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 011public class FbcModelPlugin extends SBasePlugin { 012 private long swigCPtr; 013 014 protected FbcModelPlugin(long cPtr, boolean cMemoryOwn) 015 { 016 super(libsbmlJNI.FbcModelPlugin_SWIGUpcast(cPtr), cMemoryOwn); 017 swigCPtr = cPtr; 018 } 019 020 protected static long getCPtr(FbcModelPlugin obj) 021 { 022 return (obj == null) ? 0 : obj.swigCPtr; 023 } 024 025 protected static long getCPtrAndDisown (FbcModelPlugin obj) 026 { 027 long ptr = 0; 028 029 if (obj != null) 030 { 031 ptr = obj.swigCPtr; 032 obj.swigCMemOwn = false; 033 } 034 035 return ptr; 036 } 037 038 protected void finalize() { 039 delete(); 040 } 041 042 public synchronized void delete() { 043 if (swigCPtr != 0) { 044 if (swigCMemOwn) { 045 swigCMemOwn = false; 046 libsbmlJNI.delete_FbcModelPlugin(swigCPtr); 047 } 048 swigCPtr = 0; 049 } 050 super.delete(); 051 } 052 053 public FbcModelPlugin(String uri, String prefix, FbcPkgNamespaces fbcns) { 054 this(libsbmlJNI.new_FbcModelPlugin__SWIG_0(uri, prefix, FbcPkgNamespaces.getCPtr(fbcns), fbcns), true); 055 } 056 057 public FbcModelPlugin(FbcModelPlugin orig) { 058 this(libsbmlJNI.new_FbcModelPlugin__SWIG_1(FbcModelPlugin.getCPtr(orig), orig), true); 059 } 060 061 062/** 063 * Creates and returns a deep copy of this {@link SBasePlugin} object. 064 * <p> 065 * @return a (deep) copy of this {@link SBase} object 066 */ public 067 SBasePlugin cloneObject() { 068 long cPtr = libsbmlJNI.FbcModelPlugin_cloneObject(swigCPtr, this); 069 return (cPtr == 0) ? null : new FbcModelPlugin(cPtr, true); 070 } 071 072 public SBase createObject(XMLInputStream stream) { 073 return libsbml.DowncastSBase(libsbmlJNI.FbcModelPlugin_createObject(swigCPtr, this, XMLInputStream.getCPtr(stream), stream), false); 074} 075 076 public void writeAttributes(XMLOutputStream stream) { 077 libsbmlJNI.FbcModelPlugin_writeAttributes(swigCPtr, this, XMLOutputStream.getCPtr(stream), stream); 078 } 079 080 public boolean hasRequiredElements() { 081 return libsbmlJNI.FbcModelPlugin_hasRequiredElements(swigCPtr, this); 082 } 083 084 public boolean readOtherXML(SBase parentObject, XMLInputStream stream) { 085 return libsbmlJNI.FbcModelPlugin_readOtherXML(swigCPtr, this, SBase.getCPtr(parentObject), parentObject, XMLInputStream.getCPtr(stream), stream); 086 } 087 088 089/** 090 * Returns the first child element found that has the given <code>id</code> in the model-wide SId namespace, or <code>null</code> if no such object is found. 091 * <p> 092 * @param id string representing the id of objects to find 093 * <p> 094 * @return pointer to the first element found with the given <code>id</code>. 095 */ public 096 SBase getElementBySId(String id) { 097 return libsbml.DowncastSBase(libsbmlJNI.FbcModelPlugin_getElementBySId(swigCPtr, this, id), false); 098} 099 100 101/** 102 * Returns the first child element it can find with the given <code>metaid</code>, or <code>null</code> if no such object is found. 103 * <p> 104 * @param metaid string representing the metaid of objects to find 105 * <p> 106 * @return pointer to the first element found with the given <code>metaid</code>. 107 */ public 108 SBase getElementByMetaId(String metaid) { 109 return libsbml.DowncastSBase(libsbmlJNI.FbcModelPlugin_getElementByMetaId(swigCPtr, this, metaid), false); 110} 111 112 public ListOfFluxBounds getListOfFluxBounds() { 113 long cPtr = libsbmlJNI.FbcModelPlugin_getListOfFluxBounds__SWIG_0(swigCPtr, this); 114 return (cPtr == 0) ? null : new ListOfFluxBounds(cPtr, false); 115 } 116 117 public FluxBound getFluxBound(long n) { 118 long cPtr = libsbmlJNI.FbcModelPlugin_getFluxBound__SWIG_0(swigCPtr, this, n); 119 return (cPtr == 0) ? null : new FluxBound(cPtr, false); 120 } 121 122 public FluxBound getFluxBound(String sid) { 123 long cPtr = libsbmlJNI.FbcModelPlugin_getFluxBound__SWIG_2(swigCPtr, this, sid); 124 return (cPtr == 0) ? null : new FluxBound(cPtr, false); 125 } 126 127 public int addFluxBound(FluxBound bound) { 128 return libsbmlJNI.FbcModelPlugin_addFluxBound(swigCPtr, this, FluxBound.getCPtr(bound), bound); 129 } 130 131 public FluxBound createFluxBound() { 132 long cPtr = libsbmlJNI.FbcModelPlugin_createFluxBound(swigCPtr, this); 133 return (cPtr == 0) ? null : new FluxBound(cPtr, false); 134 } 135 136 public FluxBound removeFluxBound(long n) { 137 long cPtr = libsbmlJNI.FbcModelPlugin_removeFluxBound__SWIG_0(swigCPtr, this, n); 138 return (cPtr == 0) ? null : new FluxBound(cPtr, false); 139 } 140 141 public FluxBound removeFluxBound(String sid) { 142 long cPtr = libsbmlJNI.FbcModelPlugin_removeFluxBound__SWIG_1(swigCPtr, this, sid); 143 return (cPtr == 0) ? null : new FluxBound(cPtr, false); 144 } 145 146 public long getNumFluxBounds() { 147 return libsbmlJNI.FbcModelPlugin_getNumFluxBounds(swigCPtr, this); 148 } 149 150 public ListOfObjectives getListOfObjectives() { 151 long cPtr = libsbmlJNI.FbcModelPlugin_getListOfObjectives__SWIG_0(swigCPtr, this); 152 return (cPtr == 0) ? null : new ListOfObjectives(cPtr, false); 153 } 154 155 public Objective getObjective(long n) { 156 long cPtr = libsbmlJNI.FbcModelPlugin_getObjective__SWIG_0(swigCPtr, this, n); 157 return (cPtr == 0) ? null : new Objective(cPtr, false); 158 } 159 160 public Objective getObjective(String sid) { 161 long cPtr = libsbmlJNI.FbcModelPlugin_getObjective__SWIG_2(swigCPtr, this, sid); 162 return (cPtr == 0) ? null : new Objective(cPtr, false); 163 } 164 165 public int addObjective(Objective bound) { 166 return libsbmlJNI.FbcModelPlugin_addObjective(swigCPtr, this, Objective.getCPtr(bound), bound); 167 } 168 169 public Objective createObjective() { 170 long cPtr = libsbmlJNI.FbcModelPlugin_createObjective(swigCPtr, this); 171 return (cPtr == 0) ? null : new Objective(cPtr, false); 172 } 173 174 public Objective removeObjective(long n) { 175 long cPtr = libsbmlJNI.FbcModelPlugin_removeObjective__SWIG_0(swigCPtr, this, n); 176 return (cPtr == 0) ? null : new Objective(cPtr, false); 177 } 178 179 public Objective removeObjective(String sid) { 180 long cPtr = libsbmlJNI.FbcModelPlugin_removeObjective__SWIG_1(swigCPtr, this, sid); 181 return (cPtr == 0) ? null : new Objective(cPtr, false); 182 } 183 184 public long getNumObjectives() { 185 return libsbmlJNI.FbcModelPlugin_getNumObjectives(swigCPtr, this); 186 } 187 188 public Objective getActiveObjective() { 189 long cPtr = libsbmlJNI.FbcModelPlugin_getActiveObjective__SWIG_0(swigCPtr, this); 190 return (cPtr == 0) ? null : new Objective(cPtr, false); 191 } 192 193 public int setActiveObjectiveId(String objectiveId) { 194 return libsbmlJNI.FbcModelPlugin_setActiveObjectiveId(swigCPtr, this, objectiveId); 195 } 196 197 public String getActiveObjectiveId() { 198 return libsbmlJNI.FbcModelPlugin_getActiveObjectiveId(swigCPtr, this); 199 } 200 201 public void unsetActiveObjectiveId() { 202 libsbmlJNI.FbcModelPlugin_unsetActiveObjectiveId(swigCPtr, this); 203 } 204 205 public ListOfGeneAssociations getListOfGeneAssociations() { 206 long cPtr = libsbmlJNI.FbcModelPlugin_getListOfGeneAssociations__SWIG_0(swigCPtr, this); 207 return (cPtr == 0) ? null : new ListOfGeneAssociations(cPtr, false); 208 } 209 210 public GeneAssociation getGeneAssociation(long n) { 211 long cPtr = libsbmlJNI.FbcModelPlugin_getGeneAssociation__SWIG_0(swigCPtr, this, n); 212 return (cPtr == 0) ? null : new GeneAssociation(cPtr, false); 213 } 214 215 public GeneAssociation getGeneAssociation(String sid) { 216 long cPtr = libsbmlJNI.FbcModelPlugin_getGeneAssociation__SWIG_2(swigCPtr, this, sid); 217 return (cPtr == 0) ? null : new GeneAssociation(cPtr, false); 218 } 219 220 public int addGeneAssociation(GeneAssociation association) { 221 return libsbmlJNI.FbcModelPlugin_addGeneAssociation(swigCPtr, this, GeneAssociation.getCPtr(association), association); 222 } 223 224 public GeneAssociation createGeneAssociation() { 225 long cPtr = libsbmlJNI.FbcModelPlugin_createGeneAssociation(swigCPtr, this); 226 return (cPtr == 0) ? null : new GeneAssociation(cPtr, false); 227 } 228 229 public GeneAssociation removeGeneAssociation(long n) { 230 long cPtr = libsbmlJNI.FbcModelPlugin_removeGeneAssociation__SWIG_0(swigCPtr, this, n); 231 return (cPtr == 0) ? null : new GeneAssociation(cPtr, false); 232 } 233 234 public GeneAssociation removeGeneAssociation(String sid) { 235 long cPtr = libsbmlJNI.FbcModelPlugin_removeGeneAssociation__SWIG_1(swigCPtr, this, sid); 236 return (cPtr == 0) ? null : new GeneAssociation(cPtr, false); 237 } 238 239 public int getNumGeneAssociations() { 240 return libsbmlJNI.FbcModelPlugin_getNumGeneAssociations(swigCPtr, this); 241 } 242 243 244/** 245 * Sets the parent SBML object of this plugin object to 246 * this object and child elements (if any). 247 * (Creates a child-parent relationship by this plugin object) 248 * <p> 249 * This function is called when this object is created by 250 * the parent element. 251 * Subclasses must override this this function if they have one 252 * or more child elements. Also, {@link SBasePlugin#connectToParent(SBase sbase)} 253 * must be called in the overridden function. 254 * <p> 255 * @param sbase the {@link SBase} object to use 256 * <p> 257 * @see setSBMLDocument 258 * @see enablePackageInternal 259 * @internal 260 */ public 261 void connectToParent(SBase sbase) { 262 libsbmlJNI.FbcModelPlugin_connectToParent(swigCPtr, this, SBase.getCPtr(sbase), sbase); 263 } 264 265 266/** 267 * Enables/Disables the given package with child elements in this plugin 268 * object (if any). 269 * (This is an internal implementation invoked from 270 * {@link SBase#enablePackageInternal()} function) 271 * <p> 272 * Subclasses which contain one or more {@link SBase} derived elements should 273 * override this function if elements defined in them can be extended by 274 * some other package extension. 275 * <p> 276 * @see setSBMLDocument 277 * @see connectToParent 278 * @internal 279 */ public 280 void enablePackageInternal(String pkgURI, String pkgPrefix, boolean flag) { 281 libsbmlJNI.FbcModelPlugin_enablePackageInternal(swigCPtr, this, pkgURI, pkgPrefix, flag); 282 } 283 284 public boolean acceptFbc(SWIGTYPE_p_FbcVisitor v) { 285 return libsbmlJNI.FbcModelPlugin_acceptFbc(swigCPtr, this, SWIGTYPE_p_FbcVisitor.getCPtr(v)); 286 } 287 288 public ListOfFluxBounds getFluxBoundsForReaction(String reaction) { 289 long cPtr = libsbmlJNI.FbcModelPlugin_getFluxBoundsForReaction(swigCPtr, this, reaction); 290 return (cPtr == 0) ? null : new ListOfFluxBounds(cPtr, false); 291 } 292 293}