1. mzR
  2. src
  3. random_access_gzFile.cpp
Browse code

Remove Ramp backend with dependencies

jorainer authored on 20/09/2021 12:19:56
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src/random_access_gzFile.cpp
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-// random_access_gzFile.cpp
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-// presents C-style calls based on an ifstream-derived C++ class
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-//
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-// like gzio.c from the zlib distro,
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-// but for dealing with reading >2GB files in win32, and efficient random access.
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-// Copyright (C) Insilicos LLC 2008, ALl Rights Reserved.
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-// For conditions of distribution and use, see copyright notice in zlib.h
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-//
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-// based on:
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-/* gzio.c -- IO on .gz files
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-* Copyright (C) 1995-2005 Jean-loup Gailly.
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-* For conditions of distribution and use, see copyright notice in zlib.h
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-*/
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-
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-// efficient random access stuff based on
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-/* zran.c -- example of zlib/gzip stream indexing and random access
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-* Copyright (C) 2005 Mark Adler
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-* For conditions of distribution and use, see copyright notice in zlib.h
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-Version 1.0  29 May 2005  Mark Adler */
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-
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-#include "random_access_gzFile.h"
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-#include "zlib.h"
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-
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-struct random_access_gzFile
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-{
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-    pwiz::util::random_access_compressed_ifstream *istrm;
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-};
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-
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-/* ===========================================================================
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-Opens a gzip (.gz) file for reading or writing. The mode parameter
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-is as in fopen ("rb" or "wb"). The file is given either by file descriptor
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-or path name (if fd == -1).
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-random_access_gzopen returns NULL if the file could not be opened or if there was
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-insufficient memory to allocate the (de)compression state; errno
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-can be checked to distinguish the two cases (if errno is zero, the
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-zlib error is Z_MEM_ERROR).
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-*/
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-random_access_gzFile *random_access_gzopen (const char *path)
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-{
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-    random_access_gzFile *ret = new random_access_gzFile;
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-    if (ret)
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-    {
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-        ret->istrm = new pwiz::util::random_access_compressed_ifstream(path);
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-        if (ret->istrm && !*(ret->istrm))
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-        {
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-            delete ret->istrm;
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-            delete ret;
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-            ret = NULL;
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-        }
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-    }
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-    return ret;
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-}
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-
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-/* ===========================================================================
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-Reads the given number of uncompressed bytes from the compressed file.
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-gzread returns the number of bytes actually read (0 for end of file).
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-*/
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-int random_access_gzread (random_access_gzFile *file,
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-                          char *buf,
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-                          unsigned len)
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-{
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-    file->istrm->clear(); // clear any stale failbit
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-    file->istrm->read((char *)buf,len);
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-    return file->istrm->gcount();
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-}
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-/* ===========================================================================
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-Reads one byte from the compressed file. gzgetc returns this byte
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-or -1 in case of end of file or error.
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-*/
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-int random_access_gzgetc(random_access_gzFile *file)
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-{
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-    char c;
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-    file->istrm->clear(); // clear any stale failbit
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-    file->istrm->read( &c, 1);
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-    return (file->istrm->gcount() == 1) ? (int)c : -1;
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-}
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-
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-/* ===========================================================================
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-Reads bytes from the compressed file until len-1 characters are
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-read, or a newline character is read and transferred to buf, or an
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-end-of-file condition is encountered.  The string is then terminated
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-with a null character.
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-gzgets returns buf, or Z_NULL in case of error.
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-*/
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-char * random_access_gzgets(random_access_gzFile *file, char *buf, int len)
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-{
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-    file->istrm->clear(); // clear any stale failbit
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-    file->istrm->getline(buf,len); // this does NOT retain the \n
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-    int got = file->istrm->gcount();
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-    if (got && (got < (len-1)) && !file->istrm->fail() && !file->istrm->eof())
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-    {
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-        // looks like a newline was read then discarded
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-        buf[(got-1)] = '\n';
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-        buf[got] = 0;
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-    }
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-    return (*buf?buf:NULL);
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-}
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-
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-/* ===========================================================================
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-Sets the starting position for the next gzread on the given
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-compressed file. The offset represents a number of bytes in the
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-gzseek returns the resulting offset location as measured in bytes from
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-the beginning of the uncompressed stream, or -1 in case of error.
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-NOTE - bpratt borrows zran code here for better performance
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-*/
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-random_access_gzFile_off_t random_access_gzseek (random_access_gzFile *file,
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-        random_access_gzFile_off_t offset,
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-        int whence)
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-{
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-    if (file == NULL)
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-    {
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-        return -1L;
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-    }
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-    file->istrm->clear(); // clear any stale error flags
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-    switch (whence)
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-    {
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-    case SEEK_SET:
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-        file->istrm->seekg(boost::iostreams::offset_to_position(offset));
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-        break;
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-    case SEEK_CUR:
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-        file->istrm->seekg(boost::iostreams::offset_to_position(offset),std::ios_base::cur);
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-        break;
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-    case SEEK_END:
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-        file->istrm->seekg(boost::iostreams::offset_to_position(offset),std::ios_base::end);
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-        break;
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-    }
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-    return file->istrm->tellg();
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-}
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-
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-/* ===========================================================================
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-Returns the starting position for the next gzread on the
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-given compressed file. This position represents a number of bytes in the
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-uncompressed data stream.
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-*/
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-random_access_gzFile_off_t random_access_gztell(random_access_gzFile *file)
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-{
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-    return file?(random_access_gzFile_off_t)(file->istrm->tellg()):-1;
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-}
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-
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-/* ===========================================================================
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-Returns 1 when EOF has previously been detected reading the given
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-input stream, otherwise zero.
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-*/
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-int random_access_gzeof (random_access_gzFile *s)
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-{
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-    return s?s->istrm->eof():0;
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-}
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-
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-/* ===========================================================================
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-Returns 1 if reading and doing so transparently, otherwise zero.
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-*/
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-int random_access_gzdirect(random_access_gzFile *file)
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-{
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-    if ((file == NULL) || (file->istrm == NULL))
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-    {
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-        return 0;
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-    }
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-    return !file->istrm->getCompressionType();
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-}
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-
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-/* ===========================================================================
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-Flushes all pending output if necessary, closes the compressed file
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-and deallocates all the (de)compression state.
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-*/
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-int random_access_gzclose (random_access_gzFile *file)
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-{
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-    if (file == NULL)
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-    {
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-        return Z_STREAM_ERROR;
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-    }
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-    delete file->istrm;
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-    delete file;
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-    return 0;
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-}
Browse code

Commit made by the Bioconductor Git-SVN bridge. Consists of 130 commits.

Commit information:

Commit id: 289dc240065888efcaa22ae75951e81f94fc800f

Fix package description after merge

Committed by: Steffen Neumann
Author Name: Steffen Neumann
Commit date: 2014-09-28 17:21:35 +0200
Author date: 2014-09-28 17:21:35 +0200

Commit id: 88248e8d6d86bb54dc260f0c55608dd1a949ade4

merged gsoc into master

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-09-27 08:49:45 +0100
Author date: 2014-09-27 08:49:45 +0100

Commit id: bb01e0fe0b4f04335925472a7c2b91bd22b57755

included KK's segfault patch and fixed unit test accordingly

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-09-27 08:44:50 +0100
Author date: 2014-09-27 08:44:50 +0100

Commit id: 708bd0b8ac4b2b5bae9a9b91588a260f2eeefb46

add message about pwiz backend in Bioc 3.1

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-09-25 01:20:52 +0100
Author date: 2014-09-25 01:20:52 +0100

Commit id: 4c1410ec3c8f153ad0a4b04722cad5a7d77cfd4c

restoring ramp as default backend

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-09-25 01:06:21 +0100
Author date: 2014-09-25 01:06:21 +0100

Commit id: c5d60529934813456555934bbeed29502100b41b

show pwiz method

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-09-21 21:09:38 +0100
Author date: 2014-09-21 21:09:38 +0100

Commit id: 20bfbfa1db25ec247f2313804d9b73c086a2d920

add close,mzRpwiz-method alias

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-09-21 21:04:48 +0100
Author date: 2014-09-21 21:04:48 +0100

Commit id: f80ecdc2a7f14c311b42ad279c62307a6e0aad30

test that close(pwiz) works

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-09-21 20:45:50 +0100
Author date: 2014-09-21 20:45:50 +0100

Commit id: d18dc8b0c7197c72b1bb2a70e7becfe983ced9a1

fixed signature for pwiz close method

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-09-21 20:44:41 +0100
Author date: 2014-09-21 20:44:41 +0100

Commit id: c0d7451e6b31068cde89f08ac5037a1509857cc5

fix codoc mismatch

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-09-21 19:02:00 +0100
Author date: 2014-09-21 19:02:00 +0100

Commit id: 14974a3d0890a7e2a1a7179aaa483e20a5700ef9

add close for pwiz backend to news

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-09-21 18:58:06 +0100
Author date: 2014-09-21 18:58:06 +0100

Commit id: c9d2bbb339c0ecdc9870dbd7a59bfbb94ef67f73

dummy close for pwiz backend

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-09-21 18:56:48 +0100
Author date: 2014-09-21 18:56:48 +0100

Commit id: 6d608b453328d6c751dc828d2586b016eb17b095

more close calls to remove for pwiz backend

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-09-21 18:52:55 +0100
Author date: 2014-09-21 18:52:55 +0100

Commit id: 5650801e07df64e2d74302ec98a31938bb62f11f

no isInitialised with pwiz

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-09-21 18:41:57 +0100
Author date: 2014-09-21 18:41:57 +0100

Commit id: 2a3d0eeb24673eb74c3ffa38fefb1883f9bee15d

no close with pwiz

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-09-21 17:46:38 +0100
Author date: 2014-09-21 17:46:38 +0100

Commit id: b3ae014569b6e46ccb6b396dfb9320dd7ba8fb16

bump version to avoid confusions

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-09-21 17:30:28 +0100
Author date: 2014-09-21 17:30:28 +0100

Commit id: a1bd596ffbeef73b4b505342f45742f9997e33d1

using pwiz as default raw data backend

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-09-21 17:29:02 +0100
Author date: 2014-09-21 17:29:02 +0100

Commit id: 51b4ea21d9cf034d54b0911bf281af3a937375de

Steffen's changes in v 1.11.11

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-09-20 16:21:14 +0100
Author date: 2014-09-20 16:21:14 +0100

Commit id: 81cde1ca48974585c9d6f51927087a922b13dd89

add new length to doc header

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-09-20 16:06:46 +0100
Author date: 2014-09-20 16:06:46 +0100

Commit id: 3fe883cb7ecad4867908fb907374a4df63b50a1f

show and length mzRident methods

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-09-20 15:56:26 +0100
Author date: 2014-09-20 15:56:26 +0100

Commit id: 3efb44e00fb94cdf0eb8207634218cbb47ab1b54

VignetteBuilder: knitr

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-08-27 01:03:36 +0100
Author date: 2014-08-27 01:03:36 +0100

Commit id: 73b0f902dfaa53f359318708f0606dc1f4677057

BiocStyle vig

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-08-26 23:59:29 +0100
Author date: 2014-08-26 23:59:29 +0100

Commit id: 185f281d07ed7b4a7f093eaf7b61271a88c85e20

update readme

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-08-26 23:20:02 +0100
Author date: 2014-08-26 23:20:02 +0100

Commit id: d5cc992e128594d331592b2bd57871fabf6737c9

update to build

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-08-17 22:41:17 +0100
Author date: 2014-08-17 22:41:17 +0100

Commit id: 27318416c94859102a061838a1a3f83d378414e3

bump to 1.99

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-08-17 22:12:44 +0100
Author date: 2014-08-17 22:12:44 +0100

Commit id: 13caefb4d4b469f0406ed96509ea4cebce8235b0

pulled from https://github.com/thirdwing/mzR

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-08-17 22:00:57 +0100
Author date: 2014-08-17 22:00:57 +0100

Commit id: 14822efb6c2238eda371718043bec9cc8fb27558

doc

Committed by: qkou
Author Name: qkou
Commit date: 2014-08-16 22:06:51 -0400
Author date: 2014-08-16 22:06:51 -0400

Commit id: 323424443efac769c436fb87128fad64a0358187

R_init_mzR.c

Committed by: qkou
Author Name: qkou
Commit date: 2014-08-10 00:46:14 -0400
Author date: 2014-08-10 00:46:14 -0400

Commit id: a91c0601e674efbb6949331a53ea9c6af53a4ba5

vignettes

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-08-06 21:03:23 -0400
Author date: 2014-08-06 21:03:23 -0400

Commit id: 4607e0a595f60a083d1eb90b804348ac5a8c1fb4

update with msdata

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-08-05 12:33:40 -0400
Author date: 2014-08-05 12:33:40 -0400

Commit id: cc09a790eda22b7d64226116ada89bad9089e0b2

modified: src/RcppPwiz.cpp

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-08-04 22:29:15 -0400
Author date: 2014-08-04 22:29:15 -0400

Commit id: fac511ee0f7841791bbf5380f2c948fd045b3adb

unit test against mzID

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-08-04 22:16:03 -0400
Author date: 2014-08-04 22:16:03 -0400

Commit id: 449952e31fe354b2589d8a723a4f8a842812ede6

enzymes() returns data.frame

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-08-03 16:29:59 -0400
Author date: 2014-08-03 16:29:59 -0400

Commit id: 874fba33e8029023d5e3bbd168dc998d51544c9d

writing support dropped

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-08-03 16:14:26 -0400
Author date: 2014-08-03 16:14:26 -0400

Commit id: 338f3e80dd8f98419555ab1a4aa443e14d089f24

modifications()

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-08-03 16:02:20 -0400
Author date: 2014-08-03 16:02:20 -0400

Commit id: 34ee62ee27e7b012b9ce2bd696d63e5f80185200

psms() update

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-08-03 15:41:36 -0400
Author date: 2014-08-03 15:41:36 -0400

Commit id: b8bdea9a1e2a7ab3410eea5c26566ef74e488d95

score()

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-08-03 14:14:53 -0400
Author date: 2014-08-03 14:14:53 -0400

Commit id: a42f1195b3f0b40c28aa2acfb782e517633206c9

psms()

Committed by: qkou
Author Name: qkou
Commit date: 2014-08-03 13:54:34 -0400
Author date: 2014-08-03 13:54:34 -0400

Commit id: 6c2a87019e3b328dbecc1a965d3e41e6539e0d90

para() update, numeric correction

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-08-02 23:57:41 -0400
Author date: 2014-08-02 23:57:41 -0400

Commit id: 119edf40600beb8e3b8e8006a0d955a887d06b1d

update para()

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-30 10:54:40 -0400
Author date: 2014-07-30 10:54:40 -0400

Commit id: 69ac718d0418f2ab3ba824a735975ae6c04aec00

update database()

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-30 10:38:42 -0400
Author date: 2014-07-30 10:38:42 -0400

Commit id: f7818556b2e1e3296a727eca6d2853a8b7a16b12

clean

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-29 21:35:59 -0400
Author date: 2014-07-29 21:35:59 -0400

Commit id: f67403a92b6beca4128c36b42367414463234253

database()

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-29 21:33:07 -0400
Author date: 2014-07-29 21:33:07 -0400

Commit id: 8b0255a9c7da6ccc6c7796f49f608b792bac0dfe

para()

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-29 20:33:14 -0400
Author date: 2014-07-29 20:33:14 -0400

Commit id: 183afed91ad6beb07fffb5cbe4673773619d938b

Rd

Committed by: qkou
Author Name: qkou
Commit date: 2014-07-29 00:36:40 -0400
Author date: 2014-07-29 00:36:40 -0400

Commit id: 73d380115e205eedc211869d6eace3564b3fc1cf

modified: vignettes/mzR.Rnw

Committed by: qkou
Author Name: qkou
Commit date: 2014-07-27 00:49:10 -0400
Author date: 2014-07-27 00:49:10 -0400

Commit id: 93214634ff41a9da84019320dfe6314cb7f94422

score

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-26 19:42:34 -0400
Author date: 2014-07-26 19:42:34 -0400

Commit id: cbdee47033cf10927b0dc33a02208c9ff9d89771

same header info

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-22 12:45:46 -0400
Author date: 2014-07-22 12:45:46 -0400

Commit id: 1e6ebe39851ecddedf01daa2c69fcd1f2dba906c

modified: NAMESPACE modified: R/AllGenerics.R modified: R/methods-mzRident.R modified: inst/unitTests/runit.backends.R modified: man/metadata.Rd modified: man/mzR-class.Rd

Committed by: qkou
Author Name: qkou
Commit date: 2014-07-18 00:40:10 -0400
Author date: 2014-07-18 00:40:10 -0400

Commit id: 0ed92085be5af56a78cdf0f1732a356c48d7a0f9

1.11.10

Committed by: qkou
Author Name: qkou
Commit date: 2014-07-17 21:31:27 -0400
Author date: 2014-07-17 21:31:27 -0400

Commit id: b6e254b2cca93778bfcdc549b75052d0b19bb2bb

fixed

Committed by: qkou
Author Name: qkou
Commit date: 2014-07-16 01:40:10 -0400
Author date: 2014-07-16 01:40:10 -0400

Commit id: 096aa2a6f5aebb5b99bc2e22a0fb023b1353b141

Merge pull request #3 from lgatto/master

fix backend checking
Committed by: Qiang Kou
Author Name: Qiang Kou
Commit date: 2014-07-15 21:20:15 -0400
Author date: 2014-07-15 21:20:15 -0400

Commit id: 6d8623c47c0b53e6805b9757c178c4639319a29d

fix backend checking

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-07-15 23:32:46 +0100
Author date: 2014-07-15 23:32:46 +0100

Commit id: 9060e3435a76ace952d915c3bb993e04ac93f12a

modified: src/RcppIdent.cpp

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-14 10:52:41 -0400
Author date: 2014-07-14 10:52:41 -0400

Commit id: 068ec46671400a2db3bfb10f001f30599b8495e8

modified: ChangeLog

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-12 17:29:16 -0400
Author date: 2014-07-12 17:29:16 -0400

Commit id: a8f42c9de00ed64470733eb5c63567e99d40e867

more info

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-12 14:57:33 -0400
Author date: 2014-07-12 14:57:33 -0400

Commit id: 4a88ad7c2c8ec911c44a45d16dedced9530505c2

modified: src/RcppIdent.cpp

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-12 14:13:29 -0400
Author date: 2014-07-12 14:13:29 -0400

Commit id: 935d44c5a52b895fe6ff663c062e006e4f25fab0

modified: src/RcppIdent.cpp

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-12 13:52:33 -0400
Author date: 2014-07-12 13:52:33 -0400

Commit id: f1c05ff287215f385938a116042d09bcea2aae88

modified: R/methods-mzRident.R modified: man/mzR-class.Rd modified: src/RcppIdent.cpp

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-12 11:20:58 -0400
Author date: 2014-07-12 11:20:58 -0400

Commit id: ca620536203355349c7267ad15a2ab6a2d248319

pass R CMD check

Committed by: qkou
Author Name: qkou
Commit date: 2014-07-12 00:36:08 -0400
Author date: 2014-07-12 00:36:08 -0400

Commit id: add1d1c98fe60955953036641671527337e89363

modified: R/methods-mzRident.R modified: man/metadata.Rd modified: man/mzR-class.Rd modified: src/Makevars modified: src/Makevars.win

Committed by: qkou
Author Name: qkou
Commit date: 2014-07-11 23:48:02 -0400
Author date: 2014-07-11 23:48:02 -0400

Commit id: 050051489df378a26aa97cccfefbf7ebe4102ef5

pepInfo()

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-11 18:10:10 -0400
Author date: 2014-07-11 18:10:10 -0400

Commit id: f093e39599ea2357c91816b7ff9de102f33e8e68

modified: NAMESPACE modified: R/AllGenerics.R modified: R/methods-mzRident.R modified: src/RcppIdent.cpp modified: src/RcppIdent.h modified: src/RcppIdentModule.cpp

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-11 15:12:28 -0400
Author date: 2014-07-11 15:12:28 -0400

Commit id: 3dc85db859c4d36040d3edb9ceb57074b0476f2d

modified: NAMESPACE modified: R/AllGenerics.R modified: R/methods-mzRident.R modified: src/RcppIdent.cpp modified: src/RcppIdent.h modified: src/RcppIdentModule.cpp

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-11 14:49:47 -0400
Author date: 2014-07-11 14:49:47 -0400

Commit id: ab1261cb3bfe1c02de5f7a053e6de5223686488d

modified: NAMESPACE modified: R/AllGenerics.R modified: R/methods-mzRident.R modified: src/RcppIdent.cpp modified: src/RcppIdent.h

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-11 13:47:12 -0400
Author date: 2014-07-11 13:47:12 -0400

Commit id: 01a4a2be981724624719580cd8e4f0866091f295

version

Committed by: qkou
Author Name: qkou
Commit date: 2014-07-11 01:48:50 -0400
Author date: 2014-07-11 01:48:50 -0400

Commit id: 5f49d13b736cebd65484a5993cdcce253853d4e7

remove mz5

Committed by: qkou
Author Name: qkou
Commit date: 2014-07-11 01:41:00 -0400
Author date: 2014-07-11 01:41:00 -0400

Commit id: fb3dbe2f1bf007cd033fd803426d4be2e362b3e2

Update H5public.h

Committed by: Qiang Kou
Author Name: Qiang Kou
Commit date: 2014-07-07 08:46:19 -0400
Author date: 2014-07-07 08:46:19 -0400

Commit id: 2446f08fdadd11c38a1cb54dddfe1e52b1a7bca9

modified: src/pwiz/utility/chemistry/Chemistry.hpp modified: src/pwiz/utility/misc/Std.hpp modified: src/pwiz/utility/misc/sha1calc.cpp

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-04 19:41:41 -0400
Author date: 2014-07-04 19:41:41 -0400

Commit id: b7c28c0db06b2dc9f8f5a7dcd218b7581ffd8121

compiled

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-04 18:05:54 -0400
Author date: 2014-07-04 18:05:54 -0400

Commit id: 1ffe5c024dafd51c2342f4d1dd930cb8d67d8041

modified: DESCRIPTION modified: src/Makevars.win

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-04 10:09:46 -0400
Author date: 2014-07-04 10:09:46 -0400

Commit id: 06e03716f187508072c33d3f0e9e79e135b22c05

modified: src/Makevars modified: src/hdf5/src/H5public.h

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-03 22:32:09 -0400
Author date: 2014-07-03 22:32:09 -0400

Commit id: 488ed2bd55151ece46c8cb5ac1df11f73b7c47a3

modified: src/Makevars

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-03 21:48:39 -0400
Author date: 2014-07-03 21:48:39 -0400

Commit id: 06f4d0a3832e47ad4a69e53d7b9b751dbb9f2770

modified: src/hdf5/src/H5public.h modified: src/pwiz/utility/misc/SHA1.cpp modified: src/pwiz/utility/misc/SHA1.h

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-03 21:47:50 -0400
Author date: 2014-07-03 21:47:50 -0400

Commit id: ff58989379a67f20ac8797ba437d430d8b5a2d62

modified: src/RcppIdent.cpp

Committed by: qkou
Author Name: qkou
Commit date: 2014-06-30 09:42:05 -0400
Author date: 2014-06-30 09:42:05 -0400

Commit id: 58dfa68675768c13950299c43229c1b0f1f1824b

modified: src/RcppIdent.cpp

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-28 21:17:18 -0400
Author date: 2014-06-28 21:17:18 -0400

Commit id: 6c228ae30c477e76add7e3ea805e386f1a0d862d

modified: src/RcppIdent.cpp

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-28 20:16:55 -0400
Author date: 2014-06-28 20:16:55 -0400

Commit id: 464d4e83a9e06732f7c3f1a0172a9cb2bbd53943

modified: src/RcppIdent.cpp

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-28 17:21:01 -0400
Author date: 2014-06-28 17:21:01 -0400

Commit id: ed36541a5fc99192f9df55222f2a2d9a6352ae33

idInfo

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-28 17:02:20 -0400
Author date: 2014-06-28 17:02:20 -0400

Commit id: 1ed6dceee93d2f57a66a94b15774212403d42200

modified: NAMESPACE modified: R/AllGenerics.R modified: R/methods-mzRident.R modified: src/RcppIdent.cpp modified: src/RcppIdent.h modified: src/RcppIdentModule.cpp

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-28 15:19:47 -0400
Author date: 2014-06-28 15:19:47 -0400

Commit id: 47b2a99876650729a329ebeebc174d9873919667

modified: DESCRIPTION

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-28 13:12:13 -0400
Author date: 2014-06-28 13:12:13 -0400

Commit id: ecad541c1e2d92f7be63433c5bf362d7b7f955b2

mzid supported done

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-28 13:04:27 -0400
Author date: 2014-06-28 13:04:27 -0400

Commit id: 684340ce7ee5b8fadbd4dfa839e3b0d7ba9b1c91

mzid file support

Committed by: kouqiang
Author Name: kouqiang
Commit date: 2014-06-28 01:02:19 -0400
Author date: 2014-06-28 01:02:19 -0400

Commit id: 7382b1321539a2838ae75da6f9c1ff9cbe98bb6b

mzid

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-27 23:38:36 -0400
Author date: 2014-06-27 23:38:36 -0400

Commit id: 5423b4c653762d90ce6d4bf7dcf1d591a2a9987f

modified: R/methods-mzRpwiz.R modified: R/zzz.R modified: src/RcppPwiz.cpp

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-27 23:27:36 -0400
Author date: 2014-06-27 23:27:36 -0400

Commit id: 9e20328e920207328eb68b9fa59c198d0d634a0f

Update AllGenerics.R

Committed by: Qiang Kou
Author Name: Qiang Kou
Commit date: 2014-06-27 22:52:37 -0400
Author date: 2014-06-27 22:52:37 -0400

Commit id: 19731b9e51b72027eb02ee6be5aa7343c5b12ace

modified: NAMESPACE modified: R/AllGenerics.R modified: R/methods-mzRpwiz.R modified: man/metadata.Rd modified: man/mzR-class.Rd modified: man/openMSfile.Rd modified: src/RcppPwiz.cpp modified: src/RcppPwiz.h modified: src/RcppPwizModule.cpp

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-27 22:03:31 -0400
Author date: 2014-06-27 22:03:31 -0400

Commit id: 94ac2b4ba810d0f820a9266be782667e375ede9a

modified: src/RcppPwiz.cpp

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-27 10:15:58 -0400
Author date: 2014-06-27 10:15:58 -0400

Commit id: 1259a8db48d4f7aa9ffe403dd5ee574bbfd238fb

modified: R/zzz.R modified: src/RcppPwiz.cpp

Committed by: kouqiang
Author Name: kouqiang
Commit date: 2014-06-27 00:44:31 -0400
Author date: 2014-06-27 00:44:31 -0400

Commit id: 9791bc574989cdefe279071dbf3a47232e1d8c86

identadata src

Committed by: kouqiang
Author Name: kouqiang
Commit date: 2014-06-27 00:22:35 -0400
Author date: 2014-06-27 00:22:35 -0400

Commit id: ede49e01e23c6586777d72fdd0dfef4bd40729f2

software info

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-26 22:20:57 -0400
Author date: 2014-06-26 22:20:57 -0400

Commit id: 431b2b42a93ff52a05d82801d1830ba81c72f18f

writeMSfile()

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-26 21:53:11 -0400
Author date: 2014-06-26 21:53:11 -0400

Commit id: 53a7a31378bd42adcf779cd1fbe9e2d052a507d7

deleted: src/hdf5/c++/src/H5 deleted: src/hdf5/c++/src/H5DataTy deleted: src/pwiz/data/common/BinaryIndexSt deleted: src/pwiz/data/common/ParamT deleted: src/pwiz/data/m deleted: src/pwiz/data/msdata/BinaryDataEnc deleted: src/pwiz/data/msdata/Chroma deleted: src/pwiz/data/msdata/MSNu deleted: src/pwiz/data/msdata/Seri deleted: src/pwiz/data/msdata/Serializer deleted: src/pwiz/data/msdata/Serializer_mz deleted: src/pwiz/data/msdata/Sp deleted: src/pwiz/data/msdata/Spec deleted: src/pwiz/data/msdata/mz5/Refer deleted: src/pwiz/utility/mis deleted: src/pwiz/utility/misc/IntegerS

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-26 19:04:22 -0400
Author date: 2014-06-26 19:04:22 -0400

Commit id: 359a40045162a49d94d68f0d60f2c6bb43970a2c

modified: NAMESPACE modified: R/AllGenerics.R modified: R/io.R modified: R/methods-mzRpwiz.R modified: src/RcppPwiz.cpp modified: src/RcppPwiz.h modified: src/RcppPwizModule.cpp new file: src/boost/filesystem/src/operations new file: src/hdf5/c++/src/H5 new file: src/hdf5/c++/src/H5DataTy new file: src/pwiz/data/common/BinaryIndexSt new file: src/pwiz/data/common/ParamT new file: src/pwiz/data/m new file: src/pwiz/data/msdata/BinaryDataEnc new file: src/pwiz/data/msdata/Chroma new file: src/pwiz/data/msdata/MSNu new file: src/pwiz/data/msdata/Seri new file: src/pwiz/data/msdata/Serializer new file: src/pwiz/data/msdata/Serializer_mz new file: src/pwiz/data/msdata/Sp new file: src/pwiz/data/msdata/Spec new file: src/pwiz/data/msdata/mz5/Refer new file: src/pwiz/utility/mis new file: src/pwiz/utility/misc/IntegerS

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-26 19:00:48 -0400
Author date: 2014-06-26 19:00:48 -0400

Commit id: 2ce04488e7a8e623a7dfd2b9408da0b9dd5059a4

modified: inst/unitTests/runit.backends.R modified: src/RcppPwiz.cpp modified: src/RcppPwiz.h

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-26 15:59:21 -0400
Author date: 2014-06-26 15:59:21 -0400

Commit id: 3103fd4fa92ddd63700c8b5940344db44e97be09

modified: src/RcppPwiz.cpp

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-26 13:33:44 -0400
Author date: 2014-06-26 13:33:44 -0400

Commit id: 329f7c1201360f5ebf5703d4837b25ae332e7a85

modified: man/metadata.Rd modified: man/mzR-class.Rd modified: src/RcppPwiz.cpp

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-26 11:35:13 -0400
Author date: 2014-06-26 11:35:13 -0400

Commit id: 0adf852da9ccec69103038ca96b30e8715d3c898

modified: inst/unitTests/runit.backends.R modified: src/RcppPwiz.cpp modified: src/RcppPwiz.h

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-26 11:20:03 -0400
Author date: 2014-06-26 11:20:03 -0400

Commit id: 219b5287ca5531577b4a6c80f403957ddef5ab94

modified: src/RcppPwiz.cpp

Committed by: kouqiang
Author Name: kouqiang
Commit date: 2014-06-26 01:33:43 -0400
Author date: 2014-06-26 01:33:43 -0400

Commit id: 14316dcb1c16ca922d9962ed9ecdaac324e1a151

deleted: src/R_init_mzR.c modified: src/RcppPwiz.cpp deleted: src/ramp_base64.cpp deleted: src/ramp_base64.h

Committed by: kouqiang
Author Name: kouqiang
Commit date: 2014-06-26 01:04:14 -0400
Author date: 2014-06-26 01:04:14 -0400

Commit id: efb21501a1b05b680b3d35aa124216f9977b5993

modified: src/RcppPwiz.cpp modified: src/RcppPwiz.h

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-25 23:44:07 -0400
Author date: 2014-06-25 23:44:07 -0400

Commit id: 4e9e1dec2879178547d681603aec46259a6a9978

mz5

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-25 22:54:26 -0400
Author date: 2014-06-25 22:54:26 -0400

Commit id: 0e7fc23b1ff7508fed6331c0e517a8dc6fa33a0c

mz5

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-25 22:28:24 -0400
Author date: 2014-06-25 22:28:24 -0400

Commit id: 9ad55a2cdd89791bf75ad23f0ee91b3fc70624ad

mz5

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-25 22:13:35 -0400
Author date: 2014-06-25 22:13:35 -0400

Commit id: c9fecd83ebf31f142c22030f4593fe5ac675323a

modified: R/methods-mzRpwiz.R modified: src/RcppPwiz.cpp

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-24 23:31:33 -0400
Author date: 2014-06-24 23:31:33 -0400

Commit id: 4edf517724950d6771fd19c979a460711baa5891

modified: R/methods-mzRpwiz.R modified: src/RcppPwiz.cpp modified: src/RcppPwiz.h

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-24 23:01:49 -0400
Author date: 2014-06-24 23:01:49 -0400

Commit id: 22ca998b6b6d3a7496f293f44909436a5b7d8ad0

modified: src/RcppPwiz.cpp modified: src/RcppPwiz.h

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-24 21:31:58 -0400
Author date: 2014-06-24 21:31:58 -0400

Commit id: 6beb4ce5c49cafa644766e23453ed6d10bb89c34

modified: man/metadata.Rd modified: man/mzR-class.Rd

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-22 12:02:07 -0400
Author date: 2014-06-22 12:02:07 -0400

Commit id: dc5e65d93bb67d1b4a1488b90099946e22eed13c

deleted: .travis.yml

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-22 11:26:02 -0400
Author date: 2014-06-22 11:26:02 -0400

Commit id: be53359804d6c7416c715c3eb259fb931c6c117a

modified: .travis.yml modified: src/Makevars.win

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-21 21:33:37 -0400
Author date: 2014-06-21 21:33:37 -0400

Commit id: 1afd9887dac232f3e72fe9d20d44a72b42e28461

deleted: .Rinstignore

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-21 21:27:46 -0400
Author date: 2014-06-21 21:27:46 -0400

Commit id: bd4c954bd246787137eb0d961a91bb80b774cb6a

new file: .Rbuildignore new file: .travis.yml

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-21 21:25:47 -0400
Author date: 2014-06-21 21:25:47 -0400

Commit id: 3bc8fcca8002a62458a2b2dd1c6b7cf6a8cfab9f

fixed error on windows and snow leopard

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-21 21:18:50 -0400
Author date: 2014-06-21 21:18:50 -0400

Commit id: ed9c622443eb992cf3322d687312e3f56bf8be72

Update Makevars.win

Committed by: Qiang Kou
Author Name: Qiang Kou
Commit date: 2014-06-15 00:55:16 +0800
Author date: 2014-06-15 00:55:16 +0800

Commit id: bf8c7bd931cd93b5db6d84c9c1bf323ea7702e74

new file: src/boost/signals/connection.hpp new file: src/boost/signals/detail/config.hpp new file: src/boost/signals/detail/gen_signal_N.pl new file: src/boost/signals/detail/named_slot_map.hpp new file: src/boost/signals/detail/signal_base.hpp new file: src/boost/signals/detail/signals_common.hpp new file: src/boost/signals/detail/slot_call_iterator.hpp new file: src/boost/signals/signal0.hpp new file: src/boost/signals/signal1.hpp new file: src/boost/signals/signal10.hpp new file: src/boost/signals/signal2.hpp new file: src/boost/signals/signal3.hpp new file: src/boost/signals/signal4.hpp new file: src/boost/signals/signal5.hpp new file: src/boost/signals/signal6.hpp new file: src/boost/signals/signal7.hpp new file: src/boost/signals/signal8.hpp new file: src/boost/signals/signal9.hpp new file: src/boost/signals/signal_template.hpp new file: src/boost/signals/slot.hpp new file: src/boost/signals/trackable.hpp

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-14 12:52:52 -0400
Author date: 2014-06-14 12:52:52 -0400

Commit id: 5ac3655c7e81f429859eb6b509208f8ec785e1f9

modified: src/Makevars.win

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-07 11:42:14 -0400
Author date: 2014-06-07 11:42:14 -0400

Commit id: f9f42e3d83adbaf98a201e50866821bc0e43598a

modified: ChangeLog modified: src/RcppPwiz.cpp modified: src/hdf5/src/H5FDmulti.c

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-07 11:24:01 -0400
Author date: 2014-06-07 11:24:01 -0400

Commit id: d8d6f92e46efa93f8234e542b1c4f8f98cee59e5

modified: R/zzz.R.in

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-06 17:28:36 -0400
Author date: 2014-06-06 17:28:36 -0400

Commit id: e64a8bb7bb7988047466848e5b449038ae9460b3

modified: R/zzz.R modified: src/Makevars

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-06 16:40:29 -0400
Author date: 2014-06-06 16:40:29 -0400

Commit id: 0a44cc02ea9b5417ac51f60632fc1b6100c6d160

modified: src/Makevars

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-06 16:01:08 -0400
Author date: 2014-06-06 16:01:08 -0400

Commit id: 4d19d457031e0ae9af343a44774f5deebae01cc8

modified: src/RcppPwiz.cpp modified: src/RcppPwiz.h

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-06 14:16:37 -0400
Author date: 2014-06-06 14:16:37 -0400

Commit id: effcb581a573e13b7b7cc9b459ef2dec4885b4be

modified: src/RcppPwiz.cpp

Committed by: kouqiang
Author Name: kouqiang
Commit date: 2014-06-06 04:33:43 -0400
Author date: 2014-06-06 04:33:43 -0400

Commit id: 028f6748d4cf81d47569edcd67fe25064b084e60

modified: NAMESPACE modified: R/AllGenerics.R modified: R/methods-mzRpwiz.R modified: src/RcppPwiz.cpp

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-04 23:21:43 -0400
Author date: 2014-06-04 23:21:43 -0400

Commit id: d95b557d2c637630ca784889cd0ef1f56b8423d5

Update methods-mzRpwiz.R

Committed by: Qiang Kou
Author Name: Qiang Kou
Commit date: 2014-06-04 21:51:47 -0400
Author date: 2014-06-04 21:51:47 -0400

Commit id: aad52653c2ceb33655364d5a39c0559225746cfb

Update RcppPwizModule.cpp

Committed by: Qiang Kou
Author Name: Qiang Kou
Commit date: 2014-06-04 21:50:32 -0400
Author date: 2014-06-04 21:50:32 -0400

Commit id: 4fda90cc08feb731aeb65c6015a033fbe46c372e

Update RcppPwiz.cpp

Committed by: Qiang Kou
Author Name: Qiang Kou
Commit date: 2014-06-04 21:48:06 -0400
Author date: 2014-06-04 21:48:06 -0400

Commit id: 660d2e984fabdd20997ff8b648d361c7d9aae711

modified: src/RcppPwiz.cpp modified: src/RcppPwiz.h

Committed by: qkou
Author Name: qkou
Commit date: 2014-06-02 13:07:57 -0400
Author date: 2014-06-02 13:07:57 -0400

Commit id: ec6bbdf496a57f2f39b2e4c3bbada75a060e5bbe

modified: src/boost_aux/boost/utility/singleton.hpp

Committed by: qkou
Author Name: qkou
Commit date: 2014-06-02 09:21:07 -0400
Author date: 2014-06-02 09:21:07 -0400

Commit id: a093954cb779467026288c7f51cca083e0a20661

modified: src/pwiz/data/msdata/ramp/ramp.cpp

Committed by: qkou
Author Name: qkou
Commit date: 2014-05-29 07:36:21 -0400
Author date: 2014-05-29 07:36:21 -0400

Commit id: 4510a1cda50ee8f1f43b667297918dcffed45af2

modified: src/Makevars modified: src/cramp.h modified: src/pwiz/data/msdata/ramp/ramp.cpp deleted: src/ramp.cpp deleted: src/ramp.h modified: src/rampR.cpp deleted: src/ramp_base64.cpp deleted: src/ramp_base64.h

Committed by: qkou
Author Name: qkou
Commit date: 2014-05-28 20:17:42 -0400
Author date: 2014-05-28 20:17:42 -0400


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mzR@94635 bc3139a8-67e5-0310-9ffc-ced21a209358

s.neumann authored on 28/09/2014 18:06:01
Showing1 changed files
src/random_access_gzFile.cpp
History View file @84a4b1664f
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@@ -21,8 +21,9 @@ Version 1.0  29 May 2005  Mark Adler */
21 21 
 #include "random_access_gzFile.h"
22 22 
 #include "zlib.h"
23 23
24 
-struct random_access_gzFile {
25 
-	pwiz::util::random_access_compressed_ifstream *istrm;
24 
+struct random_access_gzFile
25 
+{
26 
+    pwiz::util::random_access_compressed_ifstream *istrm;
26 27 
 };
27 28
28 29 
 /* ===========================================================================
... ... 
@@ -36,16 +37,18 @@ zlib error is Z_MEM_ERROR).
36 37 
 */
37 38 
 random_access_gzFile *random_access_gzopen (const char *path)
38 39 
 {
39 
-	random_access_gzFile *ret = new random_access_gzFile;
40 
-	if (ret) {
41 
-		ret->istrm = new pwiz::util::random_access_compressed_ifstream(path);
42 
-		if (ret->istrm && !*(ret->istrm)) {
43 
-			delete ret->istrm;
44 
-			delete ret;
45 
-			ret = NULL;
46 
-		}
47 
-	}
48 
-	return ret;
40 
+    random_access_gzFile *ret = new random_access_gzFile;
41 
+    if (ret)
42 
+    {
43 
+        ret->istrm = new pwiz::util::random_access_compressed_ifstream(path);
44 
+        if (ret->istrm && !*(ret->istrm))
45 
+        {
46 
+            delete ret->istrm;
47 
+            delete ret;
48 
+            ret = NULL;
49 
+        }
50 
+    }
51 
+    return ret;
49 52 
 }
50 53
51 54 
 /* ===========================================================================
... ... 
@@ -53,12 +56,12 @@ Reads the given number of uncompressed bytes from the compressed file.
53 56 
 gzread returns the number of bytes actually read (0 for end of file).
54 57 
 */
55 58 
 int random_access_gzread (random_access_gzFile *file,
56 
-				 char *buf,
57 
-				 unsigned len)
59 
+                          char *buf,
60 
+                          unsigned len)
58 61 
 {
59 
-	file->istrm->clear(); // clear any stale failbit
60 
-	file->istrm->read((char *)buf,len);
61 
-	return file->istrm->gcount();
62 
+    file->istrm->clear(); // clear any stale failbit
63 
+    file->istrm->read((char *)buf,len);
64 
+    return file->istrm->gcount();
62 65 
 }
63 66 
 /* ===========================================================================
64 67 
 Reads one byte from the compressed file. gzgetc returns this byte
... ... 
@@ -66,10 +69,10 @@ or -1 in case of end of file or error.
66 69 
 */
67 70 
 int random_access_gzgetc(random_access_gzFile *file)
68 71 
 {
69 
-	char c;
70 
-	file->istrm->clear(); // clear any stale failbit
71 
-	file->istrm->read( &c, 1);
72 
-	return (file->istrm->gcount() == 1) ? (int)c : -1;
72 
+    char c;
73 
+    file->istrm->clear(); // clear any stale failbit
74 
+    file->istrm->read( &c, 1);
75 
+    return (file->istrm->gcount() == 1) ? (int)c : -1;
73 76 
 }
74 77
75 78 
 /* ===========================================================================
... ... 
@@ -79,16 +82,18 @@ end-of-file condition is encountered.  The string is then terminated
79 82 
 with a null character.
80 83 
 gzgets returns buf, or Z_NULL in case of error.
81 84 
 */
82 
-char * random_access_gzgets(random_access_gzFile *file, char *buf, int len) {
83 
-	file->istrm->clear(); // clear any stale failbit
84 
-	file->istrm->getline(buf,len); // this does NOT retain the \n
85 
-	int got = file->istrm->gcount();
86 
-	if (got && (got < (len-1)) && !file->istrm->fail() && !file->istrm->eof()) {
87 
-		// looks like a newline was read then discarded
88 
-		buf[(got-1)] = '\n';
89 
-		buf[got] = 0;
90 
-	}
91 
-	return (*buf?buf:NULL);
85 
+char * random_access_gzgets(random_access_gzFile *file, char *buf, int len)
86 
+{
87 
+    file->istrm->clear(); // clear any stale failbit
88 
+    file->istrm->getline(buf,len); // this does NOT retain the \n
89 
+    int got = file->istrm->gcount();
90 
+    if (got && (got < (len-1)) && !file->istrm->fail() && !file->istrm->eof())
91 
+    {
92 
+        // looks like a newline was read then discarded
93 
+        buf[(got-1)] = '\n';
94 
+        buf[got] = 0;
95 
+    }
96 
+    return (*buf?buf:NULL);
92 97 
 }
93 98
94 99 
 /* ===========================================================================
... ... 
@@ -99,25 +104,27 @@ the beginning of the uncompressed stream, or -1 in case of error.
99 104 
 NOTE - bpratt borrows zran code here for better performance
100 105 
 */
101 106 
 random_access_gzFile_off_t random_access_gzseek (random_access_gzFile *file,
102 
-							   random_access_gzFile_off_t offset,
103 
-							   int whence)
107 
+        random_access_gzFile_off_t offset,
108 
+        int whence)
104 109 
 {
105 
-	if (file == NULL) {
106 
-			return -1L;
107 
-	}
108 
-	file->istrm->clear(); // clear any stale error flags
109 
-	switch (whence) {
110 
-		case SEEK_SET:
111 
-			file->istrm->seekg(boost::iostreams::offset_to_position(offset));
112 
-			break;
113 
-		case SEEK_CUR:
114 
-			file->istrm->seekg(boost::iostreams::offset_to_position(offset),std::ios_base::cur);
115 
-			break;
116 
-		case SEEK_END:
117 
-			file->istrm->seekg(boost::iostreams::offset_to_position(offset),std::ios_base::end);
118 
-			break;
119 
-	}
120 
-	return file->istrm->tellg();
110 
+    if (file == NULL)
111 
+    {
112 
+        return -1L;
113 
+    }
114 
+    file->istrm->clear(); // clear any stale error flags
115 
+    switch (whence)
116 
+    {
117 
+    case SEEK_SET:
118 
+        file->istrm->seekg(boost::iostreams::offset_to_position(offset));
119 
+        break;
120 
+    case SEEK_CUR:
121 
+        file->istrm->seekg(boost::iostreams::offset_to_position(offset),std::ios_base::cur);
122 
+        break;
123 
+    case SEEK_END:
124 
+        file->istrm->seekg(boost::iostreams::offset_to_position(offset),std::ios_base::end);
125 
+        break;
126 
+    }
127 
+    return file->istrm->tellg();
121 128 
 }
122 129
123 130 
 /* ===========================================================================
... ... 
@@ -127,7 +134,7 @@ uncompressed data stream.
127 134 
 */
128 135 
 random_access_gzFile_off_t random_access_gztell(random_access_gzFile *file)
129 136 
 {
130 
-	return file?(random_access_gzFile_off_t)(file->istrm->tellg()):-1;
137 
+    return file?(random_access_gzFile_off_t)(file->istrm->tellg()):-1;
131 138 
 }
132 139
133 140 
 /* ===========================================================================
... ... 
@@ -136,7 +143,7 @@ input stream, otherwise zero.
136 143 
 */
137 144 
 int random_access_gzeof (random_access_gzFile *s)
138 145 
 {
139 
-	return s?s->istrm->eof():0;
146 
+    return s?s->istrm->eof():0;
140 147 
 }
141 148
142 149 
 /* ===========================================================================
... ... 
@@ -144,10 +151,11 @@ Returns 1 if reading and doing so transparently, otherwise zero.
144 151 
 */
145 152 
 int random_access_gzdirect(random_access_gzFile *file)
146 153 
 {
147 
-	if ((file == NULL) || (file->istrm == NULL)) {
148 
-		return 0;
149 
-	}
150 
-	return !file->istrm->getCompressionType();
154 
+    if ((file == NULL) || (file->istrm == NULL))
155 
+    {
156 
+        return 0;
157 
+    }
158 
+    return !file->istrm->getCompressionType();
151 159 
 }
152 160
153 161 
 /* ===========================================================================
... ... 
@@ -156,10 +164,11 @@ and deallocates all the (de)compression state.
156 164 
 */
157 165 
 int random_access_gzclose (random_access_gzFile *file)
158 166 
 {
159 
-	if (file == NULL) {
160 
-		return Z_STREAM_ERROR;
161 
-	}
162 
-	delete file->istrm;
163 
-	delete file;
164 
-	return 0;
167 
+    if (file == NULL)
168 
+    {
169 
+        return Z_STREAM_ERROR;
170 
+    }
171 
+    delete file->istrm;
172 
+    delete file;
173 
+    return 0;
165 174 
 }
Browse code

Added the mzR package to the repository.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mzR@57456 bc3139a8-67e5-0310-9ffc-ced21a209358

c.wong authored on 15/08/2011 19:53:29
Showing1 changed files
src/random_access_gzFile.cpp
History View file @bcff5d52a8
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,165 @@
1 
+// random_access_gzFile.cpp
2 
+// presents C-style calls based on an ifstream-derived C++ class
3 
+//
4 
+// like gzio.c from the zlib distro,
5 
+// but for dealing with reading >2GB files in win32, and efficient random access.
6 
+// Copyright (C) Insilicos LLC 2008, ALl Rights Reserved.
7 
+// For conditions of distribution and use, see copyright notice in zlib.h
8 
+//
9 
+// based on:
10 
+/* gzio.c -- IO on .gz files
11 
+* Copyright (C) 1995-2005 Jean-loup Gailly.
12 
+* For conditions of distribution and use, see copyright notice in zlib.h
13 
+*/
14 
+
15 
+// efficient random access stuff based on
16 
+/* zran.c -- example of zlib/gzip stream indexing and random access
17 
+* Copyright (C) 2005 Mark Adler
18 
+* For conditions of distribution and use, see copyright notice in zlib.h
19 
+Version 1.0  29 May 2005  Mark Adler */
20 
+
21 
+#include "random_access_gzFile.h"
22 
+#include "zlib.h"
23 
+
24 
+struct random_access_gzFile {
25 
+	pwiz::util::random_access_compressed_ifstream *istrm;
26 
+};
27 
+
28 
+/* ===========================================================================
29 
+Opens a gzip (.gz) file for reading or writing. The mode parameter
30 
+is as in fopen ("rb" or "wb"). The file is given either by file descriptor
31 
+or path name (if fd == -1).
32 
+random_access_gzopen returns NULL if the file could not be opened or if there was
33 
+insufficient memory to allocate the (de)compression state; errno
34 
+can be checked to distinguish the two cases (if errno is zero, the
35 
+zlib error is Z_MEM_ERROR).
36 
+*/
37 
+random_access_gzFile *random_access_gzopen (const char *path)
38 
+{
39 
+	random_access_gzFile *ret = new random_access_gzFile;
40 
+	if (ret) {
41 
+		ret->istrm = new pwiz::util::random_access_compressed_ifstream(path);
42 
+		if (ret->istrm && !*(ret->istrm)) {
43 
+			delete ret->istrm;
44 
+			delete ret;
45 
+			ret = NULL;
46 
+		}
47 
+	}
48 
+	return ret;
49 
+}
50 
+
51 
+/* ===========================================================================
52 
+Reads the given number of uncompressed bytes from the compressed file.
53 
+gzread returns the number of bytes actually read (0 for end of file).
54 
+*/
55 
+int random_access_gzread (random_access_gzFile *file,
56 
+				 char *buf,
57 
+				 unsigned len)
58 
+{
59 
+	file->istrm->clear(); // clear any stale failbit
60 
+	file->istrm->read((char *)buf,len);
61 
+	return file->istrm->gcount();
62 
+}
63 
+/* ===========================================================================
64 
+Reads one byte from the compressed file. gzgetc returns this byte
65 
+or -1 in case of end of file or error.
66 
+*/
67 
+int random_access_gzgetc(random_access_gzFile *file)
68 
+{
69 
+	char c;
70 
+	file->istrm->clear(); // clear any stale failbit
71 
+	file->istrm->read( &c, 1);
72 
+	return (file->istrm->gcount() == 1) ? (int)c : -1;
73 
+}
74 
+
75 
+/* ===========================================================================
76 
+Reads bytes from the compressed file until len-1 characters are
77 
+read, or a newline character is read and transferred to buf, or an
78 
+end-of-file condition is encountered.  The string is then terminated
79 
+with a null character.
80 
+gzgets returns buf, or Z_NULL in case of error.
81 
+*/
82 
+char * random_access_gzgets(random_access_gzFile *file, char *buf, int len) {
83 
+	file->istrm->clear(); // clear any stale failbit
84 
+	file->istrm->getline(buf,len); // this does NOT retain the \n
85 
+	int got = file->istrm->gcount();
86 
+	if (got && (got < (len-1)) && !file->istrm->fail() && !file->istrm->eof()) {
87 
+		// looks like a newline was read then discarded
88 
+		buf[(got-1)] = '\n';
89 
+		buf[got] = 0;
90 
+	}
91 
+	return (*buf?buf:NULL);
92 
+}
93 
+
94 
+/* ===========================================================================
95 
+Sets the starting position for the next gzread on the given
96 
+compressed file. The offset represents a number of bytes in the
97 
+gzseek returns the resulting offset location as measured in bytes from
98 
+the beginning of the uncompressed stream, or -1 in case of error.
99 
+NOTE - bpratt borrows zran code here for better performance
100 
+*/
101 
+random_access_gzFile_off_t random_access_gzseek (random_access_gzFile *file,
102 
+							   random_access_gzFile_off_t offset,
103 
+							   int whence)
104 
+{
105 
+	if (file == NULL) {
106 
+			return -1L;
107 
+	}
108 
+	file->istrm->clear(); // clear any stale error flags
109 
+	switch (whence) {
110 
+		case SEEK_SET:
111 
+			file->istrm->seekg(boost::iostreams::offset_to_position(offset));
112 
+			break;
113 
+		case SEEK_CUR:
114 
+			file->istrm->seekg(boost::iostreams::offset_to_position(offset),std::ios_base::cur);
115 
+			break;
116 
+		case SEEK_END:
117 
+			file->istrm->seekg(boost::iostreams::offset_to_position(offset),std::ios_base::end);
118 
+			break;
119 
+	}
120 
+	return file->istrm->tellg();
121 
+}
122 
+
123 
+/* ===========================================================================
124 
+Returns the starting position for the next gzread on the
125 
+given compressed file. This position represents a number of bytes in the
126 
+uncompressed data stream.
127 
+*/
128 
+random_access_gzFile_off_t random_access_gztell(random_access_gzFile *file)
129 
+{
130 
+	return file?(random_access_gzFile_off_t)(file->istrm->tellg()):-1;
131 
+}
132 
+
133 
+/* ===========================================================================
134 
+Returns 1 when EOF has previously been detected reading the given
135 
+input stream, otherwise zero.
136 
+*/
137 
+int random_access_gzeof (random_access_gzFile *s)
138 
+{
139 
+	return s?s->istrm->eof():0;
140 
+}
141 
+
142 
+/* ===========================================================================
143 
+Returns 1 if reading and doing so transparently, otherwise zero.
144 
+*/
145 
+int random_access_gzdirect(random_access_gzFile *file)
146 
+{
147 
+	if ((file == NULL) || (file->istrm == NULL)) {
148 
+		return 0;
149 
+	}
150 
+	return !file->istrm->getCompressionType();
151 
+}
152 
+
153 
+/* ===========================================================================
154 
+Flushes all pending output if necessary, closes the compressed file
155 
+and deallocates all the (de)compression state.
156 
+*/
157 
+int random_access_gzclose (random_access_gzFile *file)
158 
+{
159 
+	if (file == NULL) {
160 
+		return Z_STREAM_ERROR;
161 
+	}
162 
+	delete file->istrm;
163 
+	delete file;
164 
+	return 0;
165 
+}