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// ==========================================================================
// SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2026, Knut Reinert, FU Berlin
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
// * Redistributions in binary form must reproduce the above copyright
// notice, this list of conditions and the following disclaimer in the
// documentation and/or other materials provided with the distribution.
// * Neither the name of Knut Reinert or the FU Berlin nor the names of
// its contributors may be used to endorse or promote products derived
// from this software without specific prior written permission.
//
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
// DAMAGE.
//
// ==========================================================================
// Author: David Weese <david.weese@fu-berlin.de>
// ==========================================================================
// TODO(esiragusa): tests
#ifndef SEQAN_STREAM_GUESS_FORMAT_
#define SEQAN_STREAM_GUESS_FORMAT_
namespace seqan2 {
// --------------------------------------------------------------------------
// Class FileExtensions
// --------------------------------------------------------------------------
template <typename TFormat, typename T>
struct FileExtensions;
// ============================================================================
// Functions
// ============================================================================
// --------------------------------------------------------------------------
// Function guessFormatFromStream()
// --------------------------------------------------------------------------
// Base case: we get here if the file format could not be determined.
template <typename TFileSeq>
inline bool guessFormatFromStream(TFileSeq &, TagSelector<> &)
{
return false;
}
// --------------------------------------------------------------------------
// Function guessFormatFromStream(TagSelector)
// --------------------------------------------------------------------------
template <typename TFileSeq, typename TTagList>
inline bool guessFormatFromStream(TFileSeq &seq, TagSelector<TTagList> &format)
{
typedef typename TTagList::Type TFormat;
if (value(format) == -1 || isEqual(format, TFormat()))
{
// if tagId is set to -1 (auto-detect) or the current format (TFormatTag) then test for TFormatTag format
if (guessFormatFromStream(seq, TFormat()))
{
assign(format, TFormat());
return true;
}
}
return guessFormatFromStream(seq, static_cast<typename TagSelector<TTagList>::Base &>(format));
}
// --------------------------------------------------------------------------
// Function guessFormatFromFilename()
// --------------------------------------------------------------------------
// Base case: we get here if the file format could not be determined.
template <typename TFilename>
inline bool guessFormatFromFilename(TFilename const &, TagSelector<>)
{
return false;
}
template <typename TFilename>
inline typename Prefix<TFilename const>::Type
getBasename(TFilename const & fname, TagSelector<> const &)
{
return prefix(fname, length(fname));
}
// --------------------------------------------------------------------------
// Function guessFormatFromFilename(TagSelector)
// --------------------------------------------------------------------------
template <typename TFilename, typename TTagList>
inline bool guessFormatFromFilename(TFilename const &fname, TagSelector<TTagList> &format)
{
typedef typename TTagList::Type TFormat;
if (value(format) == -1 || isEqual(format, TFormat()))
{
// if tagId is set to -1 (auto-detect) or the current format (TFormatTag) then test for TFormatTag format
if (guessFormatFromFilename(fname, TFormat()))
{
assign(format, TFormat());
return true;
}
}
return guessFormatFromFilename(fname, static_cast<typename TagSelector<TTagList>::Base &>(format));
}
template <typename TFilename, typename TTagList>
inline typename Prefix<TFilename const>::Type
getBasename(TFilename const & fname, TagSelector<TTagList> const &format)
{
typedef typename TTagList::Type TFormat;
if (isEqual(format, TFormat()))
return getBasename(fname, TFormat());
else
return getBasename(fname, static_cast<typename TagSelector<TTagList>::Base const &>(format));
}
// --------------------------------------------------------------------------
// Function guessFormatFromFilename(Tag)
// --------------------------------------------------------------------------
/*!
* @fn guessFormatFromFilename
* @headerfile <seqan/file.h>
* @brief Guesses a file format from a sequence file name.
*
* @signature bool guessFormatFromFilename(fileName, formatTag);
*
* @param[in] fileName A filename of a sequence file.
* @param[in] formatTag A file format tag.
*
* @return bool <tt>true</tt> if the format represented by <tt>formatTag</tt> was recognized in <tt>fileName</tt>.
*/
template <typename TFilename, typename TFormat_>
inline bool guessFormatFromFilename(TFilename const & fileName, Tag<TFormat_> /*formatTag*/)
{
typedef typename Value<TFilename>::Type TValue;
typedef ModifiedString<TFilename const, ModView<FunctorLowcase<TValue> > > TLowcase;
typedef Tag<TFormat_> TFormat;
TLowcase lowcaseFileName(fileName);
for (unsigned i = 0; i < sizeof(FileExtensions<TFormat>::VALUE) / sizeof(char*); ++i)
if (endsWith(lowcaseFileName, lowerString(FileExtensions<TFormat>::VALUE[i])))
return true;
return false;
}
template <typename TFilename, typename TFormat_>
inline typename Prefix<TFilename const>::Type
getBasename(TFilename const & fileName, Tag<TFormat_> const & /*formatTag*/)
{
typedef typename Value<TFilename>::Type TValue;
typedef ModifiedString<TFilename const, ModView<FunctorLowcase<TValue> > > TLowcase;
typedef Tag<TFormat_> TFormat;
TLowcase lowcaseFileName(fileName);
for (unsigned i = 0; i < sizeof(FileExtensions<TFormat>::VALUE) / sizeof(char*); ++i)
if (endsWith(lowcaseFileName, lowerString(FileExtensions<TFormat>::VALUE[i])))
return prefix(fileName, length(fileName) - length(FileExtensions<TFormat>::VALUE[i]));
return prefix(fileName, length(fileName));
}
// --------------------------------------------------------------------------
// Function _getFileExtensions()
// --------------------------------------------------------------------------
template <typename TStringSet, typename TFormat_>
inline void _getFileExtensions(TStringSet &stringSet, Tag<TFormat_> /*formatTag*/, bool primaryExtensionOnly = false)
{
typedef Tag<TFormat_> TFormat;
if (primaryExtensionOnly)
{
appendValue(stringSet, FileExtensions<TFormat>::VALUE[0]); // first is primary
}
else
{
for (unsigned i = 0; i < sizeof(FileExtensions<TFormat>::VALUE) / sizeof(char*); ++i)
appendValue(stringSet, FileExtensions<TFormat>::VALUE[i]);
}
}
template <typename TStringSet, typename TTag>
inline void _getFileExtensions(TStringSet &stringSet, TagList<TTag, void> const /*formatTag*/, bool primaryExtensionOnly = false)
{
_getFileExtensions(stringSet, TTag(), primaryExtensionOnly);
}
template <typename TStringSet, typename TTag, typename TSubList>
inline void _getFileExtensions(TStringSet &stringSet, TagList<TTag, TSubList> const /*formatTag*/, bool primaryExtensionOnly = false)
{
_getFileExtensions(stringSet, TTag(), primaryExtensionOnly);
_getFileExtensions(stringSet, TSubList(), primaryExtensionOnly);
}
template <typename TStringSet, typename TTagList>
inline void _getFileExtensions(TStringSet &stringSet, TagSelector<TTagList> const /*formatTag*/, bool primaryExtensionOnly = false)
{
_getFileExtensions(stringSet, TTagList(), primaryExtensionOnly);
}
} // namespace seqan2
#endif // #ifndef SEQAN_STREAM_GUESS_FORMAT_
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