File: SBMLReader.cs

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/* ----------------------------------------------------------------------------
 * This file was automatically generated by SWIG (http://www.swig.org).
 * Version 2.0.4
 *
 * Do not make changes to this file unless you know what you are doing--modify
 * the SWIG interface file instead.
 * ----------------------------------------------------------------------------- */

namespace libsbml {

 using System;
 using System.Runtime.InteropServices;

/** 
 * @sbmlpackage{core}
 *
@htmlinclude pkg-marker-core.html Methods for reading SBML from files and text strings.
 *
 * @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 SBMLDocument 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 SBMLDocument 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 SBMLDocument.
 *
 * For convenience as well as easy access from other languages besides C++,
 * this file also defines two global functions,
 * libsbml::readSBML(@if java String filename@endif)
 * and libsbml::readSBMLFromString(@if java String xml@endif).
 * They are equivalent to creating an SBMLReader
 * object and then calling the
 * SBMLReader::readSBML(@if java String filename@endif) or
 * SBMLReader::readSBMLFromString(@if java String xml@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
 * SBMLReader::readSBML(@if java String filename@endif) and
 * SBMLWriter::writeSBML(@if java SBMLDocument d, String filename@endif)
 * will automatically decompress and compress the file while writing and
 * reading 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 clike <a href='libsbml-installation.html'>installation instructions</a> @endif@if python <a href='libsbml-installation.html'>installation instructions</a> @endif@if java  <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.
 */

public class SBMLReader : IDisposable {
	private HandleRef swigCPtr;
	protected bool swigCMemOwn;
	
	internal SBMLReader(IntPtr cPtr, bool cMemoryOwn)
	{
		swigCMemOwn = cMemoryOwn;
		swigCPtr    = new HandleRef(this, cPtr);
	}
	
	internal static HandleRef getCPtr(SBMLReader obj)
	{
		return (obj == null) ? new HandleRef(null, IntPtr.Zero) : obj.swigCPtr;
	}
	
	internal static HandleRef getCPtrAndDisown (SBMLReader obj)
	{
		HandleRef ptr = new HandleRef(null, IntPtr.Zero);
		
		if (obj != null)
		{
			ptr             = obj.swigCPtr;
			obj.swigCMemOwn = false;
		}
		
		return ptr;
	}

  ~SBMLReader() {
    Dispose();
  }

  public virtual void Dispose() {
    lock(this) {
      if (swigCPtr.Handle != IntPtr.Zero) {
        if (swigCMemOwn) {
          swigCMemOwn = false;
          libsbmlPINVOKE.delete_SBMLReader(swigCPtr);
        }
        swigCPtr = new HandleRef(null, IntPtr.Zero);
      }
      GC.SuppressFinalize(this);
    }
  }

  public static bool operator==(SBMLReader lhs, SBMLReader rhs)
  {
    if((Object)lhs == (Object)rhs)
    {
      return true;
    }

    if( ((Object)lhs == null) || ((Object)rhs == null) )
    {
      return false;
    }

    return (getCPtr(lhs).Handle.ToString() == getCPtr(rhs).Handle.ToString());
  }

  public static bool operator!=(SBMLReader lhs, SBMLReader rhs)
  {
    return !(lhs == rhs);
  }

  public override bool Equals(Object sb)
  {
    if ( ! (sb is SBMLReader) )
    {
      return false;
    }

    return this == (SBMLReader)sb;
  }

  public override int GetHashCode()
  {
    return swigCPtr.Handle.ToInt32();
  }

  
/**
   * Creates a new SBMLReader and returns it. 
   *
   * The libSBML SBMLReader objects offer methods for reading SBML in
   * XML form from files and text strings.
   */ public
 SBMLReader() : this(libsbmlPINVOKE.new_SBMLReader(), true) {
  }

  
/**
   * Reads an SBML document from a file.
   *
   * This method is identical to SBMLReader::readSBMLFromFile(@if java String filename@endif).
   *
   * 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 SBMLDocument
   * object returned by this method.  Callers can use the methods on
   * SBMLDocument such as SBMLDocument::getNumErrors() and
   * SBMLDocument::getError(@if java long n@endif) to get the errors.  The object returned by
   * SBMLDocument::getError(@if java long n@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 SBMLError 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 clike
 @verbatim
 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.
   }
 }
 @endverbatim
 @endif@if java
 @verbatim
 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 error cases.
     }
 }
 @endverbatim
 @endif@if python
 @verbatim
 reader = SBMLReader()
 doc    = reader.readSBMLFromFile(filename)
 
 if doc.getNumErrors() > 0:
   if doc.getError(0).getErrorId() == libsbml.XMLFileUnreadable:
     # Handle case of unreadable file here.
   elif doc.getError(0).getErrorId() == libsbml.XMLFileOperationError:
     # Handle case of other file error here.
   else:
     # Handle other error cases here.
   
 @endverbatim
 @endif@if csharp
 @verbatim
 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.
     }
  }
 @endverbatim
 @endif
   *
   * *
 * 
 * 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.
 *
   *
   * *
 * 
 * To read a gzip/zip file, libSBML needs to be configured and linked with the
 * <a target='_blank' href='http://www.zlib.net/'>zlib</a> library at compile
 * time.  It also needs to be linked with the <a target='_blank'
 * href=''>bzip2</a> library to read files in <em>bzip2</em> format.  (Both of
 * these are the default configurations for libSBML.)  Errors about unreadable
 * files will be logged if a compressed filename is given and libSBML was
 * <em>not</em> linked with the corresponding required library.
 *
 *
   *
   * @param filename the name or full pathname of the file to be read.
   *
   * @return a pointer to the SBMLDocument created from the SBML content.
   *
   * * 
 * @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.
   *
   * @see SBMLError
   * @see SBMLDocument
   */ public
 SBMLDocument readSBML(string filename) {
    IntPtr cPtr = libsbmlPINVOKE.SBMLReader_readSBML(swigCPtr, filename);
    SBMLDocument ret = (cPtr == IntPtr.Zero) ? null : new SBMLDocument(cPtr, true);
    return ret;
  }

  
/**
   * Reads an SBML document from a file.
   *
   * This method is identical to SBMLReader::readSBML(@if java String filename@endif).
   *
   * 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 SBMLDocument
   * object returned by this method.  Callers can use the methods on
   * SBMLDocument such as SBMLDocument::getNumErrors() and
   * SBMLDocument::getError(@if java long n@endif) to get the errors.  The object returned by
   * SBMLDocument::getError(@if java long n@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 SBMLError 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 clike
 @verbatim
 SBMLReader reader = new SBMLReader();
 SBMLDocument doc  = reader.readSBML(filename);
 
 if (doc->getNumErrors() > 0)
 {
   if (doc->getError(0)->getErrorId() == XMLError::FileUnreadable)
   {
     // Handle case of unreadable file here.
   } 
   else if (doc->getError(0)->getErrorId() == XMLError::FileOperationError)
   {
     // 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.
   }
 }
 @endverbatim
 @endif@if java
 @verbatim
 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 error cases.
     }
 }
 @endverbatim
 @endif@if python
 @verbatim
 reader = SBMLReader()
 doc    = reader.readSBMLFromFile(filename)
 
 if doc.getNumErrors() > 0:
   if doc.getError(0).getErrorId() == libsbml.XMLFileUnreadable:
     # Handle case of unreadable file here.
   elif doc.getError(0).getErrorId() == libsbml.XMLFileOperationError:
     # Handle case of other file error here.
   else:
     # Handle other error cases here.
   
 @endverbatim
 @endif
   *
   * *
 * 
 * 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.
 *
   *
   * *
 * 
 * To read a gzip/zip file, libSBML needs to be configured and linked with the
 * <a target='_blank' href='http://www.zlib.net/'>zlib</a> library at compile
 * time.  It also needs to be linked with the <a target='_blank'
 * href=''>bzip2</a> library to read files in <em>bzip2</em> format.  (Both of
 * these are the default configurations for libSBML.)  Errors about unreadable
 * files will be logged if a compressed filename is given and libSBML was
 * <em>not</em> linked with the corresponding required library.
 *
 *
   *
   * @param filename the name or full pathname of the file to be read.
   *
   * @return a pointer to the SBMLDocument created from the SBML content.
   *
   * * 
 * @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.
   *
   * @see SBMLError
   * @see SBMLDocument
   */ public
 SBMLDocument readSBMLFromFile(string filename) {
    IntPtr cPtr = libsbmlPINVOKE.SBMLReader_readSBMLFromFile(swigCPtr, filename);
    SBMLDocument ret = (cPtr == IntPtr.Zero) ? null : new SBMLDocument(cPtr, true);
    return ret;
  }

  
/**
   * Reads an SBML document from the given XML 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
   * <code>&lt;?xml version='1.0' encoding='UTF-8'?&gt;</code>, 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 SBML.  See the method documentation for
   * SBMLReader::readSBML(@if java String filename@endif)
   * for an example of code for testing the returned error code.
   *
   * @param xml a string containing a full SBML model
   *
   * @return a pointer to the SBMLDocument created from the SBML content.
   *
   * @note When using this method to read an SBMLDocument that uses 
   * the SBML L3 Hierarchical Model Composition package (comp) the
   * document location cannot be set automatically. Thus, if the model
   * contains references to ExternalModelDefinitions, it will be necessary
   * to manually set the document URI location (setLocationURI) in order 
   * to facilitate resolving these models.
   *
   * @see SBMLReader::readSBML(@if java String filename@endif)
   */ public
 SBMLDocument readSBMLFromString(string xml) {
    IntPtr cPtr = libsbmlPINVOKE.SBMLReader_readSBMLFromString(swigCPtr, xml);
    SBMLDocument ret = (cPtr == IntPtr.Zero) ? null : new SBMLDocument(cPtr, true);
    return ret;
  }

  
/**
   * 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.
   *
   * *
 * @if python @note Because this is a static method on a class, the Python
 * language interface for libSBML will contain two variants.  One will be the
 * expected, normal static method on the class (i.e., a regular
 * <em>methodName</em>), and the other will be a standalone top-level
 * function with the name <em>ClassName_methodName()</em>. This is merely an
 * artifact of how the language interfaces are created in libSBML.  The
 * methods are functionally identical. @endif
   *
   * @see @if clike hasBzip2() @else SBMLReader::hasBzip2() @endif
   */ public
 static bool hasZlib() {
    bool ret = libsbmlPINVOKE.SBMLReader_hasZlib();
    return ret;
  }

  
/**
   * 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.
   *
   * *
 * @if python @note Because this is a static method on a class, the Python
 * language interface for libSBML will contain two variants.  One will be the
 * expected, normal static method on the class (i.e., a regular
 * <em>methodName</em>), and the other will be a standalone top-level
 * function with the name <em>ClassName_methodName()</em>. This is merely an
 * artifact of how the language interfaces are created in libSBML.  The
 * methods are functionally identical. @endif
   *
   * @see @if clike hasZlib() @else SBMLReader::hasZlib() @endif
   */ public
 static bool hasBzip2() {
    bool ret = libsbmlPINVOKE.SBMLReader_hasBzip2();
    return ret;
  }

}

}