libSBML Perl API
libSBML 5.10.0 Perl API
|
Reads an SBML Document into memory. More...
Classes | |
class | SBMLReader |
{core} Methods for reading SBML from files and text strings. More... | |
Functions | |
SBMLDocument_t * | readSBML (const char *filename) |
Reads an SBML document from the given file filename . More... | |
SBMLDocument_t * | readSBMLFromFile (const char *filename) |
Reads an SBML document from the given file filename . More... | |
SBMLDocument_t * | readSBMLFromString (const char *xml) |
Reads an SBML document from the given XML string xml . More... | |
Reads an SBML Document into memory.
SBMLDocument_t* readSBML | ( | const char * | filename | ) |
Reads an SBML document from the given file filename
.
If filename
does not exist, or it is not an SBML file, an error will be logged in the error log of the SBMLDocument object returned by this method. Calling programs can inspect this error log to determine the nature of the problem. Please refer to the definition of SBMLDocument_t for more information about the error reporting mechanism.
SBMLReader_t *sr;
SBMLDocument_t *d;
sr = SBMLReader_create();
d = SBMLReader_readSBML(reader, 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)
}
If the filename ends with .gz, the file will be read as a gzip file. Similary, if the filename ends with .zip or .bz2, the file will be read as a zip or bzip2 file, respectively. Otherwise, the fill will be read as an uncompressed file. If the filename ends with .zip, only the first file in the archive will be read if the zip archive contains two or more files.
To read a gzip/zip file, underlying libSBML needs to be linked with zlib at compile time. Also, underlying libSBML needs to be linked with bzip2 to read a bzip2 file. File unreadable error will be logged if a compressed file name is given and underlying libSBML is not linked with the corresponding required library. SBMLReader_hasZlib() and SBMLReader_hasBzip2() can be used to check whether libSBML is linked with each library.
SBMLDocument_t* readSBMLFromFile | ( | const char * | filename | ) |
Reads an SBML document from the given file filename
.
If filename
does not exist, or it is not an SBML file, an error will be logged in the error log of the SBMLDocument object returned by this method. Calling programs can inspect this error log to determine the nature of the problem. Please refer to the definition of SBMLDocument_t for more information about the error reporting mechanism.
SBMLReader_t *sr;
SBMLDocument_t *d;
sr = SBMLReader_create();
d = SBMLReader_readSBML(reader, 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)
}
If the filename ends with .gz, the file will be read as a gzip file. Similary, if the filename ends with .zip or .bz2, the file will be read as a zip or bzip2 file, respectively. Otherwise, the fill will be read as an uncompressed file. If the filename ends with .zip, only the first file in the archive will be read if the zip archive contains two or more files.
To read a gzip/zip file, underlying libSBML needs to be linked with zlib at compile time. Also, underlying libSBML needs to be linked with bzip2 to read a bzip2 file. File unreadable error will be logged if a compressed file name is given and underlying libSBML is not linked with the corresponding required library. SBMLReader_hasZlib() and SBMLReader_hasBzip2() can be used to check whether libSBML is linked with each library.
SBMLDocument_t* readSBMLFromString | ( | const char * | xml | ) |
Reads an SBML document from the given XML string xml
.
If the string does not begin with XML declaration,
<?xml version='1.0' encoding='UTF-8'?>
an XML declaration string will be prepended.
This method will report an error if the given string xml
is not SBML. The error will be logged in the error log of the SBMLDocument_t structure returned by this method. Calling programs can inspect this error log to determine the nature of the problem. Please refer to the definition of SBMLDocument for more information about the error reporting mechanism.