream2: creating new mtctx for nbWorkers=%u",
|
6161: DEBUGLOG(4, "call ZSTDMT_initCStream_internal as nbWorkers=%u", params.nbWorkers);
|
6162: FORWARD_IF_ERROR( ZSTDMT_initCStream_internal(
|
6206: DEBUGLOG(5, "ZSTD_compressStream2, endOp=%u ", (unsigned)endOp);
|
6234: FORWARD_IF_ERROR(ZSTD_CCtx_init_compressStream2(cctx, endOp, totalInputSize), "compressStream2 initialization failed");
|
6258: flushMin = ZSTDMT_compressStream_generic(cctx->mtctx, output, input, endOp);
|
6267: FORWARD_IF_ERROR(flushMin, "ZSTDMT_compressStream_generic failed");
|
6285: DEBUGLOG(5, "completed ZSTD_compressStream2 delegating to ZSTDMT_compressStream_generic");
|
6294: FORWARD_IF_ERROR( ZSTD_compressStream_generic(cctx, output, input, endOp) , "");
|
6295: DEBUGLOG(5, "completed ZSTD_compressStream2");
|
6314: /* ZSTD_compressStream2() will check validity of dstPos and srcPos */
|
6315: { size_t const cErr = ZSTD_compressStream2(cctx, &output, &input, endOp);
|
6335: size_t const result = ZSTD_compressStream2_simpleArgs(cctx,
|
6343: FORWARD_IF_ERROR(result, "ZSTD_compressStream2_simpleArgs failed");
|
6802: /* Transparent initialization stage, same as compressStream2() */
|
6805: FORWARD_IF_ERROR(ZSTD_CCtx_init_compressStream2(cctx, ZSTD_e_end, srcSize), "CCtx initialization failed");
|
6837: static ZSTD_inBuffer inBuffer_forEndFlush(const ZSTD_CStream* zcs)
|
6844: /*! ZSTD_flushStream() :
|
6850: return ZSTD_compressStream2(zcs, output, &input, ZSTD_e_flush);
|
6857: size_t const remainingToFlush = ZSTD_compressStream2(zcs, output, &input, ZSTD_e_end);
|
6858: FORWARD_IF_ERROR(remainingToFlush , "ZSTD_compressStream2(,,ZSTD_e_end) failed");
|
6864: DEBUGLOG(4, "ZSTD_endStream : remaining to flush : %u", (unsigned)toFlush);
|
1783: noRowCCtxSize = ZSTD_estimateCStreamSize_usingCCtxParams(&initialParams);
|
1785: rowCCtxSize = ZSTD_estimateCStreamSize_usingCCtxParams(&initialParams);
|
1788: return ZSTD_estimateCStreamSize_usingCCtxParams(&initialParams);
|
1795: return ZSTD_estimateCStreamSize_usingCParams(cParams);
|
1803: size_t const newMB = ZSTD_estimateCStreamSize_internal(level);
|
| affxparser:src/fusion/file/TsvFile/TsvFile.h: [ ] |
|---|
472: std::fstream m_fileStream;
|
579: int isFileOpen() { return (m_fileStream.is_open()? TSV_OK : TSV_ERR_FILEIO); }
|
581: bool is_open() { return m_fileStream.is_open(); }
|
582: bool good() { return m_fileStream.good(); }
|
| LACE:inst/htmlwidgets/lib/d3.v4.js: [ ] |
|---|
6898: function geoStream(object, stream) {
|
7424: function circleStream(stream, radius, delta, direction, t0, t1) {
|
8978: function TransformStream() {}
|
9343: point, pointStream = {point: function(x, y) { point = [x, y]; }};
|
6915: var areaStream = {
|
6921: areaStream.lineStart = areaRingStart;
|
6922: areaStream.lineEnd = areaRingEnd;
|
6935: areaStream.point = areaPointFirst;
|
6943: areaStream.point = areaPoint;
|
6972: geoStream(object, areaStream);
|
7020: var boundsStream = {
|
7025: boundsStream.point = boundsRingPoint;
|
7026: boundsStream.lineStart = boundsRingStart;
|
7027: boundsStream.lineEnd = boundsRingEnd;
|
7029: areaStream.polygonStart();
|
7032: areaStream.polygonEnd();
|
7033: boundsStream.point = boundsPoint;
|
7034: boundsStream.lineStart = boundsLineStart;
|
7035: boundsStream.lineEnd = boundsLineEnd;
|
7099: boundsStream.point = linePoint;
|
7104: boundsStream.point = boundsPoint;
|
7115: areaStream.point(lambda, phi);
|
7120: areaStream.lineStart();
|
7125: areaStream.lineEnd();
|
7151: geoStream(feature, boundsStream);
|
7200: var centroidStream = {
|
7206: centroidStream.lineStart = centroidRingStart;
|
7207: centroidStream.lineEnd = centroidRingEnd;
|
7210: centroidStream.lineStart = centroidLineStart;
|
7211: centroidStream.lineEnd = centroidLineEnd;
|
7230: centroidStream.point = centroidLinePointFirst;
|
7239: centroidStream.point = centroidLinePoint;
|
7258: centroidStream.point = centroidPoint;
|
7264: centroidStream.point = centroidRingPointFirst;
|
7269: centroidStream.point = centroidPoint;
|
7275: centroidStream.point = centroidRingPoint;
|
7310: geoStream(object, centroidStream);
|
7470: circleStream(stream, r, p, 1);
|
7906: circleStream(stream, radius, delta, direction, from, to);
|
8182: var activeStream = stream,
|
8183: bufferStream = clipBuffer(),
|
8192: var clipStream = {
|
8201: if (visible(x, y)) activeStream.point(x, y);
|
8220: activeStream = bufferStream, segments = [], polygon = [], clean = true;
|
8239: activeStream = stream, segments = polygon = ring = null;
|
8243: clipStream.point = linePoint;
|
8256: if (v__ && v_) bufferStream.rejoin();
|
8257: segments.push(bufferStream.result());
|
8259: clipStream.point = point;
|
8260: if (v_) activeStream.lineEnd();
|
8270: activeStream.lineStart();
|
8271: activeStream.point(x, y);
|
8274: if (v && v_) activeStream.point(x, y);
|
8280: activeStream.lineStart();
|
8281: activeStream.point(a[0], a[1]);
|
8283: activeStream.point(b[0], b[1]);
|
8284: if (!v) activeStream.lineEnd();
|
8287: activeStream.lineStart();
|
8288: activeStream.point(x, y);
|
8296: return clipStream;
|
8306: cacheStream,
|
8311: return cache && cacheStream === stream ? cache : cache = clipRectangle(x0, y0, x1, y1)(cacheStream = stream);
|
8314: ...(16 bytes skipped)...return arguments.length ? (x0 = +_[0][0], y0 = +_[0][1], x1 = +_[1][0], y1 = +_[1][1], cache = cacheStream = null, clip) : [[x0, y0], [x1, y1]];
|
8324: var lengthStream = {
|
8334: lengthStream.point = lengthPointFirst;
|
8335: lengthStream.lineEnd = lengthLineEnd;
|
8339: lengthStream.point = lengthStream.lineEnd = noop$1;
|
8345: lengthStream.point = lengthPoint;
|
8364: geoStream(object, lengthStream);
|
8607: var areaStream$1 = {
|
8612: areaStream$1.lineStart = areaRingStart$1;
|
8613: areaStream$1.lineEnd = areaRingEnd$1;
|
8616: areaStream$1.lineStart = areaStream$1.lineEnd = areaStream$1.point = noop$1;
|
8628: areaStream$1.point = areaPointFirst$1;
|
8632: areaStream$1.point = areaPoint$1;
|
8650: var boundsStream$1 = {
|
8686: var centroidStream$1 = {
|
8691: centroidStream$1.lineStart = centroidRingStart$1;
|
8692: centroidStream$1.lineEnd = centroidRingEnd$1;
|
8695: centroidStream$1.point = centroidPoint$1;
|
8696: centroidStream$1.lineStart = centroidLineStart$1;
|
8697: centroidStream$1.lineEnd = centroidLineEnd$1;
|
8718: centroidStream$1.point = centroidPointFirstLine;
|
8722: centroidStream$1.point = centroidPointLine;
|
8735: centroidStream$1.point = centroidPoint$1;
|
8739: centroidStream$1.point = centroidPointFirstRing;
|
8747: centroidStream$1.point = centroidPointRing;
|
8817: var lengthStream$1 = {
|
8820: lengthStream$1.point = lengthPointFirst$1;
|
8824: lengthStream$1.point = noop$1;
|
8840: lengthStream$1.point = lengthPoint$1;
|
8912: projectionStream,
|
8913: contextStream;
|
8917: if (typeof pointRadius === "function") contextStream.pointRadius(+pointRadius.apply(this, arguments));
|
8918: geoStream(object, projectionStream(contextStream));
|
8920: return contextStream.result();
|
8924: geoStream(object, projectionStream(areaStream$1));
|
8925: return areaStream$1.result();
|
8929: geoStream(object, projectionStream(lengthStream$1));
|
8930: return lengthStream$1.result();
|
8934: geoStream(object, projectionStream(boundsStream$1));
|
8935: return boundsStream$1.result();
|
8939: geoStream(object, projectionStream(centroidStream$1));
|
8940: return centroidStream$1.result();
|
8944: return arguments.length ? (projectionStream = _ == null ? (projection = null, identity$4) : (projection = _).stream, path) : projection;
|
8949: contextStream = _ == null ? (context = null, new PathString) : new PathContext(context = _);
|
8950: if (typeof pointRadius !== "function") contextStream.pointRadius(pointRadius);
|
8956: pointRadius = typeof _ === "function" ? _ : (contextStream.pointRadius(+_), +_);
|
8971: var s = new TransformStream;
|
8980: TransformStream.prototype = {
|
8981: constructor: TransformStream,
|
8994: geoStream(object, projection.stream(boundsStream$1));
|
8995: fitBounds(boundsStream$1.result());
|
9083: var resampleStream = {
|
9087: polygonStart: function() { stream.polygonStart(); resampleStream.lineStart = ringStart; },
|
9088: polygonEnd: function() { stream.polygonEnd(); resampleStream.lineStart = lineStart; }
|
9098: resampleStream.point = linePoint;
|
9109: resampleStream.point = point;
|
9115: resampleStream.point = ringPoint;
|
9116: resampleStream.lineEnd = ringEnd;
|
9121: resampleStream.point = linePoint;
|
9126: resampleStream.lineEnd = lineEnd;
|
9130: return resampleStream;
|
9163: cacheStream;
|
9180: return cache && cacheStream...(9 bytes skipped)...am ? cache : cache = transformRadians(transformRotate(rotate)(preclip(projectResample(postclip(cacheStream = stream)))));
|
9244: cache = cacheStream = null;
|
9339: cacheStream,
|
9363: return cache && cacheStream === stream ? cache : cache = multiplex([lower48.stream(cacheStream = stream), alaska.stream(stream), hawaii.stream(stream)]);
|
9385: .stream(pointStream);
|
9390: .stream(pointStream);
|
9395: .stream(pointStream);
|
9417: cache = cacheStream = null;
|
9621: cacheStream,
|
9625: cache = cacheStream = null;
|
9631: return cache && cacheStream === stream ? cache : cache = transform$$1(postclip(cacheStream = stream));
|
16942: exports.geoStream = geoStream;
|
| seqTools:src/dna_fasta_stream.h: [ ] |
|---|
52: } fafStream;
|
207: } faStream;
|
215: void faStream_destroy(faStream *fa)
|
275: faStream * faStream_init(const char* filename, unsigned k, unsigned mode)
|
135: // fasta Stream
|
54: static inline unsigned faf_isEof(fafStream *faf) { return faf->status & faf_file_eof; }
|
55: static inline unsigned faf_isOpen(fafStream *faf)
|
62: static fafStream* faf_stream_init(const char* filename, unsigned mode)
|
64: // Construct fafStream object from opened file
|
65: fafStream *faf = calloc(sizeof(fafStream), 1);
|
87: static void faf_destroy(fafStream *faf)
|
99: static size_t inline faf_read(fafStream *faf, char *dest, unsigned size)
|
187: fafStream *fasta;
|
230: int fas_fill(faStream *fa)
|
279: printf("[faStream_init] k > fas_size!\n");
|
283: faStream *fa = calloc(sizeof(faStream), 1);
|
292: printf("[faStream_init] Cannot open file '%s'!\n", filename);
|
293: faStream_destroy(fa);
|
308: printf("[faStream_init] Initial array filling failed!\n");
|
309: faStream_destroy(fa);
|
321: static inline int fas_fas_end(faStream *fa) { return fa->ffc == 0; }
|
322: static inline int fas_nuc_end(faStream *fa) { return fa->fnc == 0; }
|
333: static inline int fas_checkNewLine(faStream *fa)
|
343: static inline int fas_skipNewLine(faStream *fa)
|
366: static inline int fas_skipLine(faStream *fa)
|
386: static inline int fas_checkNewSeq(faStream *fa)
|
399: static inline int fas_skipSeqHeader(faStream *fa)
|
412: static inline int fas_checkComment(faStream *fa)
|
422: static inline int fas_skipComment(faStream *fa)
|
435: static inline int fas_checkN(faStream *fa)
|
445: static inline int fas_skipN(faStream *fa)
|
496: char * fas_getSeqName(faStream *fa)
|
551: int fas_initSeq(faStream *fa)
|
592: static inline int fas_returnFromTranfer(faStream *fa)
|
626: int fas_TransferNucArray(faStream *fa)
|
697: int fa_empty(faStream *fa) { return (fa->stream_state & fas_stream_empty); }
|
698: int fa_NucReady(faStream *fa) { return (fa->stream_state & fas_nuc_ready); }
|
699: int fa_K_Ready(faStream *fa) { return (fa->stream_state & fas_loc_kReady); }
|
700: int fa_NewSeq(faStream *fa) { return (fa->stream_state & fas_loc_newSeq); }
|
701: int fa_N_Nuc(faStream *fa) { return (ACGTN[(unsigned)*fa->iter] == nval); }
|
704: void fa_unsetNucReady(faStream *fa)
|
| interacCircos:inst/htmlwidgets/lib/d3.js: [ ] |
|---|
3639: function d3_geo_pathProjectStream(project) {
|
3271: var lower48Stream = lower48.stream(stream), alaskaStream = alaska.stream(stream), hawaiiStream = hawaii.stream(stream);
|
3274: lower48Stream.point(x, y);
|
3279: lower48Stream.sphere();
|
3284: lower48Stream.lineStart();
|
3289: lower48Stream.lineEnd();
|
3294: lower48Stream.polygonStart();
|
3299: lower48Stream.polygonEnd();
|
3255: var point, pointStream = {
|
3275: alaskaStream.point(x, y);
|
3276: hawaiiStream.point(x, y);
|
3280: alaskaStream.sphere();
|
3281: hawaiiStream.sphere();
|
3285: alaskaStream.lineStart();
|
3286: hawaiiStream.lineStart();
|
3290: alaskaStream.lineEnd();
|
3291: hawaiiStream.lineEnd();
|
3295: alaskaStream.polygonStart();
|
3296: hawaiiStream.polygonStart();
|
3300: alaskaStream.polygonEnd();
|
3301: hawaiiStream.polygonEnd();
|
3322: ...(33 bytes skipped)...slate(_).clipExtent([ [ x - .455 * k, y - .238 * k ], [ x + .455 * k, y + .238 * k ] ]).stream(pointStream).point;
|
3323: ...(79 bytes skipped)...([ [ x - .425 * k + ε, y + .12 * k + ε ], [ x - .214 * k - ε, y + .234 * k - ε ] ]).stream(pointStream).point;
|
3324: ...(80 bytes skipped)...[ [ x - .214 * k + ε, y + .166 * k + ε ], [ x - .115 * k - ε, y + .234 * k - ε ] ]).stream(pointStream).point;
|
3593: var pointRadius = 4.5, projection, context, projectStream, contextStream, cacheStream;
|
3596: if (typeof pointRadius === "function") contextStream.pointRadius(+pointRadius.apply(this, arguments));
|
3597: if (!cacheStream || !cacheStream.valid) cacheStream = projectStream(contextStream);
|
3598: d3.geo.stream(object, cacheStream);
|
3600: return contextStream.result();
|
3604: d3.geo.stream(object, projectStream(d3_geo_pathArea));
|
3609: d3.geo.stream(object, projectStream(d3_geo_pathCentroid));
|
3614: d3.geo.stream(object, projectStream(d3_geo_pathBounds));
|
3619: projectStream = (projection = _) ? _.stream || d3_geo_pathProjectStream(_) : d3_identity;
|
3624: contextStream = (context = _) == null ? new d3_geo_pathBuffer() : new d3_geo_pathContext(_);
|
3625: if (typeof pointRadius !== "function") contextStream.pointRadius(pointRadius);
|
3630: pointRadius = typeof _ === "function" ? _ : (contextStream.pointRadius(+_), +_);
|
3634: cacheStream = null;
|
| Cardinal:R/utils.R: [ ] |
|---|
370: getRNGStream <- function() {
|
379: setRNGStream <- function(seed = NULL) {
|
385: generateRNGStreams <- function(n = 1) {
|
387: s <- getRNGStream()
|
396: s <- nextRNGStream(seeds[[i - 1]])
|
| BUSseq:src/rngstream.cpp: [ ] |
|---|
303: RngStream::RngStream (const char *s) : name (s)
|
327: void RngStream::ResetStartStream ()
|
325: // Reset Stream to beginning of Stream.
|
335: // Reset Stream to beginning of SubStream.
|
345: // Reset Stream to NextSubStream.
|
3: * File: RngStream.cpp for multiple streams of Random Numbers
|
242: double RngStream::U01 ()
|
271: double RngStream::U01d ()
|
292: // declared RngStream, unless SetPackageSeed is called.
|
294: double RngStream::nextSeed[6] =
|
309: state of the stream, the starting state of the current SubStream, and the
|
313: will be the seed of the next declared RngStream. */
|
337: void RngStream::ResetStartSubstream ()
|
347: void RngStream::ResetNextSubstream ()
|
357: bool RngStream::SetPackageSeed (const unsigned long seed[6])
|
368: bool RngStream::SetSeed (const unsigned long seed[6])
|
384: void RngStream::AdvanceState (long e, long c)
|
415: void RngStream::GetState (unsigned long seed[6]) const
|
424: void RngStream::WriteState () const
|
439: void RngStream::WriteStateFull () const
|
443: cout << "The RngStream";
|
470: void RngStream::IncreasedPrecis (bool incp)
|
477: void RngStream::SetAntithetic (bool a)
|
486: double RngStream::RandU01 ()
|
498: int RngStream::RandInt (int low, int high)
|
| RProtoBufLib:src/GatingSet_pb_lib/GatingSet.pb.cc: [ ] |
|---|
1460: bool paramRange::MergePartialFromCodedStream(
|
1810: bool Range::MergePartialFromCodedStream(
|
2113: bool rangeGate::MergePartialFromCodedStream(
|
2391: bool MultiRangeGate::MergePartialFromCodedStream(
|
2724: bool paramPoly::MergePartialFromCodedStream(
|
3077: bool polygonGate::MergePartialFromCodedStream(
|
3384: bool coordinate::MergePartialFromCodedStream(
|
3729: bool ellipseGate::MergePartialFromCodedStream(
|
4131: bool BOOL_GATE_OP::MergePartialFromCodedStream(
|
4471: bool boolGate::MergePartialFromCodedStream(
|
4740: bool clusterGate::MergePartialFromCodedStream(
|
5029: bool quadGate::MergePartialFromCodedStream(
|
5519: bool gate::MergePartialFromCodedStream(
|
6100: bool POPSTATS::MergePartialFromCodedStream(
|
6499: bool calibrationTable::MergePartialFromCodedStream(
|
7150: bool biexpTrans::MergePartialFromCodedStream(
|
7573: bool fasinhTrans::MergePartialFromCodedStream(
|
7978: bool scaleTrans::MergePartialFromCodedStream(
|
8311: bool flinTrans::MergePartialFromCodedStream(
|
8628: bool logTrans::MergePartialFromCodedStream(
|
8993: bool logGML2Trans::MergePartialFromCodedStream(
|
9334: bool logicleTrans::MergePartialFromCodedStream(
|
10043: bool transformation::MergePartialFromCodedStream(
|
10821: bool trans_pair::MergePartialFromCodedStream(
|
11195: bool trans_local::MergePartialFromCodedStream(
|
11609: bool POPINDICES::MergePartialFromCodedStream(
|
12094: bool nodeProperties::MergePartialFromCodedStream(
|
12578: bool treeNodes::MergePartialFromCodedStream(
|
12875: bool populationTree::MergePartialFromCodedStream(
|
13247: bool COMP::MergePartialFromCodedStream(
|
13908: bool PARAM::MergePartialFromCodedStream(
|
14432: bool GatingHierarchy::MergePartialFromCodedStream(
|
14868: bool CytoFrame::MergePartialFromCodedStream(
|
15151: bool TRANS_TBL::MergePartialFromCodedStream(
|
15563: bool GatingSet::MergePartialFromCodedStream(
|
1461: ::PROTOBUF_NAMESPACE_ID::io::CodedInputStream* input) {
|
1533: ::PROTOBUF_NAMESPACE_ID::io::CodedOutputStream* output) const {
|
1811: ::PROTOBUF_NAMESPACE_ID::io::CodedInputStream* input) {
|
1868: ::PROTOBUF_NAMESPACE_ID::io::CodedOutputStream* output) const {
|
2114: ::PROTOBUF_NAMESPACE_ID::io::CodedInputStream* input) {
|
2156: ::PROTOBUF_NAMESPACE_ID::io::CodedOutputStream* output) const {
|
2392: ::PROTOBUF_NAMESPACE_ID::io::CodedInputStream* input) {
|
2449: ::PROTOBUF_NAMESPACE_ID::io::CodedOutputStream* output) const {
|
2725: ::PROTOBUF_NAMESPACE_ID::io::CodedInputStream* input) {
|
2783: ::PROTOBUF_NAMESPACE_ID::io::CodedOutputStream* output) const {
|
3078: ::PROTOBUF_NAMESPACE_ID::io::CodedInputStream* input) {
|
3131: ::PROTOBUF_NAMESPACE_ID::io::CodedOutputStream* output) const {
|
3385: ::PROTOBUF_NAMESPACE_ID::io::CodedInputStream* input) {
|
3442: ::PROTOBUF_NAMESPACE_ID::io::CodedOutputStream* output) const {
|
3730: ::PROTOBUF_NAMESPACE_ID::io::CodedInputStream* input) {
|
3807: ::PROTOBUF_NAMESPACE_ID::io::CodedOutputStream* output) const {
|
4132: ::PROTOBUF_NAMESPACE_ID::io::CodedInputStream* input) {
|
4205: ::PROTOBUF_NAMESPACE_ID::io::CodedOutputStream* output) const {
|
4472: ::PROTOBUF_NAMESPACE_ID::io::CodedInputStream* input) {
|
4514: ::PROTOBUF_NAMESPACE_ID::io::CodedOutputStream* output) const {
|
4741: ::PROTOBUF_NAMESPACE_ID::io::CodedInputStream* input) {
|
4787: ::PROTOBUF_NAMESPACE_ID::io::CodedOutputStream* output) const {
|
5030: ::PROTOBUF_NAMESPACE_ID::io::CodedInputStream* input) {
|
5090: ::PROTOBUF_NAMESPACE_ID::io::CodedOutputStream* output) const {
|
5520: ::PROTOBUF_NAMESPACE_ID::io::CodedInputStream* input) {
|
5670: ::PROTOBUF_NAMESPACE_ID::io::CodedOutputStream* output) const {
|
6101: ::PROTOBUF_NAMESPACE_ID::io::CodedInputStream* input) {
|
6160: ::PROTOBUF_NAMESPACE_ID::io::CodedOutputStream* output) const {
|
6500: ::PROTOBUF_NAMESPACE_ID::io::CodedInputStream* input) {
|
6652: ::PROTOBUF_NAMESPACE_ID::io::CodedOutputStream* output) const {
|
6741: target = ::PROTOBUF_NAMESPACE_ID::io::CodedOutputStream::WriteVarint32ToArray(
|
6754: target = ::PROTOBUF_NAMESPACE_ID::io::CodedOutputStream::WriteVarint32ToArray(
|
6767: target = ::PROTOBUF_NAMESPACE_ID::io::CodedOutputStream::WriteVarint32ToArray(
|
6780: target = ::PROTOBUF_NAMESPACE_ID::io::CodedOutputStream::WriteVarint32ToArray(
|
6793: target = ::PROTOBUF_NAMESPACE_ID::io::CodedOutputStream::WriteVarint32ToArray(
|
7151: ::PROTOBUF_NAMESPACE_ID::io::CodedInputStream* input) {
|
7247: ::PROTOBUF_NAMESPACE_ID::io::CodedOutputStream* output) const {
|
7574: ::PROTOBUF_NAMESPACE_ID::io::CodedInputStream* input) {
|
7670: ::PROTOBUF_NAMESPACE_ID::io::CodedOutputStream* output) const {
|
7979: ::PROTOBUF_NAMESPACE_ID::io::CodedInputStream* input) {
|
8049: ::PROTOBUF_NAMESPACE_ID::io::CodedOutputStream* output) const {
|
8312: ::PROTOBUF_NAMESPACE_ID::io::CodedInputStream* input) {
|
8369: ::PROTOBUF_NAMESPACE_ID::io::CodedOutputStream* output) const {
|
8629: ::PROTOBUF_NAMESPACE_ID::io::CodedInputStream* input) {
|
8712: ::PROTOBUF_NAMESPACE_ID::io::CodedOutputStream* output) const {
|
8994: ::PROTOBUF_NAMESPACE_ID::io::CodedInputStream* input) {
|
9051: ::PROTOBUF_NAMESPACE_ID::io::CodedOutputStream* output) const {
|
9335: ::PROTOBUF_NAMESPACE_ID::io::CodedInputStream* input) {
|
9457: ::PROTOBUF_NAMESPACE_ID::io::CodedOutputStream* output) const {
|
10044: ::PROTOBUF_NAMESPACE_ID::io::CodedInputStream* input) {
|
10246: ::PROTOBUF_NAMESPACE_ID::io::CodedOutputStream* output) const {
|
10822: ::PROTOBUF_NAMESPACE_ID::io::CodedInputStream* input) {
|
10892: ::PROTOBUF_NAMESPACE_ID::io::CodedOutputStream* output) const {
|
11196: ::PROTOBUF_NAMESPACE_ID::io::CodedInputStream* input) {
|
11269: ::PROTOBUF_NAMESPACE_ID::io::CodedOutputStream* output) const {
|
11342: target = ::PROTOBUF_NAMESPACE_ID::io::CodedOutputStream::WriteVarint32ToArray(
|
11610: ::PROTOBUF_NAMESPACE_ID::io::CodedInputStream* input) {
|
11695: ::PROTOBUF_NAMESPACE_ID::io::CodedOutputStream* output) const {
|
11758: target = ::PROTOBUF_NAMESPACE_ID::io::CodedOutputStream::WriteVarint32ToArray(
|
12095: ::PROTOBUF_NAMESPACE_ID::io::CodedInputStream* input) {
|
12198: ::PROTOBUF_NAMESPACE_ID::io::CodedOutputStream* output) const {
|
12579: ::PROTOBUF_NAMESPACE_ID::io::CodedInputStream* input) {
|
12634: ::PROTOBUF_NAMESPACE_ID::io::CodedOutputStream* output) const {
|
12876: ::PROTOBUF_NAMESPACE_ID::io::CodedInputStream* input) {
|
12918: ::PROTOBUF_NAMESPACE_ID::io::CodedOutputStream* output) const {
|
13248: ::PROTOBUF_NAMESPACE_ID::io::CodedInputStream* input) {
|
13402: ::PROTOBUF_NAMESPACE_ID::io::CodedOutputStream* output) const {
|
13570: target = ::PROTOBUF_NAMESPACE_ID::io::CodedOutputStream::WriteVarint32ToArray(
|
13909: ::PROTOBUF_NAMESPACE_ID::io::CodedInputStream* input) {
|
14007: ::PROTOBUF_NAMESPACE_ID::io::CodedOutputStream* output) const {
|
14433: ::PROTOBUF_NAMESPACE_ID::io::CodedInputStream* input) {
|
14532: ::PROTOBUF_NAMESPACE_ID::io::CodedOutputStream* output) const {
|
14869: ::PROTOBUF_NAMESPACE_ID::io::CodedInputStream* input) {
|
14913: ::PROTOBUF_NAMESPACE_ID::io::CodedOutputStream* output) const {
|
15152: ::PROTOBUF_NAMESPACE_ID::io::CodedInputStream* input) {
|
15207: ::PROTOBUF_NAMESPACE_ID::io::CodedOutputStream* output) const {
|
15564: ::PROTOBUF_NAMESPACE_ID::io::CodedInputStream* input) {
|
15719: ::PROTOBUF_NAMESPACE_ID::io::CodedOutputStream* output) const {
|
| affxparser:src/fusion/calvin_files/data/src/DataSet.cpp: [ ] |
|---|
161: void DataSet::ReadDataSetUsingStream()
|
327: void DataSet::ClearStreamData()
|
71: fileStream = 0;
|
95: fileStream = &ifs;
|
129: ReadDataSetUsingStream();
|
170: fileStream->seekg(mapStart);
|
171: fileStream->read(data, mapLen);
|
444: fileStream->seekg(mapStart);
|
445: fileStream->read(data, mapLen);
|
182: ClearStreamData();
|
438: ClearStreamData();
|
| RSeqAn:inst/include/seqan/stream/file_stream.h: [ ] |
|---|
1138: class FileStream :
|
1143: typedef typename BasicStream<TValue, TDirection>::Type TBasicStream;
|
1147: FileStream() :
|
1151: FileStream(const char * fileName, int openMode = DefaultOpenMode<FileStream>::VALUE) :
|
1157: ~FileStream()
|
1198: typedef FileStreamBuffer<TValue, TDirection, TSpec> TStream_;
|
1215: typedef FileStreamBuffer<TValue, TDirection, TSpec> TStream_;
|
804: struct FileStreamBuffer :
|
831: FileStreamBuffer()
|
836: ~FileStreamBuffer()
|
1142: typedef FileStreamBuffer<TValue, TDirection, TSpec> TStreamBuffer;
|
1115: class FileStream;
|
1119: close(FileStream<TValue, TDirection, TSpec> & stream);
|
1130: struct DefaultOpenMode<FileStream<TValue, TDirection, TSpec>, TDummy>:
|
1134: // Class FileStream
|
1139: public BasicStream<TValue, TDirection>::Type
|
1148: TBasicStream(&buffer)
|
1152: TBasicStream(&buffer)
|
1188: struct Value<FileStream<TValue, TDirection, TSpec> >:
|
1199: typedef typename TStream_::TFile TFile_;
|
1205: struct Position<FileStream<TValue, TDirection, TSpec> >:
|
1216: typedef typename TStream_::TFile TFile_;
|
1222: struct Size<FileStream<TValue, TDirection, TSpec> >:
|
1230: SEQAN_CONCEPT_IMPL((FileStream<TValue, Input, TSpec>), (InputStreamConcept));
|
1233: SEQAN_CONCEPT_IMPL((FileStream<TValue, Output, TSpec>), (OutputStreamConcept));
|
1236: SEQAN_CONCEPT_IMPL((FileStream<TValue, Bidirectional, TSpec>), (BidirectionalStreamConcept));
|
1257: open(FileStream<TValue, TDirection, TSpec> & stream, const char * fileName, int openMode = DefaultOpenMode<FileStream<TValue, TDirection, TSpec> >::VALUE)
|
1301: close(FileStream<TValue, TDirection, TSpec> & stream)
|
800: // Class FileStreamBuffer
|
1099: clear(FileStreamBuffer<TValue, TDirection, TSpec> & buffer)
|
1145: TStreamBuffer buffer;
|
1182: struct Value<FileStreamBuffer<TValue, TDirection, TSpec> >
|
1189: Value<FileStreamBuffer<TValue, TDirection, TSpec> >{};
|
1196: struct Position<FileStreamBuffer<TValue, TDirection, TSpec> >
|
1206: Position<FileStreamBuffer<TValue, TDirection, TSpec> >{};
|
1213: struct Size<FileStreamBuffer<TValue, TDirection, TSpec> >
|
1223: Size<FileStreamBuffer<TValue, TDirection, TSpec> >{};
|
1293: close(FileStreamBuffer<TValue, TDirection, TSpec> & buffer)
|
| CytoML:inst/include/CytoML/wsNode.hpp: [ ] |
|---|
43: class CytoStream : public std::ostream {
|
46: CytoStream() : std::ostream(&cytobuf){}
|
54: extern CytoML::CytoStream cytocout;
|
| RSeqAn:inst/include/seqan/basic/basic_stream.h: [ ] |
|---|
446: struct BasicStream :
|
47: struct StreamIterator;
|
56: inline void writeValue(Iter<TContainer, StreamIterator<Output> > &iter, TValue val);
|
94: // Concept StreamConcept
|
98: * @concept StreamConcept
|
103: * @signature concept StreamConcept;
|
107: * @mfn StreamConcept#Value
|
110: * @signature Value<TStream>::Type;
|
112: * @tparam TStream The stream type to query for its value type.
|
117: * @mfn StreamConcept#Size
|
120: * @signature Size<TStream>::Type;
|
122: * @tparam TStream The stream type to query for its size type.
|
127: * @mfn StreamConcept#Position
|
130: * @signature Position<TStream>::Type;
|
132: * @tparam TStream The stream type to query for its position type.
|
137: * @fn StreamConcept#position
|
143: * @return TPosition Current position in stream, see @link StreamConcept#Position Position @endlink.
|
147: * @fn StreamConcept#setPosition
|
157: * @fn StreamConcept#atEnd
|
166: SEQAN_CONCEPT(StreamConcept, (TStream))
|
174: * @concept InputStreamConcept Input StreamConcept
|
175: * @extends StreamConcept
|
178: * @signature concept InputStreamConcept : StreamConcept;
|
183: SEQAN_CONCEPT_REFINE(InputStreamConcept, (TStream), (StreamConcept))
|
185: typedef typename Value<TStream>::Type TValue;
|
186: typedef typename Size<TStream>::Type TSize;
|
187: typedef typename Position<TStream>::Type TPosition;
|
200: * @concept OutputStreamConcept Output StreamConcept
|
201: * @extends StreamConcept
|
204: * @signature concept OutputStreamConcept : StreamConcept;
|
209: SEQAN_CONCEPT_REFINE(OutputStreamConcept, (TStream), (StreamConcept))
|
211: typedef typename Value<TStream>::Type TValue;
|
212: typedef typename Size<TStream>::Type TSize;
|
213: typedef typename Position<TStream>::Type TPosition;
|
226: * @concept BidirectionalStreamConcept Bidirectional StreamConcept
|
227: * @extends StreamConcept
|
230: * @signature concept BidirectionalStreamConcept : StreamConcept;
|
235: SEQAN_CONCEPT_REFINE(BidirectionalStreamConcept, (TStream), (InputStreamConcept)(OutputStreamConcept))
|
402: * @mfn StreamConcept#DirectionIterator
|
405: * @signature DirectionIterator<TStream>::Type;
|
407: * @tparam TStream The stream to query for its direction iterator.
|
423: If<Is<StreamConcept<TObject> >,
|
424: Iter<TObject, StreamIterator<TDirection> >,
|
429: // Metafunction BasicStream
|
433: * @mfn BasicStream
|
437: * @signature BasicStream<TValue, TDirection[, TTraits]>::Type;
|
991: // NOTE(esiragusa): should it be defined for Streams and Containers?
|
1302: template <typename TStream, typename TIterator>
|
1303: inline TStream &
|
1304: operator<<(TStream & target,
|
1307: typename DirectionIterator<TStream, Output>::Type it = directionIterator(target, Output());
|
1312: template <typename TStream, typename TValue>
|
1313: inline TStream &
|
1314: operator<<(TStream & target,
|
1317: typename DirectionIterator<TStream, Output>::Type it = directionIterator(target, Output());
|
170: // Concept InputStreamConcept
|
191: SEQAN_CONCEPT_USAGE(InputStreamConcept)
|
196: // Concept OutputStreamConcept
|
217: SEQAN_CONCEPT_USAGE(OutputStreamConcept)
|
222: // Concept BidirectionalStreamConcept
|
916: inline SEQAN_FUNC_ENABLE_IF(Is< OutputStreamConcept<TTarget> >, void)
|
924: inline SEQAN_FUNC_ENABLE_IF(Is< OutputStreamConcept<TTarget> >, void)
|
994: //inline SEQAN_FUNC_ENABLE_IF(Or<Is<OutputStreamConcept<TTarget> >, Is<ContainerConcept<TTarget> > >, void)
|
1026: //inline SEQAN_FUNC_ENABLE_IF(Or<Is<OutputStreamConcept<TTarget> >, Is<ContainerConcept<TTarget> > >, void)
|
1041: //inline SEQAN_FUNC_ENABLE_IF(Or<Is<OutputStreamConcept<TTarget> >, Is<ContainerConcept<TTarget> > >, void)
|
| mzR:src/boost/nowide/fstream.hpp: [ ] |
|---|
23: struct StreamTypeIn
|
32: struct StreamTypeOut
|
41: struct StreamTypeInOut
|
56: /// \tparam T_StreamType One of StreamType* above.
|
61: typename T_StreamType,
|
72: class basic_ifstream : public detail::fstream_impl<CharType, Traits, detail::StreamTypeIn>
|
74: using fstream_impl = detail::fstream_impl<CharType, Traits, detail::StreamTypeIn>;
|
123: class basic_ofstream : public detail::fstream_impl<CharType, Traits, detail::StreamTypeOut>
|
125: using fstream_impl = detail::fstream_impl<CharType, Traits, detail::StreamTypeOut>;
|
175: class basic_fstream : public detail::fstream_impl<CharType, Traits, detail::StreamTypeInOut>
|
177: using fstream_impl = detail::fstream_impl<CharType, Traits, detail::StreamTypeInOut>;
|
272: template<typename CharType, typename Traits, typename T_StreamType, int>
|
274: public T_StreamType::template stream_base<CharType, Traits>::type
|
278: using stream_base = typename T_StreamType::template stream_base<CharType, Traits>::type;
|
310: void open(const std::string& file_name, std::ios_base::openmode mode = T_StreamType::mode())
|
316: std::ios_base::openmode mode = T_StreamType::mode())
|
320: void open(const char* file_name, std::ios_base::openmode mode = T_StreamType::mode())
|
322: if(!rdbuf()->open(file_name, mode | T_StreamType::mode_modifier()))
|
328: void open(const wchar_t* file_name, std::ios_base::openmode mode = T_StreamType::mode())
|
330: if(!rdbuf()->open(file_name, mode | T_StreamType::mode_modifier()))
|
| seqTools:src/dna_astream.h: [ ] |
|---|
87: } daStream;
|
55: dfStream *dnaf;
|
95: static inline int dasEmpty(daStream *das) { return das->r_iter == das->r_end; }
|
96: static inline int dasProcEmpty(daStream *das) { return das->p_iter == das->p_end; }
|
97: static inline int dasIsError(daStream *das) { return das->state & das_err; }
|
98: static inline int dasIsOpen(daStream *das) { return dfs_isOpen(das->dnaf); }
|
99: static inline int dasIsEof(daStream *das) { return dfs_stream_eof(das->dnaf); }
|
107: void das_destroy(daStream *das)
|
122: int das_fill(daStream *das)
|
176: daStream * das_init(const char* filename, unsigned das_size)
|
178: daStream *das = calloc(sizeof(daStream), 1);
|
| beachmat:inst/include/tatami/utils/Oracles.hpp: [ ] |
|---|
90: struct OracleStream {
|
99: OracleStream(std::unique_ptr<Oracle<Index_> > o) : oracle(std::move(o)) {}
|
78: * @brief Stream predictions from the oracle.
|
84: * The `OracleStream` is primarily intended for `Matrix` developers to use within subclass implementations that can expl...(25 bytes skipped)...
|
85: * Users should not have to construct `OracleStream` instances.
|
94: OracleStream() = default;
|
| diffUTR:README.md: [ ] |
|---|
3: ## Streamlining differential exon and 3' UTR usage analysis
|
| CoGAPS:src/utils/Archive.h: [ ] |
|---|
86: std::fstream mStream;
|
24: mStream(path.c_str(), std::ios::binary | flags)
|
43: mStream.close();
|
49: ar.mStream.write(reinterpret_cast<char*>(&val), sizeof(T)); // NOLINT
|
56: ar.mStream.read(reinterpret_cast<char*>(&val), sizeof(T)); // NOLINT
|
| BUSseq:src/rngstream.h: [ ] |
|---|
8: class RngStream
|
12: RngStream (const char *name = "");
|
18: void ResetStartStream ();
|
| beachmat:inst/include/byteme/ZlibBufferReader.hpp: [ ] |
|---|
27: struct ZStream {
|
28: ZStream(int mode) {
|
58: ~ZStream() {
|
64: ZStream(const ZStream&) = delete;
|
65: ZStream(ZStream&&) = delete;
|
66: ZStream& operator=(const ZStream&) = delete;
|
67: ZStream& operator=(ZStream&&) = delete;
|
133: ZStream zstr;
|
| chromDraw:src/libBoard/include/board/Tools.h: [ ] |
|---|
57: class MessageStream {
|
74: MessageStream::MessageStream( std::ostream & out, const char * prefix )
|
60: inline MessageStream( std::ostream & out, const char * prefix );
|
63: inline MessageStream operator<<( const T & v );
|
70: extern MessageStream error;
|
71: extern MessageStream warning;
|
72: extern MessageStream notice;
|
81: MessageStream MessageStream::operator<<( const T & v )
|
87: return MessageStream( _out, 0 );
|
| Streamer:R/stream-methods.R: [ ] |
|---|
1: .Stream_set <- function(x, ..., verbose)
|
25: .Stream$new(inputPipe=inputPipe, verbose=verbose)
|
28: setMethod(Stream, "Producer",
|
32: .Stream_set(x, verbose=verbose)
|
34: do.call(Stream, c(rev(list(..., verbose=verbose)), list(x)))
|
37: setMethod(Stream, "Consumer", .Stream_set)
|
3: ## helper used to construct Streams
|
| Streamer:R/Streamer-class.R: [ ] |
|---|
1: .Streamer <- setRefClass("Streamer",
|
6: .Streamer$methods(
|
9: "initialize 'Streamer'"
|
20: "reset Streamer() -- noop"
|
21: if (verbose) msg("Streamer$reset()")
|
27: if (verbose) msg("Streamer$yield()")
|
33: if (verbose) msg("Streamer$status()")
|
41: setMethod(reset, "Streamer", function(x, ...) x$reset())
|
43: setMethod(yield, "Streamer", function(x, ...) x$yield())
|
45: setMethod(status,"Streamer", function(x, ...) x$status())
|
| msa:src/ClustalW/src/Makefile.in: [ ] |
|---|
635: InFileStream.o: ./fileInput/InFileStream.cpp
|
642: InFileStream.obj: ./fileInput/InFileStream.cpp
|
61: InFileStream.$(OBJEXT) ClustalFileParser.$(OBJEXT) \
|
266: ./fileInput/InFileStream.cpp \
|
269: ./fileInput/InFileStream.h \
|
488: @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/InFileStream.Po@am__quote@
|
636: ...(33 bytes skipped)...FS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT InFileStream.o -MD -MP -MF $(DEPDIR)/InFileStream.Tpo -c -o InFileStream.o `test -f './fileInput/InFileStream.cpp' || echo '$(srcdir)/'`./fileInput/InFileStream.cpp
|
637: @am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/InFileStream.Tpo $(DEPDIR)/InFileStream.Po
|
638: @AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='./fileInput/InFileStream.cpp' object='InFileStream.o' libtool=no @AMDEPBACKSLASH@
|
640: ...(36 bytes skipped)...) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o InFileStream.o `test -f './fileInput/InFileStream.cpp' || echo '$(srcdir)/'`./fileInput/InFileStream.cpp
|
643: ...(33 bytes skipped)...FS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT InFileStream.obj -MD -MP -MF $(DEPDIR)/InFileStream.Tpo -c -o InFileStream.obj `if test -f './fileInput/InFileStream.cpp'; then $(CYGPATH_W) './fileInput/InFileStream.cpp'; else $(CYGPATH_W) '$(srcdir)/./fileInput/InFileStream.cpp'; fi`
|
644: @am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/InFileStream.Tpo $(DEPDIR)/InFileStream.Po
|
645: @AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='./fileInput/InFileStream.cpp' object='InFileStream.obj' libtool=no @AMDEPBACKSLASH@
|
647: ...(36 bytes skipped)...) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o InFileStream.obj `if test -f './fileInput/InFileStream.cpp'; then $(CYGPATH_W) './fileInput/InFileStream.cpp'; else $(CYGPATH_W) '$(srcdir)/./fileInput/InFileStream.cpp'; fi`
|
| msa:src/ClustalW/windows/src/Makefile: [ ] |
|---|
635: InFileStream.o: ./fileInput/InFileStream.cpp
|
642: InFileStream.obj: ./fileInput/InFileStream.cpp
|
61: InFileStream.$(OBJEXT) ClustalFileParser.$(OBJEXT) \
|
266: ./fileInput/InFileStream.cpp \
|
269: ./fileInput/InFileStream.h \
|
488: # ./$(DEPDIR)/InFileStream.Po
|
636: ...(13 bytes skipped)...FS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT InFileStream.o -MD -MP -MF $(DEPDIR)/InFileStream.Tpo -c -o InFileStream.o `test -f './fileInput/InFileStream.cpp' || echo '$(srcdir)/'`./fileInput/InFileStream.cpp
|
637: # $(am__mv) $(DEPDIR)/InFileStream.Tpo $(DEPDIR)/InFileStream.Po
|
638: source='./fileInput/InFileStream.cpp' object='InFileStream.o' libtool=no \
|
640: ...(14 bytes skipped)...) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o InFileStream.o `test -f './fileInput/InFileStream.cpp' || echo '$(srcdir)/'`./fileInput/InFileStream.cpp
|
643: ...(13 bytes skipped)...FS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT InFileStream.obj -MD -MP -MF $(DEPDIR)/InFileStream.Tpo -c -o InFileStream.obj `if test -f './fileInput/InFileStream.cpp'; then $(CYGPATH_W) './fileInput/InFileStream.cpp'; else $(CYGPATH_W) '$(srcdir)/./fileInput/InFileStream.cpp'; fi`
|
644: # $(am__mv) $(DEPDIR)/InFileStream.Tpo $(DEPDIR)/InFileStream.Po
|
645: source='./fileInput/InFileStream.cpp' object='InFileStream.obj' libtool=no \
|
647: ...(14 bytes skipped)...) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o InFileStream.obj `if test -f './fileInput/InFileStream.cpp'; then $(CYGPATH_W) './fileInput/InFileStream.cpp'; else $(CYGPATH_W) '$(srcdir)/./fileInput/InFileStream.cpp'; fi`
|
| mzR:src/pwiz/analysis/spectrum_processing/SpectrumList_MZRefiner.cpp: [ ] |
|---|
1329: shared_ptr<ofstream> statStream_;
|
1394: statStream_ = openFilestreamIfWritable(statFilepath, fileExists);
|
1395: if (!statStream_) statStream_ = openFilestreamIfWritable(statFilepath.filename(), fileExists);
|
1396: if (!statStream_) statStream_ = openFilestreamIfWritable(bfs::temp_directory_path() / statFilepath.filename(), fileExists);
|
1397: if (!statStream_) throw runtime_error("[SpectrumList_MZRefiner::configureShift] unable to open a writable mzRefinem...(17 bytes skipped)...
|
1401: *statStream_ << "ThresholdScore\tThresholdValue\tExcluded (score)\tExcluded (mass error)"
|
2236: *statStream_ << statsRow.str();
|
2237: statStream_->close();
|
| Rarr:src/compression_tools/zstd/compress/zstd_compress_internal.h: [ ] |
|---|
50: typedef enum { zcss_init=0, zcss_load, zcss_flush } ZSTD_cStreamStage;
|
1421: /*! ZSTD_initCStream_internal() :
|
1426: size_t ZSTD_initCStream_internal(ZSTD_CStream* zcs,
|
456: ZSTD_cStreamStage streamStage;
|
| DEsubs:R/subpathwayAnalysis.R: [ ] |
|---|
72: subStreamCases <- apply(cases, 1, function(x) {paste0(x, collapse='.')})
|
7: supportedMethods <- c( subTypes[['subStreamCases']],
|
89: 'subStreamCases'=subStreamCases,
|
167: if ( method %in% subTypes[['subStreamCases']] )
|
| CNEr:src/ucsc/net.c: [ ] |
|---|
27: static int netStreamSocket()
|
95: if ((sd = netStreamSocket()) < 0)
|
230: if ((sd = netStreamSocket()) < 0)
|
| lpsymphony:src/SYMPHONY/Osi/src/OsiMsk/OsiMskSolverInterface.cpp: [ ] |
|---|
99: void MSKAPI OsiMskStreamFuncLog(MSKuserhandle_t handle, MSKCONST char* str) {
|
110: void MSKAPI OsiMskStreamFuncWarning(MSKuserhandle_t handle, MSKCONST char* str) {
|
121: void MSKAPI OsiMskStreamFuncError(MSKuserhandle_t handle, MSKCONST char* str) {
|
4575: MSK_linkfunctotaskstream(getMutableLpPtr(), MSK_STREAM_LOG, messageHandler(), OsiMskStreamFuncLog);
|
4576: MSK_linkfunctotaskstream(getMutableLpPtr(), MSK_STREAM_ERR, messageHandler(), OsiMskStreamFuncWarning);
|
4577: MSK_linkfunctotaskstream(getMutableLpPtr(), MSK_STREAM_WRN, messageHandler(), OsiMskStreamFuncError);
|
4941: err = MSK_linkfunctotaskstream(task_, MSK_STREAM_LOG, messageHandler(), OsiMskStreamFuncLog);
|
4944: err = MSK_linkfunctotaskstream(task_, MSK_STREAM_WRN, messageHandler(), OsiMskStreamFuncWarning);
|
4947: err = MSK_linkfunctotaskstream(task_, MSK_STREAM_ERR, messageHandler(), OsiMskStreamFuncError);
|
| ShortRead:R/AllClasses-Base.R: [ ] |
|---|
370: .FastqStreamer_g <- setRefClass("FastqStreamer",
|
387: setClass("FastqStreamerList", contains="FastqFileList",
|
388: prototype=prototype(elementType="FastqStreamer"))
|
| ShortRead:inst/unitTests/test_ShortReadQ.R: [ ] |
|---|
97: test_FastqStreamer <- function()
|
141: test_FastqStreamer_roundtrip <- function()
|
149: test_FastqStreamer_IRanges <- function()
|
101: f <- FastqStreamer(fl, n=50)
|
112: f <- FastqStreamer(fl, n=50)
|
118: f <- FastqStreamer(fl, n=500)
|
130: f <- FastqStreamer(fl, n=50, readerBlockSize=100)
|
145: s <- FastqStreamer(out)
|
155: f <- FastqStreamer(fl, rng)
|
164: f <- FastqStreamer(fl, rng)
|
172: f <- FastqStreamer(fl, rng)
|
179: f <- FastqStreamer(fl, rng, readerBlockSize=10000)
|
185: f <- FastqStreamer(fl, rng, readerBlockSize=10000)
|
192: checkException(FastqStreamer(fl, rng), silent=TRUE)
|
194: checkException(FastqStreamer(fl, rng), silent=TRUE)
|
| velociraptor:man/plotVelocityStream.Rd: [ ] |
|---|
76: Plot velocities embedded into low-dimensional space as a stream plot. Stream
|
2: % Please edit documentation in R/plotVelocityStream.R
|
3: \name{plotVelocityStream}
|
4: \alias{plotVelocityStream}
|
7: plotVelocityStream(
|
90: Streamlines are computed by simple integration with a forward Euler method,
|
108: plotVelocityStream(out, em)
|
109: plotVelocityStream(out, em, color.streamlines = TRUE)
|
| OncoSimulR:src/UnityOncoSimul/exprtk.h: [ ] |
|---|
39336: template <typename Stream, typename Ptr>
|
39339: Stream* stream = reinterpret_cast<Stream*>(p);
|
| CancerInSilico:src/Tests/catch.h: [ ] |
|---|
639: class Stream;
|
667: Stream createStream( std::string const& streamName );
|
488: // >> +StreamEndStop
|
490: // >> stuff +StreamEndStop
|
491: struct StreamEndStop {
|
497: T const& operator + ( T const& value, StreamEndStop ) {
|
1200: struct CopyableStream {
|
1201: CopyableStream() {}
|
1202: CopyableStream( CopyableStream const& other ) {
|
1205: CopyableStream& operator=( CopyableStream const& other ) {
|
1262: CopyableStream &stream()
|
1264: if(!m_usedStream)
|
1266: m_usedStream = true;
|
1272: static CopyableStream &m_stream()
|
1274: static CopyableStream s;
|
1281: bool m_usedStream;
|
2232: __catchResult << __VA_ARGS__ + ::Catch::StreamEndStop(); \
|
2240: __catchResult << log + ::Catch::StreamEndStop(); \
|
3832: class StreamBufBase : public std::streambuf {
|
3834: virtual ~StreamBufBase() CATCH_NOEXCEPT;
|
3849: struct IStream {
|
3850: virtual ~IStream() CATCH_NOEXCEPT;
|
3854: class FileStream : public IStream {
|
3857: FileStream( std::string const& filename );
|
3858: virtual ~FileStream() CATCH_NOEXCEPT;
|
3859: public: // IStream
|
3863: class CoutStream : public IStream {
|
3866: CoutStream();
|
3867: virtual ~CoutStream() CATCH_NOEXCEPT;
|
3869: public: // IStream
|
3873: class DebugOutStream : public IStream {
|
3874: CATCH_AUTO_PTR( StreamBufBase ) m_streamBuf;
|
3877: DebugOutStream();
|
3878: virtual ~DebugOutStream() CATCH_NOEXCEPT;
|
3880: public: // IStream
|
3966: m_stream( openStream() )
|
4013: IStream const* openStream() {
|
4015: return new CoutStream();
|
4018: return new DebugOutStream();
|
4023: return new FileStream( m_data.outputFilename );
|
4027: CATCH_AUTO_PTR( IStream const ) m_stream;
|
6537: class StreamRedirect {
|
6540: StreamRedirect( std::ostream& stream, std::string& targetString )
|
6548: ~StreamRedirect() {
|
6562: // order of writes and cannot use StreamRedirect on its own
|
6839: StreamRedirect coutRedir( Catch::cout(), redirectedCout );
|
7632: class StreamBufImpl : public StreamBufBase {
|
7637: StreamBufImpl() {
|
7641: ~StreamBufImpl() CATCH_NOEXCEPT {
|
7669: FileStream::FileStream( std::string const& filename ) {
|
7678: std::ostream& FileStream::stream() const {
|
7689: DebugOutStream::DebugOutStream()
|
7690: : m_streamBuf( new StreamBufImpl<OutputDebugWriter>() ),
|
7694: std::ostream& DebugOutStream::stream() const {
|
7700: CoutStream::CoutStream()
|
7704: std::ostream& CoutStream::stream() const {
|
9108: m_usedStream( false )
|
9231: if(m_usedStream)
|
9565: struct StreamingReporterBase : SharedImpl<IStreamingReporter> {
|
9567: StreamingReporterBase( ReporterConfig const& _config )
|
9578: virtual ~StreamingReporterBase() CATCH_OVERRIDE;
|
9794: struct TestEventListenerBase : StreamingReporterBase {
|
9796: : StreamingReporterBase( _config )
|
10132: class XmlReporter : public StreamingReporterBase {
|
10135: : StreamingReporterBase( _config ),
|
10158: public: // StreamingReporterBase
|
10161: StreamingReporterBase::noMatchingTestCases( s );
|
10165: StreamingReporterBase::testRunStarting( testInfo );
|
10175: StreamingReporterBase::testGroupStarting( groupInfo );
|
10181: StreamingReporterBase::testCaseStarting(testInfo);
|
10195: StreamingReporterBase::sectionStarting( sectionInfo );
|
10284: StreamingReporterBase::sectionEnded( sectionStats );
|
10299: StreamingReporterBase::testCaseEnded( testCaseStats );
|
10315: StreamingReporterBase::testGroupEnded( testGroupStats );
|
10325: StreamingReporterBase::testRunEnded( testRunStats );
|
10595: struct ConsoleReporter : StreamingReporterBase {
|
10597: : StreamingReporterBase( _config ),
|
10632: StreamingReporterBase::sectionStarting( _sectionInfo );
|
10650: StreamingReporterBase::sectionEnded( _sectionStats );
|
10654: StreamingReporterBase::testCaseEnded( _testCaseStats );
|
10664: StreamingReporterBase::testGroupEnded( _testGroupStats );
|
10670: StreamingReporterBase::testRunEnded( _testRunStats );
|
11025: struct CompactReporter : StreamingReporterBase {
|
11028: : StreamingReporterBase( _config )
|
11077: StreamingReporterBase::testRunEnded( _testRunStats );
|
11318: IStream::~IStream() CATCH_NOEXCEPT {}
|
11319: FileStream::~FileStream() CATCH_NOEXCEPT {}
|
11320: CoutStream::~CoutStream() CATCH_NOEXCEPT {}
|
11321: DebugOutStream::~DebugOutStream() CATCH_NOEXCEPT {}
|
11322: StreamBufBase::~StreamBufBase() CATCH_NOEXCEPT {}
|
11343: StreamingReporterBase::~StreamingReporterBase() {}
|
1542: TrueType& testStreamable( std::ostream& );
|
1543: FalseType testStreamable( FalseType );
|
1548: struct IsStreamInsertable {
|
1551: enum { value = sizeof( testStreamable(s << t) ) == sizeof( TrueType ) };
|
1555: class IsStreamInsertable {
|
1623: Detail::StringMakerBase<Detail::IsStreamInsertable<T>::value> {};
|
5737: struct IStreamingReporter : IShared {
|
5738: virtual ~IStreamingReporter();
|
5770: virtual IStreamingReporter* create( ReporterConfig const& config ) const = 0;
|
5779: virtual IStreamingReporter* create( std::string const& name, Ptr<IConfig const> const& config ) const = 0;
|
5784: Ptr<IStreamingReporter> addReporter( Ptr<IStreamingReporter> const& existingReporter, Ptr<IStreamingReporter> const& additionalReporter );
|
6592: explicit RunContext( Ptr<IConfig const> const& _config, Ptr<IStreamingReporter> const& reporter )
|
6904: Ptr<IStreamingReporter> m_reporter;
|
6959: Ptr<IStreamingReporter> createReporter( std::string const& reporterName, Ptr<Config> const& config ) {
|
6960: Ptr<IStreamingReporter> reporter = getRegistryHub().getReporterRegistry().create( reporterName, config.get() );...(1 bytes skipped)...
|
6973: Ptr<IStreamingReporter> makeReporter( Ptr<Config> const& config ) {
|
6978: Ptr<IStreamingReporter> reporter;
|
6985: Ptr<IStreamingReporter> addListeners( Ptr<IConfig const> const& config, Ptr<IStreamingReporter> reporters ) {
|
6998: Ptr<IStreamingReporter> reporter = makeReporter( config );
|
7414: virtual IStreamingReporter* create( std::string const& name, Ptr<IConfig const> const& config ) const CATCH_OVERRID...(4 bytes skipped)...
|
8470: class LegacyReporterAdapter : public SharedImpl<IStreamingReporter>
|
9399: class MultipleReporters : public SharedImpl<IStreamingReporter> {
|
9400: typedef std::vector<Ptr<IStreamingReporter> > Reporters;
|
9404: void add( Ptr<IStreamingReporter> const& reporter ) {
|
9408: public: // IStreamingReporter
|
9507: Ptr<IStreamingReporter> addReporter( Ptr<IStreamingReporter> const& existingReporter, Ptr<IStreamingReporter> const& additionalReporter ) {
|
9508: Ptr<IStreamingReporter> resultingReporter;
|
9514: resultingReporter = Ptr<IStreamingReporter>( multi );
|
9627: struct CumulativeReporterBase : SharedImpl<IStreamingReporter> {
|
9816: virtual IStreamingReporter* create( ReporterConfig const& config ) const {
|
9840: // to IStreamingReporter. The "legacy" interface, IReporter, is still supported via
|
9848: virtual IStreamingReporter* create( ReporterConfig const& config ) const {
|
9869: virtual IStreamingReporter* create( ReporterConfig const& config ) const {
|
11334: IStreamingReporter::~IStreamingReporter() {}
|
| rhdf5filters:src/vbz/third_party/gsl/gsl-lite.hpp: [ ] |
|---|
4781: // Stream output for string_span types
|
4786: template< class Stream >
|
4787: void write_padding( Stream & os, std::streamsize n )
|
4793: template< class Stream, class Span >
|
4794: Stream & write_to_stream( Stream & os, Span const & spn )
|
4796: typename Stream::sentry sentry( os );
|
| chopsticks:src/deflate.h: [ ] |
|---|
58: /* Stream status */
|