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 ListOfSpecies 013 * construct. 014 <p> 015 * <p> 016 * The various ListOf___ classes in SBML 017 * are merely containers used for organizing the main components of an SBML 018 * model. In libSBML's implementation, ListOf___ 019 * classes are derived from the 020 * intermediate utility class {@link ListOf}, which 021 * is not defined by the SBML specifications but serves as a useful 022 * programmatic construct. {@link ListOf} is itself is in turn derived from {@link SBase}, 023 * which provides all of the various ListOf___ 024 * classes with common features 025 * defined by the SBML specification, such as 'metaid' attributes and 026 * annotations. 027 <p> 028 * The relationship between the lists and the rest of an SBML model is 029 * illustrated by the following (for SBML Level 2 Version 4): 030 <p> 031 * <figure> 032 <object type="image/svg+xml" data="listof-illustration.svg" class="centered"></object> 033</figure> 034 035 <p> 036 * Readers may wonder about the motivations for using the ListOf___ 037 * containers in SBML. A simpler approach in XML might be to place the 038 * components all directly at the top level of the model definition. The 039 * choice made in SBML is to group them within XML elements named after 040 * ListOf<em>Classname</em>, in part because it helps organize the 041 * components. More importantly, the fact that the container classes are 042 * derived from {@link SBase} means that software tools can add information <em>about</em> 043 * the lists themselves into each list container's 'annotation'. 044 <p> 045 * @see ListOfFunctionDefinitions 046 * @see ListOfUnitDefinitions 047 * @see ListOfCompartmentTypes 048 * @see ListOfSpeciesTypes 049 * @see ListOfCompartments 050 * @see ListOfSpecies 051 * @see ListOfParameters 052 * @see ListOfInitialAssignments 053 * @see ListOfRules 054 * @see ListOfConstraints 055 * @see ListOfReactions 056 * @see ListOfEvents 057 */ 058 059public class ListOfSpecies extends ListOf { 060 private long swigCPtr; 061 062 protected ListOfSpecies(long cPtr, boolean cMemoryOwn) 063 { 064 super(libsbmlJNI.ListOfSpecies_SWIGUpcast(cPtr), cMemoryOwn); 065 swigCPtr = cPtr; 066 } 067 068 protected static long getCPtr(ListOfSpecies obj) 069 { 070 return (obj == null) ? 0 : obj.swigCPtr; 071 } 072 073 protected static long getCPtrAndDisown (ListOfSpecies obj) 074 { 075 long ptr = 0; 076 077 if (obj != null) 078 { 079 ptr = obj.swigCPtr; 080 obj.swigCMemOwn = false; 081 } 082 083 return ptr; 084 } 085 086 protected void finalize() { 087 delete(); 088 } 089 090 public synchronized void delete() { 091 if (swigCPtr != 0) { 092 if (swigCMemOwn) { 093 swigCMemOwn = false; 094 libsbmlJNI.delete_ListOfSpecies(swigCPtr); 095 } 096 swigCPtr = 0; 097 } 098 super.delete(); 099 } 100 101 102/** 103 * Creates a new {@link ListOfSpecies} object. 104 <p> 105 * The object is constructed such that it is valid for the given SBML 106 * Level and Version combination. 107 <p> 108 * @param level the SBML Level 109 <p> 110 * @param version the Version within the SBML Level 111 */ public 112 ListOfSpecies(long level, long version) throws org.sbml.libsbml.SBMLConstructorException { 113 this(libsbmlJNI.new_ListOfSpecies__SWIG_0(level, version), true); 114 } 115 116 117/** 118 * Creates a new {@link ListOfSpecies} object. 119 <p> 120 * The object is constructed such that it is valid for the SBML Level and 121 * Version combination determined by the {@link SBMLNamespaces} object in 122 * <code>sbmlns</code>. 123 <p> 124 * @param sbmlns an {@link SBMLNamespaces} object that is used to determine the 125 * characteristics of the {@link ListOfSpecies} object to be created. 126 */ public 127 ListOfSpecies(SBMLNamespaces sbmlns) throws org.sbml.libsbml.SBMLConstructorException { 128 this(libsbmlJNI.new_ListOfSpecies__SWIG_1(SBMLNamespaces.getCPtr(sbmlns), sbmlns), true); 129 } 130 131 132/** 133 * Creates and returns a deep copy of this ListOfSpeciess instance. 134 <p> 135 * @return a (deep) copy of this ListOfSpeciess. 136 */ public 137 ListOfSpecies cloneObject() { 138 long cPtr = libsbmlJNI.ListOfSpecies_cloneObject(swigCPtr, this); 139 return (cPtr == 0) ? null : new ListOfSpecies(cPtr, true); 140 } 141 142 143/** 144 * Returns the libSBML type code for the objects contained in this {@link ListOf} 145 * (i.e., {@link Species} objects, if the list is non-empty). 146 <p> 147 * <p> 148 * LibSBML attaches an identifying code to every kind of SBML object. These 149 * are integer constants known as <em>SBML type codes</em>. The names of all 150 * the codes begin with the characters “<code>SBML_</code>”. 151 * In the Java language interface for libSBML, the 152 * type codes are defined as static integer constants in the interface class 153 * {@link libsbmlConstants}. Note that different Level 3 154 * package plug-ins may use overlapping type codes; to identify the package 155 * to which a given object belongs, call the <code>getPackageName()</code> 156 * method on the object. 157 <p> 158 * @return the SBML type code for objects contained in this list: 159 * {@link libsbmlConstants#SBML_SPECIES SBML_SPECIES} (default). 160 <p> 161 * @see #getElementName() 162 * @see #getPackageName() 163 */ public 164 int getItemTypeCode() { 165 return libsbmlJNI.ListOfSpecies_getItemTypeCode(swigCPtr, this); 166 } 167 168 169/** 170 * Returns the XML element name of this object. 171 <p> 172 * For ListOfSpeciess, the XML element name is <code>'listOfSpeciess'.</code> 173 <p> 174 * @return the name of this element, i.e., <code>'listOfSpeciess'.</code> 175 */ public 176 String getElementName() { 177 return libsbmlJNI.ListOfSpecies_getElementName(swigCPtr, this); 178 } 179 180 181/** 182 * Get a {@link Species} from the {@link ListOfSpecies}. 183 <p> 184 * @param n the index number of the {@link Species} to get. 185 <p> 186 * @return the nth {@link Species} in this {@link ListOfSpecies}. 187 <p> 188 * @see #size() 189 */ public 190 Species get(long n) { 191 long cPtr = libsbmlJNI.ListOfSpecies_get__SWIG_0(swigCPtr, this, n); 192 return (cPtr == 0) ? null : new Species(cPtr, false); 193 } 194 195 196/** 197 * Get a {@link Species} from the {@link ListOfSpecies} 198 * based on its identifier. 199 <p> 200 * @param sid a string representing the identifier 201 * of the {@link Species} to get. 202 <p> 203 * @return {@link Species} in this {@link ListOfSpecies} 204 * with the given <code>sid</code> or <code>null</code> if no such 205 * {@link Species} exists. 206 <p> 207 * @see #get(long n) 208 * @see #size() 209 */ public 210 Species get(String sid) { 211 long cPtr = libsbmlJNI.ListOfSpecies_get__SWIG_2(swigCPtr, this, sid); 212 return (cPtr == 0) ? null : new Species(cPtr, false); 213 } 214 215 216/** 217 * Removes the nth item from this ListOfSpeciess items and returns a pointer to 218 * it. 219 <p> 220 * The caller owns the returned item and is responsible for deleting it. 221 <p> 222 * @param n the index of the item to remove 223 <p> 224 * @see #size() 225 */ public 226 Species remove(long n) { 227 long cPtr = libsbmlJNI.ListOfSpecies_remove__SWIG_0(swigCPtr, this, n); 228 return (cPtr == 0) ? null : new Species(cPtr, true); 229 } 230 231 232/** 233 * Removes item in this ListOfSpeciess items with the given identifier. 234 <p> 235 * The caller owns the returned item and is responsible for deleting it. 236 * If none of the items in this list have the identifier <code>sid</code>, then 237 * <code>null</code> is returned. 238 <p> 239 * @param sid the identifier of the item to remove 240 <p> 241 * @return the item removed. As mentioned above, the caller owns the 242 * returned item. 243 */ public 244 Species remove(String sid) { 245 long cPtr = libsbmlJNI.ListOfSpecies_remove__SWIG_1(swigCPtr, this, sid); 246 return (cPtr == 0) ? null : new Species(cPtr, true); 247 } 248 249}