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 * <span class="pkg-marker pkg-color-fbc"><a href="group__fbc.html">fbc</a></span>
013 SBML Level 3 &ldquo;fbc&rdquo; to COBRA converter.
014 <p>
015 * <p style='color: #777; font-style: italic'>
016This class of objects is defined by libSBML only and has no direct
017equivalent in terms of SBML components.  It is a class used in
018the implementation of extra functionality provided by libSBML.
019</p>
020
021 <p>
022 * This converter takes a model in &ldquo;fbc&rdquo; Version&nbsp;2 format
023 * and converts it to COBRA format.
024 <p>
025 * {@link FbcToCobraConverter} is enabled by creating a {@link ConversionProperties} object
026 * with the option <code>'convert fbc to cobra'</code> (literally that
027 * full string, including the spaces), and passing this properties object to
028 * {@link SBMLDocument#convert(ConversionProperties)}.  The converter
029 * offers one option:
030 <p>
031 * <ul>
032 * <li> <code>'overwriteReactionNotes':</code> should gene associations be written into
033 * the 'notes' subelement attached to {@link Reaction} objects, even if a {@link Reaction}
034 * already has 'notes' content?
035 *
036 * </ul> <p>
037 * <p>
038 * <h2>General information about the use of SBML converters</h2>
039 <p>
040 * The use of all the converters follows a similar approach.  First, one
041 * creates a {@link ConversionProperties} object and calls
042 * {@link ConversionProperties#addOption(ConversionOption)}
043 * on this object with one argument: a text string that identifies the desired
044 * converter.  (The text string is specific to each converter; consult the
045 * documentation for a given converter to find out how it should be enabled.)
046 <p>
047 * Next, for some converters, the caller can optionally set some
048 * converter-specific properties using additional calls to
049 * {@link ConversionProperties#addOption(ConversionOption)}.
050 * Many converters provide the ability to
051 * configure their behavior to some extent; this is realized through the use
052 * of properties that offer different options.  The default property values
053 * for each converter can be interrogated using the method
054 * {@link SBMLConverter#getDefaultProperties()} on the converter class in question .
055 <p>
056 * Finally, the caller should invoke the method
057 * {@link SBMLDocument#convert(ConversionProperties)}
058 * with the {@link ConversionProperties} object as an argument.
059 <p>
060 * <h3>Example of invoking an SBML converter</h3>
061 <p>
062 * The following code fragment illustrates an example using
063 * {@link SBMLReactionConverter}, which is invoked using the option string 
064 * <code>'replaceReactions':</code>
065 <p>
066<pre class='fragment'>
067{@link ConversionProperties} props = new {@link ConversionProperties}();
068if (props != null) {
069  props.addOption('replaceReactions');
070} else {
071  // Deal with error.
072}
073</pre>
074<p>
075 * In the case of {@link SBMLReactionConverter}, there are no options to affect
076 * its behavior, so the next step is simply to invoke the converter on
077 * an {@link SBMLDocument} object.  Continuing the example code:
078 <p>
079<pre class='fragment'>
080  // Assume that the variable 'document' has been set to an {@link SBMLDocument} object.
081  status = document.convert(config);
082  if (status != libsbml.LIBSBML_OPERATION_SUCCESS)
083  {
084    // Handle error somehow.
085    System.out.println('Error: conversion failed due to the following:');
086    document.printErrors();
087  }
088</pre>
089<p>
090 * Here is an example of using a converter that offers an option. The
091 * following code invokes {@link SBMLStripPackageConverter} to remove the
092 * SBML Level&nbsp;3 <em>Layout</em> package from a model.  It sets the name
093 * of the package to be removed by adding a value for the option named
094 * <code>'package'</code> defined by that converter:
095 <p>
096<pre class='fragment'>
097{@link ConversionProperties} config = new {@link ConversionProperties}();
098if (config != None) {
099  config.addOption('stripPackage');
100  config.addOption('package', 'layout');
101  status = document.convert(config);
102  if (status != LIBSBML_OPERATION_SUCCESS) {
103    // Handle error somehow.
104    System.out.println('Error: unable to strip the {@link Layout} package');
105    document.printErrors();
106  }
107} else {
108  // Handle error somehow.
109  System.out.println('Error: unable to create {@link ConversionProperties} object');
110}
111</pre>
112<p>
113 * <h3>Available SBML converters in libSBML</h3>
114 <p>
115 * LibSBML provides a number of built-in converters; by convention, their
116 * names end in <em>Converter</em>. The following are the built-in converters
117 * provided by libSBML 5.15.2
118:
119 <p>
120 * <p>
121 * <ul>
122 * <li> ArraysFlatteningConverter
123 * <li> {@link CobraToFbcConverter}
124 * <li> {@link CompFlatteningConverter}
125 * <li> {@link FbcToCobraConverter}
126 * <li> {@link FbcV1ToV2Converter}
127 * <li> {@link FbcV2ToV1Converter}
128 * <li> {@link SBMLFunctionDefinitionConverter}
129 * <li> {@link SBMLIdConverter}
130 * <li> {@link SBMLInferUnitsConverter}
131 * <li> {@link SBMLInitialAssignmentConverter}
132 * <li> {@link SBMLLevel1Version1Converter}
133 * <li> {@link SBMLLevelVersionConverter}
134 * <li> {@link SBMLLocalParameterConverter}
135 * <li> SBMLRateOfConverter
136 * <li> {@link SBMLReactionConverter}
137 * <li> {@link SBMLRuleConverter}
138 * <li> {@link SBMLStripPackageConverter}
139 * <li> {@link SBMLUnitsConverter}
140 *
141 * </ul>
142 */
143
144public class FbcToCobraConverter extends SBMLConverter {
145   private long swigCPtr;
146
147   protected FbcToCobraConverter(long cPtr, boolean cMemoryOwn)
148   {
149     super(libsbmlJNI.FbcToCobraConverter_SWIGUpcast(cPtr), cMemoryOwn);
150     swigCPtr = cPtr;
151   }
152
153   protected static long getCPtr(FbcToCobraConverter obj)
154   {
155     return (obj == null) ? 0 : obj.swigCPtr;
156   }
157
158   protected static long getCPtrAndDisown (FbcToCobraConverter obj)
159   {
160     long ptr = 0;
161
162     if (obj != null)
163     {
164       ptr             = obj.swigCPtr;
165       obj.swigCMemOwn = false;
166     }
167
168     return ptr;
169   }
170
171  protected void finalize() {
172    delete();
173  }
174
175  public synchronized void delete() {
176    if (swigCPtr != 0) {
177      if (swigCMemOwn) {
178        swigCMemOwn = false;
179        libsbmlJNI.delete_FbcToCobraConverter(swigCPtr);
180      }
181      swigCPtr = 0;
182    }
183    super.delete();
184  }
185
186  
187/** * @internal */ public
188 static void init() {
189    libsbmlJNI.FbcToCobraConverter_init();
190  }
191
192  
193/**
194   * Creates a new {@link FbcToCobraConverter} object.
195   */ public
196 FbcToCobraConverter() {
197    this(libsbmlJNI.new_FbcToCobraConverter__SWIG_0(), true);
198  }
199
200  
201/**
202   * Copy constructor; creates a copy of an {@link FbcToCobraConverter}
203   * object.
204   <p>
205   * @param orig the {@link FbcToCobraConverter} object to copy.
206   */ public
207 FbcToCobraConverter(FbcToCobraConverter orig) {
208    this(libsbmlJNI.new_FbcToCobraConverter__SWIG_1(FbcToCobraConverter.getCPtr(orig), orig), true);
209  }
210
211  
212/**
213   * Creates and returns a deep copy of this {@link FbcToCobraConverter} object.
214   <p>
215   * @return a (deep) copy of this {@link FbcToCobraConverter}.
216   */ public
217 SBMLConverter cloneObject() {
218    long cPtr = libsbmlJNI.FbcToCobraConverter_cloneObject(swigCPtr, this);
219    return (cPtr == 0) ? null : new FbcToCobraConverter(cPtr, true);
220  }
221
222  
223/**
224   * Returns <code>true</code> if this converter object's properties match the given
225   * properties.
226   <p>
227   * A typical use of this method involves creating a {@link ConversionProperties}
228   * object, setting the options desired, and then calling this method on
229   * an {@link FbcToCobraConverter} object to find out if the object's
230   * property values match the given ones.  This method is also used by
231   * {@link SBMLConverterRegistry#getConverterFor(ConversionProperties)}
232   * to search across all registered converters for one matching particular
233   * properties.
234   <p>
235   * @param props the properties to match.
236   <p>
237   * @return <code>true</code> if this converter's properties match, <code>false</code>
238   * otherwise.
239   */ public
240 boolean matchesProperties(ConversionProperties props) {
241    return libsbmlJNI.FbcToCobraConverter_matchesProperties(swigCPtr, this, ConversionProperties.getCPtr(props), props);
242  }
243
244  
245/**
246   * Perform the conversion.
247   <p>
248   * This method causes the converter to do the actual conversion work,
249   * that is, to convert the {@link SBMLDocument} object set by
250   * {@link SBMLConverter#setDocument(SBMLDocument)} and
251   * with the configuration options set by
252   * {@link SBMLConverter#setProperties(ConversionProperties)}.
253   <p>
254   * <p>
255 * @return integer value indicating success/failure of the
256 * function.   The possible values
257 * returned by this function are:
258   * <ul>
259   * <li> {@link libsbmlConstants#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS}
260   * <li> {@link libsbmlConstants#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED}
261   * <li> {@link libsbmlConstants#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT}
262   * </ul>
263   */ public
264 int convert() {
265    return libsbmlJNI.FbcToCobraConverter_convert(swigCPtr, this);
266  }
267
268  
269/**
270   * Returns the default properties of this converter.
271   <p>
272   * A given converter exposes one or more properties that can be adjusted
273   * in order to influence the behavior of the converter.  This method
274   * returns the <em>default</em> property settings for this converter.  It is
275   * meant to be called in order to discover all the settings for the
276   * converter object.
277   <p>
278   * @return the {@link ConversionProperties} object describing the default properties
279   * for this converter.
280   */ public
281 ConversionProperties getDefaultProperties() {
282    return new ConversionProperties(libsbmlJNI.FbcToCobraConverter_getDefaultProperties(swigCPtr, this), true);
283  }
284
285}