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// --------------------------------------------------------------------------
// OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2013.
//
// This software is released under a three-clause BSD license:
// * 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 any author or any participating institution
// may be used to endorse or promote products derived from this software
// without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
// --------------------------------------------------------------------------
// 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 ANY OF THE AUTHORS OR THE CONTRIBUTING
// INSTITUTIONS 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.
//
// --------------------------------------------------------------------------
// $Maintainer: Clemens Groepl,Andreas Bertsch$
// $Authors: $
// --------------------------------------------------------------------------
#include <OpenMS/DATASTRUCTURES/BigString.h>
#include <OpenMS/CONCEPT/Exception.h>
#include <iostream>
namespace OpenMS
{
typedef std::pair<String, String> FASTAEntry;
BigString::BigString() :
big_string_("$"),
separator_('$'),
count_(1),
len_(1)
{
sep_indices_.push_back(0);
FASTA_header_.push_back("");
}
BigString::BigString(const BigString & bs) :
big_string_(bs.big_string_),
separator_(bs.separator_),
count_(bs.count_),
len_(bs.len_),
sep_indices_(bs.sep_indices_),
FASTA_header_(bs.FASTA_header_)
{
}
BigString::~BigString()
{
}
void BigString::add(FASTAEntry const & new_entry)
{
big_string_ += new_entry.second;
big_string_ += separator_;
++count_;
len_ += new_entry.second.length() + 1;
sep_indices_.push_back(len_ - 1);
FASTA_header_.push_back(new_entry.first);
}
void BigString::setSeparator(const char sep)
{
separator_ = sep;
}
char BigString::getSeparator()
{
return separator_;
}
Size BigString::size()
{
return count_;
}
Size BigString::length()
{
return len_;
}
void BigString::getPeptide(FASTAEntry & entry, Size start, Size length)
{
Size index_start = getIndex_(start);
if (index_start != getIndex_(start + length))
{
throw Exception::InvalidValue(__FILE__, __LINE__, __PRETTY_FUNCTION__, "desired peptide is part of 2 fasta entries", "");
}
entry.first = FASTA_header_[index_start];
entry.second = big_string_.substr(start, length);
return;
}
const String & BigString::getBigString() const
{
return big_string_;
}
Size BigString::getIndex_(Size index, Size start, Size end)
{
if (end - start <= 1)
{
if (sep_indices_[start] >= index)
{
return start;
}
else
{
return start + 1;
}
}
Size half = (Size) ((end - start) / 2) + start;
if (index > sep_indices_[half])
{
return getIndex_(index, half, end);
}
else if (index < sep_indices_[half])
{
return getIndex_(index, start, half);
}
else
{
return half;
}
}
Size BigString::getIndex_(Size index)
{
return getIndex_(index, 0, sep_indices_.size());
}
}
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