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 * Converter to replace reactions with SBML <em>rate rules</em>. 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 converter will take an SBML model and replace the definitions of 022 * reactions in the model with definitions of SBML rate rules. Equivalent 023 * {@link RateRule} objects are only created for species mentioned in reactions that 024 * have {@link KineticLaw} subobjects, since those are the only reactions that have 025 * an effect on the rates of change of species in the model; however, the 026 * converter removes all {@link Reaction} objects in the model after it is done. 027 <p> 028 * <h2>Configuration and use of {@link SBMLReactionConverter}</h2> 029 <p> 030 * {@link SBMLReactionConverter} is enabled by creating a {@link ConversionProperties} object 031 * with the option <code>'replaceReactions'</code>, and passing this properties object 032 * to {@link SBMLDocument#convert(ConversionProperties)}. This 033 * converter does not offer any additional configuration options. 034 <p> 035 * <p> 036 * <h2>General information about the use of SBML converters</h2> 037 <p> 038 * The use of all the converters follows a similar approach. First, one 039 * creates a {@link ConversionProperties} object and calls 040 * {@link ConversionProperties#addOption(ConversionOption)} 041 * on this object with one arguments: a text string that identifies the desired 042 * converter. (The text string is specific to each converter; consult the 043 * documentation for a given converter to find out how it should be enabled.) 044 <p> 045 * Next, for some converters, the caller can optionally set some 046 * converter-specific properties using additional calls to 047 * {@link ConversionProperties#addOption(ConversionOption)}. 048 * Many converters provide the ability to 049 * configure their behavior to some extent; this is realized through the use 050 * of properties that offer different options. The default property values 051 * for each converter can be interrogated using the method 052 * {@link SBMLConverter#getDefaultProperties()} on the converter class in question . 053 <p> 054 * Finally, the caller should invoke the method 055 * {@link SBMLDocument#convert(ConversionProperties)} 056 * with the {@link ConversionProperties} object as an argument. 057 <p> 058 * <h3>Example of invoking an SBML converter</h3> 059 <p> 060 * The following code fragment illustrates an example using 061 * {@link SBMLReactionConverter}, which is invoked using the option string 062 * <code>'replaceReactions':</code> 063 <p> 064<pre class='fragment'> 065{@link ConversionProperties} props = new {@link ConversionProperties}(); 066if (props != null) { 067 props.addOption('replaceReactions'); 068} else { 069 // Deal with error. 070} 071</pre> 072<p> 073 * In the case of {@link SBMLReactionConverter}, there are no options to affect 074 * its behavior, so the next step is simply to invoke the converter on 075 * an {@link SBMLDocument} object. Continuing the example code: 076 <p> 077<pre class='fragment'> 078 // Assume that the variable 'document' has been set to an {@link SBMLDocument} object. 079 status = document.convert(config); 080 if (status != libsbml.LIBSBML_OPERATION_SUCCESS) 081 { 082 // Handle error somehow. 083 System.out.println('Error: conversion failed due to the following:'); 084 document.printErrors(); 085 } 086</pre> 087<p> 088 * Here is an example of using a converter that offers an option. The 089 * following code invokes {@link SBMLStripPackageConverter} to remove the 090 * SBML Level 3 <em>Layout</em> package from a model. It sets the name 091 * of the package to be removed by adding a value for the option named 092 * <code>'package'</code> defined by that converter: 093 <p> 094<pre class='fragment'> 095{@link ConversionProperties} config = new {@link ConversionProperties}(); 096if (config != None) { 097 config.addOption('stripPackage'); 098 config.addOption('package', 'layout'); 099 status = document.convert(config); 100 if (status != LIBSBML_OPERATION_SUCCESS) { 101 // Handle error somehow. 102 System.out.println('Error: unable to strip the {@link Layout} package'); 103 document.printErrors(); 104 } 105} else { 106 // Handle error somehow. 107 System.out.println('Error: unable to create {@link ConversionProperties} object'); 108} 109</pre> 110<p> 111 * <h3>Available SBML converters in libSBML</h3> 112 <p> 113 * LibSBML provides a number of built-in converters; by convention, their 114 * names end in <em>Converter</em>. The following are the built-in converters 115 * provided by libSBML 5.12.0 116: 117 <p> 118 * <p> 119 * <ul> 120 * <li> {@link CobraToFbcConverter} 121 * <li> {@link CompFlatteningConverter} 122 * <li> {@link FbcToCobraConverter} 123 * <li> {@link FbcV1ToV2Converter} 124 * <li> {@link FbcV2ToV1Converter} 125 * <li> {@link SBMLFunctionDefinitionConverter} 126 * <li> {@link SBMLIdConverter} 127 * <li> {@link SBMLInferUnitsConverter} 128 * <li> {@link SBMLInitialAssignmentConverter} 129 * <li> {@link SBMLLevel1Version1Converter} 130 * <li> {@link SBMLLevelVersionConverter} 131 * <li> {@link SBMLLocalParameterConverter} 132 * <li> {@link SBMLReactionConverter} 133 * <li> {@link SBMLRuleConverter} 134 * <li> {@link SBMLStripPackageConverter} 135 * <li> {@link SBMLUnitsConverter} 136 * 137 * </ul> 138 */ 139 140public class SBMLReactionConverter extends SBMLConverter { 141 private long swigCPtr; 142 143 protected SBMLReactionConverter(long cPtr, boolean cMemoryOwn) 144 { 145 super(libsbmlJNI.SBMLReactionConverter_SWIGUpcast(cPtr), cMemoryOwn); 146 swigCPtr = cPtr; 147 } 148 149 protected static long getCPtr(SBMLReactionConverter obj) 150 { 151 return (obj == null) ? 0 : obj.swigCPtr; 152 } 153 154 protected static long getCPtrAndDisown (SBMLReactionConverter obj) 155 { 156 long ptr = 0; 157 158 if (obj != null) 159 { 160 ptr = obj.swigCPtr; 161 obj.swigCMemOwn = false; 162 } 163 164 return ptr; 165 } 166 167 protected void finalize() { 168 delete(); 169 } 170 171 public synchronized void delete() { 172 if (swigCPtr != 0) { 173 if (swigCMemOwn) { 174 swigCMemOwn = false; 175 libsbmlJNI.delete_SBMLReactionConverter(swigCPtr); 176 } 177 swigCPtr = 0; 178 } 179 super.delete(); 180 } 181 182 183/** * @internal */ public 184 static void init() { 185 libsbmlJNI.SBMLReactionConverter_init(); 186 } 187 188 189/** 190 * Creates a new {@link SBMLReactionConverter} object. 191 */ public 192 SBMLReactionConverter() { 193 this(libsbmlJNI.new_SBMLReactionConverter__SWIG_0(), true); 194 } 195 196 197/** 198 * Copy constructor; creates a copy of an {@link SBMLReactionConverter} 199 * object. 200 <p> 201 * @param obj the {@link SBMLReactionConverter} object to copy. 202 */ public 203 SBMLReactionConverter(SBMLReactionConverter obj) { 204 this(libsbmlJNI.new_SBMLReactionConverter__SWIG_1(SBMLReactionConverter.getCPtr(obj), obj), true); 205 } 206 207 208/** 209 * Creates and returns a deep copy of this {@link SBMLReactionConverter} 210 * object. 211 <p> 212 * @return a (deep) copy of this converter. 213 */ public 214 SBMLConverter cloneObject() { 215 long cPtr = libsbmlJNI.SBMLReactionConverter_cloneObject(swigCPtr, this); 216 return (cPtr == 0) ? null : new SBMLReactionConverter(cPtr, true); 217 } 218 219 220/** 221 * Returns <code>true</code> if this converter object's properties match the given 222 * properties. 223 <p> 224 * A typical use of this method involves creating a {@link ConversionProperties} 225 * object, setting the options desired, and then calling this method on 226 * an {@link SBMLReactionConverter} object to find out if the object's 227 * property values match the given ones. This method is also used by 228 * {@link SBMLConverterRegistry#getConverterFor(ConversionProperties)} 229 * to search across all registered converters for one matching particular 230 * properties. 231 <p> 232 * @param props the properties to match. 233 <p> 234 * @return <code>true</code> if this converter's properties match, <code>false</code> 235 * otherwise. 236 */ public 237 boolean matchesProperties(ConversionProperties props) { 238 return libsbmlJNI.SBMLReactionConverter_matchesProperties(swigCPtr, this, ConversionProperties.getCPtr(props), props); 239 } 240 241 242/** 243 * Perform the conversion. 244 <p> 245 * This method causes the converter to do the actual conversion work, 246 * that is, to convert the {@link SBMLDocument} object set by 247 * {@link SBMLConverter#setDocument(SBMLDocument)} and 248 * with the configuration options set by 249 * {@link SBMLConverter#setProperties(ConversionProperties)}. 250 <p> 251 * <p> 252 * @return integer value indicating success/failure of the 253 * function. The possible values 254 * returned by this function are: 255 * <ul> 256 * <li> {@link libsbmlConstants#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS} 257 * <li> {@link libsbmlConstants#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED} 258 * <li> {@link libsbmlConstants#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT} 259 * <li> {@link libsbmlConstants#LIBSBML_CONV_INVALID_SRC_DOCUMENT LIBSBML_CONV_INVALID_SRC_DOCUMENT} 260 * </ul> 261 */ public 262 int convert() { 263 return libsbmlJNI.SBMLReactionConverter_convert(swigCPtr, this); 264 } 265 266 267/** 268 * Returns the default properties of this converter. 269 <p> 270 * A given converter exposes one or more properties that can be adjusted 271 * in order to influence the behavior of the converter. This method 272 * returns the <em>default</em> property settings for this converter. It is 273 * meant to be called in order to discover all the settings for the 274 * converter object. 275 <p> 276 * @return the {@link ConversionProperties} object describing the default properties 277 * for this converter. 278 */ public 279 ConversionProperties getDefaultProperties() { 280 return new ConversionProperties(libsbmlJNI.SBMLReactionConverter_getDefaultProperties(swigCPtr, this), true); 281 } 282 283 284/** 285 * Sets the current SBML document to the given {@link SBMLDocument} object. 286 <p> 287 * @param doc the document to use for this conversion. 288 <p> 289 * <p> 290 * @return integer value indicating success/failure of the 291 * function. The possible values 292 * returned by this function are: 293 * <ul> 294 * <li> {@link libsbmlConstants#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS} 295 * </ul> 296 */ public 297 int setDocument(SBMLDocument doc) { 298 return libsbmlJNI.SBMLReactionConverter_setDocument(swigCPtr, this, SBMLDocument.getCPtr(doc), doc); 299 } 300 301}