001/* ----------------------------------------------------------------------------
002 * This file was automatically generated by SWIG (http://www.swig.org).
003 * Version 3.0.10
004 *
005 * Do not make changes to this file unless you know what you are doing--modify
006 * the SWIG interface file instead.
007 * ----------------------------------------------------------------------------- */
008
009package org.sbml.libsbml;
010
011/** 
012 *  File and text-string SBML writer.
013 <p>
014 * <p style='color: #777; font-style: italic'>
015This class of objects is defined by libSBML only and has no direct
016equivalent in terms of SBML components.  This class is not prescribed by
017the SBML specifications, although it is used to implement features
018defined in SBML.
019</p>
020
021 <p>
022 * The {@link SBMLWriter} class is the converse of {@link SBMLReader}, and provides the
023 * main interface for serializing SBML models into XML and writing the
024 * result to an output stream or to files and text strings.  The methods 
025 * for writing SBML all take an {@link SBMLDocument} object and a destination.  
026 * They return a boolean or integer value to indicate success or failure.
027 <p>
028 * <h2>Support for writing compressed files</h2>
029 <p>
030 * LibSBML provides support for writing (as well as reading) compressed
031 * SBML files.  The process is transparent to the calling
032 * application&mdash;the application does not need to do anything
033 * deliberate to invoke the functionality.  If a given SBML filename ends
034 * with an extension for the <em>gzip</em>, <em>zip</em> or <em>bzip2</em> compression
035 * formats (respectively, <code>&quot;.gz&quot;</code>,
036 * <code>&quot;.zip&quot;</code>, or <code>&quot;.bz2&quot;</code>),
037 * then the methods
038 * {@link SBMLWriter#writeSBML(SBMLDocument, String)}
039 * and {@link SBMLReader#readSBML(String)}
040 * will automatically compress and decompress the file while writing and
041 * reading it.  If the filename has no such extension, it
042 * will be written and read uncompressed as normal.
043 <p>
044 * The compression feature requires that the <em>zlib</em> (for <em>gzip</em> and 
045 * <em>zip</em> formats) and/or <em>bzip2</em> (for <em>bzip2</em> format) be available on the
046 * system running libSBML, and that libSBML was configured with their
047 * support compiled-in.  Please see the libSBML <a href='../../../libsbml-installation.html'>installation instructions</a> for 
048 * more information about this.  The methods
049 * {@link SBMLWriter#hasZlib()} and
050 * {@link SBMLWriter#hasBzip2()}
051 * can be used by an application to query at run-time whether support
052 * for the compression libraries is available in the present copy of
053 * libSBML.
054 <p>
055 * Support for compression is not mandated by the SBML standard, but
056 * applications may find it helpful, particularly when large SBML models
057 * are being communicated across data links of limited bandwidth.
058 */
059
060public class SBMLWriter {
061   private long swigCPtr;
062   protected boolean swigCMemOwn;
063
064   protected SBMLWriter(long cPtr, boolean cMemoryOwn)
065   {
066     swigCMemOwn = cMemoryOwn;
067     swigCPtr    = cPtr;
068   }
069
070   protected static long getCPtr(SBMLWriter obj)
071   {
072     return (obj == null) ? 0 : obj.swigCPtr;
073   }
074
075   protected static long getCPtrAndDisown (SBMLWriter obj)
076   {
077     long ptr = 0;
078
079     if (obj != null)
080     {
081       ptr             = obj.swigCPtr;
082       obj.swigCMemOwn = false;
083     }
084
085     return ptr;
086   }
087
088  protected void finalize() {
089    delete();
090  }
091
092  public synchronized void delete() {
093    if (swigCPtr != 0) {
094      if (swigCMemOwn) {
095        swigCMemOwn = false;
096        libsbmlJNI.delete_SBMLWriter(swigCPtr);
097      }
098      swigCPtr = 0;
099    }
100  }
101
102  /**
103   * Equality comparison method for SBMLWriter.
104   * <p>
105   * Because the Java methods for libSBML are actually wrappers around code
106   * implemented in C++ and C, certain operations will not behave as
107   * expected.  Equality comparison is one such case.  An instance of a
108   * libSBML object class is actually a <em>proxy object</em>
109   * wrapping the real underlying C/C++ object.  The normal <code>==</code>
110   * equality operator in Java will <em>only compare the Java proxy objects</em>,
111   * not the underlying native object.  The result is almost never what you
112   * want in practical situations.  Unfortunately, Java does not provide a
113   * way to override <code>==</code>.
114   *  <p>
115   * The alternative that must be followed is to use the
116   * <code>equals()</code> method.  The <code>equals</code> method on this
117   * class overrides the default java.lang.Object one, and performs an
118   * intelligent comparison of instances of objects of this class.  The
119   * result is an assessment of whether two libSBML Java objects are truly 
120   * the same underlying native-code objects.
121   *  <p>
122   * The use of this method in practice is the same as the use of any other
123   * Java <code>equals</code> method.  For example,
124   * <em>a</em><code>.equals(</code><em>b</em><code>)</code> returns
125   * <code>true</code> if <em>a</em> and <em>b</em> are references to the
126   * same underlying object.
127   *
128   * @param sb a reference to an object to which the current object
129   * instance will be compared
130   *
131   * @return <code>true</code> if <code>sb</code> refers to the same underlying 
132   * native object as this one, <code>false</code> otherwise
133   */
134  public boolean equals(Object sb)
135  {
136    if ( this == sb ) 
137    {
138      return true;
139    }
140    return swigCPtr == getCPtr((SBMLWriter)(sb));
141  }
142
143  /**
144   * Returns a hashcode for this SBMLWriter object.
145   *
146   * @return a hash code usable by Java methods that need them.
147   */
148  public int hashCode()
149  {
150    return (int)(swigCPtr^(swigCPtr>>>32));
151  }
152
153  
154/**
155   * Creates a new {@link SBMLWriter}.
156   <p>
157   * The libSBML {@link SBMLWriter} objects offer methods for writing SBML in
158   * XML form to files and text strings.
159   */ public
160 SBMLWriter() {
161    this(libsbmlJNI.new_SBMLWriter(), true);
162  }
163
164  
165/**
166   * Sets the name of this program, i.e., the program that is about to
167   * write out the {@link SBMLDocument}.
168   <p>
169   * If the program name and version are set (see
170   * {@link SBMLWriter#setProgramVersion(String)}), the
171   * following XML comment, intended for human consumption, will be written
172   * at the beginning of the XML document:
173   * <pre class='fragment'>
174 &lt;!-- Created by &lt;program name&gt; version &lt;program version&gt;
175 on yyyy-MM-dd HH:mm with libSBML version &lt;libsbml version&gt;. --&gt;
176 </pre>
177   <p>
178   * If the program name and version are not set at some point before
179   * calling the writeSBML() methods, no such comment is written out.
180   <p>
181   * @param name the name of this program (where 'this program' refers to
182   * program in which libSBML is embedded, not libSBML itself!)
183   <p>
184   * <p>
185 * @return integer value indicating success/failure of the
186 * function.   This particular
187 * function only does one thing irrespective of user input or 
188 * object state, and thus will only return a single value:
189   * <ul>
190   * <li> {@link libsbmlConstants#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS}
191   *
192   * </ul> <p>
193   * @see #setProgramVersion(String version)
194   */ public
195 int setProgramName(String name) {
196    return libsbmlJNI.SBMLWriter_setProgramName(swigCPtr, this, name);
197  }
198
199  
200/**
201   * Sets the version of this program, i.e., the program that is about to
202   * write out the {@link SBMLDocument}.
203   <p>
204   * If the program version and name are set (see
205   * {@link SBMLWriter#setProgramName(String)}), the
206   * following XML comment, intended for human consumption, will be written
207   * at the beginning of the document:
208   * <pre class='fragment'>
209 &lt;!-- Created by &lt;program name&gt; version &lt;program version&gt;
210 on yyyy-MM-dd HH:mm with libSBML version &lt;libsbml version&gt;. --&gt;
211 </pre>
212   <p>
213   * If the program version and name are not set at some point before
214   * calling the writeSBML() methods, no such comment is written out.
215   <p>
216   * @param version the version of this program (where 'this program'
217   * refers to program in which libSBML is embedded, not libSBML itself!)
218   <p>
219   * <p>
220 * @return integer value indicating success/failure of the
221 * function.   This particular
222 * function only does one thing irrespective of user input or 
223 * object state, and thus will only return a single value:
224   * <ul>
225   * <li> {@link libsbmlConstants#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS}
226   *
227   * </ul> <p>
228   * @see #setProgramName(String name)
229   */ public
230 int setProgramVersion(String version) {
231    return libsbmlJNI.SBMLWriter_setProgramVersion(swigCPtr, this, version);
232  }
233
234  
235/**
236   * Writes the given SBML document to filename.
237   <p>
238   * If the given filename ends with the suffix <code>&quot;.gz&quot;</code>
239(for example, <code>&quot;myfile.xml.gz&quot;</code>), libSBML assumes the
240caller wants the file to be written compressed in <em>gzip</em> format.
241Similarly, if the given filename ends with <code>&quot;.zip&quot;</code> or
242<code>&quot;.bz2&quot;</code>, libSBML assumes the caller wants the file to
243be compressed in <em>zip</em> or <em>bzip2</em> format (respectively).
244Files whose names lack these suffixes will be written uncompressed.
245<em>Special considerations for the zip format</em>: If the given filename
246ends with <code>&quot;.zip&quot;</code>, the file placed in the zip archive
247will have the suffix <code>&quot;.xml&quot;</code> or
248<code>&quot;.sbml&quot;</code>.  For example, the file in the zip archive
249will be named <code>&quot;test.xml&quot;</code> if the given filename is
250<code>&quot;test.xml.zip&quot;</code> or <code>&quot;test.zip&quot;</code>.
251Similarly, the filename in the archive will be
252<code>&quot;test.sbml&quot;</code> if the given filename is
253<code>&quot;test.sbml.zip&quot;</code>.
254
255   <p>
256   * @param d the SBML document to be written.
257   <p>
258   * @param filename the name or full pathname of the file where the SBML
259   * is to be written. 
260   <p>
261   * @return <code>true</code> on success and <code>false</code> if the filename could not be
262   * opened for writing.
263   <p>
264   * @note To write a gzip/zip file, libSBML needs to be configured and linked with
265the <a target="_blank" href="http://www.zlib.net/">zlib</a> library at
266compile time.  It also needs to be linked with the <a target="_blank"
267href="">bzip2</a> library to write files in <em>bzip2</em> format.  (Both
268of these are the default configurations for libSBML.)  Errors about
269unreadable files will be logged and this method will return
270<code>false</code> if a compressed filename is given and libSBML was
271<em>not</em> linked with the corresponding required library.
272
273   <p>
274   * @see #setProgramVersion(String version)
275   * @see #setProgramName(String name)
276   */ public
277 boolean writeSBML(SBMLDocument d, String filename) {
278    return libsbmlJNI.SBMLWriter_writeSBML__SWIG_0(swigCPtr, this, SBMLDocument.getCPtr(d), d, libsbml.getAbsolutePath(filename));
279  }
280
281  
282/**
283   * Writes the given SBML document to the output stream.
284   <p>
285   * @param d the SBML document to be written.
286   <p>
287   * @param stream the stream object where the SBML is to be written.
288   <p>
289   * @return <code>true</code> on success and <code>false</code> if one of the underlying
290   * parser components fail (rare).
291   <p>
292   * @see #setProgramVersion(String version)
293   * @see #setProgramName(String name)
294   */ public
295 boolean writeSBML(SBMLDocument d, OStream stream) {
296    return libsbmlJNI.SBMLWriter_writeSBML__SWIG_1(swigCPtr, this, SBMLDocument.getCPtr(d), d, SWIGTYPE_p_std__ostream.getCPtr(stream.get_ostream()), stream);
297  }
298
299  
300/** * @internal */ public
301 String writeToString(SBMLDocument d) {
302    return libsbmlJNI.SBMLWriter_writeToString(swigCPtr, this, SBMLDocument.getCPtr(d), d);
303  }
304
305  
306/**
307   * Writes the given SBML document to filename.
308   <p>
309   * If the given filename ends with the suffix <code>&quot;.gz&quot;</code>
310(for example, <code>&quot;myfile.xml.gz&quot;</code>), libSBML assumes the
311caller wants the file to be written compressed in <em>gzip</em> format.
312Similarly, if the given filename ends with <code>&quot;.zip&quot;</code> or
313<code>&quot;.bz2&quot;</code>, libSBML assumes the caller wants the file to
314be compressed in <em>zip</em> or <em>bzip2</em> format (respectively).
315Files whose names lack these suffixes will be written uncompressed.
316<em>Special considerations for the zip format</em>: If the given filename
317ends with <code>&quot;.zip&quot;</code>, the file placed in the zip archive
318will have the suffix <code>&quot;.xml&quot;</code> or
319<code>&quot;.sbml&quot;</code>.  For example, the file in the zip archive
320will be named <code>&quot;test.xml&quot;</code> if the given filename is
321<code>&quot;test.xml.zip&quot;</code> or <code>&quot;test.zip&quot;</code>.
322Similarly, the filename in the archive will be
323<code>&quot;test.sbml&quot;</code> if the given filename is
324<code>&quot;test.sbml.zip&quot;</code>.
325
326   <p>
327   * @param d the SBML document to be written.
328   <p>
329   * @param filename the name or full pathname of the file where the SBML
330   * is to be written. 
331   <p>
332   * @return <code>true</code> on success and <code>false</code> if the filename could not be
333   * opened for writing.
334   <p>
335   * @note To write a gzip/zip file, libSBML needs to be configured and linked with
336the <a target="_blank" href="http://www.zlib.net/">zlib</a> library at
337compile time.  It also needs to be linked with the <a target="_blank"
338href="">bzip2</a> library to write files in <em>bzip2</em> format.  (Both
339of these are the default configurations for libSBML.)  Errors about
340unreadable files will be logged and this method will return
341<code>false</code> if a compressed filename is given and libSBML was
342<em>not</em> linked with the corresponding required library.
343
344   <p>
345   * @see #setProgramVersion(String version)
346   * @see #setProgramName(String name)
347   */ public
348 boolean writeSBMLToFile(SBMLDocument d, String filename) {
349    return libsbmlJNI.SBMLWriter_writeSBMLToFile(swigCPtr, this, SBMLDocument.getCPtr(d), d, libsbml.getAbsolutePath(filename));
350  }
351
352  
353/**
354   * Writes the given SBML document to an in-memory string and returns a
355   * pointer to it.
356   <p>
357   * The string is owned by the caller and should be freed (with <code>free</code>())
358   * when no longer needed.
359   <p>
360   * @param d the SBML document to be written.
361   <p>
362   * @return the string on success and <code>0</code> if one of the underlying parser
363   * components fail.
364   <p>
365   * @see #setProgramVersion(String version)
366   * @see #setProgramName(String name)
367   */ public
368 String writeSBMLToString(SBMLDocument d) {
369    return libsbmlJNI.SBMLWriter_writeSBMLToString(swigCPtr, this, SBMLDocument.getCPtr(d), d);
370  }
371
372  
373/**
374   * Predicate returning <code>true</code> if this copy of libSBML has been linked
375   * with the <em>zlib</em> library.
376   <p>
377   * LibSBML supports reading and writing files compressed with either
378   * bzip2 or zip/gzip compression.  The facility depends on libSBML having
379   * been compiled with the necessary support libraries.  This method
380   * allows a calling program to inquire whether that is the case for the
381   * copy of libSBML it is using.
382   <p>
383   * @return <code>true</code> if libSBML is linked with zlib, <code>false</code> otherwise.
384   <p>
385   * 
386   <p>
387   * @see SBMLWriter#hasBzip2() 
388   */ public
389 static boolean hasZlib() {
390    return libsbmlJNI.SBMLWriter_hasZlib();
391  }
392
393  
394/**
395   * Predicate returning <code>true</code> if this copy of libSBML has been linked
396   * with the <em>bzip2</em> library.
397   <p>
398   * LibSBML supports reading and writing files compressed with either
399   * bzip2 or zip/gzip compression.  The facility depends on libSBML having
400   * been compiled with the necessary support libraries.  This method
401   * allows a calling program to inquire whether that is the case for the
402   * copy of libSBML it is using.
403   <p>
404   * @return <code>true</code> if libSBML is linked with bzip2, <code>false</code> otherwise.
405   <p>
406   * 
407   <p>
408   * @see SBMLWriter#hasZlib() 
409   */ public
410 static boolean hasBzip2() {
411    return libsbmlJNI.SBMLWriter_hasBzip2();
412  }
413
414}