001/* ----------------------------------------------------------------------------
002 * This file was automatically generated by SWIG (http://www.swig.org).
003 * Version 3.0.8
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 *  Whole-document SBML Level/Version converter.
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.  It is a class used in
017the implementation of extra functionality provided by libSBML.
018</p>
019
020 <p>
021 * This SBML converter takes an SBML document having one SBML Level+Version
022 * combination, and attempts to convert it to an SBML document having a
023 * different Level+Version combination.
024 <p>
025 * This class is also the basis for
026 * {@link SBMLDocument#setLevelAndVersion(long, long, boolean)}.
027 <p>
028 * <h2>Configuration and use of {@link SBMLLevelVersionConverter}</h2>
029 <p>
030 * {@link SBMLLevelVersionConverter} is enabled by creating a {@link ConversionProperties}
031 * object with the option <code>'setLevelAndVersion'</code>, and passing this
032 * properties object to {@link SBMLDocument#convert(ConversionProperties)}.  The target SBML Level and Version
033 * combination are determined by the value of the SBML namespace set on the
034 * {@link ConversionProperties} object (using
035 * {@link ConversionProperties#setTargetNamespaces(SBMLNamespaces targetNS)}).
036 <p>
037 * In addition, this converter offers the following options:
038 <p>
039 * <ul>
040 * <li> <code>'strict':</code> If this option has the value <code>true</code>, then the validity
041 * of the SBML document will be strictly preserved.  This means that SBML
042 * validation will be performed, and if the original model is not valid or
043 * semantics cannot be preserved in the converted model, then conversion will
044 * not be performed.  Conversely, if this option is set to <code>false</code>, model
045 * conversion will always be performed; if any errors are detected related to
046 * altered semantics, the errors will be logged in the usual way (i.e., the
047 * error log on the {@link SBMLDocument} object).
048 <p>
049 * <li> <code>'addDefaultUnits':</code> By default, a conversion from SBML Level&nbsp;2
050 * to Level&nbsp;3 will explicitly add {@link UnitDefinition} objects and unit
051 * attributes on the {@link Model} object to define units that are implicitly defined
052 * in SBML Level&nbsp;2.  This is usually desirable because in SBML
053 * Level&nbsp;3, there are no default units and a conversion from
054 * Level&nbsp;2 that did <em>not</em> add unit definitions would actually result
055 * in a loss of information.  However, some users or software tools may not
056 * need or want this, or worse, may be fooled into thinking that libSBML has
057 * somehow inferred the proper units for model quantities.  (It has not; it
058 * merely adds generic predefined units.)  This option lets callers control
059 * this behavior.
060 *
061 * </ul> <p>
062 * <p>
063 * <h2>General information about the use of SBML converters</h2>
064 <p>
065 * The use of all the converters follows a similar approach.  First, one
066 * creates a {@link ConversionProperties} object and calls
067 * {@link ConversionProperties#addOption(ConversionOption)}
068 * on this object with one arguments: a text string that identifies the desired
069 * converter.  (The text string is specific to each converter; consult the
070 * documentation for a given converter to find out how it should be enabled.)
071 <p>
072 * Next, for some converters, the caller can optionally set some
073 * converter-specific properties using additional calls to
074 * {@link ConversionProperties#addOption(ConversionOption)}.
075 * Many converters provide the ability to
076 * configure their behavior to some extent; this is realized through the use
077 * of properties that offer different options.  The default property values
078 * for each converter can be interrogated using the method
079 * {@link SBMLConverter#getDefaultProperties()} on the converter class in question .
080 <p>
081 * Finally, the caller should invoke the method
082 * {@link SBMLDocument#convert(ConversionProperties)}
083 * with the {@link ConversionProperties} object as an argument.
084 <p>
085 * <h3>Example of invoking an SBML converter</h3>
086 <p>
087 * The following code fragment illustrates an example using
088 * {@link SBMLReactionConverter}, which is invoked using the option string 
089 * <code>'replaceReactions':</code>
090 <p>
091<pre class='fragment'>
092{@link ConversionProperties} props = new {@link ConversionProperties}();
093if (props != null) {
094  props.addOption('replaceReactions');
095} else {
096  // Deal with error.
097}
098</pre>
099<p>
100 * In the case of {@link SBMLReactionConverter}, there are no options to affect
101 * its behavior, so the next step is simply to invoke the converter on
102 * an {@link SBMLDocument} object.  Continuing the example code:
103 <p>
104<pre class='fragment'>
105  // Assume that the variable 'document' has been set to an {@link SBMLDocument} object.
106  status = document.convert(config);
107  if (status != libsbml.LIBSBML_OPERATION_SUCCESS)
108  {
109    // Handle error somehow.
110    System.out.println('Error: conversion failed due to the following:');
111    document.printErrors();
112  }
113</pre>
114<p>
115 * Here is an example of using a converter that offers an option. The
116 * following code invokes {@link SBMLStripPackageConverter} to remove the
117 * SBML Level&nbsp;3 <em>Layout</em> package from a model.  It sets the name
118 * of the package to be removed by adding a value for the option named
119 * <code>'package'</code> defined by that converter:
120 <p>
121<pre class='fragment'>
122{@link ConversionProperties} config = new {@link ConversionProperties}();
123if (config != None) {
124  config.addOption('stripPackage');
125  config.addOption('package', 'layout');
126  status = document.convert(config);
127  if (status != LIBSBML_OPERATION_SUCCESS) {
128    // Handle error somehow.
129    System.out.println('Error: unable to strip the {@link Layout} package');
130    document.printErrors();
131  }
132} else {
133  // Handle error somehow.
134  System.out.println('Error: unable to create {@link ConversionProperties} object');
135}
136</pre>
137<p>
138 * <h3>Available SBML converters in libSBML</h3>
139 <p>
140 * LibSBML provides a number of built-in converters; by convention, their
141 * names end in <em>Converter</em>. The following are the built-in converters
142 * provided by libSBML 5.12.0
143:
144 <p>
145 * <p>
146 * <ul>
147 * <li> {@link CobraToFbcConverter}
148 * <li> {@link CompFlatteningConverter}
149 * <li> {@link FbcToCobraConverter}
150 * <li> {@link FbcV1ToV2Converter}
151 * <li> {@link FbcV2ToV1Converter}
152 * <li> {@link SBMLFunctionDefinitionConverter}
153 * <li> {@link SBMLIdConverter}
154 * <li> {@link SBMLInferUnitsConverter}
155 * <li> {@link SBMLInitialAssignmentConverter}
156 * <li> {@link SBMLLevel1Version1Converter}
157 * <li> {@link SBMLLevelVersionConverter}
158 * <li> {@link SBMLLocalParameterConverter}
159 * <li> {@link SBMLReactionConverter}
160 * <li> {@link SBMLRuleConverter}
161 * <li> {@link SBMLStripPackageConverter}
162 * <li> {@link SBMLUnitsConverter}
163 *
164 * </ul>
165 */
166
167public class SBMLLevelVersionConverter extends SBMLConverter {
168   private long swigCPtr;
169
170   protected SBMLLevelVersionConverter(long cPtr, boolean cMemoryOwn)
171   {
172     super(libsbmlJNI.SBMLLevelVersionConverter_SWIGUpcast(cPtr), cMemoryOwn);
173     swigCPtr = cPtr;
174   }
175
176   protected static long getCPtr(SBMLLevelVersionConverter obj)
177   {
178     return (obj == null) ? 0 : obj.swigCPtr;
179   }
180
181   protected static long getCPtrAndDisown (SBMLLevelVersionConverter obj)
182   {
183     long ptr = 0;
184
185     if (obj != null)
186     {
187       ptr             = obj.swigCPtr;
188       obj.swigCMemOwn = false;
189     }
190
191     return ptr;
192   }
193
194  protected void finalize() {
195    delete();
196  }
197
198  public synchronized void delete() {
199    if (swigCPtr != 0) {
200      if (swigCMemOwn) {
201        swigCMemOwn = false;
202        libsbmlJNI.delete_SBMLLevelVersionConverter(swigCPtr);
203      }
204      swigCPtr = 0;
205    }
206    super.delete();
207  }
208
209  
210/** * @internal */ public
211 static void init() {
212    libsbmlJNI.SBMLLevelVersionConverter_init();
213  }
214
215  
216/**
217   * Creates a new {@link SBMLLevelVersionConverter} object.
218   */ public
219 SBMLLevelVersionConverter() {
220    this(libsbmlJNI.new_SBMLLevelVersionConverter__SWIG_0(), true);
221  }
222
223  
224/**
225   * Copy constructor; creates a copy of an {@link SBMLLevelVersionConverter}
226   * object.
227   <p>
228   * @param obj the {@link SBMLLevelVersionConverter} object to copy.
229   */ public
230 SBMLLevelVersionConverter(SBMLLevelVersionConverter obj) {
231    this(libsbmlJNI.new_SBMLLevelVersionConverter__SWIG_1(SBMLLevelVersionConverter.getCPtr(obj), obj), true);
232  }
233
234  
235/**
236   * Creates and returns a deep copy of this {@link SBMLLevelVersionConverter}
237   * object.
238   <p>
239   * @return a (deep) copy of this converter.
240   */ public
241 SBMLConverter cloneObject() {
242    long cPtr = libsbmlJNI.SBMLLevelVersionConverter_cloneObject(swigCPtr, this);
243    return (cPtr == 0) ? null : new SBMLLevelVersionConverter(cPtr, true);
244  }
245
246  
247/**
248   * Returns <code>true</code> if this converter object's properties match the given
249   * properties.
250   <p>
251   * A typical use of this method involves creating a {@link ConversionProperties}
252   * object, setting the options desired, and then calling this method on
253   * an {@link SBMLLevelVersionConverter} object to find out if the object's
254   * property values match the given ones.  This method is also used by
255   * {@link SBMLConverterRegistry#getConverterFor(ConversionProperties)}
256   * to search across all registered converters for one matching particular
257   * properties.
258   <p>
259   * @param props the properties to match.
260   <p>
261   * @return <code>true</code> if this converter's properties match, <code>false</code>
262   * otherwise.
263   */ public
264 boolean matchesProperties(ConversionProperties props) {
265    return libsbmlJNI.SBMLLevelVersionConverter_matchesProperties(swigCPtr, this, ConversionProperties.getCPtr(props), props);
266  }
267
268  
269/**
270   * Perform the conversion.
271   <p>
272   * This method causes the converter to do the actual conversion work,
273   * that is, to convert the {@link SBMLDocument} object set by
274   * {@link SBMLConverter#setDocument(SBMLDocument)} and
275   * with the configuration options set by
276   * {@link SBMLConverter#setProperties(ConversionProperties)}.
277   <p>
278   * <p>
279 * @return integer value indicating success/failure of the
280 * function.   The possible values
281 * returned by this function are:
282   * <ul>
283   * <li> {@link libsbmlConstants#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS}
284   * <li> {@link libsbmlConstants#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED}
285   * <li> {@link libsbmlConstants#LIBSBML_CONV_INVALID_TARGET_NAMESPACE LIBSBML_CONV_INVALID_TARGET_NAMESPACE}
286   * <li> {@link libsbmlConstants#LIBSBML_CONV_PKG_CONVERSION_NOT_AVAILABLE LIBSBML_CONV_PKG_CONVERSION_NOT_AVAILABLE}
287   * <li> {@link libsbmlConstants#LIBSBML_CONV_INVALID_SRC_DOCUMENT LIBSBML_CONV_INVALID_SRC_DOCUMENT}
288   * </ul>
289   */ public
290 int convert() {
291    return libsbmlJNI.SBMLLevelVersionConverter_convert(swigCPtr, this);
292  }
293
294  
295/**
296   * Returns the default properties of this converter.
297   <p>
298   * A given converter exposes one or more properties that can be adjusted
299   * in order to influence the behavior of the converter.  This method
300   * returns the <em>default</em> property settings for this converter.  It is
301   * meant to be called in order to discover all the settings for the
302   * converter object.
303   <p>
304   * @return the {@link ConversionProperties} object describing the default properties
305   * for this converter.
306   */ public
307 ConversionProperties getDefaultProperties() {
308    return new ConversionProperties(libsbmlJNI.SBMLLevelVersionConverter_getDefaultProperties(swigCPtr, this), true);
309  }
310
311  
312/**
313   * Returns the target SBML Level for the conversion.
314   <p>
315   * @return an integer indicating the SBML Level.
316   */ public
317 long getTargetLevel() {
318    return libsbmlJNI.SBMLLevelVersionConverter_getTargetLevel(swigCPtr, this);
319  }
320
321  
322/**
323   * Returns the target SBML Version for the conversion.
324   <p>
325   * @return an integer indicating the Version within the SBML Level.
326   */ public
327 long getTargetVersion() {
328    return libsbmlJNI.SBMLLevelVersionConverter_getTargetVersion(swigCPtr, this);
329  }
330
331  
332/**
333   * Returns the flag indicating whether the conversion has been set to 'strict'.
334   <p>
335   * @return <code>true</code> if strict validity has been requested, <code>false</code>
336   * otherwise.
337   */ public
338 boolean getValidityFlag() {
339    return libsbmlJNI.SBMLLevelVersionConverter_getValidityFlag(swigCPtr, this);
340  }
341
342  
343/**
344   * Returns the flag indicating whether default units should be added when
345   * converting to L3 or not.
346   <p>
347   * @return <code>true</code> if default units should be added, <code>false</code>
348   * otherwise.
349   */ public
350 boolean getAddDefaultUnits() {
351    return libsbmlJNI.SBMLLevelVersionConverter_getAddDefaultUnits(swigCPtr, this);
352  }
353
354}