001/* ---------------------------------------------------------------------------- 002 * This file was automatically generated by SWIG (http://www.swig.org). 003 * Version 3.0.7 004 * 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 * Base class for SBML converters. 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 * The {@link SBMLConverter} class is the base class for the various SBML 022 * <em>converters</em>: classes of objects that transform or convert SBML documents. 023 * These transformations can involve essentially anything that can be written 024 * algorithmically; examples include converting the units of measurement in a 025 * model, or converting from one Level+Version combination of SBML to 026 * another. Applications can also create their own converters by subclassing 027 * {@link SBMLConverter} and following the examples of the existing converters. 028 <p> 029 * <p> 030 * <h2>General information about the use of SBML converters</h2> 031 <p> 032 * The use of all the converters follows a similar approach. First, one 033 * creates a {@link ConversionProperties} object and calls 034 * {@link ConversionProperties#addOption(ConversionOption)} 035 * on this object with one arguments: a text string that identifies the desired 036 * converter. (The text string is specific to each converter; consult the 037 * documentation for a given converter to find out how it should be enabled.) 038 <p> 039 * Next, for some converters, the caller can optionally set some 040 * converter-specific properties using additional calls to 041 * {@link ConversionProperties#addOption(ConversionOption)}. 042 * Many converters provide the ability to 043 * configure their behavior to some extent; this is realized through the use 044 * of properties that offer different options. The default property values 045 * for each converter can be interrogated using the method 046 * {@link SBMLConverter#getDefaultProperties()} on the converter class in question . 047 <p> 048 * Finally, the caller should invoke the method 049 * {@link SBMLDocument#convert(ConversionProperties)} 050 * with the {@link ConversionProperties} object as an argument. 051 <p> 052 * <h3>Example of invoking an SBML converter</h3> 053 <p> 054 * The following code fragment illustrates an example using 055 * {@link SBMLReactionConverter}, which is invoked using the option string 056 * <code>'replaceReactions':</code> 057 <p> 058<pre class='fragment'> 059{@link ConversionProperties} props = new {@link ConversionProperties}(); 060if (props != null) { 061 props.addOption('replaceReactions'); 062} else { 063 // Deal with error. 064} 065</pre> 066<p> 067 * In the case of {@link SBMLReactionConverter}, there are no options to affect 068 * its behavior, so the next step is simply to invoke the converter on 069 * an {@link SBMLDocument} object. Continuing the example code: 070 <p> 071<pre class='fragment'> 072 // Assume that the variable 'document' has been set to an {@link SBMLDocument} object. 073 status = document.convert(config); 074 if (status != libsbml.LIBSBML_OPERATION_SUCCESS) 075 { 076 // Handle error somehow. 077 System.out.println('Error: conversion failed due to the following:'); 078 document.printErrors(); 079 } 080</pre> 081<p> 082 * Here is an example of using a converter that offers an option. The 083 * following code invokes {@link SBMLStripPackageConverter} to remove the 084 * SBML Level 3 <em>Layout</em> package from a model. It sets the name 085 * of the package to be removed by adding a value for the option named 086 * <code>'package'</code> defined by that converter: 087 <p> 088<pre class='fragment'> 089{@link ConversionProperties} config = new {@link ConversionProperties}(); 090if (config != None) { 091 config.addOption('stripPackage'); 092 config.addOption('package', 'layout'); 093 status = document.convert(config); 094 if (status != LIBSBML_OPERATION_SUCCESS) { 095 // Handle error somehow. 096 System.out.println('Error: unable to strip the {@link Layout} package'); 097 document.printErrors(); 098 } 099} else { 100 // Handle error somehow. 101 System.out.println('Error: unable to create {@link ConversionProperties} object'); 102} 103</pre> 104<p> 105 * <h3>Available SBML converters in libSBML</h3> 106 <p> 107 * LibSBML provides a number of built-in converters; by convention, their 108 * names end in <em>Converter</em>. The following are the built-in converters 109 * provided by libSBML 5.12.0 110: 111 <p> 112 * <p> 113 * <ul> 114 * <li> {@link CobraToFbcConverter} 115 * <li> {@link CompFlatteningConverter} 116 * <li> {@link FbcToCobraConverter} 117 * <li> {@link FbcV1ToV2Converter} 118 * <li> {@link FbcV2ToV1Converter} 119 * <li> {@link SBMLFunctionDefinitionConverter} 120 * <li> {@link SBMLIdConverter} 121 * <li> {@link SBMLInferUnitsConverter} 122 * <li> {@link SBMLInitialAssignmentConverter} 123 * <li> {@link SBMLLevel1Version1Converter} 124 * <li> {@link SBMLLevelVersionConverter} 125 * <li> {@link SBMLLocalParameterConverter} 126 * <li> {@link SBMLReactionConverter} 127 * <li> {@link SBMLRuleConverter} 128 * <li> {@link SBMLStripPackageConverter} 129 * <li> {@link SBMLUnitsConverter} 130 * 131 * </ul> 132 */ 133 134public class SBMLConverter { 135 private long swigCPtr; 136 protected boolean swigCMemOwn; 137 138 protected SBMLConverter(long cPtr, boolean cMemoryOwn) 139 { 140 swigCMemOwn = cMemoryOwn; 141 swigCPtr = cPtr; 142 } 143 144 protected static long getCPtr(SBMLConverter obj) 145 { 146 return (obj == null) ? 0 : obj.swigCPtr; 147 } 148 149 protected static long getCPtrAndDisown (SBMLConverter obj) 150 { 151 long ptr = 0; 152 153 if (obj != null) 154 { 155 ptr = obj.swigCPtr; 156 obj.swigCMemOwn = false; 157 } 158 159 return ptr; 160 } 161 162 protected void finalize() { 163 delete(); 164 } 165 166 public synchronized void delete() { 167 if (swigCPtr != 0) { 168 if (swigCMemOwn) { 169 swigCMemOwn = false; 170 libsbmlJNI.delete_SBMLConverter(swigCPtr); 171 } 172 swigCPtr = 0; 173 } 174 } 175 176 protected void swigDirectorDisconnect() { 177 swigCMemOwn = false; 178 delete(); 179 } 180 181 public void swigReleaseOwnership() { 182 swigCMemOwn = false; 183 libsbmlJNI.SBMLConverter_change_ownership(this, swigCPtr, false); 184 } 185 186 public void swigTakeOwnership() { 187 swigCMemOwn = true; 188 libsbmlJNI.SBMLConverter_change_ownership(this, swigCPtr, true); 189 } 190 191 192/** 193 * Creates a new {@link SBMLConverter} object. 194 */ public 195 SBMLConverter() { 196 this(libsbmlJNI.new_SBMLConverter__SWIG_0(), true); 197 libsbmlJNI.SBMLConverter_director_connect(this, swigCPtr, swigCMemOwn, true); 198 } 199 200 201/** 202 * Creates a new {@link SBMLConverter} object with a given name. 203 <p> 204 * @param name the name for the converter to create 205 */ public 206 SBMLConverter(String name) { 207 this(libsbmlJNI.new_SBMLConverter__SWIG_1(name), true); 208 libsbmlJNI.SBMLConverter_director_connect(this, swigCPtr, swigCMemOwn, true); 209 } 210 211 212/** 213 * Copy constructor. 214 <p> 215 * This creates a copy of an {@link SBMLConverter} object. 216 <p> 217 * @param orig the {@link SBMLConverter} object to copy. 218 */ public 219 SBMLConverter(SBMLConverter orig) { 220 this(libsbmlJNI.new_SBMLConverter__SWIG_2(SBMLConverter.getCPtr(orig), orig), true); 221 libsbmlJNI.SBMLConverter_director_connect(this, swigCPtr, swigCMemOwn, true); 222 } 223 224 225/** 226 * Creates and returns a deep copy of this {@link SBMLConverter} object. 227 <p> 228 * @return the (deep) copy of this {@link SBMLConverter} object. 229 */ public 230 SBMLConverter cloneObject() { 231 return libsbml.DowncastSBMLConverter((getClass() == SBMLConverter.class) ? libsbmlJNI.SBMLConverter_cloneObject(swigCPtr, this) : libsbmlJNI.SBMLConverter_cloneObjectSwigExplicitSBMLConverter(swigCPtr, this), true); 232} 233 234 235/** 236 * Returns the SBML document that is the subject of the conversions. 237 <p> 238 * @return the current {@link SBMLDocument} object. 239 */ public 240 SBMLDocument getDocument() { 241 long cPtr = (getClass() == SBMLConverter.class) ? libsbmlJNI.SBMLConverter_getDocument__SWIG_0(swigCPtr, this) : libsbmlJNI.SBMLConverter_getDocumentSwigExplicitSBMLConverter__SWIG_0(swigCPtr, this); 242 return (cPtr == 0) ? null : new SBMLDocument(cPtr, false); 243 } 244 245 246/** 247 * Returns the default properties of this converter. 248 <p> 249 * A given converter exposes one or more properties that can be adjusted 250 * in order to influence the behavior of the converter. This method 251 * returns the <em>default</em> property settings for this converter. It is 252 * meant to be called in order to discover all the settings for the 253 * converter object. The run-time properties of the converter object can 254 * be adjusted by using the method 255 * {@link SBMLConverter#setProperties(ConversionProperties props)}. 256 <p> 257 * @return the default properties for the converter. 258 <p> 259 * @see #setProperties(ConversionProperties) 260 * @see #matchesProperties(ConversionProperties) 261 */ public 262 ConversionProperties getDefaultProperties() { 263 return new ConversionProperties((getClass() == SBMLConverter.class) ? libsbmlJNI.SBMLConverter_getDefaultProperties(swigCPtr, this) : libsbmlJNI.SBMLConverter_getDefaultPropertiesSwigExplicitSBMLConverter(swigCPtr, this), true); 264 } 265 266 267/** 268 * Returns the target SBML namespaces of the currently set properties. 269 <p> 270 * SBML namespaces are used by libSBML to express the Level+Version of the 271 * SBML document (and, possibly, any SBML Level 3 packages in 272 * use). Some converters' behavior is affected by the SBML namespace 273 * configured in the converter. For example, in {@link SBMLLevelVersionConverter} 274 * (the converter for converting SBML documents from one Level+Version 275 * combination to another), the actions are fundamentally dependent on the 276 * SBML namespaces targeted. 277 <p> 278 * @return the {@link SBMLNamespaces} object that describes the SBML namespaces 279 * in effect, or <code>null</code> if none are set. 280 */ public 281 SBMLNamespaces getTargetNamespaces() { 282 return libsbml.DowncastSBMLNamespaces((getClass() == SBMLConverter.class) ? libsbmlJNI.SBMLConverter_getTargetNamespaces(swigCPtr, this) : libsbmlJNI.SBMLConverter_getTargetNamespacesSwigExplicitSBMLConverter(swigCPtr, this), false); 283} 284 285 286/** 287 * Returns <code>true</code> if this converter matches the given properties. 288 <p> 289 * Given a {@link ConversionProperties} object <code>props</code>, this method checks that 290 * <code>props</code> possesses an option value to enable this converter. If it does, 291 * this method returns <code>true.</code> 292 <p> 293 * @param props the properties to match. 294 <p> 295 * @return <code>true</code> if the properties <code>props</code> would match the necessary 296 * properties for this type of converter, <code>false</code> otherwise. 297 */ public 298 boolean matchesProperties(ConversionProperties props) { 299 return (getClass() == SBMLConverter.class) ? libsbmlJNI.SBMLConverter_matchesProperties(swigCPtr, this, ConversionProperties.getCPtr(props), props) : libsbmlJNI.SBMLConverter_matchesPropertiesSwigExplicitSBMLConverter(swigCPtr, this, ConversionProperties.getCPtr(props), props); 300 } 301 302 303/** 304 * Sets the SBML document to be converted. 305 <p> 306 * @param doc the document to use for this conversion. 307 <p> 308 * @return integer value indicating the success/failure of the operation. 309 * The set of possible values that may 310 * be returned ultimately depends on the specific subclass of 311 * {@link SBMLConverter} being used, but the default method can return the 312 * following: 313 * <ul> 314 * <li> {@link libsbmlConstants#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS} 315 * </ul> 316 */ public 317 int setDocument(SBMLDocument doc) { 318 return (getClass() == SBMLConverter.class) ? libsbmlJNI.SBMLConverter_setDocument(swigCPtr, this, SBMLDocument.getCPtr(doc), doc) : libsbmlJNI.SBMLConverter_setDocumentSwigExplicitSBMLConverter(swigCPtr, this, SBMLDocument.getCPtr(doc), doc); 319 } 320 321 322/** 323 * Sets the configuration properties to be used by this converter. 324 <p> 325 * @param props the {@link ConversionProperties} object defining the properties 326 * to set. 327 <p> 328 * @return integer value indicating the success/failure of the operation. 329 * The set of possible values that may 330 * be returned ultimately depends on the specific subclass of 331 * {@link SBMLConverter} being used, but the default method can return the 332 * following values: 333 * <ul> 334 * <li> {@link libsbmlConstants#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS} 335 * <li> {@link libsbmlConstants#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED} 336 * 337 * </ul> <p> 338 * @see #getProperties() 339 * @see #matchesProperties(ConversionProperties) 340 */ public 341 int setProperties(ConversionProperties props) { 342 return (getClass() == SBMLConverter.class) ? libsbmlJNI.SBMLConverter_setProperties(swigCPtr, this, ConversionProperties.getCPtr(props), props) : libsbmlJNI.SBMLConverter_setPropertiesSwigExplicitSBMLConverter(swigCPtr, this, ConversionProperties.getCPtr(props), props); 343 } 344 345 346/** 347 * Returns the current properties in effect for this converter. 348 <p> 349 * A given converter exposes one or more properties that can be adjusted 350 * in order to influence the behavior of the converter. This method 351 * returns the current properties for this converter; in other words, the 352 * settings in effect at this moment. To change the property values, you 353 * can use {@link SBMLConverter#setProperties(ConversionProperties props)}. 354 <p> 355 * @return the currently set configuration properties. 356 <p> 357 * @see #setProperties(ConversionProperties) 358 * @see #matchesProperties(ConversionProperties) 359 */ public 360 ConversionProperties getProperties() { 361 long cPtr = (getClass() == SBMLConverter.class) ? libsbmlJNI.SBMLConverter_getProperties(swigCPtr, this) : libsbmlJNI.SBMLConverter_getPropertiesSwigExplicitSBMLConverter(swigCPtr, this); 362 return (cPtr == 0) ? null : new ConversionProperties(cPtr, false); 363 } 364 365 366/** 367 * Perform the conversion. 368 <p> 369 * This method causes the converter to do the actual conversion work, 370 * that is, to convert the {@link SBMLDocument} object set by 371 * {@link SBMLConverter#setDocument(SBMLDocument)} and 372 * with the configuration options set by 373 * {@link SBMLConverter#setProperties(ConversionProperties)}. 374 <p> 375 * @return integer value indicating the success/failure of the operation. 376 * The set of possible values that may 377 * be returned depends on the converter subclass; please consult 378 * the documentation for the relevant class to find out what the 379 * possibilities are. 380 */ public 381 int convert() { 382 return (getClass() == SBMLConverter.class) ? libsbmlJNI.SBMLConverter_convert(swigCPtr, this) : libsbmlJNI.SBMLConverter_convertSwigExplicitSBMLConverter(swigCPtr, this); 383 } 384 385 386/** 387 * Returns the name of this converter. 388 <p> 389 * @return a string, the name of this converter. 390 */ public 391 String getName() { 392 return libsbmlJNI.SBMLConverter_getName(swigCPtr, this); 393 } 394 395}