001/* ---------------------------------------------------------------------------- 002 * This file was automatically generated by SWIG (http://www.swig.org). 003 * Version 2.0.12 004 * 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 * Implementation of SBML Level 2's SpeciesType 013 * construct. 014 <p> 015 * The term <em>species</em> <em>type</em> refers to reacting entities independent of 016 * location. These include simple ions (e.g., protons, calcium), simple 017 * molecules (e.g., glucose, ATP), large molecules (e.g., RNA, 018 * polysaccharides, and proteins), and others. 019 <p> 020 * SBML Level 2 Versions 2–4 provide an explicit 021 * {@link SpeciesType} class of object to enable {@link Species} objects of the same type 022 * to be related together. {@link SpeciesType} is a conceptual construct; the 023 * existence of {@link SpeciesType} objects in a model has no effect on the model's 024 * numerical interpretation. Except for the requirement for uniqueness of 025 * species/species type combinations located in compartments, simulators 026 * and other numerical analysis software may ignore {@link SpeciesType} definitions 027 * and references to them in a model. 028 <p> 029 * There is no mechanism in SBML Level 2 for representing hierarchies of 030 * species types. One {@link SpeciesType} object cannot be the subtype of another 031 * {@link SpeciesType} object; SBML provides no means of defining such 032 * relationships. 033 <p> 034 * As with other major structures in SBML, {@link SpeciesType} has a mandatory 035 * attribute, 'id', used to give the species type an identifier. The 036 * identifier must be a text string conforming to the identifer syntax 037 * permitted in SBML. {@link SpeciesType} also has an optional 'name' attribute, 038 * of type <code>string.</code> The 'id' and 'name' must be used according to the 039 * guidelines described in the SBML specification (e.g., Section 3.3 in 040 * the Level 2 Version 4 specification). 041 <p> 042 * {@link SpeciesType} was introduced in SBML Level 2 Version 2. It is not 043 * available in SBML Level 1 nor in Level 3. 044 <p> 045 * @see Species 046 * @see ListOfSpeciesTypes 047 * @see CompartmentType 048 * @see ListOfCompartmentTypes 049 */ 050 051public class SpeciesType extends SBase { 052 private long swigCPtr; 053 054 protected SpeciesType(long cPtr, boolean cMemoryOwn) 055 { 056 super(libsbmlJNI.SpeciesType_SWIGUpcast(cPtr), cMemoryOwn); 057 swigCPtr = cPtr; 058 } 059 060 protected static long getCPtr(SpeciesType obj) 061 { 062 return (obj == null) ? 0 : obj.swigCPtr; 063 } 064 065 protected static long getCPtrAndDisown (SpeciesType obj) 066 { 067 long ptr = 0; 068 069 if (obj != null) 070 { 071 ptr = obj.swigCPtr; 072 obj.swigCMemOwn = false; 073 } 074 075 return ptr; 076 } 077 078 protected void finalize() { 079 delete(); 080 } 081 082 public synchronized void delete() { 083 if (swigCPtr != 0) { 084 if (swigCMemOwn) { 085 swigCMemOwn = false; 086 libsbmlJNI.delete_SpeciesType(swigCPtr); 087 } 088 swigCPtr = 0; 089 } 090 super.delete(); 091 } 092 093 094/** 095 * Creates a new {@link SpeciesType} using the given SBML <code>level</code> and <code>version</code> 096 * values. 097 <p> 098 * @param level a long integer, the SBML Level to assign to this {@link SpeciesType} 099 <p> 100 * @param version a long integer, the SBML Version to assign to this 101 * {@link SpeciesType} 102 <p> 103 * @throws SBMLConstructorException 104 * Thrown if the given <code>level</code> and <code>version</code> combination, or this kind 105 * of SBML object, are either invalid or mismatched with respect to the 106 * parent {@link SBMLDocument} object. 107 <p> 108 * <p> 109 * @note Upon the addition of a {@link SpeciesType} object to an {@link SBMLDocument} 110 * (e.g., using {@link Model#addSpeciesType(SpeciesType st)}), 111 * the SBML Level, SBML Version and XML namespace of the document 112 * <em>override</em> the values used when creating the {@link SpeciesType} object via this 113 * constructor. This is necessary to ensure that an SBML document is a 114 * consistent structure. Nevertheless, the ability to supply the values 115 * at the time of creation of a {@link SpeciesType} is an important aid to 116 * producing valid SBML. Knowledge of the intented SBML Level and 117 * Version determine whether it is valid to assign a particular value to 118 * an attribute, or whether it is valid to add an object to an existing 119 * {@link SBMLDocument}. 120 */ public 121 SpeciesType(long level, long version) throws org.sbml.libsbml.SBMLConstructorException { 122 this(libsbmlJNI.new_SpeciesType__SWIG_0(level, version), true); 123 } 124 125 126/** 127 * Creates a new {@link SpeciesType} using the given {@link SBMLNamespaces} object 128 * <code>sbmlns</code>. 129 <p> 130 * <p> 131 * The {@link SBMLNamespaces} object encapsulates SBML Level/Version/namespaces 132 * information. It is used to communicate the SBML Level, Version, and (in 133 * Level 3) packages used in addition to SBML Level 3 Core. A 134 * common approach to using libSBML's {@link SBMLNamespaces} facilities is to create an 135 * {@link SBMLNamespaces} object somewhere in a program once, then hand that object 136 * as needed to object constructors that accept {@link SBMLNamespaces} as arguments. 137 <p> 138 * It is worth emphasizing that although this constructor does not take 139 * an identifier argument, in SBML Level 2 and beyond, the 'id' 140 * (identifier) attribute of a {@link SpeciesType} object is required to have a value. 141 * Thus, callers are cautioned to assign a value after calling this 142 * constructor. Setting the identifier can be accomplished using the 143 * method {@link SBase#setId(String id)}. 144 <p> 145 * @param sbmlns an {@link SBMLNamespaces} object. 146 <p> 147 * @throws SBMLConstructorException 148 * Thrown if the given <code>level</code> and <code>version</code> combination, or this kind 149 * of SBML object, are either invalid or mismatched with respect to the 150 * parent {@link SBMLDocument} object. 151 <p> 152 * <p> 153 * @note Upon the addition of a {@link SpeciesType} object to an {@link SBMLDocument} 154 * (e.g., using {@link Model#addSpeciesType(SpeciesType st)}), 155 * the SBML Level, SBML Version and XML namespace of the document 156 * <em>override</em> the values used when creating the {@link SpeciesType} object via this 157 * constructor. This is necessary to ensure that an SBML document is a 158 * consistent structure. Nevertheless, the ability to supply the values 159 * at the time of creation of a {@link SpeciesType} is an important aid to 160 * producing valid SBML. Knowledge of the intented SBML Level and 161 * Version determine whether it is valid to assign a particular value to 162 * an attribute, or whether it is valid to add an object to an existing 163 * {@link SBMLDocument}. 164 */ public 165 SpeciesType(SBMLNamespaces sbmlns) throws org.sbml.libsbml.SBMLConstructorException { 166 this(libsbmlJNI.new_SpeciesType__SWIG_1(SBMLNamespaces.getCPtr(sbmlns), sbmlns), true); 167 } 168 169 170/** 171 * Copy constructor; creates a copy of this {@link SpeciesType}. 172 <p> 173 * @param orig the object to copy. 174 <p> 175 * @throws SBMLConstructorException 176 * Thrown if the argument <code>orig</code> is <code>null.</code> 177 */ public 178 SpeciesType(SpeciesType orig) throws org.sbml.libsbml.SBMLConstructorException { 179 this(libsbmlJNI.new_SpeciesType__SWIG_2(SpeciesType.getCPtr(orig), orig), true); 180 } 181 182 183/** 184 * Creates and returns a deep copy of this {@link SpeciesType}. 185 <p> 186 * @return a (deep) copy of this {@link SpeciesType}. 187 */ public 188 SpeciesType cloneObject() { 189 long cPtr = libsbmlJNI.SpeciesType_cloneObject(swigCPtr, this); 190 return (cPtr == 0) ? null : new SpeciesType(cPtr, true); 191 } 192 193 194/** 195 * Returns the value of the 'id' attribute of this {@link SpeciesType}. 196 <p> 197 * @return the id of this {@link SpeciesType}. 198 */ public 199 String getId() { 200 return libsbmlJNI.SpeciesType_getId(swigCPtr, this); 201 } 202 203 204/** 205 * Returns the value of the 'name' attribute of this {@link SpeciesType}. 206 <p> 207 * @return the name of this {@link SpeciesType}. 208 */ public 209 String getName() { 210 return libsbmlJNI.SpeciesType_getName(swigCPtr, this); 211 } 212 213 214/** 215 * Predicate returning <code>true</code> if this 216 * {@link SpeciesType}'s 'id' attribute is set. 217 <p> 218 * @return <code>true</code> if the 'id' attribute of this {@link SpeciesType} is 219 * set, <code>false</code> otherwise. 220 */ public 221 boolean isSetId() { 222 return libsbmlJNI.SpeciesType_isSetId(swigCPtr, this); 223 } 224 225 226/** 227 * Predicate returning <code>true</code> if this 228 * {@link SpeciesType}'s 'name' attribute is set. 229 <p> 230 * @return <code>true</code> if the 'name' attribute of this {@link SpeciesType} is 231 * set, <code>false</code> otherwise. 232 */ public 233 boolean isSetName() { 234 return libsbmlJNI.SpeciesType_isSetName(swigCPtr, this); 235 } 236 237 238/** 239 * Sets the value of the 'id' attribute of this {@link SpeciesType}. 240 <p> 241 * The string <code>sid</code> is copied. 242 <p> 243 * <p> 244 * SBML has strict requirements for the syntax of identifiers, that is, the 245 * values of the 'id' attribute present on most types of SBML objects. 246 * The following is a summary of the definition of the SBML identifier type 247 * <code>SId</code>, which defines the permitted syntax of identifiers. We 248 * express the syntax using an extended form of BNF notation: 249 * <pre style='margin-left: 2em; border: none; font-weight: bold; font-size: 13px; color: black'> 250 * letter .= 'a'..'z','A'..'Z' 251 * digit .= '0'..'9' 252 * idChar .= letter | digit | '_' 253 * SId .= ( letter | '_' ) idChar* 254 * </pre> 255 * The characters <code>(</code> and <code>)</code> are used for grouping, the 256 * character <code>*</code> 'zero or more times', and the character 257 * <code>|</code> indicates logical 'or'. The equality of SBML identifiers is 258 * determined by an exact character sequence match; i.e., comparisons must be 259 * performed in a case-sensitive manner. In addition, there are a few 260 * conditions for the uniqueness of identifiers in an SBML model. Please 261 * consult the SBML specifications for the exact details of the uniqueness 262 * requirements. 263 <p> 264 * @param sid the string to use as the identifier of this {@link SpeciesType} 265 <p> 266 * @return integer value indicating success/failure of the 267 * function. The possible values 268 * returned by this function are: 269 * <ul> 270 * <li> {@link libsbmlConstants#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS } 271 * <li> {@link libsbmlConstants#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE } 272 * </ul> 273 */ public 274 int setId(String sid) { 275 return libsbmlJNI.SpeciesType_setId(swigCPtr, this, sid); 276 } 277 278 279/** 280 * Sets the value of the 'name' attribute of this {@link SpeciesType}. 281 <p> 282 * The string in <code>name</code> is copied. 283 <p> 284 * @param name the new name for the {@link SpeciesType} 285 <p> 286 * @return integer value indicating success/failure of the 287 * function. The possible values 288 * returned by this function are: 289 * <ul> 290 * <li> {@link libsbmlConstants#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS } 291 * <li> {@link libsbmlConstants#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE } 292 * </ul> 293 */ public 294 int setName(String name) { 295 return libsbmlJNI.SpeciesType_setName(swigCPtr, this, name); 296 } 297 298 299/** 300 * Unsets the value of the 'name' attribute of this {@link SpeciesType}. 301 <p> 302 * @return integer value indicating success/failure of the 303 * function. The possible values 304 * returned by this function are: 305 * <ul> 306 * <li> {@link libsbmlConstants#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS } 307 * <li> {@link libsbmlConstants#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED } 308 * </ul> 309 */ public 310 int unsetName() { 311 return libsbmlJNI.SpeciesType_unsetName(swigCPtr, this); 312 } 313 314 315/** 316 * Returns the libSBML type code for this SBML object. 317 <p> 318 * <p> 319 * LibSBML attaches an identifying code to every kind of SBML object. These 320 * are integer constants known as <em>SBML type codes</em>. The names of all 321 * the codes begin with the characters “<code>SBML_</code>”. 322 * In the Java language interface for libSBML, the 323 * type codes are defined as static integer constants in the interface class 324 * {@link libsbmlConstants}. Note that different Level 3 325 * package plug-ins may use overlapping type codes; to identify the package 326 * to which a given object belongs, call the <code>getPackageName()</code> 327 * method on the object. 328 <p> 329 * @return the SBML type code for this object: 330 * {@link libsbmlConstants#SBML_SPECIES_TYPE SBML_SPECIES_TYPE} (default). 331 <p> 332 * <p> 333 * @warning <span class='warning'>The specific integer values of the possible 334 * type codes may be reused by different Level 3 package plug-ins. 335 * Thus, to identifiy the correct code, <strong>it is necessary to invoke 336 * both getTypeCode() and getPackageName()</strong>.</span> 337 <p> 338 * @see #getElementName() 339 * @see #getPackageName() 340 */ public 341 int getTypeCode() { 342 return libsbmlJNI.SpeciesType_getTypeCode(swigCPtr, this); 343 } 344 345 346/** 347 * Returns the XML element name of this object, which for 348 * {@link SpeciesType}, is always <code>'compartmentType'.</code> 349 <p> 350 * @return the name of this element, i.e., <code>'compartmentType'.</code> 351 */ public 352 String getElementName() { 353 return libsbmlJNI.SpeciesType_getElementName(swigCPtr, this); 354 } 355 356 357/** 358 * Predicate returning <code>true</code> if 359 * all the required attributes for this {@link SpeciesType} object 360 * have been set. 361 <p> 362 * @note The required attributes for a {@link SpeciesType} object are: 363 * <ul> 364 * <li> 'id' 365 * 366 * </ul> <p> 367 * @return a boolean value indicating whether all the required 368 * attributes for this object have been defined. 369 */ public 370 boolean hasRequiredAttributes() { 371 return libsbmlJNI.SpeciesType_hasRequiredAttributes(swigCPtr, this); 372 } 373 374}