/usr/include/sbml/SBMLReader.h is in libsbml5-dev 5.12.0+dfsg-3.
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* @file SBMLReader.h
* @brief Reads an SBML Document into memory
* @author Ben Bornstein
*
* <!--------------------------------------------------------------------------
* This file is part of libSBML. Please visit http://sbml.org for more
* information about SBML, and the latest version of libSBML.
*
* Copyright (C) 2013-2015 jointly by the following organizations:
* 1. California Institute of Technology, Pasadena, CA, USA
* 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
* 3. University of Heidelberg, Heidelberg, Germany
*
* Copyright (C) 2009-2013 jointly by the following organizations:
* 1. California Institute of Technology, Pasadena, CA, USA
* 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
*
* Copyright (C) 2006-2008 by the California Institute of Technology,
* Pasadena, CA, USA
*
* Copyright (C) 2002-2005 jointly by the following organizations:
* 1. California Institute of Technology, Pasadena, CA, USA
* 2. Japan Science and Technology Agency, Japan
*
* This library is free software; you can redistribute it and/or modify it
* under the terms of the GNU Lesser General Public License as published by
* the Free Software Foundation. A copy of the license agreement is provided
* in the file named "LICENSE.txt" included with this software distribution
* and also available online as http://sbml.org/software/libsbml/license.html
* ------------------------------------------------------------------------ -->
*
* @class SBMLReader
* @sbmlbrief{core} File and text-string SBML reader.
*
* @htmlinclude not-sbml-warning.html
*
* The SBMLReader class provides the main interface for reading SBML content
* from files and strings. The methods for reading SBML all return an
* @if python @link libsbml.SBMLDocument SBMLDocument@endlink@else SBMLDocument@endif@~
* object representing the results. In the case of failures (such as if the
* SBML contains errors or a file cannot be read), the errors will be
* recorded with the SBMLErrorLog object kept in the
* @if python @link libsbml.SBMLDocument SBMLDocument@endlink@else SBMLDocument@endif@~
* returned by SBMLReader. Consequently, immediately after calling a method
* on SBMLReader, callers should always check for errors and warnings using
* the methods for this purpose provided by @if python @link
* libsbml.SBMLDocument SBMLDocument@endlink@else SBMLDocument@endif.
*
* For convenience as well as easy access from other languages besides C++,
* this file also defines two global functions, @sbmlfunction{readSBML,
* String} and @sbmlfunction{readSBMLFromString, String}. They are
* equivalent to creating an SBMLReader object and then calling the
* @if python @link SBMLReader::readSBML() SBMLReader.readSBML()@endlink@endif@if java SBMLReader::readSBML(String)@endif@if cpp SBMLReader::readSBML()@endif@if csharp SBMLReader.readSBML()@endif@~ and
* @if python @link SBMLReader::readSBMLFromString() SBMLReader.readSBMLFromString()@endlink@endif@if java SBMLReader::readSBMLFromString(String)@endif@if cpp SBMLReader::readSBMLFromString()@endif@if csharp SBMLReader.readSBMLFromString()@endif@~ methods, respectively.
*
* @section compression Support for reading compressed files
*
* LibSBML provides support for reading (as well as writing) compressed
* SBML files. The process is transparent to the calling
* application---the application does not need to do anything
* deliberate to invoke the functionality. If a given SBML filename ends
* with an extension for the @em gzip, @em zip or @em bzip2 compression
* formats (respectively, @c .gz, @c .zip, or @c .bz2), then the methods
* @if python @link SBMLReader::readSBML() SBMLReader.readSBML()@endlink@endif@if java @link SBMLReader::readSBML(String) SBMLReader.readSBML(String)@endlink@endif@if cpp SBMLReader::readSBML()@endif@if csharp SBMLReader.readSBML()@endif@~ and
* @if python @link SBMLWriter::writeSBML() SBMLWriter.writeSBML()@endlink@endif@if java @link SBMLWriter::writeSBML(String) SBMLWriter.writeSBML(String)@endlink@endif@if cpp SBMLWriter::writeSBML()@endif@if csharp SBMLWriter.writeSBML()@endif@~
* will automatically decompress and compress the file while reading and
* writing it. If the filename has no such extension, it will be read and
* written uncompressed as normal.
*
* The compression feature requires that the @em zlib (for @em gzip and @em
* zip formats) and/or @em bzip2 (for @em bzip2 format) be available on the
* system running libSBML, and that libSBML was configured with their
* support compiled-in. Please see the libSBML
* @if java <a href="../../../libsbml-installation.html">installation instructions</a> @else <a href="libsbml-installation.html">installation instructions</a>@endif@~
* for more information about this. The methods
* @if java SBMLReader::hasZlib()@else hasZlib()@endif@~ and
* @if java SBMLReader::hasBzip2()@else hasBzip2()@endif@~
* can be used by an application to query at run-time whether support
* for the compression libraries is available in the present copy of
* libSBML.
*
* Support for compression is not mandated by the SBML standard, but
* applications may find it helpful, particularly when large SBML models
* are being communicated across data links of limited bandwidth.
*/
/**
* <!-- ~ ~ ~ ~ ~ Start of common documentation strings ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~
* The following text is used as common documentation blocks copied multiple
* times elsewhere in this file. The use of @class is a hack needed because
* Doxygen's @copydetails command has limited functionality. Symbols
* beginning with "doc_" are marked as ignored in our Doxygen configuration.
* ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ -->
*
* @class doc_sbmlreader_if_compressed
*
* @par
* If the given filename ends with the suffix @c ".gz" (for example, @c
* "myfile.xml.gz"), the file is assumed to be compressed in @em gzip
* format and will be automatically decompressed upon reading.
* Similarly, if the given filename ends with @c ".zip" or @c ".bz2", the
* file is assumed to be compressed in @em zip or @em bzip2 format
* (respectively). Files whose names lack these suffixes will be read
* uncompressed. Note that if the file is in @em zip format but the
* archive contains more than one file, only the first file in the
* archive will be read and the rest ignored.
*
* <!-- ------------------------------------------------------------------- -->
* @class doc_note_sbmlreader_error_handling
*
* @note LibSBML versions 2.x and later versions behave differently in
* error handling in several respects. One difference is how early some
* errors are caught and whether libSBML continues processing a file in
* the face of some early errors. In general, libSBML versions after 2.x
* stop parsing SBML inputs sooner than libSBML version 2.x in the face
* of XML errors, because the errors may invalidate any further SBML
* content. For example, a missing XML declaration at the beginning of
* the file was ignored by libSBML 2.x but in version 3.x and later, it
* will cause libSBML to stop parsing the rest of the input altogether.
* While this behavior may seem more severe and intolerant, it was
* necessary in order to provide uniform behavior regardless of which
* underlying XML parser (Expat, Xerces, libxml2) is being used by
* libSBML. The XML parsers themselves behave differently in their error
* reporting, and sometimes libSBML has to resort to the lowest common
* denominator.
*
* <!-- ------------------------------------------------------------------- -->
* @class doc_readsbmlfromfile
*
* Reads an SBML document from the given file.
*
* If the file named @p filename does not exist or its content is not
* valid SBML, one or more errors will be logged with the
* @if python @link libsbml.SBMLDocument SBMLDocument@endlink@else SBMLDocument@endif@~
* object returned by this method. Callers can use the methods on
* @if python @link libsbml.SBMLDocument SBMLDocument@endlink@else SBMLDocument@endif@~ such as
* @if python @link libsbml.SBMLDocument.getNumErrors() SBMLDocument.getNumErrors()@endlink@else SBMLDocument::getNumErrors()@endif@~
* and
* @if python @link libsbml.SBMLDocument.getError() SBMLDocument.getError()@endlink@endif@if java SBMLDocument::getError(long)@endif@if cpp SBMLDocument::getError()@endif@if csharp SBMLDocument::getError()@endif@~
* to get the errors. The object returned by
* @if python @link libsbml.SBMLDocument.getError() SBMLDocument.getError()@endlink@endif@if java SBMLDocument::getError(long)@endif@if cpp SBMLDocument::getError()@endif@if csharp SBMLDocument::getError()@endif@~
* is an SBMLError object, and it has methods to get the error code,
* category, and severity level of the problem, as well as a textual
* description of the problem. The possible severity levels range from
* informational messages to fatal errors; see the documentation for
* @if python @link libsbml.SBMLError SBMLError@endlink@else SBMLError@endif@~
* for more information.
*
* If the file @p filename could not be read, the file-reading error will
* appear first. The error code @if clike (a value drawn from the
* enumeration #XMLErrorCode_t)@endif@~ can provide a clue about what
* happened. For example, a file might be unreadable (either because it does
* not actually exist or because the user does not have the necessary access
* privileges to read it) or some sort of file operation error may have been
* reported by the underlying operating system. Callers can check for these
* situations using a program fragment such as the following:
* @if cpp
@code{.cpp}
SBMLReader reader;
SBMLDocument* doc = reader.readSBMLFromFile(filename);
if (doc->getNumErrors() > 0)
{
if (doc->getError(0)->getErrorId() == XMLError::XMLFileUnreadable)
{
// Handle case of unreadable file here.
}
else if (doc->getError(0)->getErrorId() == XMLError::XMLFileOperationError)
{
// Handle case of other file operation error here.
}
else
{
// Handle other cases -- see error codes defined in XMLErrorCode_t
// for other possible cases to check.
}
}
@endcode
@endif
@if conly
@code{.c}
SBMLReader_t *sr;
SBMLDocument_t *d;
sr = SBMLReader_create();
d = SBMLReader_readSBML(sr, filename);
if (SBMLDocument_getNumErrors(d) > 0)
{
if (XMLError_getId(SBMLDocument_getError(d, 0))
== SBML_READ_ERROR_FILE_NOT_FOUND)
{
...
}
if (XMLError_getId(SBMLDocument_getError(d, 0))
== SBML_READ_ERROR_NOT_SBML)
{
...
}
}
@endcode
@endif
@if java
@code{.java}
SBMLReader reader = new SBMLReader();
SBMLDocument doc = reader.readSBMLFromFile(filename);
if (doc.getNumErrors() > 0)
{
if (doc.getError(0).getErrorId() == libsbmlConstants.XMLFileUnreadable)
{
// Handle case of unreadable file here.
}
else if (doc.getError(0).getErrorId() == libsbmlConstants.XMLFileOperationError)
{
// Handle case of other file operation error here.
}
else
{
// Handle other error cases.
}
}
@endcode
@endif
@if python
@code{.py}
reader = SBMLReader()
if reader == None:
# Handle the truly exceptional case of no object created here.
doc = reader.readSBMLFromFile(filename)
if doc.getNumErrors() > 0:
if doc.getError(0).getErrorId() == XMLFileUnreadable:
# Handle case of unreadable file here.
elif doc.getError(0).getErrorId() == XMLFileOperationError:
# Handle case of other file error here.
else:
# Handle other error cases here.
@endcode
@endif
@if csharp
@code{.cs}
SBMLReader reader = new SBMLReader();
SBMLDocument doc = reader.readSBMLFromFile(filename);
if (doc.getNumErrors() > 0)
{
if (doc.getError(0).getErrorId() == libsbmlcs.libsbml.XMLFileUnreadable)
{
// Handle case of unreadable file here.
}
else if (doc.getError(0).getErrorId() == libsbmlcs.libsbml.XMLFileOperationError)
{
// Handle case of other file operation error here.
}
else
{
// Handle other cases -- see error codes defined in XMLErrorCode_t
// for other possible cases to check.
}
}
@endcode
@endif@~
*
* @copydetails doc_sbmlreader_if_compressed
*
* @copydetails doc_config_for_reading_zipped_files
*
* <!-- ------------------------------------------------------------------- -->
* @class doc_readsbmlfromstring
*
* Reads an SBML document from a text string.
*
* This method is flexible with respect to the presence of an XML
* declaration at the beginning of the string. In particular, if the
* string in @p xml does not begin with the XML declaration
* @verbatim
<?xml version='1.0' encoding='UTF-8'?>
@endverbatim
* then this method will automatically prepend the declaration
* to @p xml.
*
* This method will log a fatal error if the content given in the parameter
* @p xml is not in SBML format. See the method documentation for
* SBMLReader::readSBML(@if java String@endif) for an example of code for
* testing the returned error code.
*
* <!-- ------------------------------------------------------------------- -->
* @class doc_note_reading_comp
*
* @note When using this method to read an SBMLDocument that uses the SBML
* Level 3 Hierarchical %Model Composition package (comp) the document
* location cannot be set automatically. Thus, if the model contains
* references to ExternalModelDefinition objects, it will be necessary to
* manually set the document URI location
* (SBMLDocument::setLocationURI(@if java String@endif) in order to facilitate
* resolving these models.
*/
#ifndef SBMLReader_h
#define SBMLReader_h
#include <sbml/common/extern.h>
#include <sbml/common/sbmlfwd.h>
#include <sbml/util/util.h>
#ifdef __cplusplus
#include <string>
LIBSBML_CPP_NAMESPACE_BEGIN
class SBMLDocument;
class LIBSBML_EXTERN SBMLReader
{
public:
/**
* Creates a new SBMLReader object and returns it.
*
* The libSBML SBMLReader object offers methods for reading SBML in
* XML form from files and text strings.
*/
SBMLReader ();
/**
* Destroys this SBMLReader.
*/
virtual ~SBMLReader ();
/**
* @copydoc doc_readsbmlfromfile
*
* This method is identical to
* @if python @link SBMLReader::readSBMLFromFile() SBMLReader.readSBMLFromFile()@endlink@endif@if java @link SBMLReader::readSBMLFromFile(String) SBMLReader.readSBMLFromFile(String)@endlink@endif@if cpp SBMLReader::readSBMLFromFile()@endif@if csharp SBMLReader.readSBMLFromFile()@endif.
*
* @param filename the name or full pathname of the file to be read.
*
* @return a pointer to the SBMLDocument object created from the SBML
* content in @p filename.
*
* @copydetails doc_note_sbmlreader_error_handling
*
* @see readSBMLFromString(@if java String@endif)
* @see SBMLError
* @see SBMLDocument
*/
SBMLDocument* readSBML (const std::string& filename);
/**
* @copydoc doc_readsbmlfromfile
*
* This method is identical to
* @if python @link SBMLReader::readSBML() SBMLReader.readSBML()@endlink@endif@if java @link SBMLReader::readSBML(String) SBMLReader.readSBML(String)@endlink@endif@if cpp SBMLReader::readSBML()@endif@if csharp SBMLReader.readSBML()@endif.
*
* @param filename the name or full pathname of the file to be read.
*
* @return a pointer to the SBMLDocument object created from the SBML
* content in @p filename.
*
* @copydetails doc_note_sbmlreader_error_handling
*
* @see readSBMLFromString(@if java String@endif)
* @see SBMLError
* @see SBMLDocument
*/
SBMLDocument* readSBMLFromFile (const std::string& filename);
/**
* @copydoc doc_readsbmlfromstring
*
* @param xml a string containing a full SBML model
*
* @return a pointer to the SBMLDocument created from the SBML content,
* or a null pointer if @p xml is null.
*
* @copydetails doc_note_reading_comp
*
* @see SBMLReader::readSBML(@if java String@endif)
*/
SBMLDocument* readSBMLFromString (const std::string& xml);
/**
* Static method; returns @c true if this copy of libSBML supports
* <i>gzip</I> and <i>zip</i> format compression.
*
* @return @c true if libSBML has been linked with the <i>zlib</i>
* library, @c false otherwise.
*
* @copydetails doc_note_static_methods
*
* @see @if clike hasBzip2() @else SBMLReader::hasBzip2()@endif@~
*/
static bool hasZlib();
/**
* Static method; returns @c true if this copy of libSBML supports
* <i>bzip2</i> format compression.
*
* @return @c true if libSBML is linked with the <i>bzip2</i>
* libraries, @c false otherwise.
*
* @copydetails doc_note_static_methods
*
* @see @if clike hasZlib() @else SBMLReader::hasZlib()@endif@~
*/
static bool hasBzip2();
protected:
/** @cond doxygenLibsbmlInternal */
/**
* Used by readSBML() and readSBMLFromString().
*
* @ifnot hasDefaultArgs @htmlinclude warn-default-args-in-docs.html@endif@~
*/
SBMLDocument* readInternal (const char* content, bool isFile = true);
/** @endcond */
};
LIBSBML_CPP_NAMESPACE_END
#endif /* __cplusplus */
LIBSBML_CPP_NAMESPACE_BEGIN
BEGIN_C_DECLS
#ifndef SWIG
/**
* Creates a new SBMLReader_t and returns it.
*
* By default, XML Schema validation is off.
*
* @if conly
* @memberof SBMLReader_t
* @endif
*/
LIBSBML_EXTERN
SBMLReader_t *
SBMLReader_create (void);
/**
* Frees the given SBMLReader_t.
*
* @if conly
* @memberof SBMLReader_t
* @endif
*/
LIBSBML_EXTERN
void
SBMLReader_free (SBMLReader_t *sr);
/**
* @copydoc doc_readsbmlfromfile
*
* This function is identical to SBMLReader_readSBMLFromFile().
*
* @param sr The SBMLReader_t structure to use.
*
* @param filename a string giving the path to a file where the XML
* content is to be found.
*
* @return a pointer to the SBMLDocument structure created from the SBML
* content read from @p filename.
*
* @copydetails doc_note_sbmlreader_error_handling
*
* @if conly
* @memberof SBMLReader_t
* @endif
*/
LIBSBML_EXTERN
SBMLDocument_t *
SBMLReader_readSBML (SBMLReader_t *sr, const char *filename);
/**
* @copydoc doc_readsbmlfromfile
*
* This function is identical to SBMLReader_readSBML().
*
* @param sr The SBMLReader_t structure to use.
*
* @param filename a string giving the path to a file where the XML
* content is to be found.
*
* @return a pointer to the SBMLDocument structure created from the SBML
* content read from @p filename.
*
* @copydetails doc_note_sbmlreader_error_handling
*
* @if conly
* @memberof SBMLReader_t
* @endif
*/
LIBSBML_EXTERN
SBMLDocument_t *
SBMLReader_readSBMLFromFile (SBMLReader_t *sr, const char *filename);
/**
* @copydoc doc_readsbmlfromstring
*
* @param sr the SBMLReader_t structure to use
*
* @param xml the input xml string.
*
* @return a pointer to the SBMLDocument read.
*
* @copydetails doc_note_reading_comp
*
* @if conly
* @memberof SBMLReader_t
* @endif
*/
LIBSBML_EXTERN
SBMLDocument_t *
SBMLReader_readSBMLFromString (SBMLReader_t *sr, const char *xml);
/**
* Returns @c true if the underlying libSBML supports @em gzip and @em zlib
* format compression.
*
* This predicate tests whether the underlying copy of the libSBML library
* has been linked with the necessary libraries to support @em zlib
* compression.
*
* @return @c non-zero if libSBML is linked with zlib, @c zero otherwise.
*
* @if conly
* @memberof SBMLReader_t
* @endif
*/
LIBSBML_EXTERN
int
SBMLReader_hasZlib ();
/**
* Returns @c true if the underlying libSBML supports @em bzip2 format
* compression.
*
* This predicate tests whether the underlying copy of the libSBML library
* has been linked with the necessary libraries to support @em bzip2
* compression.
*
* @return @c non-zero if libSBML is linked with bzip2, @c zero otherwise.
*
* @if conly
* @memberof SBMLReader_t
* @endif
*/
LIBSBML_EXTERN
int
SBMLReader_hasBzip2 ();
#endif /* !SWIG */
/**
* @copydoc doc_readsbmlfromfile
*
* @if conly
* @memberof SBMLReader_t
* @endif
*/
LIBSBML_EXTERN
SBMLDocument_t *
readSBML (const char *filename);
/**
* @copydoc doc_readsbmlfromfile
*
* @param filename the name or full pathname of the file to be read.
*
* @return a pointer to the SBMLDocument structure created from the SBML
* content in @p filename.
*
* @if conly
* @memberof SBMLReader_t
* @endif
*/
LIBSBML_EXTERN
SBMLDocument_t *
readSBMLFromFile (const char *filename);
/**
* @copydoc doc_readsbmlfromstring
*
* @param xml a string containing a full SBML model
*
* @return a pointer to the SBMLDocument structure created from the SBML
* content in @p xml.
*
* @copydetails doc_note_reading_comp
*
* @if conly
* @memberof SBMLReader_t
* @endif
*/
LIBSBML_EXTERN
SBMLDocument_t *
readSBMLFromString (const char *xml);
END_C_DECLS
LIBSBML_CPP_NAMESPACE_END
#endif /* SBMLReader_h */
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