001/* ----------------------------------------------------------------------------
002 * This file was automatically generated by SWIG (http://www.swig.org).
003 * Version 2.0.11
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 * 
013 * Implementation of SBML's ListOfReactions construct.
014 * <p>
015 * The various ListOf___ classes in SBML are merely containers used for
016 * organizing the main components of an SBML model.  All are derived from
017 * the abstract class {@link SBase}, and inherit the various attributes and
018 * subelements of {@link SBase}, such as 'metaid' as and 'annotation'.  The
019 * ListOf___ classes do not add any attributes of their own.
020 * <p>
021 * The relationship between the lists and the rest of an SBML model is
022 * illustrated by the following (for SBML Level&nbsp;2 Version&nbsp;4):
023 * <p>
024 * <center><img src='listof-illustration.jpg'></center><br>
025 * 
026 * <p>
027 * Readers may wonder about the motivations for using the ListOf___
028 * containers.  A simpler approach in XML might be to place the components
029 * all directly at the top level of the model definition.  The choice made
030 * in SBML is to group them within XML elements named after
031 * {@link ListOf}<em>Classname</em>, in part because it helps organize the
032 * components.  More importantly, the fact that the container classes are
033 * derived from {@link SBase} means that software tools can add information <em>about</em>
034 * the lists themselves into each list container's 'annotation'.
035 * <p>
036 * @see ListOfFunctionDefinitions
037 * @see ListOfUnitDefinitions
038 * @see ListOfCompartmentTypes
039 * @see ListOfSpeciesTypes
040 * @see ListOfCompartments
041 * @see ListOfSpecies
042 * @see ListOfParameters
043 * @see ListOfInitialAssignments
044 * @see ListOfRules
045 * @see ListOfConstraints
046 * @see ListOfReactions
047 * @see ListOfEvents
048 */
049
050public class ListOfReactions extends ListOf {
051   private long swigCPtr;
052
053   protected ListOfReactions(long cPtr, boolean cMemoryOwn)
054   {
055     super(libsbmlJNI.ListOfReactions_SWIGUpcast(cPtr), cMemoryOwn);
056     swigCPtr = cPtr;
057   }
058
059   protected static long getCPtr(ListOfReactions obj)
060   {
061     return (obj == null) ? 0 : obj.swigCPtr;
062   }
063
064   protected static long getCPtrAndDisown (ListOfReactions obj)
065   {
066     long ptr = 0;
067
068     if (obj != null)
069     {
070       ptr             = obj.swigCPtr;
071       obj.swigCMemOwn = false;
072     }
073
074     return ptr;
075   }
076
077  protected void finalize() {
078    delete();
079  }
080
081  public synchronized void delete() {
082    if (swigCPtr != 0) {
083      if (swigCMemOwn) {
084        swigCMemOwn = false;
085        libsbmlJNI.delete_ListOfReactions(swigCPtr);
086      }
087      swigCPtr = 0;
088    }
089    super.delete();
090  }
091
092  
093/**
094   * Creates a new {@link ListOfReactions} object.
095   * <p>
096   * The object is constructed such that it is valid for the given SBML
097   * Level and Version combination.
098   * <p>
099   * @param level the SBML Level
100   * <p>
101   * @param version the Version within the SBML Level
102   */ public
103 ListOfReactions(long level, long version) throws org.sbml.libsbml.SBMLConstructorException {
104    this(libsbmlJNI.new_ListOfReactions__SWIG_0(level, version), true);
105  }
106
107  
108/**
109   * Creates a new {@link ListOfReactions} object.
110   * <p>
111   * The object is constructed such that it is valid for the SBML Level and
112   * Version combination determined by the {@link SBMLNamespaces} object in 
113   * <code>sbmlns</code>.
114   * <p>
115   * @param sbmlns an {@link SBMLNamespaces} object that is used to determine the
116   * characteristics of the {@link ListOfReactions} object to be created.
117   */ public
118 ListOfReactions(SBMLNamespaces sbmlns) throws org.sbml.libsbml.SBMLConstructorException {
119    this(libsbmlJNI.new_ListOfReactions__SWIG_1(SBMLNamespaces.getCPtr(sbmlns), sbmlns), true);
120  }
121
122  
123/**
124   * Creates and returns a deep copy of this {@link ListOfReactions} instance.
125   * <p>
126   * @return a (deep) copy of this {@link ListOfReactions}.
127   */ public
128 ListOfReactions cloneObject() {
129    long cPtr = libsbmlJNI.ListOfReactions_cloneObject(swigCPtr, this);
130    return (cPtr == 0) ? null : new ListOfReactions(cPtr, true);
131  }
132
133  
134/**
135   * Returns the libSBML type code for this SBML object.
136   * <p>
137   * LibSBML attaches an identifying code to every
138   * kind of SBML object.  These are known as <em>SBML type codes</em>.  In
139   * other languages, the set of type codes is stored in an enumeration; in
140   * the Java language interface for libSBML, the type codes are defined as
141   * static integer constants in the interface class {@link
142   * libsbmlConstants}.  The names of the type codes all begin with the
143   * characters <code>SBML_.</code> 
144   * <p>
145   * @return the SBML type code for this object, or {@link 
146   * libsbmlConstants#SBML_UNKNOWN SBML_UNKNOWN} (default).
147   * <p>
148   * @see #getElementName()
149   */ public
150 int getTypeCode() {
151    return libsbmlJNI.ListOfReactions_getTypeCode(swigCPtr, this);
152  }
153
154  
155/**
156   * Returns the libSBML type code for the objects contained in this {@link ListOf}
157   * (i.e., {@link Reaction} objects, if the list is non-empty).
158   * <p>
159   * LibSBML attaches an identifying code to every
160   * kind of SBML object.  These are known as <em>SBML type codes</em>.  In
161   * other languages, the set of type codes is stored in an enumeration; in
162   * the Java language interface for libSBML, the type codes are defined as
163   * static integer constants in the interface class {@link
164   * libsbmlConstants}.  The names of the type codes all begin with the
165   * characters <code>SBML_.</code> 
166   * <p>
167   * @return the SBML type code for the objects contained in this {@link ListOf}
168   * instance, or {@link  libsbmlConstants#SBML_UNKNOWN SBML_UNKNOWN} (default).
169   * <p>
170   * @see #getElementName()
171   */ public
172 int getItemTypeCode() {
173    return libsbmlJNI.ListOfReactions_getItemTypeCode(swigCPtr, this);
174  }
175
176  
177/**
178   * Returns the XML element name of this object
179   * <p>
180   * For {@link ListOfReactions}, the XML element name is <code>'listOfReactions'.</code>
181   * <p>
182   * @return the name of this element, i.e., <code>'listOfReactions'.</code>
183   */ public
184 String getElementName() {
185    return libsbmlJNI.ListOfReactions_getElementName(swigCPtr, this);
186  }
187
188  
189/**
190   * Get a {@link Reaction} from the {@link ListOfReactions}.
191   * <p>
192   * @param n the index number of the {@link Reaction} to get.
193   * <p>
194   * @return the nth {@link Reaction} in this {@link ListOfReactions}.
195   * <p>
196   * @see #size()
197   */ public
198 Reaction get(long n) {
199    long cPtr = libsbmlJNI.ListOfReactions_get__SWIG_0(swigCPtr, this, n);
200    return (cPtr == 0) ? null : new Reaction(cPtr, false);
201  }
202
203  
204/**
205   * Get a {@link Reaction} from the {@link ListOfReactions}
206   * based on its identifier.
207   * <p>
208   * @param sid a string representing the identifier 
209   * of the {@link Reaction} to get.
210   * <p>
211   * @return {@link Reaction} in this {@link ListOfReactions}
212   * with the given <code>sid</code> or <code>null</code> if no such
213   * {@link Reaction} exists.
214   * <p>
215   * @see #get(long n)
216   * @see #size()
217   */ public
218 Reaction get(String sid) {
219    long cPtr = libsbmlJNI.ListOfReactions_get__SWIG_2(swigCPtr, this, sid);
220    return (cPtr == 0) ? null : new Reaction(cPtr, false);
221  }
222
223  
224/**
225   * Removes the nth item from this {@link ListOfReactions} items and returns a pointer to
226   * it.
227   * <p>
228   * The caller owns the returned item and is responsible for deleting it.
229   * <p>
230   * @param n the index of the item to remove
231   * <p>
232   * @see #size()
233   */ public
234 Reaction remove(long n) {
235    long cPtr = libsbmlJNI.ListOfReactions_remove__SWIG_0(swigCPtr, this, n);
236    return (cPtr == 0) ? null : new Reaction(cPtr, true);
237  }
238
239  
240/**
241   * Removes item in this {@link ListOfReactions} items with the given identifier.
242   * <p>
243   * The caller owns the returned item and is responsible for deleting it.
244   * If none of the items in this list have the identifier <code>sid</code>, then
245   * null is returned.
246   * <p>
247   * @param sid the identifier of the item to remove
248   * <p>
249   * @return the item removed.  As mentioned above, the caller owns the
250   * returned item.
251   */ public
252 Reaction remove(String sid) {
253    long cPtr = libsbmlJNI.ListOfReactions_remove__SWIG_1(swigCPtr, this, sid);
254    return (cPtr == 0) ? null : new Reaction(cPtr, true);
255  }
256
257}