{core}
File and text-string SBML writer.
This class of objects is defined by libSBML only and has no direct
equivalent in terms of SBML components. This class is not prescribed by
the SBML specifications, although it is used to implement features
defined in SBML.
The SBMLWriter class is the converse of SBMLReader, and provides the main interface for serializing SBML models into XML and writing the result to an output stream or to files and text strings. The methods for writing SBML all take an SBMLDocument object and a destination. They return a boolean or integer value to indicate success or failure.
Support for writing compressed files
LibSBML provides support for writing (as well as reading) 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 gzip, zip or bzip2 compression formats (respectively, ".gz"
, ".zip"
, or ".bz2"
), then the methods SBMLWriter::writeSBML() and SBMLReader::readSBML() will automatically compress and decompress the file while writing and reading it. If the filename has no such extension, it will be written and read uncompressed as normal.
The compression feature requires that the zlib (for gzip and zip formats) and/or bzip2 (for bzip2 format) be available on the system running libSBML, and that libSBML was configured with their support compiled-in. Please see the libSBMLfor more information about this. The methods SBMLWriter::hasZlib() and SBMLWriter::hasBzip2() 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.
int libsbmlcs.SBMLWriter.setProgramName |
( |
string |
name | ) |
|
Sets the name of this program, i.e., the program that is about to write out the SBMLDocument.
If the program name and version are set (see SBMLWriter::setProgramVersion()), the following XML comment, intended for human consumption, will be written at the beginning of the XML document:
<!-- Created by <program name> version <program version>
on yyyy-MM-dd HH:mm with libSBML version <libsbml version>. -->
If the program name and version are not set at some point before calling the writeSBML() methods, no such comment is written out.
- Parameters
-
name | the name of this program (where 'this program' refers to program in which libSBML is embedded, not libSBML itself!) |
- Returns
- integer value indicating success/failure of the function. This particular function only does one thing irrespective of user input or object state, and thus will only return a single value:
- See also
- setProgramVersion(string version)
int libsbmlcs.SBMLWriter.setProgramVersion |
( |
string |
version | ) |
|
Sets the version of this program, i.e., the program that is about to write out the SBMLDocument.
If the program version and name are set (see SBMLWriter::setProgramName()), the following XML comment, intended for human consumption, will be written at the beginning of the document:
<!-- Created by <program name> version <program version>
on yyyy-MM-dd HH:mm with libSBML version <libsbml version>. -->
If the program version and name are not set at some point before calling the writeSBML() methods, no such comment is written out.
- Parameters
-
version | the version of this program (where 'this program' refers to program in which libSBML is embedded, not libSBML itself!) |
- Returns
- integer value indicating success/failure of the function. This particular function only does one thing irrespective of user input or object state, and thus will only return a single value:
- See also
- setProgramName(string name)
bool libsbmlcs.SBMLWriter.writeSBML |
( |
SBMLDocument |
d, |
|
|
string |
filename |
|
) |
| |
Writes the given SBML document to filename.
If the given filename ends with the suffix
".gz"
(for example,
"myfile.xml.gz"
), libSBML assumes the
caller wants the file to be written compressed in
gzip format.
Similarly, if the given filename ends with
".zip"
or
".bz2"
, libSBML assumes the caller wants the file to
be compressed in
zip or
bzip2 format (respectively).
Files whose names lack these suffixes will be written uncompressed.
Special considerations for the zip format: If the given filename
ends with
".zip"
, the file placed in the zip archive
will have the suffix
".xml"
or
".sbml"
. For example, the file in the zip archive
will be named
"test.xml"
if the given filename is
"test.xml.zip"
or
"test.zip"
.
Similarly, the filename in the archive will be
"test.sbml"
if the given filename is
"test.sbml.zip"
.
- Parameters
-
d | the SBML document to be written. |
filename | the name or full pathname of the file where the SBML is to be written. |
- Returns
true
on success and false
if the filename could not be opened for writing.
- Note
- To write a gzip/zip file, libSBML needs to be configured and linked with
the zlib library at
compile time. It also needs to be linked with the bzip2 library to write files in bzip2 format. (Both
of these are the default configurations for libSBML.) Errors about
unreadable files will be logged and this method will return
false
if a compressed filename is given and libSBML was
not linked with the corresponding required library.
- See also
- setProgramVersion(string version)
-
setProgramName(string name)
bool libsbmlcs.SBMLWriter.writeSBMLToFile |
( |
SBMLDocument |
d, |
|
|
string |
filename |
|
) |
| |
Writes the given SBML document to filename.
If the given filename ends with the suffix
".gz"
(for example,
"myfile.xml.gz"
), libSBML assumes the
caller wants the file to be written compressed in
gzip format.
Similarly, if the given filename ends with
".zip"
or
".bz2"
, libSBML assumes the caller wants the file to
be compressed in
zip or
bzip2 format (respectively).
Files whose names lack these suffixes will be written uncompressed.
Special considerations for the zip format: If the given filename
ends with
".zip"
, the file placed in the zip archive
will have the suffix
".xml"
or
".sbml"
. For example, the file in the zip archive
will be named
"test.xml"
if the given filename is
"test.xml.zip"
or
"test.zip"
.
Similarly, the filename in the archive will be
"test.sbml"
if the given filename is
"test.sbml.zip"
.
- Parameters
-
d | the SBML document to be written. |
filename | the name or full pathname of the file where the SBML is to be written. |
- Returns
true
on success and false
if the filename could not be opened for writing.
- Note
- To write a gzip/zip file, libSBML needs to be configured and linked with
the zlib library at
compile time. It also needs to be linked with the bzip2 library to write files in bzip2 format. (Both
of these are the default configurations for libSBML.) Errors about
unreadable files will be logged and this method will return
false
if a compressed filename is given and libSBML was
not linked with the corresponding required library.
- See also
- setProgramVersion(string version)
-
setProgramName(string name)