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 * Converter that removes SBML Level 3 packages. 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 and removes (strips) an SBML 022 * Level 3 package from it. No conversion is performed; the package 023 * constructs are simply removed from the SBML document. The package to be 024 * stripped is determined by the value of the option <code>'package'</code> on the 025 * conversion properties. 026 <p> 027 * <h2>Configuration and use of {@link SBMLStripPackageConverter}</h2> 028 <p> 029 * {@link SBMLStripPackageConverter} is enabled by creating a {@link ConversionProperties} 030 * object with the option <code>'stripPackage'</code>, and passing this properties 031 * object to {@link SBMLDocument#convert(ConversionProperties)}. 032 * This converter takes one required option: 033 <p> 034 * <ul> 035 * <li> <code>'package':</code> the value of this option should be a text string, the 036 * nickname of the SBML Level 3 package to be stripped from the model. 037 * 038 * </ul> <p> 039 * In addition, the converter understands an additional optional: 040 <p> 041 * <ul> 042 * <li> <code>'stripAllUnrecognized':</code> if set to <code>true</code>, the converter will 043 * remove all SBML Level 3 package constructs for Level 3 packages 044 * that this copy of libSBML does not recognize. Note that what a given copy 045 * of libSBML recognizes is determined by which plug-ins it has been 046 * configured to include. If this option is enabled, it may remove SBML 047 * Level 3 package constructs that are legitimate in the sense that they 048 * are officially defined SBML constructs, but not recognized because the 049 * running copy of libSBML has not had support enabled for them. 050 * 051 * </ul> <p> 052 * <p> 053 * <h2>General information about the use of SBML converters</h2> 054 <p> 055 * The use of all the converters follows a similar approach. First, one 056 * creates a {@link ConversionProperties} object and calls 057 * {@link ConversionProperties#addOption(ConversionOption)} 058 * on this object with one arguments: a text string that identifies the desired 059 * converter. (The text string is specific to each converter; consult the 060 * documentation for a given converter to find out how it should be enabled.) 061 <p> 062 * Next, for some converters, the caller can optionally set some 063 * converter-specific properties using additional calls to 064 * {@link ConversionProperties#addOption(ConversionOption)}. 065 * Many converters provide the ability to 066 * configure their behavior to some extent; this is realized through the use 067 * of properties that offer different options. The default property values 068 * for each converter can be interrogated using the method 069 * {@link SBMLConverter#getDefaultProperties()} on the converter class in question . 070 <p> 071 * Finally, the caller should invoke the method 072 * {@link SBMLDocument#convert(ConversionProperties)} 073 * with the {@link ConversionProperties} object as an argument. 074 <p> 075 * <h3>Example of invoking an SBML converter</h3> 076 <p> 077 * The following code fragment illustrates an example using 078 * {@link SBMLReactionConverter}, which is invoked using the option string 079 * <code>'replaceReactions':</code> 080 <p> 081<pre class='fragment'> 082{@link ConversionProperties} props = new {@link ConversionProperties}(); 083if (props != null) { 084 props.addOption('replaceReactions'); 085} else { 086 // Deal with error. 087} 088</pre> 089<p> 090 * In the case of {@link SBMLReactionConverter}, there are no options to affect 091 * its behavior, so the next step is simply to invoke the converter on 092 * an {@link SBMLDocument} object. Continuing the example code: 093 <p> 094<pre class='fragment'> 095 // Assume that the variable 'document' has been set to an {@link SBMLDocument} object. 096 status = document.convert(config); 097 if (status != libsbml.LIBSBML_OPERATION_SUCCESS) 098 { 099 // Handle error somehow. 100 System.out.println('Error: conversion failed due to the following:'); 101 document.printErrors(); 102 } 103</pre> 104<p> 105 * Here is an example of using a converter that offers an option. The 106 * following code invokes {@link SBMLStripPackageConverter} to remove the 107 * SBML Level 3 <em>Layout</em> package from a model. It sets the name 108 * of the package to be removed by adding a value for the option named 109 * <code>'package'</code> defined by that converter: 110 <p> 111<pre class='fragment'> 112{@link ConversionProperties} config = new {@link ConversionProperties}(); 113if (config != None) { 114 config.addOption('stripPackage'); 115 config.addOption('package', 'layout'); 116 status = document.convert(config); 117 if (status != LIBSBML_OPERATION_SUCCESS) { 118 // Handle error somehow. 119 System.out.println('Error: unable to strip the {@link Layout} package'); 120 document.printErrors(); 121 } 122} else { 123 // Handle error somehow. 124 System.out.println('Error: unable to create {@link ConversionProperties} object'); 125} 126</pre> 127<p> 128 * <h3>Available SBML converters in libSBML</h3> 129 <p> 130 * LibSBML provides a number of built-in converters; by convention, their 131 * names end in <em>Converter</em>. The following are the built-in converters 132 * provided by libSBML 5.12.0 133: 134 <p> 135 * <p> 136 * <ul> 137 * <li> {@link CobraToFbcConverter} 138 * <li> {@link CompFlatteningConverter} 139 * <li> {@link FbcToCobraConverter} 140 * <li> {@link FbcV1ToV2Converter} 141 * <li> {@link FbcV2ToV1Converter} 142 * <li> {@link SBMLFunctionDefinitionConverter} 143 * <li> {@link SBMLIdConverter} 144 * <li> {@link SBMLInferUnitsConverter} 145 * <li> {@link SBMLInitialAssignmentConverter} 146 * <li> {@link SBMLLevel1Version1Converter} 147 * <li> {@link SBMLLevelVersionConverter} 148 * <li> {@link SBMLLocalParameterConverter} 149 * <li> {@link SBMLReactionConverter} 150 * <li> {@link SBMLRuleConverter} 151 * <li> {@link SBMLStripPackageConverter} 152 * <li> {@link SBMLUnitsConverter} 153 * 154 * </ul> 155 */ 156 157public class SBMLStripPackageConverter extends SBMLConverter { 158 private long swigCPtr; 159 160 protected SBMLStripPackageConverter(long cPtr, boolean cMemoryOwn) 161 { 162 super(libsbmlJNI.SBMLStripPackageConverter_SWIGUpcast(cPtr), cMemoryOwn); 163 swigCPtr = cPtr; 164 } 165 166 protected static long getCPtr(SBMLStripPackageConverter obj) 167 { 168 return (obj == null) ? 0 : obj.swigCPtr; 169 } 170 171 protected static long getCPtrAndDisown (SBMLStripPackageConverter obj) 172 { 173 long ptr = 0; 174 175 if (obj != null) 176 { 177 ptr = obj.swigCPtr; 178 obj.swigCMemOwn = false; 179 } 180 181 return ptr; 182 } 183 184 protected void finalize() { 185 delete(); 186 } 187 188 public synchronized void delete() { 189 if (swigCPtr != 0) { 190 if (swigCMemOwn) { 191 swigCMemOwn = false; 192 libsbmlJNI.delete_SBMLStripPackageConverter(swigCPtr); 193 } 194 swigCPtr = 0; 195 } 196 super.delete(); 197 } 198 199 200/** * @internal */ public 201 static void init() { 202 libsbmlJNI.SBMLStripPackageConverter_init(); 203 } 204 205 206/** 207 * Creates a new {@link SBMLStripPackageConverter} object. 208 */ public 209 SBMLStripPackageConverter() { 210 this(libsbmlJNI.new_SBMLStripPackageConverter__SWIG_0(), true); 211 } 212 213 214/** 215 * Copy constructor; creates a copy of an {@link SBMLStripPackageConverter} 216 * object. 217 <p> 218 * @param obj the {@link SBMLStripPackageConverter} object to copy. 219 */ public 220 SBMLStripPackageConverter(SBMLStripPackageConverter obj) { 221 this(libsbmlJNI.new_SBMLStripPackageConverter__SWIG_1(SBMLStripPackageConverter.getCPtr(obj), obj), true); 222 } 223 224 225/** 226 * Creates and returns a deep copy of this {@link SBMLStripPackageConverter} 227 * object. 228 <p> 229 * @return the (deep) copy of this converter object. 230 */ public 231 SBMLConverter cloneObject() { 232 long cPtr = libsbmlJNI.SBMLStripPackageConverter_cloneObject(swigCPtr, this); 233 return (cPtr == 0) ? null : new SBMLStripPackageConverter(cPtr, true); 234 } 235 236 237/** 238 * Returns <code>true</code> if this converter object's properties match the given 239 * properties. 240 <p> 241 * A typical use of this method involves creating a {@link ConversionProperties} 242 * object, setting the options desired, and then calling this method on 243 * an {@link SBMLStripPackageConverter} object to find out if the object's 244 * property values match the given ones. This method is also used by 245 * {@link SBMLConverterRegistry#getConverterFor(ConversionProperties)} 246 * to search across all registered converters for one matching particular 247 * properties. 248 <p> 249 * @param props the properties to match. 250 <p> 251 * @return <code>true</code> if this converter's properties match, <code>false</code> 252 * otherwise. 253 */ public 254 boolean matchesProperties(ConversionProperties props) { 255 return libsbmlJNI.SBMLStripPackageConverter_matchesProperties(swigCPtr, this, ConversionProperties.getCPtr(props), props); 256 } 257 258 259/** 260 * Perform the conversion. 261 <p> 262 * This method causes the converter to do the actual conversion work, 263 * that is, to convert the {@link SBMLDocument} object set by 264 * {@link SBMLConverter#setDocument(SBMLDocument)} and 265 * with the configuration options set by 266 * {@link SBMLConverter#setProperties(ConversionProperties)}. 267 <p> 268 * <p> 269 * @return integer value indicating success/failure of the 270 * function. The possible values 271 * returned by this function are: 272 * <ul> 273 * <li> {@link libsbmlConstants#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS} 274 * <li> {@link libsbmlConstants#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED} 275 * <li> {@link libsbmlConstants#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE} 276 * <li> {@link libsbmlConstants#LIBSBML_CONV_PKG_CONSIDERED_UNKNOWN LIBSBML_CONV_PKG_CONSIDERED_UNKNOWN} 277 * </ul> 278 */ public 279 int convert() { 280 return libsbmlJNI.SBMLStripPackageConverter_convert(swigCPtr, this); 281 } 282 283 284/** 285 * Returns the default properties of this converter. 286 <p> 287 * A given converter exposes one or more properties that can be adjusted 288 * in order to influence the behavior of the converter. This method 289 * returns the <em>default</em> property settings for this converter. It is 290 * meant to be called in order to discover all the settings for the 291 * converter object. 292 <p> 293 * @return the {@link ConversionProperties} object describing the default properties 294 * for this converter. 295 */ public 296 ConversionProperties getDefaultProperties() { 297 return new ConversionProperties(libsbmlJNI.SBMLStripPackageConverter_getDefaultProperties(swigCPtr, this), true); 298 } 299 300 301/** 302 * @return the package to be stripped 303 */ public 304 String getPackageToStrip() { 305 return libsbmlJNI.SBMLStripPackageConverter_getPackageToStrip(swigCPtr, this); 306 } 307 308 309/** 310 * @return whether all unrecognized packages should be removed 311 */ public 312 boolean isStripAllUnrecognizedPackages() { 313 return libsbmlJNI.SBMLStripPackageConverter_isStripAllUnrecognizedPackages(swigCPtr, this); 314 } 315 316}