This file is indexed.

/usr/include/sbml/math/ASTFunction.h is in libsbml5-dev 5.13.0+dfsg-1.

This file is owned by root:root, with mode 0o644.

The actual contents of the file can be viewed below.

  1
  2
  3
  4
  5
  6
  7
  8
  9
 10
 11
 12
 13
 14
 15
 16
 17
 18
 19
 20
 21
 22
 23
 24
 25
 26
 27
 28
 29
 30
 31
 32
 33
 34
 35
 36
 37
 38
 39
 40
 41
 42
 43
 44
 45
 46
 47
 48
 49
 50
 51
 52
 53
 54
 55
 56
 57
 58
 59
 60
 61
 62
 63
 64
 65
 66
 67
 68
 69
 70
 71
 72
 73
 74
 75
 76
 77
 78
 79
 80
 81
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
/**
 * @cond doxygenLibsbmlInternal
 *
 * @file    ASTFunction.h
 * @brief   Umbrella function class for Abstract Syntax Tree (AST) class.
 * @author  Sarah Keating
 * 
 * <!--------------------------------------------------------------------------
 * This file is part of libSBML.  Please visit http://sbml.org for more
 * information about SBML, and the latest version of libSBML.
 *
 * Copyright (C) 2013-2016 jointly by the following organizations:
 *     1. California Institute of Technology, Pasadena, CA, USA
 *     2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
 *     3. University of Heidelberg, Heidelberg, Germany
 *
 * Copyright (C) 2009-2012 jointly by the following organizations: 
 *     1. California Institute of Technology, Pasadena, CA, USA
 *     2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
 *  
 * Copyright (C) 2006-2008 by the California Institute of Technology,
 *     Pasadena, CA, USA 
 *  
 * Copyright (C) 2002-2005 jointly by the following organizations: 
 *     1. California Institute of Technology, Pasadena, CA, USA
 *     2. Japan Science and Technology Agency, Japan
 * 
 * This library is free software; you can redistribute it and/or modify it
 * under the terms of the GNU Lesser General Public License as published by
 * the Free Software Foundation.  A copy of the license agreement is provided
 * in the file named "LICENSE.txt" included with this software distribution and
 * also available online as http://sbml.org/software/libsbml/license.html
 * ------------------------------------------------------------------------ -->
 */

#ifndef ASTFunction_h
#define ASTFunction_h


#include <sbml/common/extern.h>

#include <sbml/math/ASTBase.h>
#include <sbml/math/ASTFunctionBase.h>
#include <sbml/math/ASTNaryFunctionNode.h>
#include <sbml/math/ASTUnaryFunctionNode.h>
#include <sbml/math/ASTBinaryFunctionNode.h>
#include <sbml/math/ASTCiFunctionNode.h>
#include <sbml/math/ASTLambdaFunctionNode.h>
#include <sbml/math/ASTPiecewiseFunctionNode.h>
#include <sbml/math/ASTCSymbol.h>
#include <sbml/math/ASTQualifierNode.h>
#include <sbml/math/ASTSemanticsNode.h>

#ifdef __cplusplus

LIBSBML_CPP_NAMESPACE_BEGIN

class LIBSBML_EXTERN ASTFunction : public ASTBase
{
public:

  ASTFunction (int type = AST_UNKNOWN);


  /**
   * Copy constructor
   */
  ASTFunction (const ASTFunction& orig);
  

  /**
   * Assignment operator for ASTNode.
   */
  ASTFunction& operator=(const ASTFunction& rhs);


  /**
   * Destroys this ASTNode, including any child nodes.
   */
  virtual ~ASTFunction ();


  /**
   * Creates a copy (clone).
   */
  virtual ASTFunction* deepCopy () const;

  /************************************* 
   * get functions 
   */
  
  /* ast attributes */
  std::string getClass() const;
  std::string getId() const;
  std::string getStyle() const;

  /* other attributes */
  const std::string& getDefinitionURL() const;
  const std::string& getEncoding() const;
  const std::string& getName() const;

  /* user data */
  SBase* getParentSBMLObject() const;
  void *getUserData() const;
  unsigned int getNumBvars() const;

  /************************************* 
   * isSet functions 
   */
  
  /* ast attributes */
  bool isSetClass() const;
  bool isSetId() const;
  bool isSetStyle() const;


  /* other attributes */
  bool isSetDefinitionURL() const;
  bool isSetEncoding() const;
  bool isSetName() const;
  
  /* user data */
  bool isSetParentSBMLObject() const;
  bool isSetUserData() const;

  /************************************* 
   * set functions 
   */
  
  /* ast attributes */
  int setClass(std::string className);
  int setId(std::string id);
  int setStyle(std::string style);


  /* other attributes */
  int setDefinitionURL(const std::string& url);
  int setEncoding(const std::string& encoding);
  int setName(const std::string& name);

  /* user data */
  int setParentSBMLObject(SBase* sb);
  int setUserData(void *userData);

  /************************************* 
   * unset functions 
   */
  
  /* ast attributes */
  int unsetClass();
  int unsetId();
  int unsetStyle();

  /* other attributes */
  int unsetDefinitionURL();
  int unsetEncoding();
  int unsetName();  

  /* user data */
  int unsetParentSBMLObject();
  int unsetUserData();
  
  /************************************* 
   * manipulating child functions 
   */

  int addChild(ASTBase * child);

  ASTBase* getChild (unsigned int n) const;

  unsigned int getNumChildren() const;

  int insertChild(unsigned int n, ASTBase* newChild);

  int prependChild(ASTBase* newChild);

  int removeChild(unsigned int n);

  int replaceChild(unsigned int n, ASTBase* newChild, bool delreplaced);

  int swapChildren(ASTFunction* that);

  void setIsChildFlag(bool flag);

  /************************************* 
   * semantics functions 
   */
  
  int addSemanticsAnnotation (XMLNode* sAnnotation);

  unsigned int getNumSemanticsAnnotations () const;

  XMLNode* getSemanticsAnnotation (unsigned int n) const;

  
  /************************************* 
   * convenience query functions 
   */
  
  bool isAvogadro() const;
  bool isBoolean() const;
  bool isConstant() const;
  bool isFunction() const;
  bool isInfinity() const;
  bool isInteger() const;
  bool isLambda() const;
  bool isLog10() const;
  bool isLogical() const;
  bool isName() const;
  bool isNaN() const;
  bool isNegInfinity() const;
  bool isNumber() const;
  bool isOperator() const;
  bool isPiecewise() const;
  bool isQualifier() const;
  bool isRational() const;
  bool isReal() const;
  bool isRelational() const;
  bool isSemantics() const;
  bool isSqrt() const;
  bool isUMinus() const;
  bool isUnknown() const;
  bool isUPlus() const;
  
  virtual bool hasCnUnits() const;
  virtual const std::string& getUnitsPrefix() const;
  
  /************************************* 
   * access member variable functions 
   */

  ASTUnaryFunctionNode *      getUnaryFunction() const;
  ASTBinaryFunctionNode *     getBinaryFunction() const;
  ASTNaryFunctionNode *       getNaryFunction() const;
  ASTCiFunctionNode *         getUserFunction() const;
  ASTLambdaFunctionNode *     getLambda() const;
  ASTPiecewiseFunctionNode *  getPiecewise() const;
  ASTCSymbol *                getCSymbol() const;
  ASTQualifierNode *          getQualifier() const;
  ASTSemanticsNode *          getSemantics() const;


  virtual bool isWellFormedNode() const;
 
  virtual bool hasCorrectNumberArguments() const;
 
  virtual ASTBasePlugin* getPlugin(const std::string& package);
  virtual const ASTBasePlugin* getPlugin(const std::string& package) const;
  virtual ASTBasePlugin* getPlugin(unsigned int n);
  virtual const ASTBasePlugin* getPlugin(unsigned int n) const;

  ASTBase* getMember() const;

  /************************************* 
   * read/write functions 
   */
  virtual void write(XMLOutputStream& stream) const;


  virtual bool read(XMLInputStream& stream, const std::string& reqd_prefix="");

  virtual void writeNodeOfType(XMLOutputStream& stream, int type, 
    bool inChildNode = false) const;

  virtual int getTypeCode () const;


protected:

  /* sync the member variables when changing asts */
  void syncMembersAndTypeFrom(ASTNumber* rhs, int type);
  void syncMembersAndTypeFrom(ASTFunction* rhs, int type);
  void syncPackageMembersAndTypeFrom(ASTFunction* rhs, int type);
  
  int setNameAndChangeType(const std::string& name);

  void reset();

  bool readApply(XMLInputStream& stream, const std::string& reqd_prefix,
                  const XMLToken& currentElement);

  bool readLambda(XMLInputStream& stream, const std::string& reqd_prefix,
                  const XMLToken& currentElement);

  bool readPiecewise(XMLInputStream& stream, const std::string& reqd_prefix,
                  const XMLToken& currentElement);

  bool readQualifier(XMLInputStream& stream, const std::string& reqd_prefix,
                  const XMLToken& currentElement);

  bool readCiFunction(XMLInputStream& stream, const std::string& reqd_prefix,
                  const XMLToken& currentElement);

  bool readCSymbol(XMLInputStream& stream, const std::string& reqd_prefix,
                  const XMLToken& currentElement);

  bool readSemantics(XMLInputStream& stream, const std::string& reqd_prefix,
                  const XMLToken& currentElement);

  bool readFunctionNode(XMLInputStream& stream, const std::string& reqd_prefix,
                  const XMLToken& nextElement, bool& read, int type, 
                  unsigned int numChildren, ASTBasePlugin* plugin = NULL);

  bool representsQualifierNode(int type);

  friend class ASTNode;
  friend class ASTSemanticsNode;

  /* member variables */

  ASTUnaryFunctionNode *      mUnaryFunction;
  ASTBinaryFunctionNode *     mBinaryFunction;
  ASTNaryFunctionNode *       mNaryFunction;
  ASTCiFunctionNode *         mUserFunction;
  ASTLambdaFunctionNode *     mLambda;
  ASTPiecewiseFunctionNode *  mPiecewise;
  ASTCSymbol *                mCSymbol;
  ASTQualifierNode *          mQualifier;
  ASTSemanticsNode *          mSemantics;
  
  bool mIsOther;

};

LIBSBML_CPP_NAMESPACE_END

#endif /* __cplusplus */

#endif  /* ASTNode_h */
/** @endcond */