multovl
1.3
Multiple overlaps of genomic regions
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textio.hh
Go to the documentation of this file.
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/* <LICENSE>
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License for the MULTOVL multiple genomic overlap tools
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Copyright (c) 2007-2012, Dr Andras Aszodi,
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Campus Science Support Facilities GmbH (CSF),
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Dr-Bohr-Gasse 3, A-1030 Vienna, Austria, Europe.
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All rights reserved.
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Redistribution and use in source and binary forms, with or without
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modification, are permitted provided that the following conditions are
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met:
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* Redistributions of source code must retain the above copyright notice,
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this list of conditions and the following disclaimer.
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* Redistributions in binary form must reproduce the above copyright notice,
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this list of conditions and the following disclaimer in the documentation
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and/or other materials provided with the distribution.
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* Neither the name of the Campus Science Support Facilities GmbH
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nor the names of its contributors may be used to endorse
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or promote products derived from this software without specific prior
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written permission.
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THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS
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AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
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INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY
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AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL
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THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
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INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
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NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
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USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
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ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
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(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF
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THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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</LICENSE> */
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#ifndef MULTOVL_TEXTIO_HEADER
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#define MULTOVL_TEXTIO_HEADER
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// == HEADER textio.hh ==
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// -- Standard headers --
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#include <string>
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#include <vector>
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// -- Library headers --
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#include "
trackio.hh
"
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#include "
fileformat.hh
"
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namespace
multovl {
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namespace
io {
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class
Linereader;
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class
TextReader
:
public
TrackReader
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{
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public
:
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TextReader
(
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const
std::string& infname,
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Fileformat::Kind format);
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virtual
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std::string
read_into
(std::string& chrom,
Region
& reg);
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~
TextReader
();
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virtual
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void
add_error
(
const
std::string& msg);
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private
:
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bool
is_valid()
const
{
return
_valid; }
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Linereader
* _lrp;
// can be BedLinereader or GffLinereader
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std::ifstream _inf;
// input file stream
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std::string _line;
// input buffer
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unsigned
int
_linecount;
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bool
_valid;
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};
// END OF CLASS TextReader
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// -- Output --
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// Add code here if you want to do more complex output than the classic
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// "write-GFF2-to-stdout" approach.
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}
// namespace io
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}
// namespace multovl
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#endif // MULTOVL_TEXTIO_HEADER
multovl::io::TextReader::read_into
virtual std::string read_into(std::string &chrom, Region ®)
multovl::io::TrackReader
Definition:
trackio.hh:69
multovl::io::TextReader::add_error
virtual void add_error(const std::string &msg)
Adds an error message to _errors, nicely decorated with linecount.
fileformat.hh
Module to handle file format recognition.
multovl::Region
Instances of the Region class represent regions on a sequence. They have first and last coordinates...
Definition:
region.hh:65
multovl::io::Linereader
Base class of parser objects. Linereader objects process one line at a time, and change their interna...
Definition:
linereader.hh:75
multovl::io::TextReader::TextReader
TextReader(const std::string &infname, Fileformat::Kind format)
multovl::io::TextReader
Definition:
textio.hh:66
trackio.hh
Base classes to read/write input/output tracks (collections of regions).
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