001/* ---------------------------------------------------------------------------- 002 * This file was automatically generated by SWIG (http://www.swig.org). 003 * Version 3.0.8 004 * 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 * <span class="pkg-marker pkg-color-layout"><a href="group__layout.html">layout</a></span> 013 014 A glyph for an SBML species. 015 <p> 016 * In addition to the attributes it inherits from {@link GraphicalObject}, the 017 * {@link SpeciesGlyph} object has an optional 'species' attribute. 018 */ 019 020public class SpeciesGlyph extends GraphicalObject { 021 private long swigCPtr; 022 023 protected SpeciesGlyph(long cPtr, boolean cMemoryOwn) 024 { 025 super(libsbmlJNI.SpeciesGlyph_SWIGUpcast(cPtr), cMemoryOwn); 026 swigCPtr = cPtr; 027 } 028 029 protected static long getCPtr(SpeciesGlyph obj) 030 { 031 return (obj == null) ? 0 : obj.swigCPtr; 032 } 033 034 protected static long getCPtrAndDisown (SpeciesGlyph obj) 035 { 036 long ptr = 0; 037 038 if (obj != null) 039 { 040 ptr = obj.swigCPtr; 041 obj.swigCMemOwn = false; 042 } 043 044 return ptr; 045 } 046 047 protected void finalize() { 048 delete(); 049 } 050 051 public synchronized void delete() { 052 if (swigCPtr != 0) { 053 if (swigCMemOwn) { 054 swigCMemOwn = false; 055 libsbmlJNI.delete_SpeciesGlyph(swigCPtr); 056 } 057 swigCPtr = 0; 058 } 059 super.delete(); 060 } 061 062 063/** 064 * Creates a new {@link SpeciesGlyph} with the given SBML level, version, and package version 065 * and the id of the associated species set to the empty string. 066 */ public 067 SpeciesGlyph(long level, long version, long pkgVersion) throws org.sbml.libsbml.SBMLConstructorException { 068 this(libsbmlJNI.new_SpeciesGlyph__SWIG_0(level, version, pkgVersion), true); 069 } 070 071 072/** 073 * Creates a new {@link SpeciesGlyph} with the given SBML level, version, and package version 074 * and the id of the associated species set to the empty string. 075 */ public 076 SpeciesGlyph(long level, long version) throws org.sbml.libsbml.SBMLConstructorException { 077 this(libsbmlJNI.new_SpeciesGlyph__SWIG_1(level, version), true); 078 } 079 080 081/** 082 * Creates a new {@link SpeciesGlyph} with the given SBML level, version, and package version 083 * and the id of the associated species set to the empty string. 084 */ public 085 SpeciesGlyph(long level) throws org.sbml.libsbml.SBMLConstructorException { 086 this(libsbmlJNI.new_SpeciesGlyph__SWIG_2(level), true); 087 } 088 089 090/** 091 * Creates a new {@link SpeciesGlyph} with the given SBML level, version, and package version 092 * and the id of the associated species set to the empty string. 093 */ public 094 SpeciesGlyph() throws org.sbml.libsbml.SBMLConstructorException { 095 this(libsbmlJNI.new_SpeciesGlyph__SWIG_3(), true); 096 } 097 098 099/** 100 * Ctor. 101 */ public 102 SpeciesGlyph(LayoutPkgNamespaces layoutns) throws org.sbml.libsbml.SBMLConstructorException { 103 this(libsbmlJNI.new_SpeciesGlyph__SWIG_4(LayoutPkgNamespaces.getCPtr(layoutns), layoutns), true); 104 } 105 106 107/** 108 * Creates a new {@link SpeciesGlyph} with the given <code>id</code>. 109 <p> 110 * (FOR BACKWARD COMPATIBILITY) 111 */ public 112 SpeciesGlyph(LayoutPkgNamespaces layoutns, String id) throws org.sbml.libsbml.SBMLConstructorException { 113 this(libsbmlJNI.new_SpeciesGlyph__SWIG_5(LayoutPkgNamespaces.getCPtr(layoutns), layoutns, id), true); 114 } 115 116 117/** 118 * Creates a new {@link SpeciesGlyph} with the given <code>id</code> and the id of the 119 * associated species object set to the second argument. 120 <p> 121 * (FOR BACKWARD COMPATIBILITY) 122 */ public 123 SpeciesGlyph(LayoutPkgNamespaces layoutns, String id, String speciesId) throws org.sbml.libsbml.SBMLConstructorException { 124 this(libsbmlJNI.new_SpeciesGlyph__SWIG_6(LayoutPkgNamespaces.getCPtr(layoutns), layoutns, id, speciesId), true); 125 } 126 127 128/** 129 * Creates a new {@link SpeciesGlyph} from the given {@link XMLNode} 130 */ public 131 SpeciesGlyph(XMLNode node, long l2version) throws org.sbml.libsbml.SBMLConstructorException { 132 this(libsbmlJNI.new_SpeciesGlyph__SWIG_7(XMLNode.getCPtr(node), node, l2version), true); 133 } 134 135 136/** 137 * Creates a new {@link SpeciesGlyph} from the given {@link XMLNode} 138 */ public 139 SpeciesGlyph(XMLNode node) throws org.sbml.libsbml.SBMLConstructorException { 140 this(libsbmlJNI.new_SpeciesGlyph__SWIG_8(XMLNode.getCPtr(node), node), true); 141 } 142 143 144/** 145 * Copy constructor. 146 */ public 147 SpeciesGlyph(SpeciesGlyph source) throws org.sbml.libsbml.SBMLConstructorException { 148 this(libsbmlJNI.new_SpeciesGlyph__SWIG_9(SpeciesGlyph.getCPtr(source), source), true); 149 } 150 151 152/** 153 * <p> 154 * Replaces all uses of a given <code>SIdRef</code> type attribute value with another 155 * value. 156 <p> 157 * <p> 158 * In SBML, object identifiers are of a data type called <code>SId</code>. 159 * In SBML Level 3, an explicit data type called <code>SIdRef</code> was 160 * introduced for attribute values that refer to <code>SId</code> values; in 161 * previous Levels of SBML, this data type did not exist and attributes were 162 * simply described to as 'referring to an identifier', but the effective 163 * data type was the same as <code>SIdRef</code>in Level 3. These and 164 * other methods of libSBML refer to the type <code>SIdRef</code> for all 165 * Levels of SBML, even if the corresponding SBML specification did not 166 * explicitly name the data type. 167 <p> 168 * This method works by looking at all attributes and (if appropriate) 169 * mathematical formulas in MathML content, comparing the referenced 170 * identifiers to the value of <code>oldid</code>. If any matches are found, the 171 * matching values are replaced with <code>newid</code>. The method does <em>not</em> 172 * descend into child elements. 173 <p> 174 * @param oldid the old identifier 175 * @param newid the new identifier 176 */ public 177 void renameSIdRefs(String oldid, String newid) { 178 libsbmlJNI.SpeciesGlyph_renameSIdRefs(swigCPtr, this, oldid, newid); 179 } 180 181 182/** 183 * Returns the id of the associated species object. 184 */ public 185 String getSpeciesId() { 186 return libsbmlJNI.SpeciesGlyph_getSpeciesId(swigCPtr, this); 187 } 188 189 190/** 191 * Sets the id of the associated species object. 192 */ public 193 void setSpeciesId(String id) { 194 libsbmlJNI.SpeciesGlyph_setSpeciesId(swigCPtr, this, id); 195 } 196 197 198/** 199 * Returns true if the id of the associated species object is not the 200 * empty string. 201 */ public 202 boolean isSetSpeciesId() { 203 return libsbmlJNI.SpeciesGlyph_isSetSpeciesId(swigCPtr, this); 204 } 205 206 207/** 208 * Calls initDefaults from {@link GraphicalObject}. 209 */ public 210 void initDefaults() { 211 libsbmlJNI.SpeciesGlyph_initDefaults(swigCPtr, this); 212 } 213 214 215/** 216 * Returns the XML element name of 217 * this SBML object. 218 <p> 219 * @return the string of the name of this element 220 */ public 221 String getElementName() { 222 return libsbmlJNI.SpeciesGlyph_getElementName(swigCPtr, this); 223 } 224 225 226/** 227 * Creates and returns a deep copy of this {@link SpeciesGlyph}. 228 <p> 229 * @return a (deep) copy of this {@link SpeciesGlyph}. 230 */ public 231 SpeciesGlyph cloneObject() { 232 long cPtr = libsbmlJNI.SpeciesGlyph_cloneObject(swigCPtr, this); 233 return (cPtr == 0) ? null : new SpeciesGlyph(cPtr, true); 234 } 235 236 237/** 238 * Returns the libSBML type code of this object instance. 239 <p> 240 * <p> 241 * LibSBML attaches an identifying code to every kind of SBML object. These 242 * are integer constants known as <em>SBML type codes</em>. The names of all 243 * the codes begin with the characters <code>SBML_</code>. 244 * In the Java language interface for libSBML, the 245 * type codes are defined as static integer constants in the interface class 246 * {@link libsbmlConstants}. Note that different Level 3 247 * package plug-ins may use overlapping type codes; to identify the package 248 * to which a given object belongs, call the <code>getPackageName()</code> 249 * method on the object. 250 <p> 251 * @return the SBML type code for this object: 252 * {@link libsbmlConstants#SBML_LAYOUT_SPECIESGLYPH SBML_LAYOUT_SPECIESGLYPH} 253 <p> 254 * <p> 255 * @warning <span class='warning'>The specific integer values of the possible 256 * type codes may be reused by different Level 3 package plug-ins. 257 * Thus, to identifiy the correct code, <strong>it is necessary to invoke 258 * both getTypeCode() and getPackageName()</strong>.</span> 259 <p> 260 * @see #getElementName() 261 * @see #getPackageName() 262 */ public 263 int getTypeCode() { 264 return libsbmlJNI.SpeciesGlyph_getTypeCode(swigCPtr, this); 265 } 266 267 268/** 269 * Creates an {@link XMLNode} object from this. 270 */ public 271 XMLNode toXML() { 272 return new XMLNode(libsbmlJNI.SpeciesGlyph_toXML(swigCPtr, this), true); 273 } 274 275}