PLearn 0.1
RunICPVariable.h
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00001 // -*- C++ -*-
00002 
00003 // RunICPVariable.h
00004 //
00005 // Copyright (C) 2006 Olivier Delalleau
00006 //
00007 // Redistribution and use in source and binary forms, with or without
00008 // modification, are permitted provided that the following conditions are met:
00009 //
00010 //  1. Redistributions of source code must retain the above copyright
00011 //     notice, this list of conditions and the following disclaimer.
00012 //
00013 //  2. Redistributions in binary form must reproduce the above copyright
00014 //     notice, this list of conditions and the following disclaimer in the
00015 //     documentation and/or other materials provided with the distribution.
00016 //
00017 //  3. The name of the authors may not be used to endorse or promote
00018 //     products derived from this software without specific prior written
00019 //     permission.
00020 //
00021 // THIS SOFTWARE IS PROVIDED BY THE AUTHORS ``AS IS'' AND ANY EXPRESS OR
00022 // IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
00023 // OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN
00024 // NO EVENT SHALL THE AUTHORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
00025 // SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED
00026 // TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
00027 // PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
00028 // LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
00029 // NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
00030 // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
00031 //
00032 // This file is part of the PLearn library. For more information on the PLearn
00033 // library, go to the PLearn Web site at www.plearn.org
00034 
00035 // Authors: Olivier Delalleau
00036 
00040 #ifndef RunICPVariable_INC
00041 #define RunICPVariable_INC
00042 
00043 #include <plearn/var/UnaryVariable.h>
00044 #include "ChemicalICP.h"
00045 #include "Molecule.h"
00046 
00047 namespace PLearn {
00048 using namespace std;
00049 
00050 // Forward declaration.
00051 class ScoreLayerVariable;
00052 
00065 class RunICPVariable : public UnaryVariable
00066 {
00067     typedef UnaryVariable inherited;
00068 
00069 public:
00070 
00072     TVec< PP<ChemicalICP> > icp_aligners;
00073 
00074     //#####  Public Build Options  ############################################
00075 
00078 
00079 public:
00080     //#####  Public Member Functions  #########################################
00081 
00083     RunICPVariable();
00084 
00086     RunICPVariable(Variable* input);
00087 
00088     // ### If your class has parameters, you probably want a constructor that
00089     // ### initializes them
00090     // RunICPVariable(Variable* input, param_type the_parameter, ...);
00091 
00092     // Your other public member functions go here
00093 
00095     void setScoreLayer(ScoreLayerVariable* the_score_layer);
00096 
00102     void addTemplate(PP<ChemicalICP> icp_aligner, PP<Molecule> mol_template,
00103                      Var mol_coordinates);
00104 
00106     VarArray& getPathsToResize(int i);
00107 
00108     //#####  PLearn::Variable methods #########################################
00109     // (PLEASE IMPLEMENT IN .cc)
00110     virtual void recomputeSize(int& l, int& w) const;
00111     virtual void fprop();
00112     virtual void bprop();
00113 
00114     // ### These ones are not always implemented
00115     // virtual void bbprop();
00116     // virtual void symbolicBprop();
00117     // virtual void rfprop();
00118 
00119     //#####  PLearn::Object Protocol  #########################################
00120 
00121     // Declares other standard object methods.
00122     // ### If your class is not instantiatable (it has pure virtual methods)
00123     // ### you should replace this by PLEARN_DECLARE_ABSTRACT_OBJECT
00124     PLEARN_DECLARE_OBJECT(RunICPVariable);
00125 
00126     // Simply calls inherited::build() then build_()
00127     virtual void build();
00128 
00130     // (PLEASE IMPLEMENT IN .cc)
00131     virtual void makeDeepCopyFromShallowCopy(CopiesMap& copies);
00132 
00133 protected:
00134 
00136     TVec< PP<Molecule> > templates;
00137 
00142     VarArray molecule_coordinates;
00143 
00148     TVec<VarArray> paths_to_resize;
00149 
00150     //#####  Protected Options  ###############################################
00151 
00152     // ### Declare protected option fields (such as learned parameters) here
00153     // ...
00154 
00155 protected:
00156 
00159     ScoreLayerVariable* score_layer;
00160 
00161     //#####  Protected Member Functions  ######################################
00162 
00164     // (PLEASE IMPLEMENT IN .cc)
00165     static void declareOptions(OptionList& ol);
00166 
00167 private:
00168     //#####  Private Member Functions  ########################################
00169 
00171     // (PLEASE IMPLEMENT IN .cc)
00172     void build_();
00173 
00174 private:
00175     //#####  Private Data Members  ############################################
00176 
00177     // The rest of the private stuff goes here
00178 };
00179 
00180 // Declares a few other classes and functions related to this class
00181 DECLARE_OBJECT_PTR(RunICPVariable);
00182 
00183 // ### Put here a convenient method for building your variable.
00184 // ### e.g., if your class is TotoVariable, with two parameters foo_type foo
00185 // ### and bar_type bar, you could write:
00186 // inline Var toto(Var v, foo_type foo=default_foo, bar_type bar=default_bar)
00187 // { return new TotoVariable(v, foo, bar); }
00188 
00189 } // end of namespace PLearn
00190 
00191 #endif
00192 
00193 
00194 /*
00195   Local Variables:
00196   mode:c++
00197   c-basic-offset:4
00198   c-file-style:"stroustrup"
00199   c-file-offsets:((innamespace . 0)(inline-open . 0))
00200   indent-tabs-mode:nil
00201   fill-column:79
00202   End:
00203 */
00204 // vim: filetype=cpp:expandtab:shiftwidth=4:tabstop=8:softtabstop=4:encoding=utf-8:textwidth=79 :
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